Amino Acids, Proteins, and Enzymes

Draw the structure for each of the following amino acids at physiological pH:

a. glycine

b. T

c. glutamate

d. Phe

Classify each of the following proteins according to its function:

a. hemoglobin, oxygen campier in the blood

b. collagen, a major component of tendons and cartilage

c. Keratin is a protein that is found in hair.

d. amylases that catalyze the hydrolysis of search

Classify each of the following proteins according to their function:

a. insulin, a protein needed for glucose utilization

b. antibodies that disable foreign proteins

c. casein, milk protein

d. lipases that catalyze the hydrolysis of lipids.

What functional groups are found in all a-amino acids?

How does the polarity of the R group in leucine compare to the R group in serine?

Draw the structure of each of the following amino acids at physiological pH:

a. glycine

h. T

c. glutamate

d. Phi

Draw the surface for each of the following amino acids at physiological pH:

a. Lysine

b. proline

c. V

d. Tyr

Classify each of the amino acids in problem $16.5$as polar or nonpolar. If polar, indicate if the R group is neutral, acidic, or basic. Indicate if each is hydrophobic or hydrophilic.

Classify each of the amino acids in the problem  $16.6$  as polar or nonpolar. If polar, indicate if the R group is neutral, acidic, or basic. Indicate if each is hydrophobic or hydrophilic.

Give the name of the amino acid represented by each of the following abbreviations:

a. Ala

b. Q

c. K

d. Cys

Give the name of the amino acid represented by each of the following abbreviations:

a. Trp

b. M

c. Prom

d. G

Draw the condensed structural formula for each of the following pairs, and give their three-letter and one-letter abbreviations:

a. alanylations

b. serylpheaylalanine

c. glycylalanylvaline

d. valyliwoleucyltrypeophan

16.12 Draw the condensed structural formula for cach of the following peptides, and give its three-letler and one-letler abbreviations:

a. prolyl aspartate

b. threonyl leucine

c. methionylglutaminyllysine

d. histidylglycylghutamylisoleucine

Peprides isolated from rapeseed that may have limaer blond pressure have the following sequence of amino acids. Draw the structure for each peptide and write the one-letter abbreviations.

a. Arg-lle-Iyr

b. Val-Irp-lle-Ser

Pcpeides froes sweet potato with antioxidant properties has the following sequence of amino acids. Draw the structure for each peptide and write the single-letter abbreviations.

a. Asp-Cys-Gly-Tyr

b. Asn-Tyt-Asp-Gila-Tyr

Explain why each of the following pairs are complementary proteins:

a. Coen and Peas

b. rice and soy

Explain why each of the following pairs are complementary proteins:

a. beans and outs

b. almonds and peanuts

What happens when a primary structure forms a secondary structure?

What type of interaction would you expect between the R groups of the following amino acids in a tertiary structure?

a. cysteine and cysteine

b. aspartate and lysine

c. serine and aspartate

d. leucine and leucine

What type of interaction would you expect between the R groups of the following amino acids in a quaternary structure?

a. phenylalanine and isoleucine

b. glutamate and arginine

c. asparagine and tyrosine

d. alanine and proline

What is the difference in hydrogen bonding between an $\alpha$ helix and a $\beta$-pleated sheet?

In an $\alpha$ helix, how does hydrogen bonding occur between the amino acids in the polypeptide chain?

A portion of a polypeptide chain contains the following sequence of amino acids:

- Leu-Val-Cys-Asp-

a. Which amino acids are likely to be found on the inside of the protein structure? Why?

b. Which amino acids would be found on the outside of the protein? Why?

c. How does the primary structure of a protein affect its tertiary structure?

In myoglobin, about one-half of the 153 amino acids have nonpolar $\mathrm{R}$ groups.

a. Where would you expect those amino acids to be located in the tertiary structure?

b. Where would you expect the polar$R$groups to be in the tertiary structure?

c. Why is myoglobin more soluble in water than silk or wool?

Indicate whether each of the following statements describes primary, secondary, tertiary, or quaternary protein structure:

a.$R$ groups interact to form disulfide bonds or salt bridges.

b. Peptide bonds join amino acids in a polypeptide chain.

c. Several polypeptides in a beta-pleated sheet are held together by hydrogen bonds between adjacent chains.

d. Hydrogen bonding between amino acids in the same polypeptide gives a coiled shape to the protein.

Indicate whether each of the following statements describes primary, secondary, tertiary, or quaternary protein structure:

a. Hydrophobic $\mathrm{R}$groups seeking a nonpolar environment move toward the inside of the folded protein.

b. Protein chains of collagen form a triple helix.

c. An active protein contains four tertiary subunits.

d. In sickle-cell anemia, valine replaces glutamate in the $\beta$-chain.

Indicate the changes in secondary and tertiary structural levels of proteins for each of the following:

$100°\mathrm{C}$

b. Prior to giving an injection, the skin is wiped with an alcohol swab.

c. Surgical instruments are placed in a $120°\mathrm{C}$ autoclave.

d. During surgery, a wound is closed by cauterization (heat).

Indicate the changes in secondary and tertiary structural levels of proteins for each of the following:

a. Tannic acid is placed on a burn.

b. Milk is heated to ${60}^{o}C$ to make yoghurt.

c. To avoid spoilage, seeds are treated with a solution of $HgC{l}_2$.

d. Hamburger is cooked at high temperatures to destroy E. coli bacteria that may cause intestinal illness.

What are two types of secondary protein structure?

Why do chemical reactions in the body require enzymes?

How do enzymes make chemical reactions in the body proceed at faster rates?

What is the reactant for each of the following enzymes?

a. galactase

b. lipase

c. aspartase

What is the reactant for each of the following enzymes?

a. peptidase

b. cellulase

c. lactase

What is the name of the class of enzymes that would catalyze each of the following reactions?

a. hydrolysis of sucrose

b. addition of oxygen

c. converting glucose $\left({\mathrm{C}}_6{\mathrm{H}}_{12}{\mathrm{O}}_6\right)$ to fructose$\left({\mathrm{C}}_6{\mathrm{H}}_{12}{\mathrm{O}}_6\right)$

d. moving an amino group from one molecule to another

How is the $LDH$ isoenzyme in the heart different from the $LDH$ isoenzyme in the liver?

A patient arrives in an emergency department complaining of chest pains. What enzymes would you test for in the blood serum?

What is the name of the class of enzymes that would catalyze each of the following reactions?

a. addition of water to a double bond

b. removing hydrogen atoms

c. splitting peptide bonds in proteins

d. converting a tertiary alcohol to a secondary alcohol

Match the terms (1) enzyme-substrate complex, (2) enzyme, and (3) substrate with each of the following:

a. has a tertiary structure that recognizes the substrate

b. the combination of an enzyme with the substrate

c. has a structure that fits the active site of an enzyme

Match the terms (1) active site, (2) lock-and-key model, and (3) induced-fit model with each of the following:

a. the portion of an enzyme where catalytic activity occurs

b. an active site that adapts to the shape of a substrate

c. an active site that has a rigid shape

a. Write an equation that represents an enzyme-catalyzed reaction.

b. How is the active site different from the whole enzyme structure?

a. How does an enzyme speed up the reaction of a substrate?

b. After the products have formed, what happens to the enzyme?

What are isoenzymes?

A patient has elevated blood serum levels of $LDH and AST.$ What condition might be indicated?

Trypsin, a peptidase that hydrolyzes polypeptides, functions in the small intestine at an optimum $pH of 7.7 to 8.0$. How is the rate of a trypsin-catalyzed reaction affected by each of the following conditions?

a. changing the $pH to 3.0$

b. running the reaction at $75°C$

Pepsin, a peptidase that hydrolyzes proteins, functions in the stomach at an optimum $pH of 1.5 and 2.0.$ How is the rate of a pepsin-catalyzed reaction affected by each of the following conditions?

a. changing the $pH to 5.0$

b. running the reaction at $0°C$

The following graph shows the activity versus$pH$ curves for pepsin, sucrase, and trypsin. Estimate the optimum $pH$ for each.

Refer to the graph in problem $16.45$ to determine if the reaction rate in each condition will be at the optimum rate or not.

a. trypsin, $pH 5.0$

b. sucrase, $pH 5.0$

c. pepsin, $pH 4.0$

d. trypsin, $pH 8.0$

e. pepsin, $pH 2.0$

Indicate whether each of the following describes a competitive or a noncompetitive enzyme inhibitor:

a. The inhibitor has a structure similar to the substrate.

b. The effect of the inhibitor cannot be reversed by adding more substrate.

c. The inhibitor competes with the substrate for the active site,

d. The structure of the inhibitor is not similar to the substrate.

e. The addition of more substrate reverses the inhibition.

Oxaloacetate is an inhibitor of succinate dehydrogenase.

a. Would you expect oxaloacetate to be a competitive or a noncompetitive inhibitor? Why?

b. Would oxaloacetate bind to the active site or elsewhere on the enzyme?

c. How would you reverse the effect of the inhibitor?

If Jeremy's current weight is $21\mathrm{lbs}$, how many milligrams of hydroxyurea should Jeremy be given each day?