BCH 401G: Exam 1 Sapling

Suppose that an arginine residue in the active site of an enzyme was mutated to alanine. As expected, the alanine mutant was inactive, suggesting that the arginine residue was critical to the catalytic mechanism. Which mutation is most likely to restore WT level of activity to the alanine mutant?

A to K

What does an apoenzyme require to become a holoenzyme?

A cofactor

Describe a coenzyme

A small organic compound that is required for proper enzyme function

Polysaccharides are polymers of:

Monosaccharides

Functional groups common to all amino acids:

NH3+ COO-

What is the catalytic triad of chymotrypsin, a type of serine protease?

the amino acids serine, histidine, and aspartate

Predominant intermolecular forces for the following: A) Electrostatic (Ionic) Interactions B) Hydrogen Bonding C) van der Waals Interactions

A: KCl B: H2O & NH3 C: CH4

Which polypeptide, (Ala-Asp-Gly)5 or (Asn-Ser-His)5, is more soluble at pH 3?

(Asn-Ser-His)5

Which polypeptide, (Ala-Ser-Gly)5 or (Asn-Ser-His)5, is more soluble at pH 6?

(Asn-Ser-His)5

Which polypeptide, (Glu)20 or (Phe-Met)3, is more soluble at pH 7?

(Glu)20

Which polypeptide, (Gly)20 or (Lys-Ala)3, is more soluble at pH 7?

(Lys-Ala)3

True statements about SDS-PAGE under reducing conditions

-A protein binds round 1.4 times its mass of SDS, resulting in a large overall negative charge -Smaller proteins migrate faster through the polyacrylamide gel -Proteins are separated in a polyacrylamide gel matrix

True statements about enzymes

-A substrate must bind to the active site before catalysis can occur -An enzyme yields a specific product, whereas a nonbiological catalyst may produce more than one produce with the occurrence of side reactions -Generally, an enzyme is specific for a particular substrate. For ex, thrombin catalyzes the hydrolysis of the peptide bond b/t Arg & Gly -Catalysis occurs as the active site, which usually consists of a crevice on the surface of the enzyme

Statements that correctly describe hemoglobin & myoglobin structure

-Each Fe atom can form 6 coordination bonds. One of these bonds is formed b/t Fe & O2 -By itself, heme is not a good O2 carrier. It must be part of a larger protein to prevent oxidation of the Fe -Both contain a prosthetic group called heme, which contains a central Fe atom -Each hemoglobin molecule can bind 4 O2 molecules; each myoglobin can bind 1 O2 molecule

Cellulose could provide an abundant and cheap form of glucose for humans. Why is cellulose not a source of nutrients for humans?

-Humans, and most vertebrates, lack the enzyme cellulase -Vertebrate enzymes hydrolyze (alpha 1-4) glucose linkages, but not glucose in the beta configuration

Factors that directly favor the unloading of O2 from hemoglobin in the blood near metabolically active tissues

-an increase in blood temperature near the tissues -a decrease in blood pH near the tissues -the presence of a pressure gradient for O2

Scenarios which, according to the Bohr effect, result in hemoglobin's release of bound O2

-the concentration of hydrogen ions in the blood increases -CO2 levels in the blood increase

A) [S] << Km B) [S] = Km C) [S] >> Km

A: almost all active sites are empty & [Efree] is about equal of [Etotal] B: [Efree] is equal to [ES] C: [ES] is much higher than [Efree] & rxn rate is independent of [S]

A) Starch B) Glycogen C) Cellulose

A: major storage form of glucose in plants & made up of 2 polysaccharides: amylose & amylopectin B: major storage form of carbohydrates in animals C: not digestible by humans

Classify each amino acid by properties of its side chain (R group) at pH 7: A) Positively charged R group B) Negatively charged R group C) Neutral polar R group D) Nonpolar aliphatic R group E) Aromatic R group

A: Arginine B: Aspartate C: Serine D: Leucine E: Phenylalanine

A) [S] = 0.1. Km B) [S] = Km C) [S] = 10 Km

A: Doubling [S] will almost double the rate & less than 10% of the active sites are occupied by substrate B: Half of the active sites are occupied by substrate C: About 90% of the active sites are occupied by substrate, doubling [S] will have little effect of the rate, & this condition will result in the highest rate

Classify proteins according to its highest level of protein structure: A) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure

A: Gly-Ala-Val-Leu B: single helical chain of collagen C: single hemoglobin subunit with heme D: hemoglobin

A) Reversible competitive B) Reversible noncompetitive C) Irreversible

A: Inhibitor structure resembles substrate structure & inhibitor does not alter the maximum rxn rate B: inhibitor binds noncovalently at site other than active site C: inhibitor binds covalently and permanently at active site

Highest level of protein structure described by each: A) Primary structure B) Secondary structure C) Tertiary structure D)Quaternary structure

A: order of amino acids B: beta-pleated sheets & alpha-helix C: overall shape of a single polypeptide unit D: overall macromolecule structure containing more than on polypeptide chain

Match the enzymes: A) Transferase B) Ligase C) Oxidoreductase D) Lyase E) Hydrolase F) Isomerase

A: rxns involving the transfer of a functional group from one molecule to another B: energetically unfavorable rxns that require ATP to form new bonds C: oxidation-reduction rxns D: rxns that eliminate or form a double bond E: hydrolysis F: isomerization rxns

Proteins are polymers of:

Amino acids

Select the true statements about protein secondary structure: A) Disulfide bonds stabilize secondary structure B) In a beta-pleated sheet, the side chains extend above and below the sheet C) The beta-pleated sheet is held together by hydrogen bonds between adjacent segments D) In an alpha-helix, the side chains are located inside the helix E) The secondary level of protein structure refers to the spatial arrangements of short segments of the protein

B C & E

Select the phrases that describe the plasma membrane: A) Provides a rigid structure that allows the cell to hold its shape B) Creates a barrier b/t the inside & outside of the cell C) Separates the nucleus and cytosol D) Maintains the correct ion concentration inside the cell

B & D

What does oil not dissolve in H2O? A) Hydrogen bonds form between oil molecules, causing them to aggregate B) H2O molecules form stronger associations with other polar molecules that with oil C) Oil is less dense than water, which causes it to separate from water instead of dissolving D) H2O molecules form hydrogen bonds with each other and exclude oil molecules

B & D

Which statements accurately describe the polarity & electronegativity of water: A) H2O has polar bonds and a linear symmetrical shape, so it's polar B) H2O molecules have slight charges and are attracted to each other by ionic bonds C) H2O molecules are polar & thus associate with each other through hydrogen bonds D) O2 atom in H2O molecules is strong electronegative E) The atoms of the H2O molecules are held together by covalent bonds

C D & E

Which interaction can contribute to the intrinsic binding energy during enzymatic catalysis? A) Permanent covalent bonding B) nucleophilic attack by serine C) van der Waals interactions D) hydrogen bonding E) electrostatic interactions

C D & E

All of the cells in the body need oxygen. Hemoglobin molecules in RBCs transport O2 through the bloodstream. O2 is loaded onto the hemoglobin molecules in the lungs and unloaded from the hemoglobin molecules in the tissues. What drives the unloading of O2 from hemoglobin molecules in the tissues?

Low partial pressure of O2 in the tissues

Hemoglobin vs Myoglobin

Hemoglobin: -O2 dissociation curve is sigmoidal shaped -as O2 binds to this molecule the shape the molecule changes, enhancing further O2 binding -the binding pattern for this molecule is considered cooperative -this molecule delivers O2 more efficiently to tissues Myoglobin: -O2 dissociation curve is hyperbolic shaped -this molecule has a greater affinity for O2

Nucleic acids are polymers of:

Nucleotides

In the lungs, O2 diffuses into the blood & is loaded onto hemoglobin for transport. In, the tissues, O2 is unloaded from hemoglobin and diffuses from the blood into nearby cells. What drives the diffusion of O2?

Partial pressure of O2

Protein vs Glycogen Structure

Protein: Linear & AA polymer Glycogen: Branched & Glucose polymer

Reversible vs Irreversible Inhibition

Reversible: -forms an ionic bond with the enzyme -can be removed from the active site by dilution with the substrate -prevents the cell from producing unneeded resources Irreversible: -forms a covalent bond with the enzyme -permanently modifies the structure of the active site -can interfere with the production of vital cellular resources

A protein was purified to homogeneity. The determination of the mass by gel-filtration chromatography yields a value of 60 kDa. Chromatography in the presence of urea results in a 30 kDa species. Repeating the chromatography in the presence of both urea and beta-mercaptoethanol, however, results in a single molecular species of 15 kDa. What does the data suggest about the structure of the protein?

The 60 kDa protein is composed of two 30 kDa subunits linked by noncovalent interactions. Each 30 kDa subunit is composed of two 15 kDa subunits joined by disulfide bonds