Study Guide Exam 2

Note: Any and all material discussed in lecture can be used for questions on the exam. The outline
below contains the main points that I expect everyone to know if they wish to pass the exam and
subsequently pass the course. Use this study guide as well as the objectives from the Objectives &
Figures Documents to organize your studying.

Protein Structure and Function Chap 18

I. General Comments.
A. Know the functions of proteins in the body.
1. Enzymes (Catalysis).
2. Protective.
3. Transport.
4. Regulatory (Hormones).
5. Structural.
6. Motility or Contractile.
7. Nutrient or Storage.
8. Exotics (Miscellaneous).
II. The Amino Acids.
A. What is an amino acid?
B. Know the difference between an alpha () amino acid and the other possible types of amino acids.
C. Zwitterions.
1. What is a zwitterion (dipolar ion)?
2. Know why amino acids exist as zwitterions in neutral solutions.
a) what charge do amino acids have at pH 2?
b) what charge do amino acids have at pH 13?
D. Know how the isoelectric point (isoelectric pH) of an amino acid is defined.
a) what charge do amino acids have when the pH is less than the pI?
b) what charge do amino acids have when the pH is greater than the pI?
c) what charge do amino acids have when the pH is equal to the pI?
E. Know the four major classes of amino acids.
1. Know the names of the 20 amino acids used by living organisms and the class to which they
belong.
a) non-polar.
(1) glycine (gly), alanine (ala), valine (val), leucine (leu), isoleucine (ile), proline (pro),
phenylalanine (phe), methionine (met) & tryptophan (trp)
b) polar uncharged.
(1) serine (ser), threonine (thr), cysteine (cys), tyrosine (tyr), asparagine (asn), & glutamine
(gln)
(2) what chemical reaction can cysteine (cys) undergo?
c) polar negatively charged.
(1) glutamate (glu) & aspartate (asp)
(2) what is the relationship between glu, gln, asp, & asn?
(3) pKa of the side chain carboxyl group?
d) polar positively charged.

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 (1) lysine (lys), arginine (arg) & histidine (his)
(2) pKa of lys side chain; pKa of arg side chain; pKa of his side chain?
2. Be able to recognize and differentiate between the structures of the 20 amino acids.
a) be able to recognize and/or name the two sulfur containing amino acids.
(1) methionine (met) & cysteine (cys)
b) be able to recognize and/or name the three aromatic amino acids.
(1) phenylalanine (phe), tyrosine (tyr), & tryptophan (trp)
c) where in a properly folded protein would the four types of amino acids be found?
F. Stereochemistry.
1. Know which of the amino acid(s) contain a chiral carbon atom.
2. Which enantiomeric form of the amino acids is used by living organisms D or L?
III. Peptides and Proteins.
A. How do amino acids react with each other to form peptides and proteins?
1. What type of reaction occurs between two amino acids?
2. What type of organic functional group is formed?
3. What is the special name given to this type of bond when present in peptides or proteins?
4. What special properties does this bond have when present in peptides or proteins?
5. How many amino acids are there in a
a) dipeptide?
b) tripeptide?
c) peptide?
d) oligopeptide
e) polypeptide?
f) protein?
6. What is the difference between a polypeptide and a protein?
7. Be able to recognize the peptide bond in a peptide / protein structure.
B. Know the convention for writing the sequence of a peptide or protein.
1. What is the amino terminal or N-terminal of a peptide or protein?
2. Using the convention be able to identify the amino terminal or N-terminal of a peptide or
protein.
3. What is the carboxyl terminal or C-terminal of a peptide or protein?
4. Using the convention be able to identify the carboxyl terminal or C-terminal of a peptide or
protein.
IV. Higher Order Structures of Proteins.
A. Primary (1) Structure.
1. What is the primary (1) structure of a peptide or protein?
2. What chemical bonds and/or intermolecular forces stabilize the primary (1) structure of a
peptide or protein?
a) what group or groups on an amino acid are involved in stabilizing the primary (1)
structure?
3. What information does the primary (1) structure of a peptide or protein contain?
a) what happens to a protein if the primary (1) structure is changed?
4. On a schematic diagram of a peptide or protein be able to identify the primary (1) structure.
B. Secondary (2) Structure.
1. What is the secondary (2) structure of a peptide or protein?

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 2. What feature of the peptide bond limits the number of possible secondary structures?
3. What are the three most abundant types of secondary (2) structure?
a) what is an alpha () helix?
b) how is an alpha () helix characterized?
c) how many amino acids per turn of the helix?
d) what group or groups of the amino acid when incorporated into the protein are involved in
stabilizing an alpha () helix?
e) what is the spacing between the amino acids involved in the hydrogen bonds the stabilize
the alpha () helix?
f) what is a beta () sheet?
g) how is a beta () sheet characterized?
h) what group or groups of the amino acid when incorporated into the protein are involved in
stabilizing a beta () sheet?
i) what is the difference between a parallel and an antiparallel beta () sheet?
j) what is a turn or bend ( bend or turn)?
k) how is a turn or bend ( bend or turn) characterized?
l) how many amino acids per turn?
m) what group or groups of the amino acid when incorporated into the protein are involved in
stabilizing a turn?
4. On a schematic diagram of a peptide or protein be able to identify the secondary (2) structure.
5. What is the fourth allowed secondary structure?
a) a triple helix present in glycine rich proteins - collagen triple helix.
C. Tertiary (3) Structure.
1. What is the tertiary (3) structure of a peptide or protein?
a) what is non-regular, non-repeating structure?
b) how is non-regular, non-repeating structure characterized?
2. What chemical bonds and/or intermolecular forces stabilize the tertiary (3) structure of a
peptide or protein?
a) what group or groups of the amino acid when incorporated into the protein are involved in
stabilizing the tertiary (3) structure of a peptide or protein?
3. On a schematic diagram of a peptide or protein be able to identify the tertiary (3) structure.
D. Quaternary (4) Structure.
1. What is the quaternary (4) structure of a peptide or protein?
a) what is a subunit?
(1) identical versus non-identical.
b) what is a monomeric protein?
c) what is a polymeric protein?
2. What chemical bonds and/or intermolecular forces stabilize the quaternary (4) structure of a
peptide or protein?
a) what group or groups of the amino acid when incorporated into the protein are involved in
stabilizing the quaternary (4) structure of a peptide or protein?
3. On a schematic diagram of a peptide or protein be able to identify the quaternary (4) structure.
E. Know the general structural types of proteins.
1. globular versus fibrous versus membrane.
a) shape differences.

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 b) size differences.
c) functional differences.
d) solubility differences.
F. Know how the isoelectric point (isoelectric pH) of an a peptide/protein is defined.
a) what charge do peptides/proteins have when the pH is less than the pI?
b) what charge do peptides/proteins have when the pH is greater than the pI?
c) what charge do peptides/proteins have when the pH is equal to the pI?
G. Denaturation.
1. What is hydrolysis?
2. What is denaturation?
3. How is denaturation different from hydrolysis?
a) what happens to the 1 structure of a peptide or protein when it is denatured?
b) what happens to the 2 structure of a peptide or protein when it is denatured?
c) what happens to the 3 structure of a peptide or protein when it is denatured?
d) what happens to the 4 structure of a peptide or protein when it is denatured?
4. What are some common denaturing agents?
a) how do these individual agents denature peptides and proteins?
V. Conjugated Proteins.
A. What are conjugated proteins?
B. What group or groups can be attached to conjugated proteins?
1. What is a Prosthetic Group?
2. What is the Apoprotein?
3. What is the Holoprotein?
VI. Selected Fibrous Proteins.
A. Know the function of collagen in the body.
1. Know the structure of collagen and how it is assembled.
a) 1 structure
b) 2 structure
c) 3 structure
d) 4 structure
VII. Diseases of Abnormal Protein Folding.
A. Prions.
1. What diseases are caused by abnormally folded prions?
2. In the familial type diseases what causes the prion to fold abnormally?
3. What are some of the properties of the abnormal prion protein?
4. How does the abnormally folded prion protein effect the normal protein in the infectious form
of the disease?
5. How is the disease treated?

Enzymes and Vitamins (Coenzymes) Chapter 19

I. General Comments.
A. What is an enzyme?
B. What makes enzymes different from man made catalysts?
1. Efficiency (speed).
2. Specificity.

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 a) absolute.
b) group.
c) linkage.
d) stereo.
e) product.
II. Naming & Classifying Enzymes.
A. What is the normal suffix for enzymes?
B. What are the six major classes of enzymes?
1. What type of reaction is catalyzed by Oxidoreductases?
a) what type of reaction is catalyzed by an Oxidase?
b) what type of reaction is catalyzed by a Reductase?
c) what type of reaction is catalyzed by a Dehydrogenase?
d) what type of reaction is catalyzed by a Oxygenase?
e) what type of reaction is catalyzed by a Peroxidase?
2. What type of reaction is catalyzed by Transferases?
a) what type of reaction is catalyzed by a Transaminase?
b) what type of reaction is catalyzed by a Aminotransferase?
c) what type of reaction is catalyzed by a Kinase?
d) what type of reaction is catalyzed by a Methyltransferase?
3. What type of reaction is catalyzed by Hydrolases?
a) what type of reaction is catalyzed by a Esterase?
b) what type of reaction is catalyzed by a Amidase?
c) what type of reaction is catalyzed by a Peptidase?
d) what type of reaction is catalyzed by a Glycosidase?
e) what type of reaction is catalyzed by a Lipase?
4. What type of reaction is catalyzed by Lyases?
a) what type of reaction is catalyzed by a Synthase?
b) what type of reaction is catalyzed by a Decarboxylase?
c) what type of reaction is catalyzed by a Dehydrase?
d) what type of reaction is catalyzed by a Deaminase?
5. What type of reaction is catalyzed by Isomerases?
a) what type of reaction is catalyzed by a Mutase?
b) what type of reaction is catalyzed by a Epimerase?
6. What type of reaction is catalyzed by Ligases?
a) what type of reaction is catalyzed by a Synthetase?
b) what type of reaction is catalyzed by a Carboxylase?
C. Enzyme Nomenclature.
1. How are the majority of enzymes named?
2. How are synthases and synthetases named?
3. Common Names.
III. Common Terms in Enzyme Chemistry.
A. What is the Substrate?
B. What is the Product?
C. What is the Substrate Binding Site?
D. What is the Active Site?

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IV. Factors Affecting Enzyme Activity.
A. At a constant (fixed) substrate concentration what happens to the initial rate of the reaction when:
1. The enzyme concentration is decreased?
2. The enzyme concentration is increased?
B. At a constant (fixed) enzyme concentration what happens to the initial rate of the reaction when:
1. The temperature of the reaction is increased?
a) why?
2. The pH of the reaction is increased or decreased?
a) why?
3. The substrate concentration is increased?
a) what is meant by enzyme saturated with its substrate?
b) what is meant by saturation kinetics?
c) why does an enzyme become saturated with its substrate?
d) understand the Michaelis-Menton equation.
e) what is Vmax?
f) what is the Km?
g) what are the units of Km?
h) how is the value of Km defined / determined?
i) how does Km relate to affinity of enzyme for substrate?
V. Mechanism of Enzyme Action.
A. What is the enzyme-substrate complex?
B. Explain the Lock-and-Key Model of enzyme activity.
1. What is the Lock?
2. What is the Key?
3. What aspect of enzyme activity does the Lock-and-Key Model explain well?
4. What aspect(s) of enzyme activity does the Lock-and-Key Model explain poorly?
C. Explain the Induced-Fit Model of enzyme activity.
1. How is it different from the Lock-and-Key Model?
2. How is it better than the Lock-and-Key Model?
D. How do enzymes increase the rate of a reaction? / How do they perform their catalytic role?
1. Stress and strain on a bond to be broken.
2. Proper positioning of two molecules to be joined.
3. Acid-base catalysis.
4. Metal catalysis.
VI. Enzyme Inhibition.
A. What is meant by enzyme inhibition?
B. What are the two primary types of enzyme inhibition?
C. What is Irreversible Inhibition?
1. How does an irreversible inhibitor interact with an enzyme?
2. Why is it called irreversible inhibition?
D. What is Reversible Inhibition?
1. How does a reversible inhibitor interact with an enzyme?
2. Why is it called reversible inhibition?
3. What is Competitive Reversible Inhibition?
a) what does a competitive inhibitor look like?

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 b) where on the enzyme does a competitive inhibitor bind?
c) why is it called competitive inhibition?
d) what happens to the rate of a competitively inhibited enzyme reaction as the concentration
of substrate is increased?
4. What is Noncompetitive Reversible Inhibition?
a) what does a noncompetitive inhibitor look like?
b) where on the enzyme does a noncompetitive inhibitor bind?
c) why is it called noncompetitive inhibition?
d) what happens to the rate of a non competitively inhibited enzyme reaction as the
concentration of substrate is increased?
E. What are the medical uses for enzyme inhibitors?
VII. Enzyme Regulation and Allosterism.
A. What mechanisms are available to the cell for controlling the rates of enzyme catalyzed reactions?
B. Substrate availability.
C. Equilibrium Considerations.
1. Maintaining the [S] and [P] near the equilibrium position.
2. Maintaining the [S] distant from the equilibrium position.
3. Maintaining the [P] distant from the equilibrium position.
D. Feedback inhibition.
1. What is the general mechanism of feedback inhibition?
2. What molecule feeds back?
3. Where does it bind on the enzyme?
4. This mechanism is similar to _________________ inhibition.
E. Synthesis.
1. How does the cell control enzyme activity by changing the rate/amount of protein synthesis?
F. Irreversible covalent modification zymogen activation.
1. What is a zymogen? What is a proenzyme?
2. How are zymogens (proenzymes) converted to active enzymes?
3. What type of enzyme catalyzes the activation of zymogens (proenzymes)?
4. Why does the cell synthesize some enzymes as zymogens (proenzymes)?
5. Zymogens (proenzymes) are found where, in what metabolic systems?
G. Reversible covalent modification.
1. In general how does this mechanism for controlling enzyme activity function.
2. What group is usually added to the enzyme to activate it?
a) What is the source of this group?
3. What group is usually removed from the enzyme to activate it?
a) What is the source of this group?
4. What group is usually added to the enzyme to inactivate it?
a) what is the source of this group?
5. What group is usually removed from the enzyme to inactivate it?
a) What is the source of this group?
6. What type of enzyme adds the group to the protein?
7. What type of enzyme removes the group from the protein?
H. Allosteric enzymes.
1. How is an allosteric enzyme structurally different from a non allosteric enzyme?

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 a) how many subunits does an allosteric enzyme contain?
b) do all allosteric enzymes have 4 structure?
c) how many binding sites does an allosteric enzyme have?
2. How is an allosteric enzyme kinetically different from a non allosteric enzyme?
a) what is the shape of the kinetic curve?
b) activity at low substrate concentrations
(1) Tense (T) state
(2) low affinity state
(3) high Km state
c) activity at high substrate concentrations
(1) Relaxed (R) state
(2) high affinity state
(3) low Km state
d) activity at very high substrate concentrations
3. What is a regulator (modulator, effector) molecule?
a) what does a positive regulator (modulator, effector) molecule do to the activity of an
allosteric enzyme?
(1) where does it bind?
b) what does a negative regulator (modulator, effector) molecule do to the activity of an
allosteric enzyme?
(1) Where does it bond?
4. How / why does Hemoglobin fit the model of an allosteric protein?
a) shape of oxygen saturation curve.
b) negative allosteric effectors.
(1) hydrogen ion.
(2) 2,3-bisphosphoglycerate.
c) how do the negative allosteric affect the affinity of hemoglobin toward oxygen?
d) how does allosteric nature of hemoglobin allow the molecule to perform its function
exceedingly well?
VIII. Isoenzymes.
A. What is an isoenzyme?
1. Are they composed of one or many protein subunits?
a) are the subunits the same or different?
2. Do they catalyze the same or different reactions?
3. Do different tissues contain different isoenzymes?
B. Lactate Dehydrogenase is an isoenzyme
1. What type(s) of subunits are found in the heart form of Lactate Dehydrogenase?
2. What type(s) of subunits are found in the muscle form of Lactate Dehydrogenase?
3. What type(s) of subunits are found in the liver form of Lactate Dehydrogenase?
IX. Vitamins & Coenzymes.
A. What is a Cofactor?
B. What is a Coenzyme?
C. What is a Cosubstrate?
1. What is/are the difference(s) between a cofactor, coenzyme, and cosubstrate?
2. What dietary requirements often become coenzymes or cosubstrates?

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D. What is an Apoenzyme?
E. What is a Holoenzyme?
1. Are apoenzymes able to catalyze metabolic reactions why or why not?
2. Are holoenzymes able to catalyze metabolic reactions why or why not?
F. The Big Seven Coenzymes/Cosubstrates
1. Adenosine Triphosphate (ATP).
a) What are the functions of ATP in the cell?
b) Be able to identify the structure of ATP.
(1) be able to identify its component parts.
c) Be able to identify the high energy chemical bonds within ATP.
(1) what type of bonds are they.
d) Know the relationships between ATP, ADP and AMP and how they are interconverted.
e) Function of cyclic AMP (cAMP).
2. Guanosine Triphosphate (GTP).
a) What are the functions of GTP in the cell?
b) Be able to identify the structure of GTP.
(1) be able to identify its component parts.
c) Be able to identify the high energy chemical bonds within GTP.
(1) what type of bonds are they?
d) Know the relationships between GTP, GDP and GMP and how they are interconverted.
3. Nicotinamide Adenine Dinucleotide (NAD+) & Nicotinamide Adenine Dinucleotide Phosphate
(NADP+).
a) What is the function of NAD+ in the cell?
b) What is the function of NADP+ in the cell?
c) What vitamin is necessary for the synthesis of NAD+ (NADP+)?
d) Which part (region) of the molecule that accepts or donates electrons / hydrogen atoms?
4. Flavin Mononucleotide (FMN) & Flavin Adenine Dinucleotide (FAD).
a) What is the function of FMN & FAD in the cell?
b) Be able to identify the structure of a FMN & FAD?
c) What vitamin is necessary for the synthesis of FMN & FAD?
d) Which part (region) of the molecule that accepts electrons / hydrogen atoms when FAD is
reduced to FADH2?
5. Coenzyme A (CoA-SH).
a) What is the function of CoA-SH in the cell?
b) Be able to identify the structure of CoA-SH.
(1) be able to identify its component parts.
(2) be able to identify that part that comes from a vitamin.
(3) which vitamin is it.
c) Which part (region) of the molecule that accepts carboxylic acid groups when CoA-SH
accepts a carboxylic acid?
G. The Minor Coenzymes/Cosubstrates
1. Describe precursor vitamin, if present, and biological function of the coenzymes:
a) Uridine Triphosphate (UTP).
b) Cytidine Triphosphate (CTP).
c) Thiamine pyrophosphate.

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 d) Pyridoxal phosphate.
e) Tetrahydrofolate.
f) Lipoic Acid.
g) Biotin.
h) Ascorbic acid.
i) Vitamin K.

kkkkkkkkkkk

Some Practice Questions

1 Which of these can be classified as a structural protein?

a. insulin
b. trypsin
c. collagen
d. immunoglobulin

2. An apoenzyme is which portion of an enzyme?

a. the protein portion
b. a vitamin B molecule
c. a metallic ion
d. an inactive precursor

3. The number of subunits (polypeptide chains) and their entanglements provide which structures of
proteins?
a. primary
b. secondary
c. tertiary
d. quarternary

4. The rate of an enzyme-catalyzed reaction is directly proportional to the

a. substrate concentration
b. square of the substrate concentration
c. reciprocal of the substrate concentration
d. none of these

5. Human and bovine (beef) insulin differ from each other

a. only in their secondary structures
b. only in their tertiary structures
c. only in their quaternary structures
d. in their primary structures

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6. The rate of enzyme-catalyzed reactions
a. increases with increasing temperature
b. decreases with increasing temperature
c. is at a maximum at a certain optimum temperature
d. is at a minimum at a certain optimum temperature

7. Lysine is which kind of amino acid?

a. acidic
b. basic
c. polar neutral
d. nonpolar neutral

8. The active site of an enzyme is composed of

a. only one amino acid residue
b. two or a few amino acids connected to each other in the protein chain
c. two or a few amino acids which may be located in different parts of the protein chain
d. one whole subunit of the protein

9. Intermolecular hydrogen bonding between the backbones of protein chains can be found in
a. the alpha helix
b. the beta-pleated sheet
c. tertiary structures
d. none of these

10. Most globular proteins have

a. only alpha-helical structures
b. only random coil structures
c. predominantly beta-pleated sheet structures
d. a combination of all of these

11. Which does not contribute to the tertiary structures of proteins?

a. salt bridges
b. disulfide bridges
c. covalent cross linking
d. intramolecular hydrogen bonding between backbones

12. The quaternary structure of a protein describes

a. the spatial relationship of subunits within the protein
b. the number of S-S bridges
c. the non-helical portions of globular proteins
d. the number of hydrophobic interactions between the non-adjacent parts of the same polypeptide
chain

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13. Which of these statements about the structure of hemoglobin is false?
a. it has a quaternary structure
b. it contains a prosthetic group
c. it has a quarter-stagger alignment
d. it has four chains, called globins

14. Detergents such as sodium dodecyl sulfate can denature proteins by

a. opening up hydrophobic regions
b. disrupting the salt bridges
c. removing heavy metals
d. breaking hydrogen bonds

15. The triple helix found in collagen is which kind of structure?

a. primary
b. secondary
c. tertiary
d. quaternary

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