CHAPTER 4
CARBON AND THE MOLECULAR DIVERSITY OF LIFE

1. Differentiate between inorganic and organic chemistry, and identify the central role of carbon in organic and biochemistry..

• Organic chemistry is the study of carbon compounds, exclusive of the oxides and carbonates of carbon.
• Inorganic chemistry involves the study of all other compounds.
• Organic compounds are based upon the ability of carbon to form four covalent bonds, thus carbon can form chains or rings or carbon that can form compounds up to molecular weights of hundreds of thousands.

2. Recognize the structure of the organic functional groups listed in the table below.

3. Define the term isomer and recognize structural, geometric and optical isomers.

• Structural Isomers - Same chemical formula but a different arrangement of atoms in the molecule.
• Geometric Isomers - Same chemical and structural formula but a different arrangement of atoms in space.
• Optical Isomers or Enantiomers - Same chemical and structural formula, but the arrangement of atoms of atoms in space are such that the molecules are mirror images of each other.

1. Define the following.

• Monomer - An organic compound composed of a single simple organic molecule or subunit such as a simple sugar.
• Macromolecule - A large molecule composed of many organic subunits such as starch or a protein.
• Polymer - An organic compound composed of many repeating subunits such as starch which is composed of hundreds of simple sugars (monomers) linked in chains to form a single large molecule.
• Oligomer - An organic molecule composed of a few (3 to 10) repeating subunits such as simple sugars.

2. Explain the formation of polymers through dehydration synthesis or condensation.

• Condensation or Dehydration Synthesis- A type of reaction by which monomers are linked, resulting in the removal of an OH from one molecule and an H from the other molecule involved in the reaction. This removal of water (OH and H) results in a bond (glycosidic bond) between the two monomers. This type of reaction is responsible for the formation of polymers such as carbohydrates, lipids and proteins.
• Hydrolysis - The opposite of condensation; the addition of an OH and H to two monomers to break the glycosidic bond linking them together.

3. List the basic properties of carbohydrates.

• Carbohydrates - Composed of C, H and O in a ratio of CH₂O. The ratio of O to H is the same as in water. Carbohydrates are used for energy, food or energy storage, as raw materials for the synthesis of more complex organic compounds and as structural substances.
• Monosaccharides - Simple sugars, composed of a single sugar molecule such as glucose or fructose. Monosaccharides can be composed of 3, 4, 5, 6 or more carbons.
• Disaccharide - A sugar composed of two monosaccharides. A double sugar such as sucrose.
• Oligosaccharides - Carbohydrates composed of a few simple sugar units such as the carbohydrate units associated with the surface of animal cell membranes.
• Polysaccharides - A complex carbohydrate composed of many monosaccharide units such as starch, glycogen, cellulose or chitin.

4. List the basic characteristics of lipids, the various types and why they represent a heterogeneous group of compounds.

• Lipids are a heterogeneous group of nonpolar compounds composed of C, H, and O in a ratio different from 2H to 1O as in water or carbohydrates, usually a higher ratio of H.
• Neutral fats - Fats and oils, composed of glycerol and fatty acids. Fatty acids are long hydrocarbon chains terminating with a carboxyl group. Neutral fats are formed through a condensation reaction which forms a bond between the fatty acid carboxyl group and a hydroxyl group of glycerol. One, two or three fatty acids may bond to glycerol forming monoacylglycerides, diacylglycerides or triacylglycerides. Fatty acids may be saturated or unsaturated, depending on the number of hydrogens associated with the fatty acid chain. Saturated fats have a maximum number of H’s associated with each C in the fatty acid chain, thus there are no double or triple bonds between carbons. Unsaturated fats have either double or triple bonds between two or more carbons of the fatty acid chain reducing the number of H associated with the chain. Neutral fats are primarily used for food storage, insulation and for the reduction of shock.
• Phospholipids - Phospholipids are composed of glycerol with fatty acids associated with the first two carbons of glycerol, while a phosphate and choline group is associated with the number three carbon. Phospholipids have both polar and nonpolar regions and thus are the major structural component of cellular membranes.
• Waxes - Waxes are composed of long fatty acids linked to chain alcohols or carbon rings. They are used for protection, lubrication or pliability of body surfaces. They are often involved in waterproofing of bird feathers and the surface of green plant tissues.
• Carotenoids - Yellow to orange plant pigments, function as accessory pigments in plants and produce vitamin A and retinol in animals.
• Steroids - Composed of four linked carbon rings with various functional groups and side chains attached. Involved with the initiation and regulation of certain metabolic activities. Often involved with growth, development and behavior.

5. Review the structure and function of proteins and amino acids.

• Proteins are composed of C, H, O, N and sometimes sulfur.
• Each protein is composed of a chain or chains of amino acids (polypeptides). Each amino acid is composed of an alpha carbon with an amino group and carboxyl group attached along with H and a side chain the "R" group.
• Amino acids are linked into chains (polypeptides) by peptide bonds which result from condensation between the amino group of one amino acid and the carboxyl of another.
• A polypeptide may be a functional protein or the protein may be composed of two or more polypeptides linked into a three dimensional structure.
• The shape and structure of a protein is critical to its function.
• Proteins function as enzymes, structural components, antibodies, transport compounds or as an energy source.
• PROTEIN STRUCTURE:

• Primary structure - The number, kind and sequence of the amino acids that make up a polypeptide.
• Secondary structure - A repeating pattern of coiling or folding such as the alpha helix or beta pleated sheet.
• Tertiary structure - Three dimensional folding of a single polypeptide.
• Quaternary structure - The combination of two or more polypeptides to form a single protein.

• Protein structure and function can be modified by changes, such as temperature, pH and other physical factors, in the proteins environment. Changes in structure result from the breaking or formation of additional internal bonds which modify the three dimensional structure of the polypeptide.

6. Review the structure and function of nucleic acids.

• Nucleic acids are composed of C, H, O, N and P, organized into structural units called nucleotides. Each nucleotide is composed of a nitrogen base, a five carbon sugar and a phosphate group. The identity of the nucleotide is determined by its nitrogen base. There are two classes of nitrogen bases, pyrimidines which are single ring structures and purines which are double ring structures.
• Nucleic acid function - DNA functions as the genetic material in all cellular organisms, while RNA is involved with the translation of the genetic code into the production of proteins, serves as a structural component in ribosomes and in some rare cases serve as enzymes (ribozymes).
• Nitrogen bases - The pyrimidines are cytosine, thymine and uracil. Uracil is found only in RNA while thymine is found in only DNA. Purines are adenine and guanine. In DNA and RNA bases pair together forming double stranded molecules. Bases always pair in a specific manner. This is necessary for the formation of the genetic code, protein synthesis and nucleic acid duplication.  All of these concepts will be explored in later units. In DNA, adenine and thymine always pair and guanine and cytosine always pair, while adenine pairs which uracil in RNA.
• Sugars - Ribose sugar is found in RNA while deoxyribose is found in DNA.
• Nucleotides are linked together into chains by phosphoester bonds between sugars. The backbone of the DNA or RNA molecule is composed of an alternating sequence of sugar-phosphate-sugar-phosphate-etc., with nitrogen bases attached to each sugar. Refer to your text for illustrations of the above molecules.
• Contrast DNA and RNA

1. Metabolism - the sum of the chemical activity that occurs in the cellor organism.

• Metabolic Pathway - A series of reactions that leads from a set of reactants to a final end product.
• Anabolism - A type of metabolic path that results in the synthesis of a more complex product from simple substrates.
• Catabolism - A type of metabolic path that results in the break down of complex molecules to simpler molecules.

2. Define energy and explain two types of energy, potential and kinetic.

• Energy - The capacity to do work or cause change or the ability to produce a change in the state or motion of matter.
• Matter - Anything that has mass and occupies space.
• Potential energy - Stored energy; energy by its position or state.
• Kinetic energy - Energy at work or energy in motion.

3. Review the first and second laws of thermodynamics and their application to living things and to the ecosphere.

• The First Law of Thermodynamics - The law of conservation of energy. The quantity of energy in the university is constant, that is energy is neither created nor destroyed.
• The Second Law of Thermodynamics - All systems tend toward disorder or randomness (entropy). The entropy of a system is continuously increasing.

4. Define free energy, entropy and enthalpy.

• Entropy - An increase in randomness. (S)
• Free energy - The portion of energy in a system that is available to do work. (G)
• Enthalpy - The total heat content or total potential energy of the system. (H)  There is an inverse relationship between free energy (G) and entropy (S). As entropy increases free energy decreases.

5. CHEMICAL REACTIONS:

• Reactants - The substances that enter into a chemical reaction.
• Products - The substance present at the conclusion of reaction.

• Transition State - A complex of reactants that will proceed to the product.
• Activation Energy - The quantity of energy needed to raise the reactants to the transition state.
• Exergonic Reaction - A chemical reaction that releases energy to the environment. This means that the product of the reaction contain less energy than the reactants of  the reaction.

• Endergonic Reaction - A chemical reaction that absorbs energy from the environment. In this reaction the product contains more energy than the reactants.

ENDERGONIC REACTION MECHANISM        ILLUSTRATTION Under construction!

• Reversible Chemical Reaction - A reaction that can proceed in either direction depending upon the relative concentrations that exist between the reactants and products.

• Chemical Equilibrium - a condition that exist in a chemical reaction in which the rate of change in one direction is equal to the rate of change in the other direction.
• Spontaneous Reaction - A reaction that produces products with less free energy than the reactants. A spontaneous reaction occurs without an input of outside energy, although the reaction may not be instantaneous.

6. Factors that influence the rate of chemical reactions.

• Temperature
• Pressure
• Concentration
• Catalyst/enzymes

7. Discuss how exergonic and endergonic reactions may be coupled in living organisms so that energy can be made available for life processes

• Coupled Reactions - In many metabolic processes such as protein synthesis the total process is endergonic. Energy to drive the endergonic reactions of the pathway is derived from exergonic reactions coupled to the pathway. The total process is exergonic.

8. Define the term enzyme and catalyst and explain how they work.

• Catalyst - A substance that promotes a chemical reaction.   Inorganic catalyst are normally not very specific as to the reactions they promote, while organic catalyst are usually very specific.
• Enzyme - A biological or organic catalyst. Normally very specific as to the reactants with which it interacts. Almost all enzymes are proteins.
• Induced Fit Hypothesis - This hypothesis states that the active sites of each substrate are located some distance from each other, and that binding of the substrate to the enzyme causes a change in shape of the enzyme that brings the substrates together so that they react forming the product.

9. Identify the properties of enzymes and factors involved in enzyme action.

• Enzymes do not cause a reaction to happen that could not occur on its own. They simply speed the reaction by at least a million times.
• The enzyme is not altered or used up by the reaction, thus an enzyme may be used over and over many times.
• An enzyme is highly selective as to the substrates with which it interacts.
• An enzyme is able to recognize both the reactants and products of a reaction as substrate.
• Intermediates - Compounds formed between the start and end of a metabolic pathway.
• Cofactor - a metal ion required for the function of an enzyme.
• Coenzyme - A non-protein organic molecule that is necessary for the function of an enzyme.
• Apoenzyme - The protein portion of an enzyme/coenzyme or cofactor complex.
• End products - Substance(s) present at the end of a metabolic pathway.

10. Discuss mechanisms for enzyme regulation such as feedback control and allosteric enzymes. Be able to explain competitive, noncompetitive, reversible and irreversible inhibition.

• Feedback Control - A type of control in which the product or an intermediate of a pathway blocks or inhibits the pathway by interacting with one of the enzymes of the pathway.
• Competitive Inhibition - A type of control in which the inhibitor binds to and blocks one or more of the active sites of an enzyme.
• Allosteric or Noncompetitive Inhibition - A type of control in which the inhibitor binds to a second type of binding site on the enzyme(allosteric site) changing the shape of the substrate active sites thus blocking enzyme activity.
• Reversible Inhibition - Enzyme can be alternately active or blocked by an inhibitor.
• Nonreversible Inhibition - The inhibitor permanently blocks the activity of the enzyme.

11. Effects of changes in temperature or pH on enzyme activity - Changes in eithertemperature or pH will change the shape of the enzyme causing reduced enzyme activity.
12. Ribozymes are RNA molecules that act as enzymes.
13. ATP - A nucleotide phosphate that serves as an energy transfer molecule commonly involved in biochemical reactions. ATP has three phosphates associated with the no. 5 C of the sugar. The last two of these phosphates are bonded by high energy bonds. Energy is transferred by the transfer of the terminal phosphate to a substrate molecule causing molecular change.