Unit 1

Question 1

Which universal law do metabolic redox reactions follow?

Answer 1

First law of thermodynamics

Question 2

Structure determines function, however structure alone is not always
sufficient to predict function, especially for proteins. One way to
understand the
association between protein structure and protein function,
even if it is not absolute, is to use analogies. Based on the following protein
examples, match the analogy with the protein pair.

Option 1: same structure protein, but one is green and one is red (ribonucleotide reductase)
Option 2: similar structure and color protein, but one is thick and wider than the other (porin channel protein)
Option 3: Similar structure and color patter, but the middle alpha helix on one is stretched out more than the other (GR transcription factor)

1. boat and submarine
2. Apple tree and pear tree
3. lemon and tennis ball

a. ribonucleotide reductase (bacteria) and ribonucleotide reductase (mouse)
b. porin channel protein and green fluorescent protein
c. GR transcription factor and GCN4 transcription factor

Answer 2

1. Boat and submarine (c)
2. Apple tree and pear tree (a)
3. lemon and tennis ball (b)

Question 3

Which personal observation most directly reflects DNA as the chemical basis of heredity?

Answer 3

a family with several members who share red hair

Question 4

Put the following hierarchical levels in the correct order representing the
structured organization of life on Earth. The number 1 is the lowest
hierarchical level (base of the pyramid) and the number 7 if the highest
hierarchical level (tip of the pyramid)
1.glucose
2. hydroxyl group
3. glycolysis
4. great barrier reef
5. manta ray
6. glycogen
7. liver cell

Answer 4

1. hydroxyl group 2. glucose 3. glycogen 4. glycolysis 5. liver cell 6. manta ray 7. great barrier reef

Question 5

Which example best illustrates the second law of thermodynamics in
biological systems?
a) DNA replication producing identical strands.
b) A calorimeter measuring bond energy release.
c) Cow bones decomposing in the desert.
d) A seedling germinating in sunlight to build ordered cells.
e) Water forming hydrogen bonds at a liquid surface.

Answer 5

c) Cow bones decomposing in the desert.

Question 6

A mutation changes the active site of an enzyme critical for metabolism.
Which outcome is most likely?
A) The protein stops being heritable.
B) The protein retains identical function.
C) The protein increases entropy of the system.
D) The protein function changes due to altered molecular structure.
E) The protein mutates back to its original sequence.

Answer 6

D) The protein function changes due to altered molecular structure.

Question 7

Although Watson and Crick could construct a DNA double helix with A-A
and C-C base pairs, there were two reasons why this arrangement was
unlikely to be valid. Choose the two reasons from the list below.
a) Chargaff’s rule says the abundance of adenine and cytosine nucleotides are
equal in DNA from different species, which is inconsistent with A-A and C-C.
B) Distance between the ribose sugars in A-A and C-C base pairs are
significantly different, whereas purine-pyrimidine base pairs are equally
spaced.
C) Erwin Chargaff showed that the abundance of A equaled T and G equaled C
nucleotides, so A-A and C-C base pairs is inconsistent with these data.
D) It was known that purine and pyrimidine nucleotides have complementary
sp2 orbitals and are more likely to form hydrogen bonds than A-A and C-C.
E) There are three times more adenine nucleotides in DNA compared to
cytosine nucleotides, which is inconsistent with A-A and C-C base pairs.
F) The A-A and C-C base pairing structures would not allow for RNA
transcription because U-U base pairing would be required and Watson
already knew this

Answer 7

B) Distance between the ribose sugars in A-A and C-C base pairs are
significantly different, whereas purine-pyrimidine base pairs are equally
spaced.
C) Erwin Chargaff showed that the abundance of A equaled T and G equaled C
nucleotides, so A-A and C-C base pairs is inconsistent with these data.

Question 8

Why was Pauling’s DNA model with phosphates inside and bases outside
chemically unfavorable?
A) Bases require ionic bonding
B) Bases are charged and stable in water
C) Phosphates are hydrophobic
D) It predicted only one DNA strand
E) Phosphates repel each other and bases are hydrophobic

Answer 8

E) Phosphates repel each other and bases are hydrophobic

Question 9

Why was Franklin’s B-form DNA diffraction pattern so decisive in solving
the DNA structure?
A) It proved phosphates were internal
B) It demonstrated the equal ratios of bases
C) It showed DNA was a triple helix
D) It showed DNA was composed of amino acids
E) It revealed helical geometry with uniform spacing

Answer 9

E) It revealed helical geometry with uniform spacing

Question 10

A mutation removes most of the lysine and arginine residues from SSB’s
DNA-binding domain, but the tetramer still assembles normally. What is the
most likely outcome?
A) SSB recruits helicase more efficiently to origins of replication
B) SSB binds DNA more tightly, blocking DNA polymerase loading
C) SSB continues to bind DNA but with increased sequence specificity
D) SSB fails to bind DNA because of reduced positive surface charge
E) SSB binding switches to double-stranded DNA regions

Answer 10

D) SSB fails to bind DNA because of reduced positive surface charge

Question 11

If single-stranded DNA binding were mediated by sequence-specific
recognition instead of electrostatic interactions, what major problem would
arise during genome replication?
A) DNA ligase would not be able to join adjacent fragments.
B) Helicase would be unable to unwind the double helix.
C) DNA polymerase would incorporate incorrect bases opposite lesions.
D) SSB would fail to protect most ssDNA regions from re-annealing.
E) Okazaki fragments would be elongated in the wrong orientation.

Answer 11

D) SSB would fail to protect most ssDNA regions from re-annealing.

Question 12

Match the letter on the left corresponding to the figure below with the
descriptions on the right.

A) Nitrogenous base
B) Left-handed helix
C) Ribose sugar
D) Phosphoryl group
E) Phosphoethyl linkage
F) 3’ hydroxyl
G) Minor groove
H) 5’ hydroxyl
I) Fructose sugar
J) Ionic bond
K) Major groove
L) Hydrogen bond

Answer 12

K) groove that forms a positive slope H) red molecule on bottom left of DNA structure L) forms in-between strand so of DNA to keep structure together D) on outer edge of DNA structure, 4 red balls sit together A) Bottom of DNA structure, towards the middle of DNA G) groove that forms a negative slope on dna C) rings on outer corner of DNA

Question 13

Match the description of PrP protein diseases on the left with the clinical
term on the right.
1. Sporadic PrP misfolding with or without a
PrP DNA mutation
2. Presence of an inherited PrP genetic
mutation that causes PrP misfolding
3. Consuming meat with misfolded PrP
protein without the transfer of pathogenic
DNA
A) Spontaneous
TSE
B) Familial TSE
C) Infectious
TSE

Answer 13

1. A
2. B
3. C

Question 14

Which statement below best describes the Prion Hypothesis first proposed
by Stanley Prusiner in 1982?
a) The Prion Hypothesis is an unproven theory that suggests alzheimer’s disease
is caused by Familial b) TSE that is transmitted by the mitochondria of infected
males as a result of contact sports.
TSEs of all three types are caused by misfolded prion proteins that convert
normal prion proteins into misfolded prion proteins, which form protein
aggregates that kill neurons.
C) Mad Cow disease is a TSE that is caused by viruses that transmit misfolded
prion proteins to neurons in infected individuals who come in contact with
cow’s milk from farm animals living near hospitals.
D) Familial TSE and infectious TSE are caused by misfolded prion proteins that
convert normal prion proteins into misfolded prion proteins, whereas
spontaneous TSE is caused by DNA mutations that kill neurons.

Answer 14

b) TSE that is transmitted by the mitochondria of infected
males as a result of contact sports.
TSEs of all three types are caused by misfolded prion proteins that convert
normal prion proteins into misfolded prion proteins, which form protein
aggregates that kill neurons.

Question 15

Which method could distinguish familial TSE from infectious or
spontaneous TSE?
A) Protein electrophoresis
B) DNA sequencing of PrP gene
C) Measuring ATP hydrolysis
D) Western blot of GroEL
E) Blood cholesterol testing

Answer 15

B) DNA sequencing of PrP gene

Question 16

A patient presents in your clinic with what appears to be spontaneous TSE.
a) What type of biochemical test would be the most definitive to distinguish
between a case of spontaneous TSE in a patient that resulted from sporadic
PrP protein misfolding in brain cells or the result of a somatic DNA mutation
in the PrP gene?
b) Regardless of the molecular basis of spontaneous TSE in this patient, is
the probability of their children getting
spontaneous TSE later in life high or
low?

a) Obtain protein from cells in the region of several brain plaques in the
patient and determine the structure of PrP protein molecules.
b) Probability is high.

a) Obtain DNA from cells in the region of several brain plaques in the patient
and sequence the PrP gene.
b) Probability is low.

a) Obtain protein from cells in the region of several brain plaques in the
patient and determine the structure of PrP protein molecules.
b) Probability is low.

a) Obtain DNA from cells in the region of several brain plaques in the patient
and sequence the PrP gene.
b) Probability is high.

Answer 16

a) Obtain DNA from cells in the region of several brain plaques in the patient
and sequence the PrP gene.
b) Probability is low.

Question 17

Match the description of a disease caused by misfolded protein on the left
with the correct phenotype on the right.
1. Protein aggregates form spontaneously from
misfolded protein in cells with no DNA
mutations in the corresponding gene.
2. Protein misfolding occurs spontaneously and
the protein is rapidly degraded by the
proteasome.
3. DNA mutation encodes a protein that is
misfolded when synthesized and it forms large
aggregates.
4. DNA mutation encodes a protein that is
misfolded when synthesized and is quickly
degraded by the proteasome.
5. Protein aggregates from in cells as a result of
consuming meat from an animal with Mad
Cow Disease.
A) Gain-of-
function
B) Loss-of-
function

Answer 17

1–>Gain of function
2–> Loss of function
3–> gain of function
4–> loss of function
5–> gain of function

Question 18

Put the following steps in the GroEL/ES cycle into the correct order.
1) ATP hydrolysis in the upper chamber facilitates protein
refolding and resets the lower chamber.
2) A new unfolded protein enters the lower chamber and the
cycle continues.
3) Following ADP dissociation, GroES dissociates and folded
proteins is released from the lower chamber.
4) GroES and ATP bind to the GroEL ring and trap unfolded
protein in the upper chamber.

Answer 18

order: 3,4,2,1

Question 19

Which two statements below best describe autotrophs and heterotrophs?
A) The majority of heterotrophs on Earth do not use aerobic respiration as a
form of energy conversion.
B) There are no metabolic differences between autotrophs and heterotrophs.
C) Heterotrophs evolved on Earth before autotrophs.
D) Heterotrophs are dependent on autotrophs to generate O2 from H2O in
order to support aerobic respiration.
E) Autotrophs depend on heterotrophs to oxidize sugar and release CO2 into
the atmosphere.
F) Heterotrophs depend on autotrophs for conversion of light energy to
chemical energy.
G) Heterotrophs that do not eat autotrophs every day will die in a short time.

Answer 19

D) Heterotrophs are dependent on autotrophs to generate O2 from H2O in
order to support aerobic respiration.
F) Heterotrophs depend on autotrophs for conversion of light energy to
chemical energy.

Question 20

Choose the two correct answers below that most accurately describe the
difference between the actual change in free energy (delta G) and the
standard change in free energy (delta Gº’).
A) The standard change of free energy is a function of time where as the actual
change in free energy is a function of the rate constant.
B) There is no difference between the actual change in free energy and the
standard change in free energy as long as the concentration of H2O is 55 M.
C) The actual change in free energy is dependent on temperature whereas the
standard change in free energy is dependent on pressure but not
temperature.
D) The standard change in free energy reflects the potential energy in reactants
and products independent of concentration whereas the actual change in
free energy is dependent on the concentration of reactants and products
under steady state conditions.
E) The actual change in free energy changes in response to the environment
whereas the standard change in free energy is a constant for a given
reaction

Answer 20

D) The standard change in free energy reflects the potential energy in reactants
and products independent of concentration whereas the actual change in
free energy is dependent on the concentration of reactants and products
under steady state conditions.
E) The actual change in free energy changes in response to the environment
whereas the standard change in free energy is a constant for a given
reaction

Question 21

Which TWO of the following processes are driven by the hydrophobic effect?
A) Melting of ice
B) Sequestration of hydrophobic groups to the interior of a folded protein
C) Separation of oil and water
D) Dissolving sodium chloride in water

Answer 21

B) Sequestration of hydrophobic groups to the interior of a folded protein
C) Separation of oil and water

Question 22

Select the four TRUE statements below describing the standard free
energy change (delta G) and the equilibrium constant (Keq).
A) The value for the equilibrium constant can be experimentally determined for
a given reaction.
B) The standard free energy change is a function of enzyme concentration in the
reaction.
C) If the value of the equilibrium constant is known, the value for the standard
free energy change can be determined.
D) The equilibrium constant is the ratio of product and reactant concentrations
at equilibrium.
E) A reaction is spontaneous when the standard free energy change and the
equilibrium constant are both negative values.
F) The equilibrium constant is equal to ratio of the concentration of reactants
over products at equilibrium.
G) The value for the standard free energy change is constant for a given
reaction.

Answer 22

A), C), D), G)

Question 23

The equilibrium constant Keq for the reaction A<–>B is 1x105 at 25ºC.
Calculate the delta Gº’ for this reaction.
A) -14.25 jK/mol
B) -28.5 kJ/mol
C) +28.5kJ/mol
D) +57.0 kJ/mol

Answer 23

B) -28.5 kJ/mol

Question 24

Identify the THREE conditions in the list below that BEST describe low
energy charge in a cell.
A) The energy charge ratio is above 0.85.
B) Low ATP concentrations.
C) AMP concentrations are very low.
D) High glucose concentrations.
E) The amount of stored glycogen in the cell is high.
F) High ATP concentrations.
G) High AMP concentrations.
H) Flux in anabolic pathways > catabolic pathways.
I) The energy charge ratio is below 0.70.
J) Very low ADP concentrations

Answer 24

B) Low ATP concentrations.
G) High AMP concentrations.
I) The energy charge ratio is below 0.70.

Question 25

Calculate the delta Gº’ for the conversion of Glucose-6-P <-> Fructose-6-P using the delata Gº’ values shown below. G-6-P --> F-6P DG = ? F-6P --> F-1-6-BP DG = +16.3 ATP --> ADP +Pi DG = -30.5 G-6P + ATP --> F1-6-BP + ADP DG = -12.5 A) +1.7 kJ/mol B) -1.7 kJ/mol C) +30.5 kJ/mol D) -14.2 kJ/mol

Answer 25

A) +1.7 kJ/mol

Question 26

Why is it energetically favorable to form one large oil droplet (protein complex) rather than many oil droplets (protein monomers) in an aqueous solution? A) Because large oil droplets have a more positive standard change in free energy than do small water droplets, so it is more favorable. B) Because there are more ordered water molecules with large oil droplets, so higher entropy in the system C) Because there are fewer ordered water molecules with large oil droplets, so lower entropy in the system D) Because there are fewer ordered water molecules with large oil droplets, so higher entropy in the system.

Answer 26

D) Because there are fewer ordered water molecules with large oil droplets, so higher entropy in the system.

Question 27

The H2CO3 <--> H+ + HCO3- buffering system in blood plasma maintains blood pH at 7.40. Although the p Ka of this reaction is only 6.1, this buffering system works well because 1) CO2(gas) is removed from the lungs by breathing, 2) carbonic anhydrase interconverts CO2(aqueous) + H2O <-- > H2CO3, and 3) excretion or retention of HCO3- by the kidneys regulates HCO3- levels, which in turn regulates H+ levels. Calculate the ratio of bicarbonate to carbonic acid in blood plasma at pH 7.4. A) 5.0 x 10^2 B) 1.2 x 10-3 C) 1.1 x 10-1 D) 2.0 x 10^1 E) 2.6 x 10-1

Answer 27

D) 2.0 x 10^1

Question 28

Why are A-T rich regions more susceptible to DNA denaturation than G-C rich regions? A) The primary reason G-C rich regions are more stable is that G-C base pairs have three hydrogen bonds, and A-T base pairs have only two hydrogen bonds. B) Counterions (like Mg2+) bind preferentially to G-C rich regions, enhancing their stability. C) G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions D) More DNA binding proteins bind to G-C rich regions, and therefore stabilize these structures

Answer 28

C) G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

Question 29

What is the isoelectric point (pI) of the free amino acid lysine, which has the following three pKa values: 2.1 for the α-carboxyl group 9.7 for the α-amino group 10.5 for the side chain amino group A) 6.3 B) 10.1 C) 5.9 D) 7.0

Answer 29

B) 10.1

Question 30

The DNA of a bacterial strain was isolated, and it was determined that 15% of the DNA is composed of cytosine. What percentage of the bacterial DNA is adenine? A) 70% B) 30% C) 35% D) 15%

Answer 30

C) 35%

Question 31

A peptide bond consists of what two functional groups listed below? A) an alcohol and an amide group B) a carboxyl group and an amino group C) a methyl group and amine group D) an amino group and a thiol

Answer 31

B) a carboxyl group and an amino group

Question 32

Name the six amino acids shown in the box: 1: 5 point ring structure with a COO^- off a carbon 2: 3 carbon chain with R group with two O's 3: 5 ring chain with a nitrogen in the middle 4: has sulfur, and 4 carbons 5: ring structure in R group with 2 carbons 6: has an amino group and a double bond oxygen A) 1:Pro, 2:Asp, 3:His, 4:Met, 5:Phe, 6:Gln B) 1:Pro, 2:Glu, 3:Tyr, 4:Cys, 5:Phe, 6:Asn C) 1:Phe, 2:Asp, 3:Pro, 4:Met, 5:His, 6:Gln D) 1:Phe, 2:Glu, 3:Pro, 4:Cys, 5:Phe, 6:Asn E) 1:Tyr, 2:Asp, 3:His, 4:Met, 5:Trp, 6:Arg

Answer 32

A) 1:Pro, 2:Asp, 3:His, 4:Met, 5:Phe, 6:Gln

Question 33

A homopolymer of lysine residues (polylysine) can adopt an alpha-helical conformation or a random coil conformation depending on the pH of the solution. Predict whether the conformation of polylysine would be a-helical or random coil at a pH of 1, 7, and 11. Choose a total of THREE answers. Choose either helix or random coil for pH 1, pH 7, and pH 11. A) pH 1 - helix B) pH 7 - random coil C) pH 11 - helix D) pH 11 - random coil E) pH 7 - helix F) pH 1 - random coil

Answer 33

B) pH 7 - random coil C) pH 11 - helix F) pH 1 - random coil

Question 34

he keratin coiled-coil is a ________________-handed homodimer structure whereas each individual keratin strand is a _______________-handed alpha helix. The collagen fiber contains ______________subunits that wrap around each other to form a _______________-handed triple helix. Structures of a) keratin and b) collagen are shown below. A) left; right; three; left B) right; left; three; right C) right; left; two; right D) left; right; three; right

Answer 34

D) left; right; three; right

Question 35

Prion disease is due to the accumulation of misfolded protein aggregates that lead to neurodegeneration. Which of the following statements could be the possible reason why prion protein aggregates form in cells? A) Misfolded prion proteins undergo a conformational change that stimulates subunit proteolysis leading to the formation of highly charged cationic protein nanotubes, which associate with anionic nanotubes. B) Misfolded prion proteins are ubiquitinated and targeted to the proteasome where large protein complexes are unable to degrade the misfolded ubiquitinated prion proteins, thereby stimulating aggregation. C) Phosphorylated prion proteins are very stable in the unfolded conformation and activation of cellular kinases result in prion aggregation owing to the stabilization of the phosphorylated unfolded protein. D) Mutations in the prion gene results in the synthesis of prion proteins that form multiple hydrogen bonds with water, which are stabilized by salt bridges forming between phosphate groups and arginine residues. E) Misfolded prion proteins expose a hydrophobic region that associates with the hydrophobic region of other misfolded prion proteins to initiate subunit aggregation involving beta sheets and beta stacks

Answer 35

E) Misfolded prion proteins expose a hydrophobic region that associates with the hydrophobic region of other misfolded prion proteins to initiate subunit aggregation involving beta sheets and beta stacks

Question 36

You need to separate two proteins from each other; one is Protein X = 80 kDa, which has a net negative charge at pH 7, and the other is Protein Y = 10 kDa, which has a net positive charge at pH 7. a) Which protein will elute first from a size exclusion column? b) Which protein will migrate slower in an SDS polyacrylamide gel? c) Which protein will elute first on a pH 7 cation exchange column? d) Which protein will elute first on a pH 7 anion exchange column? (a) Y, (b) Y, (c) X, (d) Y (a) X, (b) X, (c) Y, (d) X (a) X, (b) Y, (c) Y, (d) X (a) Y, (b) X, (c) Y, (d) X (a) X, (b) X, (c) X, (d) Y

Answer 36

(a) X, (b) X, (c) X, (d) Y

Question 37

There are seven hierarchical levels of organization in living systems. Rank the following levels of organization from the most complex to the least complex. The most complex level, ecosystems, has been given to you at the very top of the ranking list.

Answer 37

Least complex 1. Organisms 2. cells 3. metabolism 4. macromolecules 5. biomolecules 6. elements and functional groups

Question 38

Difference between hydrogen bond donor and an acceptor

Answer 38

Hydrogen bond acceptor: does not include the hydrogen, maybe an oxygen molecule Hydrogen bond donor: circled with the H, can be attached to N or O

Question 39

Which of the following statements about phospholipids is false? Choose one: A. The hydrocarbon tail of phospholipids is hydrophobic. B. The polar head group of phospholipids is hydrophilic. C. Phospholipids orient in lipid bilayers with the hydrophobic tails pointing inward, interacting with each other. D. The polar head group of phosphatidylcholine cannot form hydrogen bonds.

Answer 39

D. The polar head group of phosphatidylcholine cannot form hydrogen bonds.

Question 40

A molecule with peptide bonds and amino acids belongs to what structure?

Answer 40

protein

Question 41

Label a lipid bilayer

Answer 41

Head: polar, hydrophilic Tail: nonpolar, hydrophobic

Question 42

Which of the following statements about redox reactions is correct? Choose one: A. A reduced compound becomes oxidized only when it acquires an electron from an oxidized compound. B. An oxidized compound has fewer protons than its reduced counterpart. C. A reduced compound has more carbon atoms than its oxidized counterpart. D. A reduced compound becomes oxidized only when it transfers an electron to an oxidized compound.

Answer 42

D. A reduced compound becomes oxidized only when it transfers an electron to an oxidized compound.

Question 43

Which best describes the pKa of a weak acid? Choose one: A. The pKa value depends on the concentration of the molecule present. B. The pKa value depends on the pH. C. pKa values change over the course of a titration. D. The pKa is an intrinsic property of a molecule in question and depends on how tightly bound the acidic H+ is.

Answer 43

D. The pKa is an intrinsic property of a molecule in question and depends on how tightly bound the acidic H+ is.

Question 44

Describe the ph graph in terms of pka

Answer 44

As ph increases, base equivalent increases. Below the line to the left: HA > A- Below the line to the right: HA< A- Above the line: HA = A

Question 45

What type of histone amino acid substitution mutation would be least likely to impact the histone–DNA interaction? Choose one: A. arginine to glycine B. arginine to leucine C. arginine to alanine D. arginine to lysine

Answer 45

D. arginine to lysine

Question 46

What is the molecular geometry of the constituents of the peptide plane? Choose one: A. The amide nitrogen is tetrahedral and the carbonyl carbon is trigonal planar. B. The amide nitrogen is trigonal bipyramidal and the carbonyl carbon is trigonal planar. C. The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar. D. The amide nitrogen is tetrahedral and the carbonyl carbon is also tetrahedral.

Answer 46

C. The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar.

Question 47

It has been observed that in a few cases, the peptide plane is actually bent 4°–5° from being a flat plane. What is the most plausible explanation? Choose one: A. The skewed peptide plane is a result of misformed disulfide bonds, causing the protein to denature. B. Some other restraint is causing the peptide plane to adopt an unfavorable state. The favorable energetics of the other restraint offset the energetic unfavorability of the skewed peptide plane. C. This is not possible. The apparent skewing of the peptide plane must be due to error in the structural measurement. D. The fast, dynamic motions in a protein cause the peptide plane to be non-ideal over the lifetime of the protein.

Answer 47

B. Some other restraint is causing the peptide plane to adopt an unfavorable state. The favorable energetics of the other restraint offset the energetic unfavorability of the skewed peptide plane.

Question 48

Of all the different bond types found in proteins, which has partial double bond character? Choose one: A. A peptide bond B. An ionic bond C. A disulfide bond D. A hydrogen bond

Answer 48

A. A peptide bond

Question 49

What is a major consequence of the partial double bond character? Choose one: A. Unrestricted rotational freedom B. Greatly increased rotational freedom compared to the φ (phi)/ψ (psi) torsion angles C. Minimal difference in rotational freedom compared to the φ (phi)/ψ (psi) torsion angles D. Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles

Answer 49

D. Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles

Question 50

What is the isoelectric point (pI) of lysine, which has pKa values of 2.1 for the α carboxyl group, 9.7 for the α amino group, and 10.5 for the side chain amino group? Choose one: A. 5.9 B. 7.0 C. 6.3 D. 10.1

Answer 50

D. 10.1

Question 51

What nitrogenous bases are purines and which are pyrimidines

Answer 51

Purine: Adenine, Guanin Pyrimidine: Uracil, Cytosine, Thymine

Question 52

Sort the following as belonging to both DNA and RNA, DNA only, or RNA only.

Answer 52

DNA: deoxyribose sugar, thymine, usually forms dobled-stranded double helix RNA: ribose sugar, uracil, is base labile, used in translation, usually forms single strands, multiple conformations DNA and RNA: phosphate group, nitrogenous bases, guanine, adenine, cytosine, used in transcription

Question 53

The secondary structure of DNA is often B-DNA, which is a double helix that contains a minor groove and a major groove. When dying DNA molecules for DNA laboratory techniques, there are two general types of dyes that specifically bind to DNA to make it fluorescent. One type of dye, such as ethidium bromide, intercalates in between bases inside the DNA, and is only fluorescent when it is intercalated into DNA. Another type of dye rests in the major or minor groove of DNA, such as SYBR Green, and is only fluorescent when it is bound in the groove of DNA. Intercalating dyes are considered to be more carcinogenic than groove-binding DNA dyes if they are absorbed through the skin of the researcher. Which of the following options is the most reasonable explanation for this? Choose one: A. The intercalated dyes will lead to increased mutations upon DNA replication since they are inserted into the bases that are used as a template for DNA replication. B. The groove-binding dyes increase the chance of mutation when DNA is being replicated because the sugar phosphate backbone is used as a template during DNA replication. C. The intercalated dyes emit more UV light, causing more damage to the DNA than the groove-binding dyes. D. The intercalated dyes attract more carcinogens in the cell to the DNA than the groove-binding dyes.

Answer 53

A. The intercalated dyes will lead to increased mutations upon DNA replication since they are inserted into the bases that are used as a template for DNA replication.

Question 54

Tyrosine is an amino acid whose side chain has a pKa of 10.1. At pH 7, what protonation form would you expect to find it in? protonated or deprotonated?

Answer 54

protonated

Question 55

You are an undergraduate research student working in the lab and have been asked to prepare phosphorylated tyrosine. Theoretically, based on the pKa of the amino acid, which of the following might you expect to be true? Choose one: A) Phosphorylation of tyrosine is independent of pH. B) Tyrosine will be more easily phosphorylated at low pH because the proton can be removed more easily. C) Tyrosine will be more easily phosphorylated at high pH because the proton can be removed more easily. D) Tyrosine will be more easily phosphorylated at neutral pH because the proton can be removed more easily.

Answer 55

C) Tyrosine will be more easily phosphorylated at high pH because the proton can be removed more easily.

Question 56

Now that you have successfully phosphorylated tyrosine, your boss wants you to dephosphorylate it. What strategy would be the most successful in your endeavor? Choose one: add more kinase and some ATP add a phosphatase and some water add a reducing agent reduce the pH

Answer 56

add a phosphatase and some water

Question 57

Which amino acids contain sulfur? Choose one or more: A. methionine B. arginine C. cysteine D. glutamine E. proline

Answer 57

A. methionine C. cysteine

Question 58

Which amino acid is able to form disulfide bonds?

Answer 58

cysteine

Question 59

The various chemical properties of the amino acid side chains determine the chemical properties and the three-dimensional structures of proteins. What are the four groups that amino acids can be divided into? Choose one: A. charged; aromatic; lipophilic; sulfur-containing B. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic C. short-chain Polar; long-chain aliphatic; aromatic; unreactive D. polar; nonpolar; aerobic; hydrophobic or aliphatic

Answer 59

B. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic

Question 60

Sickle cell anemia patients suffer from distorted red blood cell shape and an anemic condition as a result of a genetic mutation in the HBB gene, which codes for the hemoglobin β subunits. This mutation changes a Glu to a Val at position 6 in the protein, and these patients express two alleles (one from each parent) with this mutation. When individuals inherit just one copy of this mutated gene, they are considered carriers, and have very few symptoms. Based on the quaternary structure of hemoglobin, what can you predict about the assembly of hemoglobin in sickle cell anemia patients versus carriers of the sickle cell trait? Choose one: In sickle cell anemia patients, 100% of the hemoglobin is fully functional, whereas in those that carry the trait, there is no functional hemoglobin assembled. In sickle cell anemia patients, 100% of the hemoglobin assembled contains the mutant β globin, while in carriers, 50% of the hemoglobin assembled contains the mutated version. In individuals with the sickle cell mutation, hemoglobin α subunits cannot bind to β globin at all, and the quaternary structure cannot assemble. In sickle cell anemia patients, the α globin subunits have complementary mutations to ensure the quaternary structure of hemoglobin is attained.

Answer 60

In sickle cell anemia patients, 100% of the hemoglobin assembled contains the mutant β globin, while in carriers, 50% of the hemoglobin assembled contains the mutated version.

Question 61

Take a moment to examine the junctions between hemoglobin subunits in the above model. Which of the following might you say is a reasonable assumption? Choose one: A small molecule inhibitor that prevents association of oxygen with the heme should disrupt quaternary assembly of hemoglobin. Altered structure of one subunit may cause a structural shift in a neighboring subunit. Each subunit functions independently of all of the others. Hemoglobin should be able to function with all α or all β subunits since each has a heme group.

Answer 61

Altered structure of one subunit may cause a structural shift in a neighboring subunit.

Question 62

What level of protein structure describes the spatial location of every atom in a protein? Choose one: A. 2° B. 4° C. 3° D. 1°

Answer 62

C. 3°

Question 63

Indicate where the protein secondary structures are found on the Ramachandran plot by dragging each letter to the correct circle in the plot. Where is the beta sheet, alpha helix, unfavored region, and left handed alpha helix?

Answer 63

Alpha helix: -40 and -60 (bottom left) Beta sheet: 120, -120 (left top) Unfavored region: 120, -60 (right bottom) Left-handed alpha helix: rights side middle of chart

Question 64

Seperate dieases to which proteins are degraded and which are aggregated: Phenylketonuria Cystic fibrosis Hypercholesterolemia Tay-Sachs Alzheimer's sickle cell anemia Huntingons Creutzfe-jakob and kuru

Answer 64

Proteins aggregates: Alzheimer's sickle cell anemia Huntingons Creutzfe-jakob and kuru protein is degraded: Phenylketonuria Cystic fibrosis Hypercholesterolemia Tay-Sachs

Question 65

Cystic fibrosis is caused by a point mutation in CFTR, a chloride channel responsible for regulating fluid accumulation in the lungs. This mutation tricks the cell into thinking it is misfolded and it is subsequently degraded by the ubiquitin–proteasome pathway. Which of the following strategies do you think has the highest probability of curing the patient? Choose one: increasing the patient's chloride intake treating the patient with ubiquitin–proteasome inhibitors initiating aggregation of cellular CFTR delivering the correct CFTR gene to lung cells by gene therapy

Answer 65

delivering the correct CFTR gene to lung cells by gene therapy

Question 66

Based on the prion hypothesis, proposed by Dr. Prusiner at UCSF Medical School, which do you think is the best approach to developing a treatment for Creutzfeldt–Jakob disease? Choose one: Develop a biochemical that prevents aggregation of the prion protein. Provide the cell with more ATP to better handle the misfolded protein load. Initiate prion protein misfolding. Use gene therapy to prevent the mutation from occurring.

Answer 66

Develop a biochemical that prevents aggregation of the prion protein.

Question 67

Upon reading a primary article, you discover that negative, long-term prognosis for Huntington's patients is directly related to the size of the polyglutamine track expansion in the patient's DNA. Which of the following must be true? Choose one: As the number of glutamines present in the patient's huntingtin protein increases, the lower the probability of protein aggregation. As the number of glutamines present in the patient's huntingtin protein increases, the higher the probability of protein aggregation. As the number of glutamines present in the patient's DNA increases, the lower the probability of protein aggregation. As the number of glutamines present in the patient's DNA increases, the greater the probability of protein aggregation.

Answer 67

As the number of glutamines present in the patient's huntingtin protein increases, the higher the probability of protein aggregation.

Question 68

An antigen binds to an antibody at which of the following locations? Choose one: A. Only at the heavy chain B. At the variable domain C. At the constant domain D. Only at the light chain

Answer 68

B. At the variable domain

Question 69

Difference between parallel and antiparallel beta sheets

Answer 69

parallel: C will match up with C, OH will match up with OH antiparallel: C match up with OH

Question 70

Rhodopsin is made up of amphipathic α helices and is embedded in the lipid membrane. __________ amino acids are likely to be found on the interior-facing helical surface. Choose one: A. Hydrophobic B. Aromatic C. Hydrophilic D. Non-polar

Answer 70

C. Hydrophilic

Question 71

Which of the following statements could be considered true for both the Hsp70-mediated and GroEL–GroES-mediated protein-folding processes? Choose one: Both Hsp70 and GroEL–GroES are considered chamber-type chaperones. Proteins are typically released from both complexes in a partially folded form and the folding cycle may need to be repeated multiple times. Exposed hydrophilic patches on the surface of unfolded proteins initiate recognition with chaperones. ADP hydrolysis is critical to completion of the protein-folding cycle.

Answer 71

Proteins are typically released from both complexes in a partially folded form and the folding cycle may need to be repeated multiple times.

Question 72

The Hsp70 and GroEL–GroES chaperones initiate protein folding in which cellular compartment? Choose one: plasma membrane nucleus mitochondria cytosol

Answer 72

cytosol

Question 73

Cellular chaperones are incredibly important for human health. Which of the following do you think would be most detrimental to protein folding in the cell and necessitate upregulation of chaperone activity to maintain homeostasis? Choose one: migration to high altitude low blood oxygen levels accelerated cell division high fever

Answer 73

high fever

Question 74

Which of the following protein-folding diseases is a loss-of-function disease? Choose one: A. Huntington’s disease B. Alzheimer’s disease C. Creutzfeldt-Jakob disease D. Cystic fibrosis

Answer 74

D. Cystic fibrosis