EXAM 2 Flashcards by Kaman Hung

Which percentage of polyacrylamide would give the best separation for large proteins?

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In isoelectric focusing, a protein with a pH below the pI would __________.

Migrate towards the cathode

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A polypeptide was digested by trypsin and chymotrypsin. What is the sequence?

LMYKWDERMGFCE

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Which technique is the only choice for studying protein unfolding?

NMR

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The five major protein classes are __________, structural proteins, __________, genomic caretaker proteins, and __________.

Metabolic enzymes, transport proteins, cell signaling proteins

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Identify three proteins that are considered to be genomic caretaker proteins.

DNA polymerase
RNA polymerase
Topoisomerase

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Which statement applies to hemoglobin but not to myoglobin?

Subunit interactions are critical for function

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What is the role of the proximal histidine in globin proteins?

Moves toward the heme group in response to oxygen binding

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What are the primary functions of myoglobin and hemoglobin?

Myoglobin stores oxygen and hemoglobin transports oxygen

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Oxygen binding to hemoglobin causes all subunits to switch to the R state. This is an example of the __________ model of allostery.

Concerted

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Which allosteric effectors contribute to the Bohr effect?

2,3-bisphosphoglycerate
H+
CO2

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Why is the sickle cell anemia trait prevalent in Africa?

Heterozygous individuals carrying the Val-6 mutation are less susceptible to malaria

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What type of transport is characterized by molecules moving down a concentration gradient?

Passive transport

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If RTln(C2/C1) is zero, then __________.

No net transport will occur

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What accounts for some specificity of the K+ channel?

The orientation of backbone carbonyl oxygen atoms in the channel

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The selectivity of aquaporin for H2O relies on which three features?

Hydrogen bonding to Asn
Inverted alpha-helix dipoles
A 2.8 A constriction within the protein

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What is the transport system depicted in the figure?

Secondary active symporter

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Primary active ABC transporters and P-type transporters both require __________.

A protein conformational change to function

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Thick filaments __________, but thin filaments do not.

contain myosin

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If SERCA is not functioning in a myoblast, what may occur?

The myofibrils can shorten but not lengthen

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What is the rate enhancement from the presence of an enzyme if the uncatalyzed rate is 1.2 × 102 mmol/sec and the catalyzed rate is 2.4 × 104 mmol/sec?

200

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In a reaction coordinate diagram, X is __________ and Y is __________.

ΔG± of uncatalyzed reaction; transition state

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An enzyme can increase the rate of a reaction by __________ the energy of the __________.

Lowering; transition state

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The change in activation energy due to an enzyme is illustrated by the energy of __________ minus the energy of __________.

B & C

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If an enzyme carries out acid-base catalysis, which amino acid could act as a general acid?

Histidine

Identify the three types of enzyme-mediated reactions.

* Metabolite transformation reactions * Reversible covalent modification reactions * Coenzyme-dependent redox reactions

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin?

His57

The glutamate side chain in HMG-CoA reductase acts as a general base after __________.

A conformational change triggers the exchange for NADP+ for NADPH

In the figure, Km is indicated at __________.

A kinase adds a phosphate group to a target enzyme, altering the catalytic efficiency. This is an example of __________.

Covalent modification

In isoelectric focusing, a protein that is initially below the pI would __________.

Migrate toward the cathode

Biochemical assays are important in isolating proteins because they __________.

Uniquely identify one protein

In the oxygen binding curve for myoglobin, which statement is correct?

The lower pO2 in active muscle leads to release of O2 from myoglobin

If [L] = 5 mM, [P] = 3 mM, and [PL] = 2 mM, what is the dissociation constant?

7.5 mM

What may cause the oxygen binding curve of hemoglobin to change from sigmoidal to hyperbolic?

The protein dissociated into individual subunits

Which curve represents the binding of oxygen to myoglobin?

Curve A

Predict the fragments of the peptide DASRTYPECHI after cleavage by trypsin.

* DASR * TYPECHI

When oxygen binds to hemoglobin, what occurs?

The heme group becomes planar

Calculate the purification of the target protein with a 30% decrease in activity and a 55% decrease in total protein.

1.6-fold

True or False: Protein sequencing by Edman degradation does not require purified protein but sequencing by mass spectrometry does.

False

True or False: The N-terminal residue removed by acid treatment in Edman degradation is always a methionine.

False

True or False: Trypsin and chymotrypsin treatment often provides identical peptide fragments for Edman degradation.

False

True or False: Genomic sequences are needed to predict protein sequences by the mass spectrometry method.

False

True or False: Trypsin treatment provides useful sequence information when analyzing data from mass spectrometry.

True

Match each major class of protein with the best representative protein.

* Structural proteins = Actin * Genomic caretaker proteins = Histone * Metabolic enzymes = Pepsin * Transport proteins = Aquaporin * Cell signaling proteins = Adenylate cyclase

What happens first in the oxygen binding process?

O2 binds to the iron of heme

For reversible binding between a protein and a ligand, __________.

The larger the Ka, the higher the affinity between the protein and ligand

Start with 100 units of protein activity and 100 grams of total protein. After centrifugation, what is the fold-purification?

4.2-fold

Which two statements about x-ray crystallography are true?

* Only crystallized proteins can be analyzed * The x-ray beam is scattered by the protein sample

The fractional saturation of hemoglobin binding to oxygen is illustrated by __________.

[HbO2] / ([HbO2] + [Hb])

A structural change that does NOT play a role in translating local binding of oxygen to global protein conformational change is the different __________.

location of the distal histidine

Which is a positive effector for oxygen binding to hemoglobin?

Using SDS gel electrophoresis, __________ proteins migrate the fastest in the gel and move farther away from the __________ because of their __________ charge.

small; cathode; negative

Which protein is the largest in the gel filtration chromatography figure?

Squares

Curve Y represents a system at pH 7.4 with normal physiological levels of 2,3-BPG. Curve X represents a system that __________.

has a higher pH with a normal physiological level of 2,3-BPG

A mutation in the beta subunit of hemoglobin reduces the affinity of 2,3-BPG binding. Which mutation is likely to have this consequence?

Lys82 ’ Asp82

The mutation leading to the most dramatic effect on Ca2+ transport is a mutation of __________.

Asp351 in SERCA

The K+ channel protein does not allow Na+ ions to pass through because __________.

It is unfavorable for the Na+ ions to lose their associated water molecules

Binding of the negatively charged allosteric effector 2,3-bisphosphoglycerate stabilizes the T state of hemoglobin. A substitution of a lysine by an asparagine would be expected to have __________.

an increased affinity for oxygen in the presence of 2,3-BPG

If the histidine on the E helix (His E7) that coordinates O2 is mutated to alanine, what effect would likely occur?

Oxygen binding would not cause the movement of the F helix

What is the free energy change for the transport of glucose from outside to inside the cell at 37ºC when the concentrations are 5 mM outside and 0.1 mM inside?

-10.1 kJ/mol

In a hemoglobin mutant where a hydrogen bond stabilizing the T state is eliminated, would you expect the O2 affinity to be higher or lower compared to normal protein?

Higher O2 affinity

For a cell with a membrane potential of -60 mV, what is the free energy change for glucose transport at 25 °C with concentrations of 5 mM outside and 150 mM inside?

8.43 kJ/mol

Which of the following is true of sickle cell anemia?

It is caused by a mutation in the beta-globin gene

The lactose permease from E. coli and the molybdate transporter from Archaeoglobus fulgidus both __________.

Undergo a conformational change that occurs on substrate binding

After __________ induced changes in the structure of thin filament, myosin heads containing __________ will bind with high affinity to actin subunits.

Ca2+; ADP + Pi

Leghemoglobin is an oxygen-binding protein in root nodules. If leghemoglobin is more like myoglobin than hemoglobin, what is TRUE?

The O2 binding curve is hyperbolic

The change in free energy for Solute A concentration across a membrane is calculated to be -10 kJ/mol. What is the maximum concentration ratio that can be achieved for Solute B if transported against its gradient using a secondary active symporter?

50:1

A conformational change in troponin that opens the myosin-binding sites on actin is triggered by the __________.

Release of Ca2+ by the sarcoplasmic reticulum

What may result from a His143 --> Ala143 mutation in adult hemoglobin?

Reduced affinity for 2,3-BPG

The sarcomere length of isolated heart myoblasts can be measured over time in the laboratory. If EDTA is added, what effect might it have?

What triggers action in muscle contraction?

Release of Ca2+ by the sarcoplasmic reticulum

If EDTA is included in the buffer during a sarcomere length experiment, how would the length change compare to a control experiment without EDTA?

Decreased

What effect does a higher pH have on the oxygen binding curve for hemoglobin?

Shifts the curve to the left

What occurs when Pi is released from myosin?

The power stroke occurs

What type of transport is depicted by molecules moving down a concentration gradient?

Passive transport

Both passive and active transport proteins are needed to transport _____ across membranes.

Polar molecules and ions

What type of transport is indicated when no external energy input is needed and the translocation rate reaches a plateau?

Passive transport carrier

What is the significance of the HbS mutation (Glu6 --> Val6)?

Provides heterozygous individuals protection from malaria

What is the maximum velocity in enzyme kinetics?

The velocity at very high substrate concentrations where it no longer increases

What mechanism is demonstrated when a histidine residue at an enzyme's active site transfers a H+ to a substrate?

General acid catalysis mechanism

Which assumption is made when using Michaelis-Menten kinetics?

The conversion of EP---> E + P is rapid

What does it imply if an enzyme has less activity after size-exclusion chromatography?

There is a metabolite in the mixture that is required for full enzyme activity

What is an example of covalent modification in enzymatic activity?

A kinase adds a phosphate group to a target enzyme

Which amino acid is involved in forming the oxyanion hole in chymotrypsin, but is not part of the catalytic triad?

Gly 193

What is the Keq for the uncatalyzed reaction with kF = 10^-5/s and kR = 10^-2/s?

10^-3

What is the rate enhancement for the catalyzed forward reaction if kF(cat) = 10^7/s?

10^12

What finding supports the transition state theory of enzyme catalysis?

Transition state analogs bind tightly to enzyme active sites

What does a reaction coordinate diagram illustrate about an enzyme?

Stabilizes the transition state

What is true if Km does not change but kcat increases as the pH goes above 7?

A chemical group within the enzyme with a pKa around 7 is likely involved

Place the steps of HMG-CoA reductase in the correct order: Reduction of aldehyde, Breakdown of hemithioacetal, Reduction of thioester, Cofactor exchange.

C, D, B, A