BIOLOGY [Greek, from bios, life.] [Greek, from Logos, Study/Logic.]

Biology is the study of life and living organisms. And perhaps, most importantly today, how we humans interact with and impact the lives of each other and the other organisms that share our earth. By studying the hundreds of thousands of living organisms with which humans share this earth, biologists try to answer questions about diversity and about the common characteristics of living organisms. We try, in science to make "sense" of all we see in our world around us. We shall look at some of the "themes" of biology this term; others will have to wait for other courses. But, for a beginning, let's look at what "life" is - some of the characteristics of living organisms, and then look a bit at how science asks questions about the world in which we live. These topics are addressed in the introductory chapter of your textbook.


Biological spectrum or Levels of Organization: elementary particle, atom, molecule, (virus*) organelle, cell, tissue, organ, organ system, organism, population, community, ecosystem, Biome, Biosphere. 


Characteristics of Life


Complexity, order, Regulation, Growth, metabolism, Response, Reproduction and Evolution.


Read: Natural selection, DNA-Watson and Crick, Rosalind Franklin and Cellular disorders.


Living Organisms are virtually everywhere on earth, and are found in all sizes, shapes and colors. From bacteria to aspen groves, blue whales and California redwood trees, there is a remarkable array of living organisms to catalog (or classify) and observe on earth. All of us have some understanding of what it is to be alive and what non-living stuff is. However, coming up with a good definition of life is not so easy. There are a number of things we can state which are characteristics of living organisms, the sum of which can be of help to us in distinguishing life from non-life: Although both living and non-living things share the same fundamental properties of matter and energy (which we shall look at) living organisms and non-living materials differ in the degree to which energy is used and materials are organized. To help us determine how life and non-life can be distinguished we can study some of the following common "features" of living organisms:




Your text states that DNA is the signature molecule of life. By this we mean that all living organisms have a common molecular inheritance based on the nuclei acid, DNA. DNA contain the instructions for the structure and function of cells, the common structural component of living organisms. DNA guides growth, development and maintenance of tissues and organs of multicellular organisms. DNA instructions are passed from generation to generation (inherited) by the process of reproduction.




All organisms require energy input to maintain the processes of life. Living organisms must have the capacity to obtain and convert energy from their surroundings to grow and maintain themselves. In biology this is known asmetabolism. Response to Stimuli Organisms constantly sense changes in their surroundings and make controlled responses to those changes. Organisms have specialized receptors that detect environmental stimuli, and their cells adjust metabolism in response to signals from receptors. This constant monitoring and interaction between cells and their environment is called homeostasis.


Cellular Organization


Living organisms have an organized structure, composed of cells. All living organisms are composed of one or more cells, the smallest unit of life.


Life Organization


Organisms can be unicellular, aggregates or multicellular, in which cells become specialized and interdependent, organized into tissues and organs under controlled conditions. Groups of organisms form populations and groups of different populations (or species) living in the same geographical area form communities and ecosystems.


Interdependence of Life


Just as the cells of multicellular organisms are dependent upon each other for the survival of the organism, life on earth involves an interdependence of energy and nutrients in ecological processes. Much of biology focuses on the linking of life processes:


The dependence of life processes on each other.

The interaction of organisms with their environment.

The changes that occur in groups of organisms through time.

The mechanisms of evolution as a foundation for change.


While looking for the unity of life processes, we recognize the great diversity of appearance and behavior of species on this earth, as well. Species differ greatly in their adaptations to the many distinct environments on earth. Both the unity and diversity of organisms can be explained by the mechanisms of evolution.


Diversity of Life


For thousands of years humans have categorized living organisms into groups sharing some kind of common features. In the 1700's, Linnaeus proposed a hierarchical scheme, which we continue to follow. For some time, biologists grouped organisms into general groups, called Kingdoms, based on broad general features (which are not so easy to see all of the time). Recently, biologists added a new category above Kingdom, called Domain. Your textbook uses Domains in its classification of living organisms. There are three Domains:


Domains: Archaea, Bacteria and Eukarya.


Kingdoms: Monera, Archaebacteria, Protista, Algae, Apicomplexans, Fungi, Plantae and Animalia.


At times during Biology 101, we will have reason to look a little more closely at the characteristics of these domains and kingdoms, and for those who go on to study diversity in other courses, you'll have the opportunity for greater observations. Unfortunately, we do not have time in Biology 101 to study the wonderful diversity of life on earth in any detail. Biology 102, will have diversity sections.


Evolution as the Guiding theme of Biology


Both the unity and diversity of organisms is explained by the mechanisms of evolution. The processes of evolution outline the mechanisms by which species genetically change from generation to generation, in response to the "forces" of their surroundings which favor some genetic trait over another less suited to the surroundings in which the organisms live. We shall spend some time this term looking at the mechanisms of evolution, as well as seeing the results of evolution as we study the structure and functioning of cells.


How Biologists Ask Questions


Before we leave our introduction, we need to mention how biologists look at the world around them. Each of us is curious about any number of things. Often when we are curious we ask questions to try and find out whatever it is that we are curious about. Biologists try and find answers to their questions about living things by using the scientific method of problem solving, or some variant of this method, to study the processes of life.


Scientific Principles


A Scientific Principle is an idea supported by repeated experiments and observations. The assumptions behind which scientific principles are based have been thoroughly tested and found valid over many years.


How the Scientific Process Works (SCIENTIFIC METHOD):


Make observations about whatever it is you are questioning to produce a "model" or preliminary explanation for your question


Find something about which you are curious and ask a question about it.


Based on your observations and model, make a testable hypothesis. By using the information available to make a general conclusive statement (called the hypothesis). Predict what will happen if the hypothesis is correct.


Test the hypothesis by models, controlled experiments and observations. Repeat tests to see if results are consistent with the hypothesis.


Note the results and begin to draw conclusions.


(Examine alternative hypotheses in the same manner)


Scientists work in as many different ways as there are scientists; but all share a critical attitude that requires being shown, not being told, and a logic to their thinking. Conclusions drawn support evidence and observations using deductive (making inferences about specifics based on hypothesis, or an "if-then" process) and inductive (making a general statement based on specific tests) reasoning. Science is limited to questions that can be tested. Experimental design is important. When possible, science uses controlled studies, in which the control group is a standard for comparison with the experimental group. The variables of the experiment are aspects, events or objects that may differ or change over time. When testing a hypothesis, scientists are as prepared to find the hypothesis false as they are for validating the hypothesis. Tested and supported hypotheses in science are known as theories. In this sense, theory is not the same as in some fields where theory means a speculation. A science theory has tested evidence that supports and lacks evidence that disproves it. Other fields may look at issues and ideas that are untestable. These ideas are not appropriate for science. This term, in Biology 101 we will look at some of these life processes. Chapter One of your text reviews many of the ideas I've mentioned here. Read this chapter with thought. Much of what is written there may help you think more deeply and with greater understanding of what we are to do in Biology 101 as well as in subsequent biology courses you will take.


How Biologists Ask Questions:

indoctrination, is based on faith not facts. In science one can think of a testimonial as an example of the scientific method in reverse. The conclusion coming first and then stating that it might be possible to prove the conclusion. Example: This pill will make you taller----try it, you have nothing to lose?

Before we leave our introduction, we need to mention how biologists look at the world around them. Each of us is curious about any number of things. Often when we are curious we ask questions to try and find out whatever it is that we are curious about. Biologists try and find answers to their questions about living things by using the scientific method of problem solving, or some variant of this method, to study the processes of life.


Critical Thinking encompasses the understanding that there must be experimental and conclusive proof before conclusions can be reached. Testimonials are never reliable because they represent opinions of a few and do not represent the results of experimentation and a in-depth study of a population(s).

You can’t prove a negative----a matter of debate? Scientists, as you and I, must deal with the real world of "cause and effect" or "stimulus and response". However, there are individuals who have a need for the metaphysical, a world or universe outside of anything we know. These are people who, as in the past during the time of Galileo, do not accept the scientific method for its truthful purpose and have constructed their own set of rules and logic to prove or disprove whatever they like. THIS IS NOT SCIENCE. If it is philosophy, it is in a domain of its own. Science has been criticized for not obeying philosophical rules of logic. Scientific logic is not the same as philosophic logic. Science is based on facts, not propositions and the abstract.

Example: In order to give credence to the possibility that ghosts exist, some field of thought other than science must do away with the laws of physics as we know them and apply a criterion that defies our understanding of the real world of physics. For example, do ghost have mass or weight and since they float around, are they affected by gravity?

Oftentimes, in the course of debate, we find ourselves in the awkward position of claiming that a certain assertion is false. Are aliens visiting Earth? Is there a Santa Claus? I don't know about you, but I want to smile or answer "no" to each of these questions. The problem arises when your adversary responds by saying, "Oh yeah? Prove it!”

Is there a Santa Claus? As critical thinkers, we can say: Well, I can't say for certain, but I don't see any affirmative evidence demonstrating his existence...Or, we can say: No, I can’t prove there is not a Santa Claus. BUT, I can give you many good reasons why there is probably not. (Remember, science even critiques or limits its own domain).

However, some people just won't let up. For them, this expression of healthy skepticism comes across as weasel-speak (double talk). Or, it is used to assert the philosophical premise or argument to claim that the positive and negative position are equivalent; neither proved nor disproved and thus equal. This can be extremely frustrating, especially in situations where there have been extensive investigations that have failed to prove the assertion.

For example, for years, children across the globe have attempted to catch a glimpse of Santa Claus, often going to extraordinary measures to achieve discovery. To my knowledge, no child has yet succeeded.

So, when the adversary claims that neither the "Santa Claus exists" or the "Santa Claus does not exist" proposition has been proved and, therefore, each position has equal merit, I tend to get a little annoyed.

Since science is not trying to win an argument or indoctrinate, the best answer to these arguments is: “It is impossible to enumerate through all possibilities within the domain in a reasonable amount of time -- and thus, the burden of proof is yours!” So, for everyone out there who believes in ghosts, aliens on Earth, Santa Claus, or etc. -- the burden of proof is still yours. Step up if you can. Otherwise, don't let the door hit you on the way out.



Chemistry of Life

elements - single substances that can not be broken down into simpler substance.

atom- smallest particle of an element that still has all of the properties of that element

symbol - letter or letters representing an element

compound - the chemical combination of two or more elements

molecule - smallest part of a compound which still has all of the properties of that compound.

The cell - smallest unit of life. A complex chemical factory containing some of the same elements found in the nonliving environment. Carbon, hydrogen, oxygen, and nitrogen are present in the greatest percentages.

Organism - a complete living thing that consist of both organic and inorganic compounds.



1. organic--always contain carbon--especially in C-C and C-H bonds-associated with living things and their products

exs. carbohydrates, lipids, proteins, and nucleic acids

2. inorganic- usually lack carbon--when carbon is present it is usually combined with oxygen. Exs. carbon dioxide, inorganic acids, salts, water, and bases.



Chemical bonds ( Ionic and covalent ) hold the atoms in a molecule together. In general, the more chemical bonds a molecule has the more energy it contains.

Formula- shows the composition of a compound



1. Structural Formula--indicates the kinds of atoms in a molecule, their proportions, and how the atoms are arranged or held together

2. General or Molecular formula--indicates the actual nos. and kinds of atoms in a molecule --does NOT indicate structural setup.

3. Empirical Formula--shows the symbols of the elements in a compound followed by small subscript numbers showing the ratio of atoms in the compound

Acids: proton donors or substances which ionize into positively charged hydrogen ions in a water solution (H + ions) ex. HCl ----> H+ + Cl-

Bases: proton acceptors or substances which ionize into negatively charged hydroxide ions in a water solution (OH-)ex. KOH ---- K+  +  OH-

Neutralization Reactions: -- important in living things

Acid + Base ----> Salt + Water. [ex. HCl + NaOH ---> NaCl + HOH] (This is how stomach antacids work.) pH scale: measures degree of substance alkalinity or acidity. alkaline = base. Most body fluids have a neutral pH (6-8) (Major Types of Reactions in Living Things)

1. Dehydration Synthesis or Condensation: chemical combination of two small molecules to make another larger molecule with water being driven off.

2. Hydrolysis: (enzymatic hydrolysis) (digestion) -- addition of water to a larger molecule to form two or more smaller molecules -- opposite of dehydration synthesis



An atom is composed of a nucleus and electrons.

a. The nucleus contains protons and neutrons.

b. Electrons are found outside the nucleus in energy clouds or energy levels.

c. The atomic number is defined as the number of protons; protons and electrons are equal in number when the atom is in the ground state (i.e. without an electrical charge).

d. The atomic mass (rounded off) is defined as the number of protons plus the number of neutrons found in the nucleus.

e. Isotopes of an atom differ in atomic mass (i.e. the number of neutrons) but have similar chemical properties.

f. Most elements in nature exist as a mixture of isotopes.

g. Ions are defined as atoms in which the number of protons and number of electrons differ.

(1). Ions with a greater number of protons carry a positive charge  and are called cations.

(2). Ions with a greater number of electrons carry a negative charge and are called anions.

h. Atoms are stable when the outer electron shell is filled or complete.

i. Valence electrons are found in the outermost energy level and are involved in forming chemical bonds.

Chemical bonds

A. Ionic bonds are formed between atoms that have formed cations and atoms that have formed anions.

1. An atom that loses one or more electrons has been oxidized and forms a cation. Cations have a positive charge.

2. An atom that gains one or more electrons has been reduced and forms an anion. Anions have a negative charge.

3. Positively charged cations are attracted to negatively charged anions and this attraction is what holds the ionic bond together.

4. With ionic compounds, the positive and negative charges must be balanced.

5. Ionic bonds form between metals and nonmetals.

B. Covalent bonds:

1. Covalent bonds form between nonmetals.

2. Covalent bonds form through the sharing of valence electrons.

3. Covalent bonds may be polar or nonpolar; polarity is determined by the electronegativity and mass of the elements involved in the bond.

C. Hydrogen bonds result from electrostatic attraction between oppositely charged portions of neighboring polar molecules.

D. Van der Waals interactions are much weaker than ionic or hydrogen bonds and occur between electrically neutral molecules or parts of molecules.

E. Hydrophobic bonds result when nonpolar molecules are mixed with polar molecules, particularly water.

4. Chemistry of Water

a. Life on earth is dependent on water; 70-90% of living tissue is water and all biochemical reactions occur in water.

b. Because water is polar, both ionic and polar covalent molecules are soluble in water; it is the universal solvent.

c. Hydrophobic refers to molecules that are electrically neutral, nonpolar, and insoluble in water (eg. fats and oils).

d. Hydrogen bonds between water molecules result in strong ordering of the molecules. This ordering results in physical properties such as high surface tension, high boiling point, high melting point, high heat capacity and high heat of vaporization.

e. Water serves as a temperature regulator.

f. Water will spontaneously ionize to form hydrogen ions and hydroxyl ions.

g. When water dissociates (through ionization) the number of hydrogen or hydronium ions is equal to the number of hydroxyl ions; [HOH + HOH ----> H3O++ OH-] this is the basis for the pH scale.

1. Substances which donate hydrogen ions to a solution when dissolved in water are called acids.

2. Substances which accept hydrogen ions in a water solution are called bases. Bases commonly dissociate to form hydroxyl ions which combine with hydrogen ions to form water.

3. Mathematically pH is defined as:

pH = -log [H+ or H3O+].

5. Organic molecules are the basic building blocks of living organisms on earth.

a. Organic molecules may be viewed as a carbon core with various functional groups.

b. Some molecules in organisms are simple organic molecules, while others are complex macromolecules.

c. Important functional groups include: hydroxyl, sulfhydryl, carboxyl, amino or amine, aldehyde, ether, ester, ketone, and phosphate groups. These groups are all derivatives of hydrocarbons. Radical groups (R)consist mainly of alkyl groups. ex. methyl, ethyl etc.[CH3-, CH3-CH2- etc.]

d. Condensation reactions (dehydration synthesis) are important for combining two or more organic molecules to form more complex molecules such as ethers, esters, amides (salts of amines).

Macromolecules found in organisms include carbohydrates, lipids, proteins, and nucleic acids. Each of these macromolecules is composed of simple organic compounds, combined through condensation reactions. For example, many lipids are synthesized when an alcohol condenses with an acid for form an ester linkage.

f. Amino acids are unique organic molecules, which always have an amino and a carboxyl group, that are used for synthesis of protein.

g. Enzymes are biological catalysts that are usually protein molecules. Catalysts reduce the overall time (not the reaction rate) for a chemical reaction to occur, by substantially lowering the energy of activation.


The Chemical Basis of Life

Major concepts: "Cells obey the laws of chemistry". Cells are living things, but they are made up of chemical compounds. The dominant element in the chemicals of living things is carbon. A whole variety of carbon compounds are the structural components of cells.

Carbohydrates: (sugars)

1. Monosaccharides: Glucose, fructose and Galactose

2. Disaccharides: Sucrose, Maltose and Lactose

3. Polysaccharides: Starch, Glycogen and Cellulose.

Lipids: Neutral Lipids, Triglycerides, Phospholipids and Steroids.

Proteins are one type of carbon compounds found in cells. They have special properties that are essential to life. Many proteins actually function by promoting specific chemical reactions on which living cells depend. These proteins are called enzymes.

Proteins fold into complex three-dimensional structures. The function of proteins is determined by their structure.

Nucleic acids are the carriers of genetic information ("genes").

There are two forms of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

Nucleic acids have distinct functions in the cell. DNA is an information storage structure; it contains the stable form of genetic information that is passed on from one generation to another. RNA is a impermanent form of that same information. RNA serves as a messenger that the cell uses to "read" the information in genes. That reading process, termed translation, results in the synthesis of proteins whose structure is specified by the sequence in the RNA.


Structure of biological macromolecules.[(macro) Greek makro-, from makros, large.]

The important structural and informational molecules of the cells are commonly formed by joining together smaller molecules into chains. These long, multimeric molecules are called macromolecules.

Macromolecules are formed by condensation reactions which fuse the monomeric units.

Many condensation (dehydration) reactions involve the removal of a molecule of water by the reaction of two hydroxyl groups:

Monomers may be joined in linear chains, or in branched structures.


A protein is an example of a linear chain of monomers. Other examples of linear macromolecules include the nucleic acids.

Some macromolecules are branched, such as the storage form of the important sugar, glucose, which is called glycogen. Other structural molecules, such as cellulose (which makes up the cell walls of higher plants) and mannan (which makes up the cell walls of various microorganisms) are highly branched, giving them a mat-like appearance.

Macromolecules can either be regular in their structure (consisting of identical repetitive units of monomers) or irregular (consisting of variable repeats of monomers).


The information content in a molecule is related to how complex its structure is.

Regular macromolecules often consist of one or two monomeric units (e.g., glycogen consists entirely of glucose and various mannans consists of mannose).

The gross features of the macromolecule often depend on the way in which the monomers are linked.

Both glycogen and cellulose are constructed from glucose monomers, yet they are joined together in distinct ways:


The regularity of the linkages in glycogen cause the macromolecule to coil in space, creating a helix. This is a common feature of macromolecules and is especially important in the structure of proteins and nucleic acids.The repeating alternating linkages of cellulose lead to a uncoiled structure. Cellulose forms fibers in which individual macromolecules interact with each other by hydrogen bonding using the hydroxyl groups shown. These form higher order structures consisting of bundles of these fibers, giving the rigidity of the cellulose structure. We will also see formation of higher-order structures again in the structures of proteins and nucleic acids. Irregular molecules can consist of repeating units of several monomers. Proteins are especially diverse in their structure, consisting of 20 different monomers called amino acids. Nucleic acids consist of four repeating units termed nucleic acids. In both cases, the order of these monomers is irregular, though not random. Both of these types of molecules are informational, that is the order of the monomeric units is critical to their function.

Nucleic acids store genetic instructions. The order of their nucleic acid monomers is a code which the cell uses to store information essential to the formation of new cells and cellular structures.

Proteins are not information storage molecules, but the complexity of the structures which they can form make them ideal for the role of catalyzing biochemical reactions and forming complex cellular structures.

Types of macromolecules present in cells. [(macro) Greek makro-, from makros, large.]

We have already introduced one type of macromolecule--polysaccharides.

There are a wide variety of polysaccharides. They perform either a structural (cellulose, chitin) or a storage (glycogen, starch) role. The synthesis and degradation of these molecules is specifically catalyzed by enzymes.

Lipids are another macromolecule with roles in cell structure and food storage. They are structurally a diverse group that can be divided into four major types: fatty acids, neutral fats, phospholipids and sterols. They are different from the polysaccharides in that they are determinate, that is a particular lipid molecule has a precise size, very much smaller than the indeterminate polysaccharides.


Fatty acids are in fact a basic constituent of both neutral fats and phospholipids. A fatty acid is any of a large group of monobasic acids, especially those found in animal and vegetable fats and oils, having the general formula CnH(2n+1)COOH. Characteristically made up of saturated or unsaturated aliphatic compounds with an even number of carbon atoms, this group of acids includes palmitic, stearic, and oleic acids. Neutral lipids or fats are commonly found in cells as storage fats and oils, are so called because at cellular pH, they bear no charged groups. Generally, they are completely nonpolar, with no affinity for water. Almost all neutral lipids are a combination of fatty acids with the polyhydric alcohol glycerol.


Saturated fats and trans fats are considered health hazards because they "hydrogen bond" easily; making the blood thicker and thus promoting atherosclerosis (narrowing of blood vessels by plaque deposition on the arterial walls) which can result in arteriosclerosis (narrow or blocked blood vessels)

The terms cis and trans are from Latin, in which cis means "on the same side" and trans means "on the other side" or "across". Cis fats have hydrogen atoms on the same side which breaks the easy hydrogen bonding, making the blood less viscous (thick). 
Fatty acids are molecules with a long hydrocarbon chain, made up of repeating CH2 units, sometimes called a "tail", and a carboxylate "head group". Fatty acids differ in length of the hydrocarbon tail, and in degree of saturation. The changes to the tail affect the physical characteristics of the fatty acid. Neutral fats (or triglycerides) are formed by joining three fatty acids by ester linkages to a single molecule of glycerol       (CH2OH-CHOH-CH2OH)   

Phospholipids are similar to triglycerides, except one of the three fatty acids is replaced by a hydrophilic group: In this case the hydrophilic group is a complex phosphate group [phosphoserine, an amino acid (serine) linked to a single phosphate by an ester linkage]. The hydrophilic group is linked to the rest of the molecule (diacyl glycerol) by another ester linkage. This creates a phosphodiester linkage, a linkage that also occurs in the structure of nucleic acids.


Neutral fats are commonly used as storage molecules, and phospholipids are important constituents of cellular membranes.


Another common constituent of animal membranes is cholesterol, a member of a group of lipids called sterols. Sterols have a common overall structure. The various forms differ in the chemical side-groups added to this structure. Some sterols have a structural role (e.g., cholesterol as a part of the cell membrane). Other sterols are hormones, for example estrogen and testosterone. Finally, vitamin D is derived from cholesterol, though its structure is slightly different


All of these molecules are regular:  They are constructed of a small set of smaller molecules (monomers). The monomers are connected in stereotyped ways, consistent across the entire structure, but, though the structure may be indeterminate in its length (e.g., glycogen), it has a predictable repeating structure such that all molecules have the same overall structure. Proteins are examples of irregular macromolecules.  Proteins are irregular in their structure. They are also constructed of a small set of monomers (the 20 amino acids), all amino acid monomers are connected to each other in the same way with the protein being a linear array of amino acids, however, the sequence of monomer amino acids in any protein is unique, so that all proteins have unique overall structures. The structure of proteins define their function (Structure/Function). Just as the structure of each of the regular macromolecules suit it to its molecular function (or role), the structure of individual protein molecules have evolved to allow the protein to play a very specific role. Some proteins have structural roles, some have enzymatic roles, and some rare proteins are actually used for food storage. Amino acids, or more properly, are acids which have an amino group attached to the same carbon to which the carboxyl (acid) group is attached. The identity of the amino acid depends on the nature of a variable group, the "R-group", that is also attached to the alpha carbon.

So, if the only difference among proteins is in the order of amino acids , then the differences in protein structure really depends on the differences among the amino acids.


Non-polar or hydrophobic R-groups

Polar, uncharged R-groups

Positively-charged R-groups.

Negatively-charged R-groups.


It is the chemical nature of the R-group (acidic, basic, hydrophobic, or hydrophilic) which determines its effect on the protein's function. In a protein, the amino acids are linked in a linear structure, a chain. Proteins are not branched, as is glycogen. This linear array of amino acids is termed the protein's primary structure (often called primary sequence, though that is perhaps redundant).

Therefore, the primary structure of a protein can be represented by simply listing the order of successive amino acids in the protein.

The fact that there are 20 amino acids means that a remarkably large number of proteins can conceivably be constructed, far more in fact than ever have actually existed.


The average protein contains about 300 amino acids. The number of possible 300 amino acid proteins is 20 raised to the 300th power, or 2 x 10390! This number is astonishingly large, and the size of the number is emphasized by the fact that the number of distinct proteins present in a cell is probably below 105!

So, the amount of variability possible with only 20 amino acids is unimaginably huge.


Proteins are organized into higher order structures.

Proteins do not function as linear structures. The activity of a protein depends on its ability to fold up into a distinct structure. The structure of a protein is defined by its primary structure, though the relationship between primary structure and higher order structures is still very obscure.


The next order of structure of proteins is called secondary structure and describes the ways in which the chain of amino acids can fold in space. The ways that proteins fold depends on the details of the way in which amino acids are joined together.


The bond joining two amino acids is called a peptide bond. Because of the bond's electronic structure (the way electrons are shared) the atoms involved in the bond lie in a plane. This creates a repeating flat structure which is important in the overall structure of proteins. The carbonyl (C=O) and amino (NH) groups extending in opposite directions can interact by hydrogen bonding. This hydrogen bonding stabilizes the two basic secondary structures: alpha helix, and beta sheet.

In these structures the R-groups extend out from the structures to interact with other portions of the same or different proteins.

Interactions between R-groups (ionic interactions between charged residues, hydrophobic interactions between non-polar groups, hydrogen bond interactions, and other interactions) cause the protein to bend in space to define its next level of structure, tertiary structure (the tertiary structure of the protein is the shape that the whole molecule adopts).

The same types of interactions can cause polypeptides to interact to form aggregates.

Many proteins consist of multimers of polypeptide chains (e.g., hemoglobin consists of four chains of two types--two "alpha globins" and two "beta globins"). The structure formed by interaction of distinct polypeptide chains is termed quaternary structure.

We know a lot about the ways in which the primary structure of a protein defines its secondary structure (though not enough to accurately predict that structure) and some things about how it specifies tertiary and quaternary structure, but without being able to predict either.


Nucleic acids are also irregular macromolecules. While proteins are the workhorses of the cell, catalyzing most of its chemical reactions, nucleic acids are the information storehouses of the cell.

Nucleic acids come in two forms, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). DNA is a permanent form of genetic information because the molecule is chemically extremely stable.

RNA is an impermanent form of nucleic acid since it is rapidly destroyed in the cell. While DNA is the repository of genetic information passed from one generation to the next, RNA is a messenger molecule which allows the instructions in the DNA to be used in specifying the sequence of the proteins to be expressed in the cell.

Nucleic acids are made of monomers called nucleotides.

Arguably, the most familiar nucleotide is adenosine triphosphate (ATP) which we will see is extremely important as a molecule used to store chemical energy.

Nucleotides are made up of three parts: One to three phosphate groups (AMP, ADP, and ATP have 1, 2, and 3 phosphates, respectively), a sugar, ribose in RNA and deoxyribose in DNA and a planar molecule called a "base". Bases themselves come in five kinds of two general types. Bases can be pyrimidines (consisting of one six member ring). Examples of these are cytosine (C), thymine (T), or uracil (U). Thymine is a modified form of uracil which is found in DNA; uracil is only found in RNA. Bases can also be purines (consisting of fused six and five member rings)-purines are either guanine (G) or adenine (A).

RNA consists of a linear arrangement of these nucleotides joined by phosphate groups linking successive ribose sugars. DNA consists of two strands of nucleotides, running in opposite directions, and interacting by hydrogen bonding between sets of pyrimidines and purines. A hydrogen-bonded pair of nucleotides is called a "base pair", and G will only base pair with C, and A with T.


The origin of the cell theory: Before the invention of microscopes there was no way to observe the small-scale structure of living things. Starting in the 17th century technology began to develop to enable scientists and others (microscopes were used for what amounted to parlor tricks by untrained people!) to see cells or microbes, and to see the cellular structure of larger animals. The understanding that larger animals were multicellular was relatively slow in develop. It was not until the 19th century that the idea that all animals and plants were constructed of cells, and that cells have a kind of life-cycle of their own: cells are derived from other pre-existing cells which reproduce by binary division.

These are still the basic tenets of the cell theory:


All organisms are composed of cells

Cells are the basic unit of life

Cells arise only from other pre-existing cells


The fundamental structures of cells

All cells have certain characteristics: They are surrounded by a lipid membrane which separates them from their environment-the "plasma membrane". However, membranes are not impermeable. Various substances move both into and out of cells across membranes; this is probably their most important characteristic. Since cells must both generate all of the biological molecules necessary for their functioning, and reproduce themselves, they all include DNA as genetic material, which is segregated into a DNA-containing region. All cells also include a region distinct from the DNA-containing region within which much of the biochemical activity of the cell proceeds.

The structure of the cell membrane. The plasma membrane is a bilayer of lipid molecules, largely phospholipids.


Since phospholipids include a very hydrophobic region (the fatty acid tails) and a very hydrophilic region (the head group), they spontaneously self-assemble into a structure consisting of two layers of phospholipids, the hydrophobic tails on the inside away from the aqueous solvent, and the hydrophilic head groups on the outside, interacting with the water.


The very "fatty" interior of the membrane provides a barrier against the free movement of water soluble molecules, such as the contents of the cell.


Prokaryotes are the simplest cells

Prokaryotic cells have the simplest overall structure. The prokaryotic cell is bounded by a lipid bilayer membrane, but does not contain any internal membrane-bound organelles.

It contains a region rich in DNA called a nucleoid. The nucleoid contains a circular molecule of DNA which is the cells genetic material, or genome.

Surrounding the nucleoid is a region of cytoplasm rich in ribosomes, small protein-RNA structures which do the job of synthesizing proteins. Finally, surrounding the plasma membrane is a cell wall

Prokaryotes can have surface appendages which do particular jobs. Flagella are used for locomotion. Pili are used for sexual reproduction (mating). One of the more surprising aspects of cell structure is the way that DNA molecules are packaged into cells. The genome of a common bacterium like the gut bacterium Escherichia coli which is about 1.5 millimeters in length, but the length of the bacterium is about 1000 times shorter.

In the nucleoid, the DNA is both compacted so as to fit within the bacterium, and yet is still accessible to the machinery necessary both to read the genetic instructions (synthesize RNA) and to copy the DNA (replicate).


Eukaryotic cells are much more complex

By contrast to prokaryotic cells, eukaryotic cells are much more complicated. Much of the cell is taken up by subcellular organelles bound by their own membranes (analogous to the plasma membrane surrounding the cell)


Most importantly, eukaryotic cells have a nucleus which contains all of the cell's DNA. In fact, "eukaryote" means "true nucleus" while "prokaryote" means "before the nucleus". This emphasizes the central importance of the nucleus to the eukaryotic cell, and suggests that prokaryotes are more primitive organisms, and that eukaryotes evolved from them by, among other things, acquiring a true nucleus.


The problem of packaging DNA is greater in eukaryotes. A human genome would stretch about 1 meter, but must fit in a cell 50,000 times smaller. However, eukaryotic cells (which included plants, animals, and fungi) include many other subcellular structures with important roles in cellular metabolism


Structure of a "typical" plant cell

There is of course no "typical" plant cell-all are unique. However, we can imagine a hypothetical plant cell which includes all of the features found in the various plants.


The most obvious feature of plant cells, in contrast to prokaryotes, is the existence of elaborate subcellular structure:


Italicized are found only in plants:


Nucleus: Contains DNA. Genetic information storage. Expressed into RNA

Nucleolus: Rich in RNA. Site of ribosomal RNA synthesis. Assembly of ribosomes

Chloroplast: Photosynthetic. Conversion of light energy into chemical energy. Chlorophyll-rich membranes

Mitochondrion: Respiration. Site of aerobic metabolism, converts food energy into useful form (ATP)

Vacuole: A membraneous storage organ. Storage of nutrients and water. Most obvious feature of plant cells.

Endoplasmic reticulum: A membraneous structure. Starts at the nuclear membrane, extends into the cytoplasm. Rough E.R.contains ribosomes. Smooth E.R. does not. Rough ER or RER synthesizes and exports proteins. Smooth E.R. or SER Synthesizes lipids. Membraneous. Intermediate in protein export.

Cell Wall External structure. Rigid structure, provides support and protection.

Ribosomes: Ribosomes are small organelles composed of ribosomal RNA (rRNA) and 80 some different proteins. rRNA is synthesized in the nucleolus and the ribosomal subunits are assembled there from rRNA and imported cytoplasmic made proteins. Once assembled, the subunits pass through the nuclear pores to the cytoplasm where they take part in protein synthesis. Some ribosomes are free in the cytoplasm and can be recruited to a polyribosomal structure when a messenger RNA (mRNA) strand is to be translated into a cytoplasmic protein. Other ribosomes are attached to the endoplasmic reticulum where the protein is formed within the interior to the endoplasmic reticulum. These proteins are destined for secretion, storage or incorporation into membranes.

Golgi complex (apparatus/body): The Golgi, a curved membrane stack resembling a stack of pancakes, finishes the post-transitional modifications, concentrates and packages proteins for export or storage. It also adds directions for the destination of the protein package. Proteins made within the rough ER bud off in vesicles and are transported to the Golgi where the vesicles fuse with the membrane and the components are further modified, concentrated and packaged by the time they bud off as vesicles on the opposite side of the Golgi. Therefore, the Golgi shows a polarity in that one side accepts incoming vesicles (convex or cis face) and the final product vesicles bud off the opposite side (concave or trans face). In fact, biochemical studies have shown that the enzymes present within the Golgi are different at different levels of the membrane stack.

Lysosomes: Lysosomes are membrane bound vesicles (0.05 to 0.5 micron) containing more than 40 hydrolytic enzymes that can digest most biological macromolecules. These organelles are the sites of intracellular digestion that are more numerous in cells performing phagocytosis. The limiting membrane keeps the digestive enzymes separate from the cytoplasm. The most common lysosomal enzymes are acid phosphatase, ribonuclease, deoxyribonuclease, proteases, sulfatases, and lipases. The enzymes function optimally at pH 5 and are mostly inactive at the pH of the cytosol (7.2). This taken with the limiting membrane protects the cell from digesting itself. Lysosomal enzymes are synthesized on the rough ER, transferred to the Golgi for modification and packaging. The cellular machinery attaches a directional signal to the enzymes (mannose-6-phosphate) that allows the ER and Golgi to sort these proteins and, via a receptor mediated process, segregate them to forming lysosomes. Primary lysosomes are small concentrated sacs of enzymes that are not digesting anything. Primary lysosomes fuse with a phagocytic vacuole to become secondary lysosomes or phagolysosomes where digestion begins. As the substances are digested the nutrients diffuse through the lysosomal membrane to the cytosol. Residual bodies are formed when indigestible things remain in the vacuoles. In cells with a long life span such as cardiac muscle cells, residual bodies are more numerous and are referred to lipofuscin or age pigment. Lysosomes also participate in the turnover of cellular organelles. Cytoplasmic components become enclosed in a membrane that fuses with a primary lysosome to become an autophagosome. In bone, the lysosomal enzymes are released from osteoclasts to digest surrounding bone during the process of remodeling. Lysosomal enzymes are also involved in the process of inflammation.

Peroxisomes: These small (0.5 to 1.2 microns) containing oxidative enzymes. Peroxisomes contain amino oxidases, hydroxyacid oxidase and catalase. Catalase protects the cell from hydrogen peroxide damage. Enzymes involved in lipid metabolism are also found in peroxisomes. Peroxisomal enzymes are synthesized on the free cytosolic ribosomes with a signal sequence that directs them to peroxisomes. As enzymes are added the peroxisome grows and then splits into two smaller peroxisomes.

Cytoskeleton: Within the cell is a complex network of filaments, anchor proteins, and protein motors that form a support and transportation scaffolding. This network provides shape to the cell and participates in cellular movement.

Microtubules: These variable length tubules have an outer diameter of 24 nm, a dense 5nm thick wall and central hollow core. Microtubule lengths are variable and can reach several micrometers. Microtubules are composed of repeating heterodimers of alpha and beta tubulin. The heterodimers, under the proper conditions, will spontaneously assemble into tubules in vitro (in an artificial environment outside the living organism) or in vivo (within a living organism). Growth of existing microtubules is generally directional with one end growing faster than the other. Various microtubular organizing centers (MOC), such as basal bodies, centrioles and centromeres, direct the assembly and disassembly of microtubules. Microtubular life span is variable with some, as in those of the mitotic spindle, being transient, while others, such as those in cilia, being very stable. Some antimitotic alkaloids are useful as cancer chemotherapy agents. Taxol increases the formation of microtubules and stabilizes them so that there is no free tubulin for the formation of mitotic spindles. Vinblastine causes the disassembly of formed microtubules and causes the aggregation of crystaline tubulin. Because tumor cells multiply faster than normal cells they are more susceptible to antimitotic drugs. Some body systems are more affected than others based on their normal turnover rate. For instance, the cells of the gastrointestinal lining and blood forming system have rapid turnover rates and are therefore susceptible to the inhibition of mitosis caused by the chemotherapy agents. Microtubules provide the necessary intracellular highway system for the movement of organelles and vesicles from one place to another. Molecular motors such as dynien and kinesin transport packages along this highway in an energy requiring process.

Microfilaments: Actin and myosin are microfilament proteins responsible for contraction in muscle cells. All cells have actin in some form. Myosin in motile nonmuscle cells is present in unpolymerized form. It polymerizes only to participate in cell movement. In most cells, microfilaments form thin sheath just under the cell membrane that is associated with the cellular functions of endocytosis, exocytosis and cell movement. Microfilaments are involved with the movement of vesicles, granules and cytoplasmic organelles. In association with myosin, microfilaments form a "purse-string" ring that constricts and results in the cleavage of mitotic cells. Most of a nonmuscle cell's actin is soluble and microfilaments readily dissociate and reassemble under the influence of cellular calcium and cAMP (cyclic adenosine monophosphate) levels.

Intermediate Filaments: Intermediate filaments are important components of the cell's cytoskeletal system. They may stabilize organelles, like the nucleus, or they may be involved in specialized junctions. They are distinguished from "thin filaments" by their size (8-10 nm) and the fact that thin filaments are obviously motile. However recent evidence indicates that Intermediate Filaments may also have other dynamic properties.  Intermediate filaments seemed to be involved in the connection of microfiliaments and microtubules. They are made of several proteins dependent on the cell or tissue type. The proteins differ chemically and in their cellular roles. 1. Keratins are a family of proteins (40-68 kDa) found in most epithelial cells. The variety of keratins speaks to the variety of functions performed by skin, hair, nails in protection from abrasion and desiccation. 2. Vinmentin (56-58 kDa) filaments are found in cells of mesenchymal origin such as fibroblasts, macrophages, endothelial cells, and chondroblasts. 3. Desmin (53-55 kDa) is found in smooth muscle and in the Z lines of skeletal and cardiac muscle. 4. Glial Fibrillary Acidic Protein (51 kDa) is only found in glial cells (astrocytes). 5. Neurofilaments are found in most neurons and are composed of at least three polypeptides (68, 140 and 210 kDa). 6. Nuclear Laminins (65-75 kDa) are found in the nuclear lamina of cells.

Centrioles: These cylindrical organelles participate in cell division as microtubule organizing centers. They are in fact composed of tubulin in a characteristic arrangement of nine microtubular triplets. A single pair of centrioles oriented at a 90 degree angle to one another is found near the Golgi complex in non-dividing cells. Before cell division each centriole replicates itself. During mitosis a pair of centrioles moves to opposite poles of the cell to become organizing centers for the mitotic spindle.

Cilia and Flagella: Cilia and flagella have at their core a motile highly organized microtubular structure. Flagella usually exist as one process ranging in length from 100 to 200 microns. Sperm cells have a flagellum. Ciliated cells, such as those lining the respiratory tree, normally have numerous cilia ranging in length from 2 to 10 microns. Both types of cellular processes contain the same core organization of a 9 + 2 arrangement of microtubules within a cell membrane covering. This structure, called an axoneme, consists of 9 microtubular doublets surrounding an inner core of two sheathed microtubules. Adjacent doublets are linked to one another by protein bridges called nexins and to the central pair by radial spokes. The tubules of each peripheral pair are called subfibers A and B. Subfiber A is a complete microtubule containing 13 tubulin heterodimers in cross section, while subfiber B shares part of the wall of subfiber A and has only 10 or 11 heterodimers in cross section. Protein arms of the protein dynein extend from subfiber A. At the base of each cilia or flagella is a centriole-like structure called the basal body. Cilia and flagella are motile structures. Movement is accomplished by the sliding of adjacent doublets over one another by an energy requiring process. The dynein arms have an ATPase activity and an affinity for tubulin. These arms are thought to bind and "walk" along the surface of the adjacent doublet.

Plasma membrane: A phospholipid bilayer made up of two lipid layers; surface and embedded proteins with attached carbohydrates. Semifluid cell boundary; controls passage of materials into and out of cell.




Animal cells lack cell walls and chloroplasts.

The most important difference between plant and animal cells is the fact that plant cells do not have the capacity for movement.

Movement of animal cells is important in normal cell function (e.g., phagocytic cells). Movement is critical in development.

Animal cells are also not able to trap energy from light since they lack chloroplasts. They are required to get energy necessary to life by eating other living things.

The major constituents are lipids, including phospholipids. However, the bilayer is interrupted by the inclusion of membrane proteins.

Membrane proteins have hydrophobic surfaces which allow them to associate in the hydrophobic core of the membrane. These surfaces also exclude them from the aqueous phase (cytoplasm or exterior of the cell).

The cytoplasmic face of the membrane is covered with a mesh of cytoskeletal proteins.

Cytoskeletal proteins form protein chains which give the cell it's shape. Some cytoskeletal proteins are motors which move cellular contents through the cytoplasm

The "fluid mosaic" model of the membrane states that the membrane is fluid-that is, that the molecules that make up the membrane are in constant motion rather than being fixed in space. The membrane is a mosaic-made up of lipids of various kinds, and of various proteins. Increased saturation of the fatty acids in phospholipids tends to disrupt the ordered structure of the membrane since saturation "kinks" the hydocarbon chain.

The two layers of the membrane (the inner and outer "leaflet") are isolated from each other.

Lipids move extremely quickly within one a leaflet. However, they can not move easily from one leaflet to the other since the hydrophobic head group "anchors" them. Specific proteins catalyze the movement of lipids between the leaflets. Because of the specificity of those proteins the two leaflets are different in the composition.

The proteins in the membrane may associate in a variety of ways.

They may span both leaflets or they may reside entirely in one leaflet; both of these are termed "integral membrane proteins".

They may associate only peripherally with the hydrophilic head groups, or with integral membrane proteins (those inserted within one or both leaflets). Like the phospholipids, the membrane proteins present in the two leaflets may differ. Since the proteins can be different at each end the two sides of the membrane may differ functionally.

Membrane proteins provide many functions including: Ions and many molecules can not freely pass through the hydrophobic membrane.

so: proteins must provide a means to move them into or out of cells.

Some proteins bind to small molecules (a "ligand")proteins which have polysaccharide antennae [glycocalyx] in the extracellular space.

They can signal the presence of these molecules by interacting with cytoplasmic proteins.

Recognition proteins

Especially in the immune system, membrane proteins can be used to identify a cell as "self" rather than "non-self".

Such proteins can also identify a cell in terms of its function in the immune system

Adhesion proteins

Certain glycoproteins (proteins with attached short polysaccharide chains) hold cells together.

They can create "tight junctions" which form between adjacent epithelial cells, for example lining the stomach or intestine, so that the contents can not leak into the adjoining tissue.

Membranes provide a barrier to diffusion

Lets consider the role of transport proteins.

Some transport proteins allow essential molecules to pass into the cell.

Glucose can not pass through a cell membrane, and must be brought into cells via a specific transporter.

The transporter is specific for glucose, and will not transport related saccharides.

Ions (Na+, K+, Cl-, Ca++) can not pass and also must be transported.

The transporters, or "channels" often are highly specific. Some channels catalyze the exchange of ions (e.g., Na+ for K+).

The high concentration of proteins and other molecules in cells dilutes the water concentration in cells. Water will enter cells if the concentration outside the cell excedes that inside (movement of water across a membrane in response to a concentration gradient is termed "osmosis"). Water channels can force water out against the gradient. Entry of water can be counteracted by internal pressure within the cell


Protein-mediated transport


Passive transport depends on the existence of a concentration gradient. A molecule present in the extracellular space but is consumed inside the cell will pass down the concentration gradient created by passive diffusion. This is the case for glucose, which is present outside cells, but is consumed inside them. Active transport: to move a molecule against gradient requires energy. Proteins that move molecules against their concentration gradient often use the energy in ATP. The energy in ATP is used to force the movement of the molecule across the membrane. The mechanism may involve an induced change in the shape of the protein which changes the ability of the protein to bind the molecue.

A second type of active transport involves the exchange of molecule. An example of this is the Na-K pump. This pump exchanges one K+ going into the cell for one Na+ going out. The action of the pump creates a gradient with Na+ more concentrated outside and K+ more concentrated inside the cell. Such a pump creates the concentration gradient necessary for the function of neurons.

Endocytosis and exocytosis:

The other way that proteins cross the plasma membrane is in vesicles. Proteins are delivered to the cell membrane by a process called "exocytosis". Proteins are translated directly across the membrane of the endoplasmic reticulum (the rough E.R.). They are modified by the addition of saccharide molecules (oligosaccharides). The proteins then travel in spherical membrane-bound vesicles to the Golgi body, which acts as a switching station. Some molecules are targeted to the plasma membrane while others are targeted to various organelles. More modification occurs.


Proteins destined for the plasma membrane are located in the membrane of the vesicle and proteins destined for export are in the liquid inside the vesicle (the "fluid phase"). The membrane surrounding the vesicles fuses with the plasma membrane.

This releases the contents of the vesicle into the extracellular space. The membrane portion of the vesicle becomes part of the plasma membrane. Proteins in the membrane become plasma membrane proteins

Proteins can also be imported into the cell by a process called "endocytosis". Vesicles bud into the cell at the plasma membrane. Proteins bound to surface receptors can be incorporated into the vesicle. This is termed "receptor mediated endocytosis" Proteins can enter in the fluid carried by the vesicle. This is termed "fluid phase endocytosis". Vesicles are delivered to an intracellular organelle, often the lysosome.


Metabolic energy


The first law of thermodynamics (the science of energy) states that "energy is neither created nor destroyed--it can only be converted from one form to another".


This is a difficult concept for us since from a macroscopic point of view energy appears to be created when we run up and down stairs or pump a bicycle.

Of course, as anyone know who has gone without food for any appreciable period, our energy only comes from the conversion of food.


Humans are warm-blooded animals, which means that we maintain a constant internal temperature. We do this by converting the energy in food to heat energy. Our bodies create as much heat as a 100 W lightbulb while resting


That means that in a football stadium filled with 100,000 people their bodies are creating about 10 megawatts of power even if they are all sitting on their hands. That's enough to run a rather powerful radio station!


So the energy created by our bodies by metabolism (conversion of food materials in the body) is considerable.


(Metabolism is derived from a Greek word meaning "change")


It is important to recognize that energy is not recycled by cells (for example, energy expended as heat can not be recovered). Cells do recycle (or convert) the potential energy in molecules. Metabolism involves conversion of molecules from one form to another with either the release of energy (in breaking down molecules-a process called catabolism, meaning to "change downward") or consumption of energy (building up molecules-a process called anabolism, meaning to "change upward").


Most people have heard of "anabolic steriods". These are hormones which stimulate productive metabolism, anabolism (for example, synthesizing muscle proteins), and therefore encourage bulking up by athletes.


Much of the energy released during catabolism is lost as heat, however most of the energy is recovered in a useful form. During the next three lectures we will discuss how cells capture energy and how that energy is used.


Living things and entropy


The second law of thermodynamics states that "in a closed system, the order of the system is constantly decreasing"


Entropy is a measure of the disorder in a system. As entropy increases, disorder increases. The entropy of a system which must always increase. That is a law as universally applicable as that two bodies may not occupy the same space at the same time, or that like electrical charges repel, or that gravitation tends to pull to objects together. The only way to overcome the constant increase in entropy is to add energy to the system to increase its organization.


Living things overcome the tendency to disorder by using up metabolic energy.


It takes energy to synthesize macromolecules, and to deliver them to the correct subcellular location. It takes energy to transport ions in and out of the cell to create the appropriate gradients. It takes energy to bring food molecules in and send by-products out


Enzymes accelerate the rate of reactions


In catabolic metabolism food molecules like glucose are broken down to smaller and simpler units.


The net energy contained in the units is less than that present in glucose.

so: Catabolism of glucose will yield excess energy. If not harnessed in some way, this energy would be dissipated as heat.


In anabolic metabolism smaller and simpler units are combined to produce more complex molecules.


The net energy in the larger molecule is greater than the sum of that in the parts.

so: Anabolism requires input of energy

These reactions can occur spontaneously, though as we will see, extremely slowly.

The energy necessary to drive the reaction would have to come from heat.


Most of the reactions of metabolic pathways normally proceed extremely slowly. Proteins interact with the molecules undergoing a reaction to accelerate its rate greatly These proteins are called enzymes.


Features of enzymes:


Enzymes accelerate reactions that happen slowly by themselves

The enzymes are not altered in the reaction

The enzyme can catalyze both forward and reverse reactions

Enzymes are highly selective for substrates

The "induced-fit model"


Dan Koshland's "induced-fit model":


The structure of substrates almost, but not quite, match the structure of the enzymes active site.

Binding to the active site alters the structure of the substrate, straining some of the bonds.

Strained bonds are easier to break, or rearrange.

so The enzyme greatly stimulates the rate of the reaction.

Enzymes stabilize what is called a "transition state"-a higher energy structure which can break down to form either the original reactants, or the products.


In enzymatically catalyzed reactions the products will be in a lower energy state than were the reactants. This can be understood as an energy hill diagram. Think of a large bolder on a hill.  The transition state is at the top of the energy curve so that it can fall into the  lower energy state easily. The enzyme lowers the energy needed to achieve the transition state.


Regulation of Enzyme Activity


While it is clear that enzymes are responsible for the catalysis of almost all biochemical reactions, it is important to also recognize that rarely, if ever, do enzymatic reactions proceed in isolation. The most common scenario is that enzymes catalyze individual steps of multi-step metabolic pathways, as is the case with glycolysis. As a consequence of these lock- step sequences of reactions, any given enzyme is dependent on the activity of preceding reaction steps for its substrate. In humans, substrate concentration is dependent on food supply and is not usually a physiologically important mechanism for the routine regulation of enzyme activity. Enzyme concentration, by contrast, is continually modulated in response to physiological needs. Three principal mechanisms are known to regulate the concentration of active enzyme in tissues: 1. Regulation of gene expression controls the quantity and rate of enzyme synthesis. 2. Proteolytic enzyme activity determines the rate of enzyme degradation. 3. Covalent modification of preexisting pools of inactive proenzymes produces active enzymes. Enzyme synthesis and proteolytic degradation are comparatively slow mechanisms for regulating enzyme concentration, with response times of hours, days or even weeks. Proenzyme activation is a more rapid method of increasing enzyme activity but, as a regulatory mechanism, it has the disadvantage of not being a reversible process. Proenzymes are generally synthesized in abundance, stored in secretory granules and covalently activated upon release from their storage sites. Examples of important proenzymes include pepsinogen, trypsinogen and chymotrypsinogen, which give rise to the proteolytic digestive enzymes. Likewise, many of the proteins involved in the cascade of chemical reactions responsible for blood clotting are synthesized as proenzymes. Other important proteins, such as peptide hormones and collagen, are also derived by covalent modification of precursors. Another mechanism of regulating enzyme activity is to sequester enzymes in compartments where access to their substrates is limited. For example, the proteolysis of cell proteins and glycolipids by enzymes responsible for their degradation is controlled by sequestering these enzymes within the lysosome. In contrast to regulatory mechanisms that alter enzyme concentration, there is an important group of regulatory mechanisms that do not affect enzyme concentration, are reversible and rapid in action, and actually carry out most of the moment- to- moment physiological regulation of enzyme activity. These mechanisms include allosteric regulation, regulation by reversible covalent modification and regulation by control proteins such as calmodulin. Reversible covalent modification is a major mechanism for the rapid and transient regulation of enzyme activity. The best examples, again, come from studies on the regulation of glycogen metabolism where phosphorylation of glycogen synthase and glycogen phosphorylase kinase results in the stimulation of glycogen degradation while glycogen synthesis is coordinately inhibited. Numerous other enzymes of intermediary metabolism are affected by phosphorylation, either positively or negatively. These covalent phosphorylations can be reversed by a separate sub-subclass of enzymes known as phosphatases. Recent research has indicated that the aberrant phosphorylation of growth factor and hormone receptors, as well as of proteins that regulate cell division, often leads to unregulated cell growth or cancer. The usual sites for phosphate addition to proteins are the serine, threonine and tyrosine R group hydroxyl residues.



Allosteric Enzymes


In addition to simple enzymes that interact only with substrates and inhibitors, there is a class of enzymes that bind small, physiologically important molecules and modulate activity in ways other than those described above. These are known as ; the small regulatory molecules to which they bind are known as . Allosteric effectors bring about catalytic modification by binding to the enzyme at distinct allosteric sites, well removed from the catalytic site, and causing conformational changes that are transmitted through the bulk of the protein to the catalytically active site(s). The hallmark of effectors is that when they bind to enzymes, they alter the catalytic properties of an enzyme's active site. Those that increase catalytic activity are known as positive effectors. Effectors that reduce or inhibit catalytic activity are negative effectors. Most allosteric enzymes are oligomeric (consisting of multiple subunits); generally they are located at or near branch points in metabolic pathways, where they are influential in directing substrates along one or another of the available metabolic paths. The effectors that modulate the activity of these allosteric enzymes are of two types. Those activating and inhibiting effectors that bind at allosteric sites are called heterotropic effector(Thus there exist both positive and negative heterotropic effectors.) These effectors can assume a vast diversity of chemical forms, ranging from simple inorganic molecules to complex nucleotides such as cyclic adenosine monophosphate (cAMP). Their single defining feature is that they are not identical to the substrate. In many cases the substrate itself induces distant allosteric effects when it binds to the catalytic site. Substrates acting as effectors are said to be homotropic effectors. When the substrate is the effector, it can act as such, either by binding to the substrate-binding site, or to an allosteric effector site. When the substrate binds to the catalytic site it transmits an activity-modulating effect to other subunits of the molecule. Often used as the model of a homotropic effector is hemoglobin, although it is not a branch-point enzyme and thus does not fit the definition on all counts. There are two ways that enzymatic activity can be altered by effectors: the Vmax can be increased or decreased, or the Km can be raised or lowered. Enzymes whose Km is altered by effectors are said to be K-type enzymes and the effector a K-type effector. If Vmax is altered, the enzyme and effector are said to be V-type. Many allosteric enzymes respond to multiple effectors with V-type and K-type behavior. Here again, hemoglobin is often used as a model to study allosteric interactions, although it is not strictly an enzyme. In the preceding discussion we assumed that allosteric sites and catalytic sites were homogeneously present on every subunit of an allosteric enzyme. While this is often the case, there is another class of allosteric enzymes that are comprised of separate catalytic and regulatory subunits. The archetype of this class of enzymes is cAMP-dependent protein kinase (PKA), whose mechanism of activation is unknown. The enzyme is tetrameric, containing two catalytic subunits and two regulatory subunits, and enzymatically inactive. When intracellular cAMP levels rise, one molecule of cAMP binds to each regulatory subunit, causing the tetramer to dissociate into one regulatory dimer and two catalytic monomers. In the dissociated form, the catalytic subunits are fully active; they catalyze the phosphorylation of a number of other enzymes, such as those involved in regulating glycogen metabolism. The regulatory subunits have no catalytic activity.


Properties of Allosteric Enzymes


Polymeric structure

One thing that all allosteric enzymes and proteins have in common is that they they have a polymeric or quaternary structure. That's to say that a complete allosteric protein will consist of a number of separate protein chains, or subunits,  which are linked to each other by weak interactions such as hydrogen bonds and hydrophobic linkages.

This polymeric structure is vital to the mechanism of allostery. An allosteric enzyme will contain a number of active sites, in the simplest arrangement one on each subunit, each of which can carry out the catalytic reaction for which the enzyme is responsible. It's interaction between these different sites which is responsible for substrate cooperativity. So, in a typical allosteric enzyme, binding of a substrate molecule to one of the active sites would initiate a conformational change which would increase the ability of the other active sites to bind substrate. This is positive substrate cooperativity.


Since the subunits are attached to each other by weak bonds they can quite easily detach and reattach themselves. As a result an allosteric enzyme will often exist in solution as an equilibrium between the complete enzyme and individual subunits. In a complex enzyme there may be intermediates between these extremes in which some subunits are interlinked but fewer than would be found in the complete enzyme. In this sort of circumstance a single subunit may not be catalytically active. The smallest catalytically active structure is called a protomer. This can give rise to quite a complex equilibrium between the full enzyme, individual subunits and structures in between these two. Very often binding of ligands (substrates, products or effectors) to the enzyme will change the position of this equilibrium.






To grow, function, and reproduce, cells must: 1) synthesize new cellular components such as cell walls, cell membranes, nucleic acids, ribosomes, proteins, flagella, etc., and; 2) harvest energy and convert it into a form that is usable to do cellular work. Catabolism refers to the exergonic process by which energy released by the breakdown of organic compounds such as glucose can be used to synthesize ATP, the form of energy required to do cellular work. Anabolism is the process that uses the energy stored in ATP to synthesize the building blocks of the macromolecules that make up the cell. As can be seen, these two metabolic processes are closely linked. Another factor that links catabolic and anabolic pathways is the generation of precursor metabolites. Precursor metabolites are intermediate molecules in catabolic and anabolic pathways that can be either oxidized to generate ATP or can be used to synthesize macromolecular subunits such as amino acids, lipids, and nucleotides. In this section we will concentrate primarily on harvesting energy and converting it to energy stored in ATP through the process of cellular respiration, but we will also look at some of the key precursor metabolites that are produced during this process.Cellular respiration is the process cells use to convert the energy in the chemical bonds of nutrients to ATP energy. Depending on the organism, cellular respiration can be aerobic, anaerobic, or both. Aerobic respiration is an exergonic pathway that requires molecular oxygen (O2). Anaerobic exergonic pathways do not require oxygen and include anaerobic respiration and fermentation. We will now look at these three pathways.

Aerobic respiration is the aerobic catabolism of nutrients to carbon dioxide, water, and energy, and involves an electron transport system in which molecular oxygen is the final electron acceptor. Most eukaryotes and prokaryotes use aerobic respiration to obtain energy from glucose. The overall reaction is:


C6H12O6 + 6O2 yields 6CO2 + 6H2O + energy (as ATP)


Note that glucose (C6H12O6 ) is oxidized to produce carbon dioxide (CO2) and oxygen (O2) is reduced to produce water (H2O).


This type of ATP production is seen in aerobes and facultative anaerobes. Aerobes are organisms that require molecular oxygen because they produce ATP only by aerobic respiration. Facultative anaerobes, on the other hand are capable of aerobic respiration but can switch to fermentation, an anaerobic ATP-producing process, if oxygen is unavailable.


Aerobic respiration involves four stages: glycolysis, a transition reaction that forms acetyl coenzyme A, the citric acid (Krebs) cycle, and an electron transport chain and chemiosmosis. We will now look at each of these stages.


Function: Glycolysis is a partial breakdown of a six-carbon glucose molecule into two, three-carbon molecules of pyruvate, 2NADH +2H+, and 2 net ATP as a result of substrate-level phosphorylation, as shown in Glycolysis occurs in the cytoplasm of the cell. The overall reaction is:


glucose (6C) + 2 NAD+ 2 ADP +2 inorganic phosphates (Pi)


yields 2 pyruvate (3C) + 2 NADH + 2 H+ + 2 net ATP


Glycolysis also produces a number of key precursor metabolites


Glycolysis does not require oxygen and can occur under aerobic and anaerobic conditions. However, during aerobic respiration, the two reduced NADH molecules transfer protons and electrons to the electron transport chain  to generate additional ATPs by way of oxidative phosphorylation .


The glycolysis pathway involves 9 distinct steps, each catalyzed by a unique enzyme. You are not responsible for knowing the chemical structures or enzymes involved in the steps below. They are included to help illustrate how the molecules in the pathway are manipulated by the enzymes in order to to acheive the required products.


1. To initiate glycolysis in eukaryotic cells , a molecule of ATP is hydrolyzed to transfer a phosphate group to the number 6 carbon of glucose to produce glucose 6-phosphate. In prokaryotes, the conversion of phosphoenolpyruvate (PEP) to pyruvate provides the energy to transport glucose across the cytoplasmic membrane and, in the process, adds a phosphate group to glucose producing glucose 6-phosphate. (See group translocation in Unit 1.)


2. The glucose 6-phosphate is rearranged to an isomeric form called fructose 6-phosphate.


3. A second molecule of ATP is hydrolyzed to transfer a phosphate group to the number 1 carbon of fructose 6-phosphate to produce fructose 1,6-biphosphate.


4. The 6-carbon fructose 1,6 biphosphate is split to form two, 3-carbon molecules: glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The dihydroxyacetone phosphate is then converted into a second molecule of glyceraldehyde 3-phosphate. Two molecules of glyceraldehyde 3-phosphate will now go through each of the remaining steps in glycolysis producing two molecules of each product.


5. As each of the two molecules of glyceraldehyde 3-phosphate are oxidized, the energy released is used to add an inorganic phosphate group to form two molecules of 1,3-biphosphoglycerate, each containing a high-energy phosphate bond. During these oxidations, two molecules of NAD+ are reduced to form 2NADH + 2H+ . During aerobic respiration, the 2NADH + 2H+ carry protons and electrons to the electron transport chain to generate additional ATP by oxidative phosphorylation.


6. As each of the two molecules of 1,3-biphosphoglycerate are converted to 3-phosphoglycerate, the high-energy phosphate group is added to ADP producing 2 ATP by substrate-level phosphorylation.


7. The two molecules of 3-phosphoglycerate are rearranged to form two molecules of 2-phosphoglycerate.


8. Water is removed from each of the two molecules of 2-phosphoglycerate converting the phosphate bonds to a high-energy phosphate bonds as two molecules of phosphoenolpyruvate are produced.


9. As the two molecules of phosphoenolpyruvate are converted to two molecules of pyruvate, the high-energy phosphate groups are added to ADP producing 2 ATP by substrate-level phosphorylation.


Through an intermediate step called the transition reaction, the two molecules of pyruvate then enter the citric acid cycle to be further broken down and generate more ATPs by oxidative phosphorylation.



 The transition reaction connects glycolysis to the citric acid (Krebs) cycle. Through a process called oxidative decarboxylation, the transition reaction converts the two molecules of the 3-carbon pyruvate from glycolysis (and other pathways) into two molecules of the 2-carbon molecule acetyl Coenzyme A (acetyl-CoA) and 2 molecules of carbon dioxide. First, a carboxyl group of each pyruvate is removed as carbon dioxide and then the remaining acetyl group combines with coenzyme A (CoA) to form acetyl-CoA. As the two pyruvates undergo oxidative decarboxylation, two molecules of NAD+ become reduced to 2NADH + 2H+. The 2NADH + 2H+ carry protons and electrons to the electron transport chain to generate additional ATP by oxidative phosphorylation. The overall reaction for the transition reaction is:


2 pyruvate + 2 NAD+ + 2 coenzyme A


yields 2 acetyl-CoA + 2 NADH + 2 H+ + 2 CO2


In prokaryotic cells, the transition step occurs in the cytoplasm; in eukaryotic cells the pyruvates must first enter the mitochondria because the transition reaction and the citric acid cycle take place in the matrix of the mitochondria.


The two molecules of acetyl-CoA can now enter the citric acid cycle. Acetyl-CoA is also a precursor metabolite for fatty acid synthesis.



Learning Objectives for this Section


Taking the pyruvates from glycolysis (and other pathways), by way of the transition reaction mentioned above, and completely breaking them down into CO2 molecules, H2O molecules, and generating additional ATPs by oxidative phosphorylation.


In prokaryotic cells, the citric acid cycle occurs in the cytoplasm; in eukaryotic cells the citric acid cycle takes place in the matrix of the mitochondria.


The reaction for the citric acid cycle is: acetyl + 3 NAD+ +  FAD +  ADP +  P

yields 2 CO2 + 3NADH + 3 H+ +  FADH2 +  ATP

or the overall reaction with both sides of the split glucose forming two 3 carbon structures going through glycolysis and the intermediate phase and on to the citric acid cyle: 2 acetyl groups + 6 NAD+

+ 2 FAD + 2 ADP + 2 P  yields 4 CO2 + 6 NADH + 6H+  + 2 FADH2 + 2 ATP  

The citric acid cycle provides a series of intermediate compounds that donate protons and electrons to the electron transport chain by way of the reduced coenzymes NADH and FADH2. The electron transport chain then generates additional ATPs by oxidative phosphorylation. The citric acid cycle also produces 2 ATP by substrate phosphorylation.


In addition to their roles in generating ATP, the citric acid cycle also plays an important role in the flow of carbon through the cell by supplying precursor metabolites for various biosynthetic pathways.


The citric acid cycle involves 8 distinct steps, each catalyzed by a unique enzyme. You are not responsible for knowing the chemical structures or enzymes involved in the steps below. They are included to help illustrate how the molecules in the pathway are manipulated by the enzymes in order to to acheive the required products.


1. The citric acid cycle begins when Coenzyme A transfers its 2-carbon acetyl group to the 4-carbon compound oxaloacetate to form the 6-carbon molecule citric acid.


2. The citrate is rearranged to form an isomeric form, isocitrate.


3. The 6-carbon isocitrate is oxidized and a molecule of carbon dioxide is removed producing the 5-carbon molecule alpha-ketoglutaric acid. During this oxidation, NAD+ is reduced to NADH + H+.


4. Alpha-ketogluteric acid is oxidized, carbon dioxide is removed, and coenzyme A is added to form the 4-carbon compound succinyl-CoA. During this oxidation, NAD+ is reduced to NADH + H+.


5. CoA is removed from succinyl-CoA to produce succinic acid. The energy released is used to make guanosine triphosphate (GTP) from guanosine diphosphate (GDP) and Pi by substrate-level phosphorylation. GTP can then be used to make ATP.


6. Succinic acid is oxidized to fumic acid. During this oxidation, FAD is reduced to FADH2 .


7. Water is added to fumeric acid to form malic acid.


8. Malic acid is oxidized to produce oxaloacetic acid, the starting compound of the citric acid cycle. During this oxidation, NAD+ is reduced to NADH + H+ .


The NADH + H+ and FADH2 carry protons and electrons to the electron transport chain to generate additional ATP by oxidative phosphorylation.



Learning Objectives for this Section


Function: During various steps in glycolysis and the citric acid cycle, the oxidation of certain intermediate precursor molecules causes the reduction of NAD+ to NADH + H+ and FAD to FADH2. NADH and FADH2 then transfer protons and electrons to the electron transport chain to produce additional ATPs from oxidative phosphorylation. As mentioned in the previous section on energy, during the process of aerobic respiration, coupled oxidation-reduction reactions and electron carriers are often part of what is called an electron transport chain, a series of electron carriers that eventually transfers electrons from NADH and FADH2 to oxygen. The diffusible electron carriers NADH and FADH2 carry hydrogen atoms (protons and electrons) from substrates in exergonic catabolic pathways such as glycolysis and the citric acid cycle to other electron carriers that are embedded in membranes. These membrane-associated electron carriers include flavoproteins, iron-sulfur proteins, quinones, and cytochromes. The last electron carrier in the electron transport chain transfers the electrons to the teminal electron acceptor, oxygen.


The chemiosmotic theory explains the functioning of electron transport chains. According to this theory, the tranfer of electrons down an electron transport system through a series of oxidation-reduction reactions releases energy. This energy allows certain carriers in the chain to transport hydrogen ions (H+ or protons) across a membrane.


Depending on the type of cell, the electron transport chain may be found in the cytoplasmic membrane or the inner membrane of mitochondria.

In prokaryotic cells, the protons are transported from the cytoplasm of the bacterium across the cytoplasmic membrane to the periplasmic space located between the cytoplasmic membrane and the cell wall .

In eukaryotic cells, protons are transported from the matrix of the mitochondria across the inner mitochondrial membrane to the intermembrane space located between the inner and outer mitochondrial membranes.

As the hydrogen ions accumulate on one side of a membrane, the concentration of hydrogen ions creates an electrochemical gradient or potential difference (voltage) across the membrane. (The fluid on the side of the membrane where the protons accumulate acquires a positive charge; the fluid on the opposite side of the membrane is left with a negative charge.) The energized state of the membrane as a result of this charge separation is called proton motive force or PMF.


This proton motive force provides the energy necessary for enzymes called ATP synthases, also located in the membranes mentioned above, to catalyze the synthesis of ATP from ADP and phosphate. This generation of ATP occurs as the protons cross the membrane through the ATP synthase complexes and re-enter either the bacterial cytoplasm or the matrix of the mitochondria. (Proton motive force is also used to transport substances across membranes during active transport and to rotate bacterial flagella.)


At the end of the electron transport chain involved in aerobic respiration, the last electron carrier in the membrane transfers 2 electrons to half an oxygen molecule (an oxygen atom) that simultaneously combines with 2 protons from the surrounding medium to produce water as an end product.



Determining the exact yield of ATP for aerobic respiration is difficult for a number of reasons. In addition to generating ATP by oxidative phosphorylation in prokaryotic cells, proton motive force is also used for functions such as transporting materials across membranes and rotating flagella. Also, some bacteria use different carriers in their electron transport chain than others and the carriers may vary in the number of protons they transport across the membrane. Furthermore, the number of ATP generated per reduced NADH or FADH2 is not always a whole number. For every pair of electrons transported to the electron transport chain by a molecule of NADH, between 2 and 3 ATP are generated. For each pair of electrons transferred by FADH2, between 1 and 2 ATP are generated. In eukaryotic cells, unlike prokaryotes, NADH generated in the cytoplasm during glycolysis must be transported across the mitochondrial membrane before it can transfer electrons to the electron transport chain and this requires energy. As a result, between 1 and 2 ATP are generated from these NADH.


For simplicity, however, we will look at the theoretical maximum yield of ATP per glucose molecule oxidized by aerobic respiration. We will assume that for each pair of electrons transferred to the electron transport chain by NADH, 3 ATP will be generated; for each electron pair transferred by FADH2, 2 ATP will be generated. Keep in mind, however, that less ATP may actually be generated.


As seen above, one molecule of glucose oxidized by aerobic respiration in prokaryotes yields the following:




2 net ATP from substrate-level phosphorylation

2 NADH yields 6 ATP (assuming 3 ATP per NADH) by oxidative phosphorylation




Transition (intermediate) Reaction


2 NADH yields 6 ATP (assuming 3 ATP per NADH) by oxidative phosphorylation




Citric Acid Cycle


2 ATP from substrate-level phosphorylation

6 NADH yields 18 ATP (assuming 3 ATP per NADH) by oxidative phosphorylation

2 FADH2 yields 4 ATP (assuming 2 ATP per FADH2) by oxidative phosphorylation


Total Theoretical Maximum Number of ATP Generated per Glucose in Prokaryotes


38 ATP: 4 from substrate-level phosphorylation; 34 from oxidative phosphorylation.


In eukaryotic cells, the theoretical maximum yield of ATP generated per glucose is 36 to 38, depending on how the 2 NADH generated in the cytoplasm during glycolysis enter the mitochondria and whether the resulting yield is 2 or 3 ATP per NADH.




Some prokaryotes are able to carry out anaerobic respiration, respiration in which an inorganic molecule other than oxygen (O2) is the final electron acceptor. For example, some bacteria called sulfate reducers can transfer electrons to sulfate (SO42-) reducing it to H2S. Other bacteria, called nitrate reducers, can transfer electrons to nitrate (NO3-) reducing it to nitrite (NO2-). Other nitrate reducers can reduce nitrate even further to nitrous oxide (NO) or nitrogen gas (N2).


Like aerobic respiration, anaerobic respiration involves glycolysis, a transition reaction, the citric acid cycle, and an electron transport chain. The total energy yield per glucose oxidized is less than with aerobic respiration with a theoretical maximum yield of 36 ATP or less.


Fermentation is an anaerobic breakdown of carbohydrates in which an organic molecule is the final electron acceptor. It does not involve an electron transport system. Furthermore,:


it is a partial breakdown of glucose giving a little energy, 2 net ATP's per glucose by way of substrate-level phosphorylation;

it involves only glycolysis; and

is found in anaerobic and facultative anaerobic bacteria.

A. Glycolysis during Fermentation


Function: As during aerobic respiration, glycolysis is a partial breakdown of a six-carbon glucose molecule into two, three-carbon molecules of pyruvate, 2NADH +2H+, and 2 net ATP as a result of substrate-level phosphorylation. Glycolysis occurs in the cytoplasm of the cell. As mentioned above, the overall reaction is:


glucose (6C) + 2 NAD+ +2 ADP +2 inorganic phosphates (Pi)


yields 2 pyruvate (3C) + 2 NADH + 2 H+ + 2 net ATP


Glycolysis also produces a number of key precursor metabolites.


Since there is no electron transport system, the protons and electrons donated by certain intermediate precursor molecules during glycolysis generate no additional molecules of ATP. Instead, they combine with the coenzyme NAD+, the organic molecule which serves as the final electron and proton acceptor, reducing it to NADH + H+.


The 2 pyruvic acids are then converted into one of many different fermentation end products in several non-energy-producing steps.


B. Fermentation end products


Some fermentation end products produced by microorganisms are very beneficial to humans and are the basis of a number of industries (brewing industry, dairy industry, etc.). Examples of fermentation end products include:


Saccharomyces: ethyl alcohol and CO2

Streptococcus and Lactobacillus: lactic acid

Propionibacterium: proprionic acid, acetic acid, and CO2

Escherichia coli: acetic acid, lactic acid, succinic acid, ethyl alcohol, CO2, and H2

Enterobacter: formic acid, ethyl alcohol, 2,3-butanediol, lactic acid, CO2, and H2

Clostridium: butyric acid, butyl alcohol, acetone, isopropyl alcohol, CO2, and H2



Autotrophs are organisms that are able to synthesize organic molecules from inorganic materials. Photoautotrophs absorb and convert light energy into the stored energy of chemical bonds in organic molecules through a process called photosynthesis.


Plants, algae, and bacteria known as cyanobacteria are known as oxygenic photoautotrophs because they synthesize organic molecules from inorganic materials, convert light energy into chemical energy, use water as an electron source, and generate oxygen as an end product of photosynthesis. Some bacteria, such as the green and purple bacteria, are known as anoxygenic phototrophs. Unlike the oxygenic plants, algae, and cyanobacteria, anoxygenic phototrophs do not use water as an electron source and, therefore, do not evolve oxygen during photosynthesis. The electrons come from compounds such as hydrogen gas, hydrogen sulfide, and reduced organic molecules. In this section on photosynthesis, we be concerned with the oxygenic phototrophs.


Photosynthesis is composed of two stages: the light-dependent reactions and the light-independent reactions. The light-dependent reactions convert light energy into chemical energy, producing ATP and NADPH. The light-independent reactions use the ATP and NADPH from the light-dependent reactions to reduce carbon dioxide and convert the energy to the chemical bond energy in carbohydrates such as glucose. Before we get to these photosynthetic reactions however, we need to understand a little about the electromagnetic spectrum and chloroplasts.


1. The Electromagnetic Spectrum


Visible light constitutes a very small portion of a spectrum of radiation known as the electromagnetic spectrum. All radiations in the electromagnetic spectrum travel in waves and different portions of the spectrum are catagorized by their wavelength. A wavelength is the distance from the peak of one wave to that of the next. At one end of the spectrum are television and radio waves with longer wavelengths and low energy. At the other end of the spectrum are gamma rays with a very short wavelength and a great deal of energy. Visible light is the range of wavelengths of the electromagnetic spectrum that humans can see, a mixture of wavelengths ranging from 380 nanometers to 760 nanometers. It is this light that is used in photosynthesis.


Light and other types of radiation are composed of individual packets of energy called photons. The shorter the wavelength of the radiation, the greater the energy per photon. As will be seen shortly, when photons of visible light energy strike certain atoms of pigments during photosynthesis, that energy may push an electron from that atom to a higher energy level where it can be picked up by an electron acceptor in an electron transport chain. ATP can then be generated by chemiosmosis.


Animation showing photons exciting an electron to a higher energy level.



2. Chloroplasts


In eukaryotic cells, photosynthesis takes place in organelles called chloroplasts. Like mitochondria, chloroplasts are surrounded by an inner and an outer membrane. The inner membrane encloses a fluid-filled region called the stroma that contains enzymes for the light-independent reactions of photosynthesis. Infolding of this inner membrane forms interconnected stacks of disk-like sacs called thylakoids, often arranged in stacks called grana. The thylakoid membrane, which encloses a fluid-filled thylakoid interior space, contains chlorophyll and other photosynthetic pigments as well as electron transport chains. The light-dependent reactions of photosynthesis occur in the thylakoids. The outer membrane of the chloroplast encloses the intermembrane space between the inner and outer chloroplast membranes.


The thylakoid membranes contain several pigments capable of absorbing visible light. Chlorophyll is the primary pigment of photosynthesis. Chlorophyll absorbs light in the blue and red region of the visible light spectrum and reflects green light. There are two major types of chlorophyll, chlorophyll a that initiates the light-dependent reactions of photosynthesis, and chlorophyll b, an accessory pigment that also participates in photosynthesis. The thylakoid membranes also contain other accessory pigments. Carotenoids are pigments that absorb blue and green light and reflect yellow, orange, or red. Phycocyanins absorb green and yellow light and reflect blue or purple. These accessory pigments absorb light energy and transfer it to chlorophyll.


Photosynthetic prokaryotic cells do not possess chloroplasts. Instead, thylakoid membranes are usually arranged around the periphery of the bacterium as infoldings of the cytoplasmic membrane.


3. Photosynthesis


As mentioned above, photoautotrophs use sunlight as a source of energy and through the process of photosynthesis, reduce carbon dioxide to form carbohydrates such as glucose. The radient energy is converted to the chemical bond energy within glucose and other organic molecules.


The overall reaction for photosynthesis is as follows:       6 CO2 + 12 H2O in the presence of light and chlorophyll yields C6H12O6 + 6 O2 + 6 H2O.  Note that carbon dioxide (CO2) is reduced to produce glucose (C6H12O6 ) while water (H2O) is oxidized to produce oxygen (O2).


Photosynthesis is composed of two stages: the light-dependent reactions and the light independent reactions. We will now look at the role of each in the next two sections.



The exergonic light-dependent reactions of photosynthesis convert light energy into chemical energy, producing ATP and NADPH. These reactions occur in the thylakoids of the chloroplasts. The products of the light-dependent reactions, ATP and NADPH, are both required for the endergonic light-independent reactions.


The light-dependent reactions can be summarized as follows:


12 H2O + 12 NADP+ + 18 ADP + 18 Pi + light and chlorophyll  yields 6 O2 + 12 NADPH + 18 ATP


The light-dependent reactions involve two photosystems called Photosystem I and Photosystem II. These photosystems include units called antenna complexes composed of chlorophyll molecules and accessory pigments located in the thylakoid membrane. Photosystem I contain chlorophyll a molecules called P700 because they have an absorption peak of 700 nanometers. Photosystem II contains chlorophyll a molecules referred to as P680 because they have an absorption peak of 680 nanometers.


Each antenna complex is able to trap light and transfer energy to a complex of chlorophyll molecules and proteins called the reaction center. As photons are absorbed by chlorophyll and accessory pigments, that energy is eventually transfered to the reaction center where, when absorbed by an excitable electron, moves it to a higher energy level. Here the electron may be accepted by an electron acceptor molecule of an electron transport chain where the light energy is converted to chemical energy by chemiosmosis.


The most common light-dependent reaction in photosynthesis is called noncyclic photophosphorylation. Noncyclic photophosphorylation involves both Photosystem I and Photosystem II and produces ATP and NADPH. During noncyclic photophosphorylation, the generation of ATP is coupled to a one-way flow of electrons from H2O to NADP+. We will now look at Photosystems I and II and their roles in noncyclic photophosphorylation.


1. As photons are absorbed by pigment molecules in the antenna complexes of Photosystem II, excited electrons from the reaction center are picked up by the primary electron acceptor of the Photosystem II electron transport chain. During this process, Photosystem II splits molecules of H2O into 1/2 O2, 2H+, and 2 electrons. These electrons continuously replace the electrons being lost by the P680 chlorophyll a molecules in the reaction centers of the Photosystem II antenna complexes.


During this process, ATP is generated by the Photosystem II electron transport chain and chemiosmosis. According to the chemiosmosis theory, as the electrons are transported down the electron transport chain, some of the energy released is used to pump protons across the thylakoid membrane from the stroma of the chloroplast to the thylakoid interior space producing a proton gradient or proton motive force. As the accumulating protons in the thylakoid interior space pass back across the thylakoid membrane to the stroma through ATP synthetase complexes, this proton motive force is used to generate ATP from ADP and Pi.

  2. Meanwhile, photons are also being absorbed by pigment molecules in the antenna complex of Photosystem I and excited electrons from the reaction center are picked up by the primary electron acceptor of the Photosystem I electron transport chain. The electrons being lost by the P700 chlorophyll a molecules in the reaction centers of Photosystem I are replaced by the electrons traveling down the Photosystem II electron transport chain. The electrons transported down the Photosystem I electron transport chain combine with 2H+ from the surrounding medium and NADP+ to produce NADPH + H+.   


Cyclic photophosphorylation occurs less commonly in plants than noncyclic photophosphorylation, most likely occurring when there is too little NADP+ available. It is also seen in certain photosynthetic bacteria. Cyclic photophosphorylation involves only Photosystem I and generates ATP but not NADPH. As the electrons from the reaction center of Photosystem I are picked up by the electron transport chain, they are transported back to the reaction center chlorophyll. As the electrons are transported down the electron transport chain, some of the energy released is used to pump protons across the thylakoid membrane from the stroma of the chloroplast to the thylakoid interior space producing a proton gradient or proton motive force. As the accumulating protons in the thylakoid interior space pass back across the thylakoid membrane to the stroma through ATP synthetase complexes, this energy is used to generate ATP from ADP and Pi.



The endergonic light-independent reactions of photosynthesis use the ATP and NADPH synthesized during the exergonic light-dependent reactions to provide the energy for the synthesis of glucose and other organic molecules from inorganic carbon dioxide and water. This is done by "fixing" carbon atoms from CO2 to the carbon skeletons of existing organic molecules. These reactions occur in the stroma of the chloroplasts.


The light-independent reactions can be summarized as follows:


12 NADPH + 18 ATP + 6 CO2 yields C6H12O6 (glucose) + 12 NADP+ + 18 ADP + 18 Pi + 6 H2O


Most plants use the Calvin (C3) cycle to fix carbon dioxide. C3 refers to the importance of 3-carbon molecules in the cycle. Some plants, known as C4 plants and CAM plants, differ in their initial carbon fixation step.



1. The Calvin (C3) Cycle

There are three stages to the Calvin cycle: 1) CO2 fixation; 2) production of G3P; and 3) regeneration of RuBP. We will now look at each stage.


stage 1: CO2 fixation


To begin the Calvin cycle, a molecule of CO2 reacts with a five-carbon compound called ribulose bisphosphate (RuBP) producing an unstable six-carbon intermediate which immediately breaks down into two molecules of the three-carbon compound phosphoglycerate (PGA). The carbon that was a part of inorganic CO2 is now part of the carbon skeleton of an organic molecule. The enzyme for this reaction is ribulose bisphosphate carboxylase or Rubisco. A total of six molecules of CO2 must be fixed this way in order to produce one molecule of the six-carbon sugar glucose.


stage 2: Production of G3P from PGA


The energy from ATP and the reducing power of NADPH (both produced during the light-dependent reactions) is now used to convert the molecules of PGA to glyceraldehyde-3-phosphate (G3P), another three-carbon compound. For every six molecules of CO2 that enter the Calvin cycle, two molecules of G3P are produced. Most of the G3P produced during the Calvin cycle - 10 of every 12 G3P produced - are used to regenerate the RuBP in order for the cycle to continue. Some of the molecules of G3P, however, are used to synthesize glucose and other organic molecules. As can be seen in, two molecules of the three-carbon G3P can be used to synthesize one molecule of the six-carbon sugar glucose. The G3P is also used to synthesize the other organic molecules required by photoautotrophs.


stage 3: Regeneration of RuBP from G3P


As mentioned in the previous step, most of the G3P produced during the Calvin cycle - 10 of every 12 G3P produced - are used to regenerate the RuBP so that the cycle may continue. Ten molecules of the three-carbon compound G3P eventually form six molecules of the four-carbon compound ribulose phosphate (RP). Each molecule of RP then becomes phosphorylated by the hydrolysis of ATP to produce ribulose bisphosphate (RuBP), the starting compound for the Calvin cycle.





The entry and exit of gasses in plants is through small pores called stomata located on the underside of leaves. Carbon dioxide, the gas required for the Calvin cycle, is not a very abundant gas in nature. Under hot and dry environmental conditions the stomata close to reduce the loss of water vapor, but this also results in a greatly diminished supply of CO2 for the plant. Plants that normally live in dry, hot climates have adapted different ways of initially fixing CO2 prior to its entering the Calvin cycle. These pathways of carbon fixation, know as the C4 and the CAM pathways, take place in the cytoplasm of the cell.


A. The C4 pathway:  The C4 pathway is designed to efficiently fix CO2 at low concentrations and plants that use this pathway are known as C4 plants. These plants first fix CO2 into a four carbon compound (C4) called oxaloacetate. This occurs in cells called mesophyll cells. First, CO2 is fixed to a three-carbon compound called phosphoenolpyruvate to produce the four-carbon compound oxaloacetate. The enzyme catalyzing this reaction, PEP carboxylase, fixes CO2 very efficiently so the C4 plants don't need to to have their stomata open as much.


The oxaloacetate is then converted to another four-carbon compound called malate in a step requiring the reducing power of NADPH. The malate then exits the mesophyll cells and enters the chloroplasts of specialized cells called bundle sheath cells. Here the four-carbon malate is decarboxylated to produce CO2, a three-carbon compound called pyruvate, and NADPH. The CO2 combines with ribulose bisphosphate and goes through the Calvin cycle while the pyruvate re-enters the mesophyll cells, reacts with ATP, and is converted back to phosphoenolpyruvate, the starting compound of the C4 cycle.


B. The CAM pathway


CAM plants live in very dry condition and, unlike other plants, open their stomata to fix CO2 only at night. Like C4 plants, the use PEP carboxylase to fix CO2, forming oxaloacetate. The oxaloacetate is converted to malate which is stored in cell vacuoles. During the day when the stomata are closed, CO2 is removed from the stored malate and enters the Calvin cycle.





Major concepts:

One way that cells can propagate is by dividing into two identical copies. Eukaryotic cells undergo a process called mitosis. Most importantly, during mitosis each resulting cell must have a complete copy of the genetic information present in the parental cells DNA.

Mitosis generates exact copies of each of chromosomes present in the parental cell and places one copy of each into each daughter cell. By so doing mitosis creates exact genetic replicas of the original cell.

Cell division is an elaborate process. During mitosis the cell first replicates all of the DNA present in the chromosomes, generating a second copy of each one. Later, these chromosomes segregate to the two daughter cells. In eukaryotic cells the processes of DNA replication and division are separated in time. Cells have a schedule for accomplishing these two processes; this schedule is called the cell cycle.

Passage of genetic information to succeeding  generations


The fundamental fact about living things is that they have a limited lifetime-a fact that most people, especially younger people, have inadequately dealt with ("THE PETER PAN" or  "FOREVER YOUNG SYNDROME"). Since young people do grow old and die like everyone else---the most important function of a organism is to replace itself.


The thing which identifies biological entities most clearly is their ability to reproduce.


Even viruses, which show no other traits associated with life, are able to reproduce themselves


Here we will consider the mechanisms that allow eukaryotic cells to faithfully reproduce themselves.


The forms of cell division.


The simplest form of cell division occurs in bacteria. Bacteria divide by a process called binary fission, a process of asexual reproduction. Essentially, the process involves the equal (or sometimes unequal) division of the cell and all of its contents.


The DNA content of the cell is divided between the two daughter cells. The actual division involves extending the plasma membrane and external cell wall across the bacterium to create two independent cells


The process of divsion in bacteria is highly regulated, as we will see is true of eukaryotes, but it occurs without an overt change in the appearance of the cell before the actual division.


Eukaryotes, because their cells are much larger in size and contain a much greater amount of DNA, divide by processes which are much more elaborate. The form of cell division which we will consider today is mitosis.


Mitosis is a process which generates two daughter cells which are genetically identical to the parent (in a sense, they are clones of the mother cell). Mitosis is an asexual process (meaning that it does not involve the generation of new individuals by fusion of unique germ cells, or gametes). It is used as a form of asexual reproduction by single-celled eukaryotes. Bodily growth in multi-cellular eukaryotes occurs by mitosis


The second form of cell division in eukaryotes, which we will get to next time, is meiosis.


It is essential that you recognize the fundamental difference between these two processes. Meiosis importantly creates cells that differ from the mother cell. Since meiosis is the mechanism by which gametes are formed it is important that they be unique to allow for genetic variability in a species. Since gametes must fuse to form a new organism in sexual reproduction, they must have half the number of chromosomes present in a somatic cell.


("Somatic" means literally "of the body" ("soma" = "body" in Greek), but refers to all cells which are not of the germ line, cells set aside for sexual reproduction.)


Eukaryotic DNA is organized into chromosomes


Chromosomes were discovered in the 19th century by microscopists who looked at cells stained with special dyes.


Chromosomes took up some of these dyes, and were therefore colored ("chromosome" = "colored body"--it is from the same Greek root as somatic). The microscopists had no idea what the function of these bodies was, but they were seen to divide evenly between cells.


When the seminal work on genetics done by the Czech monk, Gregor Mendel, was rediscovered around 1900 (after being ignored for about half a century) these bodies were associated with the genetic traits he described.


Chromosomes contain linear molecules of DNA-one per chromosome-packaged into a complex structure with special protein molecules

Before a cell can divide, its DNA content must be duplicated (so that identical copies can be passed on to the next generation),


This creates the familiar X-shaped structures that you probably associate with chromosomes. In these are two identical structures, called sister chromatids. Perhaps counterintuitively, both the linear structure and the X-shaped structure (before and after replication) are called chromosomes


Sister chromatids refer to the two halves of the duplicated chromosome. When mitosis occurs sister chromatids separate, move to separate cells, and become chromosomes.


The place where the sister chromatids touch (the crossing point of the X) is called the centromere. This is an important structure since it is the place at which the machinery responsible for moving DNA into the new daughter cells attaches.


"Ploidy" and chromosome number


Most organisms have two parents--a mother and a father-both of whom contribute genetic material. These organisms must have a maternal and a paternal copy of each chromosomes, the highest level of organization of genetic material.


A cell carrying two copies of each chromosome is called diploid. (One with four copies, which occurs in some plants, is called tetraploid, and one with only a single copy, as occurs in germ cells, is called haploid)


Human cells have 23 pairs of chromosomes, or 46. Some species have very few chromosomes (four pairs in the fruit fly, Drosophila melanogaster), while some have enormous numbers (such as the 108 pairs in the Horsetail). But each is still matched with one and only one identical partner.


The schedule of DNA replication and separation: the cell cycle


Since cells contain large amounts of DNA organized in large numbers of chromosome pairs, the process of replication and segregation of the chromosomes must be carefully regulated. Cells organize the processes of replication and segregation temporally into something called the cell cycle.


Among identical cells in a population the events of cell growth, DNA replication, chromosome separation, and cell division occur on a common schedule. Cells continuously increase in size after dividing. After it has grown to a particular size (which corresponds to a particular time after division) each cell will begin to duplicate its DNA. DNA duplication, or "replication", takes about the same length of time in all cells.


(What would the ploidy of a cell be after this process is finished?)


After duplication cells continue to grow. They then begin to divide at about the same size, at about the same time after replication ends.


This process can be envisioned as a clock separated into four major sectors




 Nuclear division (chromosome segregation) and cell division


 Gap 1

 Period of growth before beginning DNA replication


 DNA Synthesis

 Period of DNA replication


 Gap 2

 Second period of growth following the end of DNA synthesis


The three periods--G1, S, and G2--are also referred to collectively as interphase since they constitute the period between successive mitoses. They are also pooled collectively because the cells do not differ morphologically during this phase, and early microscopists could only distinguish mitotic from interphase cells


(If the cells can not be distinguished by appearance, how do we know that a cell is in G1, S, or G2?)


The cell cycle for an "average" human cell is about a day, while for a yeast cell it is 90 minutes.


Chromosomes condense during mitosis


During mitosis you can not see the chromosomes. It is only as cells enter mitosis that they begin to condense and begin to appear as we normally think of them. As they are condensing the cell membrane disassembles


After they condense the chromosomes attach to a special structure called a spindle, which consists of a set of microscopic filaments called microtubules

The microtubules attach to the position of the centromere and act as tiny ropes, pulling the chromosomes apart. Each of the pairs of sister chromatids separate at this stage and move to the opposite poles of the cell.


After they have moved to the opposite poles two nuclear membranes begin to form around the separated groups of chromosomes, which then decondense and return to the interphase state. Microscopists have invented names to describe each of these stages of mitosis:


Prophase: chromosomes begin to condense (early) and the nucleus disassembles (late)

Metaphase: the chromosomes attach to the spindle and line up at the midpoint of the spindle (the "metaphase plate")

Anaphase: the chromosomes move to the two poles of the spindle

Telophase: chromosomes decondense and the nuclear membrane reforms (from vesicles derived from the previous nuclear membrane).


The spindle is an interesting structure. The microtubules form an interdigitated structure, and that proteins which are microscopic motors push the "fingers" of the structure in opposite directions. This moves the two ends of the spindle apart. Second, the chromosomes are attached to the ends of the spindle by other microtubules which shorten as mitosis continues


The combination of effects moves the chromosomes to the poles of the cell.


Cell division

The process of cell division proceeds only after the pairs of chromosomes are separated. Cell division occurs by different mechanisms in plants and animals




Division involves laying down of a division plate within the dividing cell. This grows until it bridges the entire width of the cell, dividing it into two. Actually, the plate is two new plasma membranes, separated by two new cell walls, and actually cemented together by adhesive molecules.




Animal cells divide by "pinching in two". A microfilament ring immediately below the surface of the cell becomes gradually smaller, cinching a furrow around the cell. This continues until the membrane fuses in the middle, separating the two daughter cells.


The process of mitosis, by dividing the two identical sister chromatids and separating them to the two daughter cells, produces two identical cells (at least genetically).


A process insures genetic diversity by producing random assortments of genes in cells carrying randomly selected chromosomes, and even segments of chromosomes-meiosis.




Major concepts:


Diploid cells have two sets of chromosomes, one maternal and one paternal. This derives from the fact that each organism derives from the fusion of two haploid reproductive cells (gametes).

Gametes are generated in a process called meiosis. Meiosis has two objects: reduction of the number of chromsomes by half (2N to 1N) and random segregation of chromosomes to the cells that result.

Before meiosis begins the cells make copies of each of their chromosomes (replication) as normal during cell division. During the first meiotic division (Meiosis I) the each pair of maternal and paternal chromosomes segregate from each other.

The cells then divide again without the chromosomes being replicated. In this division (Meiosis II) the paired identical maternal or paternal chromosomes divide and segregate. The haploid cells that result will later develop into mature gametes.

As described mitosis is the process eukaryotic cells use to produce identical copies of cells.


The essential fact about mitosis is that at metaphase each duplicated chromosome lines up on the metaphase plate and the two sister chromatids separate and move to opposite poles of the cell. Since the two sister chromatids are the same this ensures that each of the unique DNA molecules in the cell are transmitted to the next generation.


What would happen if a single pair of chromatids did not separate and move to opposite poles? Why would this be detrimental to the resulting cells?


Nondisjunction (the name of this event) results in cells with too few or too many chromosomes. Most of the resulting cells are dead, but sometimes they survive.


Aneuploids (cells with abnormal chromosome numbers) can survive sometimes, and are often profoundly abnormal. Down's syndrome is an example of a relatively benign aneuploidy.


So clearly, the process of mitosis is essential in the short term to the ability of organisms to survive. Another process of cell division is essential to the long-term survival of a species--meiosis.


The concept of homologous chromosomes


I have already discussed the idea that each of your cells contains two copies of each unique chromosome This is easiest to envision when talking about the sex chromosomes:


In humans, the sex of each individual is determined by the identity of the two sex chromosomes. There are two types of sex chromosomes, the X and the Y. A male receives an X chromosome from his mother and a Y from his father.


This is the clearest example of the idea of there being a "mother's" chromosome and a "father's" chromosome.


A female receives an X chromosome from each parent.


However, the existence of a maternal chromosome and a paternal chromosome is not limited to the sex chromosomes. Each of the somatic chromosomes (chromosomes not involved in sex determination, not "chromosomes involved in body formation") also comes as a maternal and a paternal copy.


Are these chromosomes likely to be identical?. In fact, the two chromosomes in any pair are not identical since the parents are individuals with very different genetic makeups.


This difference is at the level of genes, as we shall see. Mutations in particular genes cause differences that we can see--we call those phenotypes.


The two chromosomes which make up a pair are called homologous, which literally means that they have a common origin (evolutionarily).


It does not mean that they are identical. It means that almost all of their sequences are exactly alike, with only small differences which generate phenotypic differences.


Two such chromosomes are termed homologues.



The mechanics of meiosis


Meiosis consists of two successive divisions without an intervening DNA replication. Each of the divisions looks similar to a mitotic division, though the first involves a separation of chromosomes which is unlike mitosis (the second is simply a mitotic division).


The two divisions are called Meiosis I and Meiosis II. In each of these divisions the intervals within are designated with a I or II (e.g, Prophase I and Prophase II).


Meiosis I


Meiosis I begins as Mitosis, with the disassembly of the nuclear membrane and condensation of the chromosomes (Prophase).


Meiosis is made up by two subsequent processes, both of which resemble mitosis. In the first process the homologous chromosomes are separated. It has an unusually long prophase that is subdivided into different stages: leptotene, zygotene, pachytene, diplotene and diakinesis. They are followed by metaphase, anaphase and telophase.

leptotene. This phase differs only slightly from the early stages of mitosis. The cells and nuclei of meiotic tissues are usually bigger than that of their neighboring tissues and they do often seem to be longer and are longitudinally structured. At regular intervals thickenings can be found, like beads on a string: the chromomeres. Their number, size and positioning is constant in each species.During leptotene homologs begin to search for each other.

zygotene. During this phase the pairing of homologous chromosomes begins. It is also called synapsis and the resulting structure synaptonemic complex. Directly after initiation of the process the pairing spreads like a zipper across the whole length of the chromosome. 

pachytene. During the pachytene the pairing stabilizes. The number of synaptic complexes corresponds to the number of chromosomes in a haploid set of the respective species. Crossing over occurs during this subphase. The pairs are also called bivalents.

diplotene. The bivalents separate again. During this process it emerges that each chromosome is built of two chromatids, so that the whole complex harbours four strands during the separation. Normally the separation is not accomplished, but the homologous chromosomes stick together at certain points, the chiasmata (sing. chiasma). This state is marked by the formation of cross-like structures, single or multiple loops.During the diplotene stage, chiasmata appear to move towards the ends of the synapsed chromosomes in the process of terminalization and ultimately to slip off the ends.

diakinesis is the continuation of the diplotene. It is usually difficult demarcate both states. The chromosomes condense and become more compact. The chromosomes begin to coil and so become shorter and thicker. Terminalization is completed. The nucleolus detaches from the nucleolar organizer and disappears completely. The nuclear envelope starts to degenerate and spindle formation is well under the way.

The duplicated chromosomes (each with two sister chromatids) attach to the spindle and move to the metaphase plate (Metaphase I).

Each pair of duplicated chromosomes is still paired. They therefore align with each other at the metaphase plate. The centromeric regions of each duplicated chromosome is fused into one structure which is attached to one of the spindle poles by microtubules.


The spindle pulls the duplicated chromosomes to the poles (Anaphase I). At this stage the maternal and paternal chromosomes are separated from each other. This is the separation which is random, giving rise to the large number of possible segregation patterns. The chromosomes dissociate from the spindle (Telophase I).


Meiosis II


This occurs after cell division-two cells are now involved. The two resulting cells then proceed directly to the next division with the assembly of new spindles in each cell, and attachment of the still condensed chromosomes to it (Prophase II).


Each sister chromatid must attach to a different spindle in preparation for division of the sister chromatids from each other.


The chromosomes line up on the metaphase plate (Metaphase II).


Since each of the duplicated chromosomes in these cells are unique they can not pair with each other. Each chromosome must line up by itself on the plate. This is a mitotic division, but unlike normal mitosis the cells are diploid and will give haploid progeny (mitosis in diploid somatic tissue occurs by a tetraploid producing two diploid cells).


Each pair of sister chromatids then separates and moves to opposite poles of the cell (Anaphase II). The chromosomes decondense and the nuclear membrane reforms (Telophase II).


The result is the production of four haploid cells each containing a single copy of each chromosome.


DNA recombination and meiosis


There is another level at which the collection of genes in the genome are randomized-DNA recombination.


During prophase I the chromosomes pair with each other so that the maternal and paternal chromosomes are in close contact. Enzymes in the cell recognize regions of identical sequence in the chromosomes. They catalyze the breakage and rejoining of DNA strands to exchange sequences between non-sister chromatids. This changes the linkage of genes on the chromosome.


Remember that the two homologous chromosomes are not identical in every way. They carry sequence differences between the genome of the mother and the father. These differences are called alleles. The father's chromosome will have a set of alleles on each chromosome many of which will be different from those on the mother's chromosome. Recombination puts some of the mother's alleles and some of the father's alleles on the same DNA molecule


So, since in Anaphase I the paternal and maternal chromosomes separate to the two poles of the cell, what is the effect of recombination on segregation of maternal and paternal alleles? How does this influence the amount of variability in the products of meiosis?


The take-home-esson for meiosis is that random segregation of chromosomes at Anaphase I and the shuffling of sequences by recombination during Prophase I provides an immense variability in the products of meiosis.


The segregation provides over 8 million possible ways chromosomes can segregate into the gametes. Recombination greatly increases this number since each chromosome probably undergoes at least one recombination per chromosome arm per meiotic prophase. In combination with the great diversity of alleles present in a population, this random assortment of alleles provides for an immense number of possible gametes. Fusion of two such gametes creates a new individual who is almost certainly unique genetically






For thousands of years farmers and herders have been selectively breeding their plants and animals to produce more useful hybrids.   It was somewhat of a hit or miss process since the actual mechanisms governing inheritance were unknown.  Knowledge of these genetic mechanisms finally came as a result of careful laboratory breeding experiments carried out over the last century and a half.


By the 1890's, the invention of better microscopes allowed biologists to discover the basic facts of cell division and sexual reproduction.  The focus of genetics research then shifted to understanding what really happens in the transmission of hereditary traits from parents to children.  A number of hypotheses were suggested to explain heredity, but Gregor Mendel, a little known Central European monk, was the only one who got it more or less right.  His ideas had been published in 1866 but largely went unrecognized until 1900, which was long after his death.  His early adult life was spent in relative obscurity doing basic genetics research and teaching high school mathematics, physics, and Greek in Brno (now in the Czech Republic).  In his later years, he became the abbot of his monastery and put aside his scientific work.


While Mendel's research was with plants, the basic underlying principles of heredity that he discovered also apply to people and other animals because the mechanisms of heredity are essentially the same for all complex life forms.


Through the selective cross-breeding of common pea plants (Pisum sativum) over many generations, Mendel discovered that certain traits show up in offspring without any blending of parent characteristics.   For instance, the pea flowers are either purple or white--intermediate colors do not appear in the offspring of cross-pollinated pea plants.  Mendel observed seven traits that are easily recognized and apparently only occur in one of two forms:



 flower color is purple or white


 seed color is yellow or green


 flower position is axil or terminal      


 pod shape is inflated or constricted


 stem length is long or short


 pod color is yellow or green


 seed shape is round or wrinkled




This observation that these traits do not show up in offspring plants with intermediate forms was critically important because the leading theory in biology at the time was that inherited traits blend from generation to generation.  Most of the leading scientists in the 19th century accepted this "blending theory."  Charles Darwin proposed another equally wrong theory known as "pangenesis".  This held that hereditary "particles" in our bodies are affected by the things we do during our lifetime.  These modified particles were thought to migrate via blood to the reproductive cells and subsequently could be inherited by the next generation.  This was essentially a variation of Lamarck's incorrect idea of the "inheritance of acquired characteristics."


Mendel picked common garden pea plants for the focus of his research because they can be grown easily in large numbers and their reproduction can be manipulated.  Pea plants have both male and female reproductive organs.  As a result, they can either self-pollinate themselves or cross-pollinate with another plant.  In his experiments, Mendel was able to selectively cross-pollinate purebred plants with particular traits and observe the outcome over many generations.  This was the basis for his conclusions about the nature of genetic inheritance.


In cross-pollinating plants that either produce yellow or green peas exclusively, Mendel found that the first offspring generation (f1) always has yellow peas.   However, the following generation (f2) consistently has a 3:1 ratio of yellow to green.


This 3:1 ratio occurs in later generations as well.   Mendel realized that this was the key to understanding the basic mechanisms of inheritanceHe came to three important conclusions from these experimental results:



 that the inheritance of each trait is determined by "units" or "factors" that are passed on to descendents unchanged      (these units are now called genes )


 that an individual inherits one such unit from each parent for each trait


 that a trait may not show up in an individual but can still be passed on to the next generation.


It is important to realize that, in this experiment, the starting parent plants were homozygous for pea color.  That is to say, they each had two identical forms (or alleles ) of the gene for this trait--2 yellows or 2 greens.  The plants in the f1 generation were all heterozygous .   In other words, they each had inherited two different alleles--one from each parent plant.  It becomes clearer when we look at the actual genetic makeup, or genotype , of the pea plants instead of only the phenotype , or observable physical characteristics.


Note that each of the f1 generation plants (shown above) inherited a Y allele from one parent and a G allele from the other.  When the f1 plants breed, each has an equal chance of passing on either Y or G alleles to each offspring.


With all of the seven pea plant traits that Mendel examined, one form appeared dominant over the other.  Which is to say, it masked the presence of the other allele.  For example, when the genotype for pea color is YG (heterozygous), the phenotype is yellow.  However, the dominant yellow allele does not alter the recessive green one in any way.   Both alleles can be passed on to the next generation unchanged.


Mendel's observations from these experiments can be summarized in two principles:



 the principle of segregation


 the principle of independent assortment


According to the principle of segregation, for any particular trait, the pair of alleles of each parent separate and only one allele passes from each parent on to an offspring.  Which allele in a parent's pair of alleles is inherited is a matter of chance.  We now know that this segregation of alleles occurs during the process of sex cell formation.

According to the principle of independent assortment, different pairs of alleles are passed to offspring independently of each other.  The result is that new combinations of genes present in neither parent are possible.  For example, a pea plant's inheritance of the ability to produce purple flowers instead of white ones does not make it more likely that it will also inherit the ability to produce yellow peas in contrast to green ones.  Likewise, the principle of independent assortment explains why the human inheritance of a particular eye color does not increase or decrease the likelihood of having 6 fingers on each hand.  Today, we know this is due to the fact that the genes for independently assorted traits are located on different chromosomes .

These two principles of inheritance, along with the understanding of unit inheritance and dominance, were the beginnings of our modern science of genetics.  However, Mendel did not realize that there are exceptions to these rules.  Some of these exceptions will be explored in the third section of this tutorial and in the Synthetic Theory of Evolution tutorial.




NOTE:  One of the reasons that Mendel carried out his breeding experiments with pea plants was that he could observe inheritance patterns in up to two generations a year.  Geneticists today usually carry out their breeding experiments with species that reproduce much more rapidly so that the amount of time and money required is significantly reduced.  Fruit flies and bacteria are commonly used for this purpose now.  Fruit flies reproduce in about 2 weeks from birth, while bacteria, such as E. coli found in our digestive systems, reproduce in only 3-5 hours.


 Since Mendel's time, our knowledge of the mechanisms of genetic inheritance has grown immensely.  For instance, it is now understood that inheriting one allele can, at times, increase the chance of inheriting another or can affect how and when a trait is expressed in an individual's phenotype.  Likewise, there are degrees of dominance and recessiveness with some traits.  The simple rules of Mendelian inheritance do not apply in these and other Polygenic Traits


Some traits are determined by the combined effect of more than one pair of genes.  These are referred to as polygenic, or continuous, traits.  An example of this is human stature.  The combined size of all of the body parts from head to foot determines the height of an individual.  There is an additive effect.  The sizes of all of these body parts are, in turn, determined by numerous genes.   Human skin, hair, and eye color are also polygenic traits because they are influenced by more than one allele at different loci.  The result is the perception of continuous gradation in the expression of these traits.


  Intermediate Expression


Apparent blending can occur in the phenotype when there is incomplete dominance resulting in an intermediate expression of a trait in heterozygous individuals.  For instance, in primroses, snapdragons, and four-o'clocks, red or white flowers are homozygous while pink ones are heterozygous.  The pink flowers result because the single "red" allele is unable to code for the production of enough red pigment to make the petals dark red.


Another example of an intermediate expression may be the pitch of human male voices.  The lowest and highest pitches apparently are found in men who are homozygous for this trait (AA and aa), while the intermediate range baritones are heterozygous (Aa).  The child-killer disease known as Tay-Sachs is also characterized by incomplete dominance.  Heterozygous individuals are genetically programmed to produce only 40-60% of the normal amount of an enzyme that prevents the disease.


Fortunately for Mendel, the pea plant traits that he studied were controlled by genes that do not exhibit an intermediate expression in the phenotype.  Otherwise, he probably would not have discovered the basic rules of genetic inheritance.




For some traits, two alleles can be codominant.   That is to say, both are expressed in heterozygous individuals.  An example of this is people who have an AB blood type for the ABO blood system.  When they are tested, these individuals actually have the characteristics of both type A and type B blood.  Their phenotype is not intermediate between the two.


Type AB blood testing as both A and B


Multiple-allele Series


The ABO blood type system is also an example of a trait that is controlled by more than just a single pair of alleles.  In other words, it is due to a multiple-allele series.  In this case, there are three alleles (A, B, and O), but each individual only inherits two of them (one from each parent).


Some traits are controlled by far more alleles.  For instance, the human HLA system, which is responsible for identifying and rejecting foreign tissue in our bodies, can have at least 30,000,000 different genotypes.  It is the HLA system which causes the rejection of organ transplants. The more we learn about human genetics the more it becomes clear that multiple-allele series are very common.  In fact, it now appears that they are more common than simple two allele ones.


Modifying and Regulator Genes


There are two classes of genes that can have an effect on how other genes function.  They are called modifying genes and regulator genes.


Modifying genes alter how certain other genes are expressed in the phenotype.  For instance, there is a dominant cataract gene which will produce varying degrees of vision impairment depending on the presence of a specific allele for a companion modifying gene.  However, cataracts also can be promoted by diabetes and common environmental factors such as excessive ultraviolet radiation.


Regulator genes can either initiate or block the expression of other genes.  They control the production of a variety of chemicals in plants and animals.   For instance, the time of production of specific proteins that will be new structural parts of our bodies can be controlled by such regulator genes.  Shortly after conception, regulator genes work as master switches orchestrating the timely development of our body parts.  They are also responsible for changes that occur in our bodies as we grow older.  In other words, they control the maturation and aging processes.  Regulator genes are also referred to as homeotic genes.


Incomplete Penetrance


Some genes are incompletely penetrant.   That is to say, their effect does not normally occur unless certain environmental factors are present.  For example, you may inherit a gene for diabetes but never get the disease unless you become greatly overweight, persistently stressed psychologically, or do not get enough sleep on a regular basis.   Similarly, the gene that causes the chronic disease known as multiple sclerosis may be triggered by the Epstein-Barr virus


Sex Related Genetic effects


There are three categories of genes that may have different effects depending on an individual's gender.   Sex-controlled genes are expressed in both sexes but differently.  An example of this is gout, a disease that causes painfully inflamed joints.  If the gene is present, men are nearly eight times more likely than women to have severe symptoms.


Some genes are known to have a different effect depending on the gender of the parent from whom they are inherited. This phenomenon is referred to as genome imprinting or genetic imprinting.  Apparently, diabetes , psoriasis , and some rare genetically inherited diseases, such as a form of mental retardation known as Angelman syndrome , can follow this inheritance pattern.




A single gene may be responsible for a variety of traits.  This is called pleiotropy. The complex of symptoms that are collectively referred to as sickle-cell trait , or sickle-cell anemia, is an example.  A single gene results in irregularly shaped red blood cells that painfully block blood vessels, cause poor overall physical development, as well as related heart, lung, kidney, and eye problems.  Another pleiotropic trait is albinism.  The gene for this trait not only results in a deficiency of skin, hair, and eye pigmentation but also causes defects in vision.


Stuttering Alleles


Lastly, it is now known that some genetically inherited diseases have more severe symptoms each succeeding generation due to segments of the defective genes being doubled in their transmission to children (as illustrated below).  These are referred to as stuttering alleles or unstable alleles.  Examples of this phenomenon are Huntington's disease, fragile-X syndrome, and the myotonic form of muscular dystrophy .


Unstable allele doubling each generation


Mendel believed that all units of inheritance are passed on to offspring unchanged.  Unstable alleles are an important exception to this rule.


Environmental Influences


The phenotype of an individual is not only the result of inheriting a particular set of parental genes.  The specific environmental characteristics of the uterus in which a fertilized egg is implanted and the health of the mother can have major impacts on the phenotype of the future child.  For instance, oxygen deprivation or inappropriate hormone levels can cause lifelong, devastating effects.  Likewise, accidents, poor nutrition, and other environmental influences throughout life can alter an individual's phenotype. 


Geneticists study identical or monozygotic twins to determine which traits are inherited and which ones were acquired following conception.  Since monozygotic twins come from the same zygote, they are essentially identical in their genetic makeup.  If there are any differences in their phenotypes, the environment is virtually always responsible.  Such differences show up in basic capabilities such as handedness, which had been assumed to be entirely genetically determined.  In rare instances, one monozygotic twin will be clearly right-handed while the other will be left-handed.  This suggests that there may be both genetic and environmental influences in the development of this trait.



 Gregor Mendel, the Austrian monk who figured out the rules of hereity.


Mendel reasoned an organism for genetic experiments should have:


a number of different traits that can be studied

plant should be self-fertilizing and have a flower structure that limits accidental contact

offspring of self-fertilized plants should be fully fertile.

Mendel's experimental organism was a common garden pea (Pisum sativum), which has a flower that lends itself to self-pollination. The male parts of the flower are termed the anthers. They produce pollen, which contains the male gametes (sperm). The female parts of the flower are the stigma, style, and ovary. The egg (female gamete) is produced in the ovary. The process of pollination (the transfer of pollen from anther to stigma) occurs prior to the opening of the pea flower. The pollen grain grows a pollen tube which allows the sperm to travel through the stigma and style, eventually reaching the ovary. The ripened ovary wall becomes the fruit (in this case the pea pod). Most flowers allow cross-pollination, which can be difficult to deal with in genetic studies if the male parent plant is not known. Since pea plants are self-pollinators, the genetics of the parent can be more easily understood. Peas are also self-compatible, allowing self-fertilized embryos to develop as readily as out-fertilized embryos. Mendel tested all 34 varieties of peas available to him through seed dealers. The garden peas were planted and studied for eight years. Each character studied had two distinct forms, such as tall or short plant height, or smooth or wrinkled seeds. Mendel's experiments used some 28,000 pea plants.


Some of Mendel's traits as expressed in garden peas.



Mendel's contribution was unique because of his methodical approach to a definite problem, use of clear-cut variables and application of mathematics (statistics) to the problem. Gregor Using pea plants and statistical methods, Mendel was able to demonstrate that traits were passed from each parent to their offspring through the inheritance of genes.


Mendel's work showed:


Each parent contributes one factor of each trait shown in offspring.

The two members of each pair of factors segregate from each other during gamete formation.

The blending theory of inheritance was discounted.

Males and females contribute equally to the traits in their offspring.

Acquired traits are not inherited.

Principle of Segregation

Mendel studied the inheritance of seed shape first. A cross involving only one trait is referred to as a monohybrid cross. Mendel crossed pure-breeding (also referred to as true-breeding) smooth-seeded plants with a variety that had always produced wrinkled seeds (60 fertilizations on 15 plants). All resulting seeds were smooth. The following year, Mendel planted these seeds and allowed them to self-fertilize. He recovered 7324 seeds: 5474 smooth and 1850 wrinkled. To help with record keeping, generations were labeled and numbered. The parental generation is denoted as the P1 generation. The offspring of the P1 generation are the F1 generation (first filial). The self-fertilizing F1 generation produced the F2 generation (second filial).


Inheritance: Mendel studied seven traits which appeared in two discrete forms, rather than continuous characters which are often difficult to distinguish. When "true-breeding" tall plants were crossed with "true-breeding" short plants, all of the offspring were tall plants. The parents in the cross were the P1 generation, and the offspring represented the F1 generation. The trait referred to as tall was considered dominant, while short was recessive. Dominant traits were defined by Mendel as those which appeared in the F1 generation in crosses between true-breeding strains. Recessives were those which "skipped" a generation, being expressed only when the dominant trait is absent. Mendel's plants exhibited complete dominance, in which the phenotypic expression of alleles was either dominant or recessive, not "in between".


When members of the F1 generation were crossed, Mendel recovered mostly tall offspring, with some short ones also occurring. Upon statistically analyzing the F2 generation, Mendel determined the ratio of tall to short plants was approximately 3:1. Short plants have skipped the F1 generation, and show up in the F2 and succeeding generations. Mendel concluded that the traits under study were governed by discrete (separable) factors. The factors were inherited in pairs, with each generation having a pair of trait factors. We now refer to these trait factors as alleles. Having traits inherited in pairs allows for the observed phenomena of traits "skipping" generations.


Summary of Mendel's Results:


The F1 offspring showed only one of the two parental traits, and always the same trait.

Results were always the same regardless of which parent donated the pollen (was male).

The trait not shown in the F1 reappeared in the F2 in about 25% of the offspring.

Traits remained unchanged when passed to offspring: they did not blend in any offspring but behaved as separate units.

Reciprocal crosses showed each parent made an equal contribution to the offspring.



Mendel's Conclusions:


Evidence indicated factors could be hidden or unexpressed, these are the recessive traits.

The term phenotype refers to the outward appearance of a trait, while the term genotype is used for the genetic makeup of an organism.

Male and female contributed equally to the offsprings' genetic makeup: therefore the number of traits was probably two (the simplest solution).

Upper case letters are traditionally used to denote dominant traits, lower case letters for recessives.

Mendel reasoned that factors must segregate from each other during gamete formation (remember, meiosis was not yet known!) to retain the number of traits at 2. The Principle of Segregation proposes the separation of paired factors during gamete formation, with each gamete receiving one or the other factor, usually not both. Organisms carry two alleles for every trait. These traits separate during the formation of gametes.


A hypertext version (in German or English, annotated also available) of Mendel's 1865 paper is available by clicking here.


Dihybrid Crosses

When Mendel considered two traits per cross (dihybrid, as opposed to single-trait-crosses, monohybrid), The resulting (F2) generation did not have 3:1 dominant:recessive phenotype ratios. The two traits, if considered to inherit independently, fit into the principle of segregation. Instead of 4 possible genotypes from a monohybrid cross, dihybrid crosses have as many as 16 possible genotypes.


Mendel realized the need to conduct his experiments on more complex situations. He performed experiments tracking two seed traits: shape and color. A cross concerning two traits is known as a dihybrid cross.


Crosses With Two Traits


Smooth seeds (S) are dominant over wrinkled (s) seeds.


Yellow seed color (Y) is dominant over green (g).


Inheritance of two traits simultaneously, a dihybrid


Again, meiosis helps us understand the behavior of alleles.


The inheritance of two traits on different chromosomes can be explained by meiosis.


Methods, Results, and Conclusions


Mendel started with true-breeding plants that had smooth, yellow seeds and crossed them with true-breeding plants having green, wrinkled seeds. All seeds in the F1 had smooth yellow seeds. The F2 plants self-fertilized, and produced four phenotypes:


315 smooth yellow


108 smooth green


101 wrinkled yellow


32 wrinkled green


Mendel analyzed each trait for separate inheritance as if the other trait were not present.The 3:1 ratio was seen separately and was in accordance with the Principle of Segregation. The segregation of S and s alleles must have happened independently of the segregation of Y and y alleles. The chance of any gamete having a Y is 1/2; the chance of any one gamete having a S is 1/2.The chance of a gamete having both Y and S is the product of their individual chances (or 1/2 X 1/2 = 1/4). The chance of two gametes forming any given genotype is 1/4 X 1/4 (remember, the product of their individual chances). Thus, the Punnett Square has 16 boxes. Since there are more possible combinations to produce a smooth yellow phenotype (SSYY, SsYy, SsYY, and SSYy), that phenotype is more common in the F2.


From the results of the second experiment, Mendel formulated the Principle of Independent Assortment -- that when gametes are formed, alleles assort independently. If traits assort independent of each other during gamete formation, the results of the dihybrid cross can make sense. Since Mendel's time, scientists have discovered chromosomes and DNA. We now interpret the Principle of Independent Assortment as alleles of genes on different chromosomes are inherited independently during the formation of gametes. This was not known to Mendel.


Punnett squares deal only with probability of a genotype showing up in the next generation. Usually if enough offspring are produced, Mendelian ratios will also be produced.


Step 1 - definition of alleles and determination of dominance.


Step 2 - determination of alleles present in all different types of gametes.


Step 3 - construction of the square.


Step 4 - recombination of alleles into each small square.


Step 5 - Determination of Genotype and Phenotype ratios in the next generation.


Step 6 - Labeling of generations, for example P1, F1, etc.


While answering genetics problems, there are certain forms and protocols that will make unintelligible problems easier to do. The term "true-breeding strain" is a code word for homozygous. Dominant alleles are those that show up in the next generation in crosses between two different "true-breeding strains". The key to any genetics problem is the recessive phenotype (more properly the phenotype that represents the recessive genotype). It is that organism whose genotype can be determined by examination of the phenotype. Usually homozygous dominant and heterozygous individuals have identical phenotypes (although their genotypes are different). This becomes even more important in dihybrid crosses.



Hugo de Vries, one of three turn-of-the-century scientists who rediscovered the work of Mendel, recognized that occasional abrupt, sudden changes occurred in the patterns of inheritance in the primrose plant. These sudden changes he termed mutations. De Vries proposed that new alleles arose by mutations. Charles Darwin, in his Origin of Species, was unable to describe how heritable changes were passed on to subsequent generations, or how new adaptations arose. Mutations provided answers to problems of the appearance of novel adaptations. The patterns of Mendelian inheritance explained the perseverance of rare traits in organisms, all of which increased variation, as you recall that was a major facet of Darwin's theory.


Mendel's work was published in 1866 but not recognized until the early 1900s when three scientists independently verified his principles, more than twenty years after his death. Ignored by the scientific community during his lifetime.


Genetic Terms

Definitions of terms. While we are discussing Mendel, we need to understand the context of his times as well as how his work fits into the modern science of genetics.


Gene - a unit of inheritance that usually is directly responsible for one trait or character.


Allele - an alternate form of a gene. Usually there are two alleles for every gene, sometimes as many a three or four.


Homozygous - when the two alleles are the same.


Heterozygous - when the two alleles are different, in such cases the dominant allele is expressed.


Dominant - a term applied to the trait (allele) that is expressed irregardless of the second allele.


Recessive - a term applied to a trait that is only expressed when the second allele is the same (e.g. short plants are homozygous for the recessive allele).


Phenotype - the physical expression of the allelic composition for the trait under study.


Genotype - the allelic composition of an organism.


Punnett squares - probability diagram illustrating the possible offspring of a mating.





Mendel's Laws are as follows:


1.      The Law of Dominance


2.      The Law of  Segregation


3.      The Law of Independent Assortment



Notice in that very brief description of his work that the words "chromosomes" or "genes" are nowhere to be found.  That is because the role of these things in relation to inheritance & heredity had not been discovered yet. What makes Mendel's contributions so impressive is that he described the basic patterns of inheritance before the mechanism for inheritance (namely genes) was even discovered.



Vocabulary terms

GENOTYPE = the genes present in the DNA of an organism.  We will use a pair of letters (ex: Tt or YY or ss, etc.) to represent genotypes for one particular trait.  There are always two letters in the genotype because (as a result of sexual reproduction) one code for the trait comes from mama organism & the other comes from papa organism, so every offspring gets two codes (two letters).


There are three possible GENOTYPES - two big letters ("TT"), one of each ("Tt"), or two lowercase letters ("tt"). When we have two capital or two lowercase letters in the GENOTYPE (TT or tt) it's called HOMOZYGOUS ("homo" means "the same"). Sometimes the term "PURE" is used instead of homozygous. When the GENOTYPE is made up of one capital letter and one lower case letter it's called HETEROZYGOUS ("hetero" means "other").  A heterozygous genotype can also be referred to as a HYBRID


Genotype = genes present in an organism (usually abbreviated as two letters)

TT = homozygous = pure

Tt  = heterozygous = hybrid

 tt  = homozygous = pure



PHENOTYPE: how the trait physically shows-up in the organism.  Examples of phenotypes: blue eyes, brown fur, striped fruit, yellow flowers.


ALLELES: alternative forms of the same gene. Alleles for a trait are located at corresponding positions on homologous chromosomes.






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