biochem final (multiple choice)

weak forces create constantly forming and breaking interactions at physiological temperatures, but cumulatively impart stability to biological structures generated by their collective activity include all except

a. hydrogen bonds

b. van der Waals forces

c. covalent bonds

d. ionic interactions

e. hydrophobic interactions

covalent bonds

which of the following fibrous proteins is composed exclusively of a-helices (alpha-helices)?

a. collagen

b. fibroin

c. a-keratin (alpha-keratin)

d. B-keratin (beta-keratin)

e. hemoglobin

a-keratin (alpha-keratin)

a two-domain protein composed of a single polypeptide (a/alpha) may have formed (during evolution) by _____, but a large protein composed of seven identical subunits (a₇) may be an example of _____.

a. post-translational modification, cooperativity

b. gene fusion, genetic economy

c. stabilization, collective motion

gene fusion, genetic economy

in micelles, 

a. polar ends form hydrophobic interactions with water

b. nonpolar ends form hydrophilic interactions with water

c. hydrocarbon tails form hydrophobic interactions with water

d. polar ends are hydrophobic and nonpolar ends are hydrophilic

e. hydrocarbon tails are excluded from the water into hydrophobic domains

hydrocarbon tails are excluded from the water into hydrophobic domains

in order to _____ the osmotic pressure created by the contents of the cytosol, cells tend to store substances such as amino acids and sugars in ____ form.

a. increase, monomeric

b. minimize, polymeric

c. minimize, monomeric

d. maximize, polymeric

e. increase, polymeric

minimize, polymeric

grapefruit juice at pH 3.2 contains about ___ times as much H⁺ as orange juice at pH 4.3

a. 0.9

b. 10^-7.5

c. 12

e 101

12

in a four-helix-bundle protein, the amino acid residues on the interior faces of the a-helices (alpha-helices) are typically

a. arranged to form salt bridges

b. negatively charged

c. hydrophobic

d. positively charged

hydrophobic

Enthalpy change is

a. the sum of heat absorbed and work

b. not a thermodynamic state function

c. a measure of disorder in a system

d. equal to the heat transferred at constant pressure

e. determined by pressure change at a constant temperature

equal to the heat transferred at constant pressure

“high-energy” compounds that exhibit a large negative free energy of hydrolysis (delta G knot prime < -25 kJ/mol) include all except

a. phosphate esters

b. enol phosphates

c. phosphate anhydrides

d. acyl phosphates

e. guanidino phosphates

f. thioesters

phosphate esters

when ATP hydrolysis (to ADP + P_i, (ΔG°’= -35.7 kJ/mol) is coupled to an unfavorable reaction, the equilibrium position of that reaction is shifted by a factor of

a. 10

b. 100

c. 10⁴

d. 10⁶

e. 10⁸

10⁶

which of the following amino acids has more than one chiral carbon?

a. serine

b. lysine

c. threonine

d. cysteine

e. aspartic acid

threonine

glutamic acid has pKa’s of 2.2, 4.3, and 9.7. what is the isoelectric point of glutamic acid?

a. 3.25

b. 4.3

c. 5.4

d. 7.0

e. 8.65

3.25

which of these peptides would absorb light at 280nm?

a. ala-lys-his

b. ser-gly-asn

c. ala-ala-trp

d. val-pro-leu

ala-ala-trp

glyphosate (the old “Roundup”) is ____ and an effective herbicide at a level of ____ per acre, but imazapyr and imazapic (“Arsenal” and “Chopper”) are ____ and effective at a level of ___ per acre.

a. persistent, pounds, biodegradable, grams

b. biodegradable, pounds, persistent, grams

c. persistent, grams, biodegradable, pounds

d. biodegradable, grams, persistent, pounds

biodegradable, pounds, persistent, grams

a common reaction of two cysteine residues in protein results in the formation of ____.

a. thioester bonds

b. disulfide bonds

c. dithiol bonds

d. thioester bonds

e. none of the above

disulfide bonds

protein isolation and purification techniques include all the following methods except

a. gas-liquid chromatography

b. affinity chromatography

c. electrophoresis

d. solubility (“salting in” and “salting out”)

e. ion exchange chromatography

gas-liquid chromatography

α-Helices and β-sheets are components of ____ structures.

a. primary

b. secondary

c. tertiary

d. quaternary

e. all are true

secondary

reaction of peptide, ala-met-ser, which phenylisothiocyanate at pH 8.0 followed by mild acidification (the first cycle of the Edman method) would release (“PTH” stands for phenylthiohydantoin)

a. the labeled peptide ala-met-lys-ser-PTH

b. PTH-ser and the peptide ala-met-lys

c. PTH-ala, PTH-ser, PTH-lys and PTH-met

d. PTH-ala and the peptide met-lys-ser

PTH-ala and the peptide met-lys-ser

the C-terminal residue of a polypeptide can be found by first cleaving the polypeptide with

a. chymotrypsin

b. carboxypeptidase

c. trypsin

d. CNBr

e. none of the above

carboxypeptidase

all of the information necessary for folding the peptide chain into its “native” structure is contained in the _____ of the peptide.

a. amino acid sequence

b. amino acid composition

c. configuration

d. amino acid side chain charges

e. post-translational modifications

amino acid sequence

which are the four most common elements in the human body?

a. H, Ca, O, Na

b. H, O, Fe, C

c. H, O, C, N

d. O, C, Fe, N

H, O, C, N

by limiting the orientation that neighboring water molecules can assume, solutes give _____ to the solvent and _____ the dynamic interplay among H₂O molecules that occurs in pure water.

a. pressure, disrupt

b. disorder, increase

c. disorder, decrease

d. order, diminish

e. order, increase

order, diminish

the “Good” buffers have all the following characteristics except:

a. they are relatively expensive

b. they are strong nucleophiles

c. they show small changes of pK_a with temperature

d. they contain nitrogen heterocycles and sulfonic acid groups

they are relatively expensive

an interaction between two subunits of a protein was determined to have a delta G degree’ = -57.05 kJ/mol. what is the K_eq for the reaction at 25 degrees C?

a. 1.02

b. 1.32

c. 10^-10

d. 10¹⁰

10¹⁰

an “antiparallel hairpin” is composed of

a. an alpha-helix, a beta-turn, and a second alpha- helix

b. a strand of beta-sheet, a beta-turn, and a second strand of beta-sheet

c. a strand of beta-sheet, an alpha-helix, and a second strand of beta-sheet

d. an alpha-helix, a strand of random coil, and a second alpha-helix

a strand of beta-sheet, a beta-turn, and a second strand of beta-sheet

all the statements about the classification of these amino acids are correct except:

a. aspartic and asparagine are acidic

b. alanine and valine are neutral, nonpolar

c. serine and glutamine are polar, uncharged

d. lysine and arginine are basic

e. tyrosine and phenylalanine are aromatic

aspartic and asparagine are acidic amino acids

which equation defines a system at equilibrium?

a. ΔG > 0

b. ΔG° = delta G

c ΔG = 0

d. ΔG° = 0

e. ΔG = RT ln ([products]/[reactants])

ΔG = 0

rank the following compounds in the order of increasing (i.e., more negative) free energy of hydrolysis

A: acetyle phosphate

B: 1,3-diphosphoglycerate

C: pyrophosphate

D: AMP

a. A, B, C, D

b. D, C, B, A

c. B, C, A, D

d. C, D, B, A

e. D, C, A, B

D, C, B, A (-14.2, -19.2, -43.1, -49.4 kJ/mol)

using a cation exchange resin (such as Dowex-50), a mixture of four amino acids is separated using an eluting gradient of increasing NaCl concentration. what would be the likely elution sequence?

a. asp, arg, ser, lys

b. arg, asp, lys, ser

c. lys, arg, asp, ser

d. asp, ser, lys, arg

e. ser, asp, lys, arg

asp, ser, lys, arg

which of the following is NOT a common post-translational modification of a protein?

a. prenylation

b. arylation

c. phosphorylation

d. methylation

e. ADP-ribosylation

arylation

quaternary structures may be used to

a. increase protein stability

b. provide genetic economy 

c. bring catalytic sites together

d. provide a, b, and c

provide a, b, and c

ninhydrin has all these properties except

a. it can be used to detect amino acids following chromatography

b. it produces a purple-colored product reaction with alanine

c. it provides a yellow product upon reaction with histidine

d. it can be used to quantify most amino acids

it provides a yellow product upon reaction with histidine

which of the following sugar alcohols yield a cold, sweet tase and is used in many candy bars?

xylitol

glycerol

ribitol

ethylene

xylitol

gram-positive bacteria possess which of the following?

lipopolysaccharide layer

inner and outer membranes

peptidoglycan

all the above

peptidoglycan

the most abundant lipid in red blood cell membranes is

phosphatidylcholine

cholesterol

phosphatidylinositol

phosphatidylserine

cholesterol

A-DNA and A-RNA double helices are ___-handed, B-DNA double helices are ___-handed, and Z-DNA double helices are ___- handed.

right, right, left

which of the following properties of sucrose is responsible for the fact that it does not undergo mutarotation when dissolved in water?

sucrose is composed entirely of D-sugars

sucrose is more than 10 carbons

sucrose is not a reducing sugar

sucrose has both furanose and pyranose substructures

sucrose is not a reducing sugar

which of the following class of enzymes does not require ATP?

flippases

floppases

type II restriction endonucleases

type II restriction endonucleases

which of the following polysaccharides is not synthesized by any mammal?

glycogen

chitin

heparin

chondroitin sulfate

chitin

to judge from the illustrations in your textbook (and in class), the outer branches of the oligosaccharides of glycoproteins are particularly rich in

ribose

mannose

galactose

arabinose

mannose

which of the following proteins does not catalyze active transport?

bacteriorhodopsin

KcsA

gastric H+,K+ ATPase

KcsA

the reason that the blood of humans is a saturated solution of uric acid, which may crystallize in the extremities to cause gout, is thought to be:

humans lack the enzyme urate oxidase

uric acid is an excellent antioxidant and may help to prevent cancer

gout usually occurs late in life, and thus has little effect on procreation

all three reasons are true

all three reasons are true

which class of lipids would be found on the skin of an apple or the feathers of a duck?

glycerophospholipids

triacylglycerols

sphingolipids

waxes

terpenes

steroids

waxes

which class of lipids is the main target for hydrolysis by enzymes in rattlesnake venom?

glycerophospholipids

triacylglycerols

sphingolipids

waxes

terpenes

steroids

glycerophospholipids

which of the following polynucleotides does not (usually) have a well-defined secondary or tertiary structure?

mRNA

rRNA

tRNA

DNA

mRNA

the thickness of a typical phospholipid membrane bilayer is:

4 Å

15 Å

26 Å

37 Å

48 Å

37Å

a bacterial protein toxin that creates an open channel in the victim’s cell membrane is using what form of membrane transport to kill the cell?

passive diffusion

facilitated diffusion

active transport

facilitated diffusion

assuming a random distribution of the four DNA bases, a restriction endonuclease that recognizes a 6-base sequence will encounter that sequence once in every how many bases?

128

2401

4096

16,384

65,536

4096

the most important factor governing the high selectivity of the KcsA protein’s potassium channel is:

the pH-gating of the channel

the construction of the channel from 12 alpha-helices

the presence of four K⁺ binding sites

the channel’s mimic of normal K⁺ hydration

the hydrolysis of ATP to drive K⁺ transport

the channel’s mimic of normal K⁺ hydration

the “Central Dogma of Molecular Biology” (as well more tangible evidence) suggests that which type of molecule held the central role in primordial life?

DNA

RNA

protein

polysaccharide

complex lipid

RNA

β-D-Galactose and β-D-mannose are

enantiomers

diastereomers

anomers

epimers

all the above

diastereomers

the presence of thymine, rather than uracil, as a base in DNA is thought to facilitate what process?

detection of errors caused by chemical degradation of DNA

more rapid uncoiling of DNA for replication

removal of the 2’-hydroxy group in ribonucleotides during DNA synthesis

steric inhibition of incorrect base pairing

detection of errors caused by chemical degradation of DNA

which of the following sugars is an aldopentose?

ribitol

ribulose

xylose

xylulose

mannose

ribose

xylose, ribose

if carbon 1 is the carbonyl group of galactose, which carbon determines if the sugar is a D- or L-stereoisomer?

C-1

C-2

C-3

C-4

C-5

C-6

C-5

all of the statements about the following pairs of sugars are correct EXCEPT:

galactose and mannose are epimers

L-galactose and D-galactose are enantiomers

glucose and mannose are epimers

glucose has fewer chiral centers than sucrose and fructose

Galactose and mannose are diastereomers.

Glyceraldehyde and dihydroxyacetone are stereoisomers

glucose and galactose are epimers

glucose has fewer chiral centers than sucrose and fructose

which of the following disaccharides contains an α(1—>4) glycosidic bond?

sucrose

lactose

maltose

cellobiose

cellulose

maltose

glucaric acid is formed by oxidation of which carbon of glucuronic acid?

C-1

C-2

C-5

C-6

both C-1 and C-6

both C-1 and C-6

in the Gram stain procedure, a brief treatment with ethanol or acetone washes away the outer membrane of Gram ___ bacteria, exposing their ___ layer of peptidoglycan (as compared to Gram ___ bacteria), from which the crystal violet is easily extracted.

negative; thicker; positive

positive; thicker; negative

negative; thinner; positive

positive; thinner; negative

negative; thinner; positive

cellulose is extremely resistant to hydrolysis, but cellulase catalyzes the hydrolysis and comes from:

the pancreas

bacteria that live in the rumen

the liver

protons secreted into the rumen

the intestinal wall.

bacteria that live in the rumen

dietary essential fatty acids for humans include

linolenic and oleic acids

palmitic and oleic acids

oleic and linoleic acids

linoleic and linolenic acids

linoleic acid (an omega-6) and alpha-linolenic acid (ALA) (an omega-3)

glycosphingolipids consist of a ___ with one or more ___ residues in a ___ linkage at the 1-hydroxy moiety.

sugar; fatty acids; esters

ceramide; sugar; β-glycosidic

ceramide; fatty acids; amide

glycerol; fatty acids; ester

ceramide; sugar; β-glycosidic

a triterpene that is both the biosynthetic precursors of all steroids and a lubricant for delicate machinery where a free-flowing lipid with very low vapor pressure is required is

lanosterol

cortisone

β-carotene

squalene

squalene

membranes with unsaturated fatty acids in their components are more flexible and fluid because:

unsaturated fatty acids pack closely together to from ordered arrays

unsaturated fatty acids bend at the double bond preventing close packing

saturated fatty acids have a “kink” that produces more fluid aggregates

unsaturated fatty acids have cis double bonds that block “kink” formation

all are correct

unsaturated fatty acids bend at the double bond preventing close packing

in most cases, glycerophospholipids have ___ fatty acid at position 1 and ___ fatty acid at position 2 of the glycerol.

a saturated; a saturated

a saturated; an unsaturated

an unsaturated; a saturated

an unsaturated; an unsaturated

a saturated; an unsaturated

cholesterol is a component of all the following except:

lipoproteins

plant cell plasma membranes

animal cell membranes

membranes of intracellular organelles

all are true

plant cell plasma membranes

steroid hormones include all the following except:

stigmasterol

progesterone

cortisone

estradiol

testosterone

stigmasterol

which of the following would be the most likely interaction between a peripheral membrane protein that contained a high lysine content and a membrane?

ionic interaction

hydrophobic interaction

lipid insertion

covalent bonding

amide hydrolysis

ionic interaction

in passive diffusion, the transported species moves across the membrane in the _____ favored direction _____.

kinetically; using a transport protein

kinetically; without a specific transport system/molecule

thermodynamically; using a transport protein

thermodynamically; without a specific transport system/molecule

thermodynamically; without a specific transport system/molecule

β-Fluoroalanine, an excellent drug that was never approved for human use by the FDA, is

a non-steroidal anti-inflammatory drug that selectively inhibits COX-2

an anti-hypercholesteremic drug that inhibits HMG-CoA reductase

an anti-bacterial agent that inhibits cell wall biosynthesis

a form of vitamin A that was shown to cause cancer in humans

a masking agent for performance-enhancing drugs, chiefly testosterone.

an anti-bacterial agent that inhibits cell wall biosynthesis

flippases are enzymes that flip:

fatty acids from one position on glycerol to another position

glucose form α- to β-glucose

amino acids from one position to another in a protein

cholesterol from one organelle to another

phospholipids across to the other side of a membrane

phospholipids across to the other side of a membrane

Lipids that spontaneously form micelles, monolayers and bilayers have what property?

waxy

polar

amphipathic

bipolar

polyisoprenoid

amphipathic

In eukaryotic cells phospholipids, glycolipids and cholesterol are synthesized by enzymes located in the ____ and ____, and flow of these components to other membranes in the cell is mediated by ____.

plasma membrane; mitochondria; osmosis

endoplasmic reticulum; Golgi; osmosis

plasma membrane, Golgi; lipid transfer proteins

endoplasmic reticulum; Golgi; lipid transfer proteins

endoplasmic reticulum; plasma membrane; flippases

endoplasmic reticulum; Golgi; lipid transfer proteins

the effect of the KscA potassium channel is an example of

passive diffusion

facilitated diffusion

active transport

membrane skeleton fencing

facilitated diffusion

the most highly oxidized purine is ____, but it is ___ found in nucleic acids.

guanine; always

adenine; always

hypoxanthine; never

xanthine; always

uric acid; never

caffeine; never

uric acid; never

cAMP and cGMP are ___ with phosphate esterified as cyclic ___ and are important as ___ of cellular metabolism.

nucleotides; phosphodiesters; inhibitors

nucleotides; phosphomonoesters, regulators

nucleotides; phosphodiesters, regulators

nucelosides; phosphomonoesters, stimulators

nucleotides; phosphodiesters, regulators

The net charge on nucleotide monophosphates is:

a. +1

b. 0

c. -1

d. -2

e. -3

-2

in double-stranded DNA containing 32%, cytosine, the percentage of adenine would be:

32%

68%

18%

0%

insufficient information to answer question

18%

Which molecule contains an acid anhydride bond?

a. DNA
b. ATP
c. UMP
d. RNA
e. cAMP

ATP

The methyl group of thymine is ultimately an evolutionary response to

the ease of hydrolysis of RNA

the need for extra solubility in membranes

photochemical dimerization in DNA

the nonenzymatic deamination of cytosine

the nonenzymatic deamination of cytosine

In eukaryotic cells, a class of ____- and ____-rich proteins called ____ interact ionically with the anionic phosphate groups in the DNA backbone to form ____.

a. lysine; leucine; prions; ribosomes

b. arginine; lysine; histones; nucleosomes

c. arginine; alanine; histones; nucleosomes

d. arginine; lysine; prions; ribosomes

e. none are true

arginine; lysine; histones; nucleosomes

RNA is ____ stable to alkaline hydrolysis than DNA because RNA’s vicinal ____ group makes the 3’-phosphodiester bond susceptible to ____ cleavage.

less; 3’-OH; nucleophilic

less; 2’-OH; nucleophilic

more; 2’-OH; electrophilic

more; 2’-OH; nucleophilic

less; 2’-OH; nucleophilic

which of the following statements correctly identifies a type II restriction endonuclease?

they work on both DNA and RNA

they recognize a palindromic sequence and cut just before the palindromic sequence

the result of this endonuclease is blunt ends

they degrade DNA by removing bases from each end

they cut DNA at sites in specific nucleotide sequences with a 2-fold axis symmetry

they cut DNA at sites in specific nucleotide sequences with a 2-fold axis symmetry

the chief fatty acid of olive oil (and clearly “empty calories”) is

palmitic acid

palmitoleic acid

oleic acid

linoleic acid

oleic acid

which of the following isoprenoid vitamins is derived from a steroid?

vitamin A

vitamin D

vitamin E

vitamin K

vitamin D

which of the following molecules would be an unlikely lipid anchor for a peripheral membrane protein?

an amide-linked myristoyl group

a thioester-linked stearoyl group

a thioether-linked farnesyl group

an ester-linked cholesteryl group

an ester-linked cholesteryl group

which of the following is not a selectivity filter for a protein involved in facilitated diffusion?

a narrow constriction in the pore formed by the protein

a requirement that several ions be transported together

a requirement for hydrolysis of ATP along with transport

a pH-switchable gate over the pore formed by the protein

a requirement for hydrolysis of ATP along with transport

The Na⁺, K⁺-ATPase of animal cells transports ___ sodium ions and hydrolyzes ___ molecules of ATP for each potassium ion transported

3;1

2; 1

1.5; 0.5

1; 1

3; 1

the DNA-directed synthesis of RNA is known as

replication

transcription

translation

termination

transcription

the long term stability of DNA is enhanced by

steric hindrance from the thymine methyl groups

easy protonation of the nucleotide bases

lack of 2’-hydroxyl groups of he deoxyriboses

small cross section of the minor groove

lack of 2’-hydroxyl groups of he deoxyriboses

which mechanism of enzyme catalysis is illustrated by the role of the serine hydroxyl group in reactions catalyzed by chymotrypsin?

approximation

tight binding of transition states

covalent intermediates

use of general acids and bases

covalent intermediates

benzene, a hydrocarbon, has a poor solubility in water chiefly because of

the hydrophobic effect

the amphiphiliity of water

the high polarity of benzene

poor solvation of benzene molecules

the hydrophobic effect (benzenes nonpolar)

HEPES is superior to phosphate or Tris as a buffer for biological experiments chiefly because of

its low cost

its pk_a of 7.55

its low MW

its low Δpk_a/degrees C

its low Δpk_a/degrees C

the presence of magnesium ions typically makes the hydrolysis of ATP ____ due to ____

more favorable; reduced charge-charge repulsion among the phosphates

less favorable; reduced charge-charge repulsion among the phosphates

more favorable; increased charge-charge repulsion among the phosphates

less favorable; increased charge-charge repulsion among the phosphates

more favorable; reduced charge-charge repulsion among the phosphates

which of the following amino acids has a side chain group that is less acidic than a typical α-ammonium group (the protonated α-amino group of an amino acid)?

asp

cys

glu

tyr

cys

the genetic defect that makes an individual unable to convert phenylalanine to tyrosine leads to the very serious disease ___, but a genetic defect that causes urine to turn black in air is the hallmark of the much less serious disease ____.

acromegaly; hypercholesteremia

hyperthyroidism; Marfan’s syndrome

phenylketonuria; alkaptonuria

Marfan’s syndrome; phenylketonuria

phenylketonuria; alkaptonuria

the arrangement of the subunits in a protein is an element of ____ structure.

primary

secondary

tertiary

quaternary

quaternary

disulfide bonds are most frequently stabilized ___ structure in proteins

primary

secondary

tertiary

quaternary

tertiary

in order to cleave a polypeptide “to the right” of methionine residues, one should treat the peptide with..

trypsin

chymotrypsin

cyanogen bromide

carboxypeptidase

cyanogen bromide

which of the following secondary structures has a strong dipole that is used by some proteins for charge neutralization?

α-helices

parallel β-sheet

antiparallel β-sheet

β-turn

α-helices

in a four-helix-bundle protein, the amino acid residues on the interior faces of the α-helices are typically

arranged to form salt bridges

negatively charged

hydrophobic

positively charged

hydrophobic