Biochem 310 Final Study Set

Shared intermediated can be defined as a molecule that is

A final product of one pathway and a reactant of the next

Which of the following is not an important metal in biological systems?

Al3+

Place the following steps in proper order. A. Phosphorylation of RTK cytoplasmic tails B. Activation of downstream signaling pathway C. Ligand binding, receptor dimerization; kinase activation D. Protein binding to RTK phosphotyrosines and phosphorylation of target proteins

C, A, D, B

In the figure below, Km is indicated at

D

Below is a schematic representation of a dimerized receptor tyrosine kinase. Where is the kinase function located

D- at the bottom

Calculate net delta G for the following reactions: A <-> B (delta G= 4 kJ/mol) and B <-> C (delta G= -10 kJ/mol)

-6 kJ/mol

Great Salt Lake City, UT has a pH of 10.2. What is the [OH-] in the lake?

1.58x10^-4 M

How many ATP are produced from 2 turns of the citrate cycle?

20

Below are the steps of solid-phase peptide synthesis. Which is the appropriate order of steps? 1. Protecting group of amino acids is removed 2. Peptide is released from solid support resin 3. Incoming amino acid is activated at carboxyl group by DCC and added to the column 4. Fmoc is removed by treatment with base and c-terminal amino acid is attached to resin molecule

4, 3, 5, 1, 2

Which reaction in the citrate cycle produces GTP?

5 (succinyl-CoA synthetase)

Which of the following best defines substrate-level phosphorylation

Direct transfer of Pi to ADP

Which stabilizing force in protein tertiary structure is a covalent binding force?

Disulfide binding

Which of the following is true of the tetrahedral intermediate in the chymotrypsin mechanism?

It contains an oxyanion

If ATP is required to make a polymeric macromolecule , which of the following will happen if no ATP is available?

The polymer is broken down to release ATP

What are the 3 letter and 1 letter abbreviations for tyrosine?

Tyr, Y

Which of the following is activated or increased in liver cell exposure to either glucagon or epinephrine?

cAMP

Below is a pentose in RNA. Which OH group differs between ribonucleotides and deoxyribonucleotides?

(Sorry I don't have the picture) the OH on the bottom right carbon

Which represents the correct arrangement of bonding in peptide bond?

(Sorry it's a picture) C-CO-NH-C

Below is a Lineweaver-Burk plot in which the axis labels have been removed interpret the plot to get Km

(Sorry no pic) 33

What is the PI of dipeptide shown?

(Sorry no pic) PI= 5

What is the full name of the amino acid below?

(Sorry no pic) arginine

What is the full name of this amino acid below?

(Sorry no pic) histidine

Which gives rise to a favorable enthalpic (delta S) driving force for protein folding?

(This is the question that was misworded) the decrease in ordered water molecules as hydrophobic amino acids pack together

Calculate delta E of the coupled redox reaction with O2 and Fe2+

1.25 (.82+.43)

Consider a weak acid whose pKa is 6.45. What is the ratio of conjugate base to conjugate acid needed to make a solution at pH 7.5?

11.2

As 18 Na+ ions are exported out of the cell by NaK ATPase membrane transport protein ___ K+ ions are transported into the cell

12

In two turns of the citrate cycle, how many electrons are transferred from intermediated to NAD+ and FAD?

16

The mechanism of HMG-CoA rid tase involves

2 NADPH

Which reactions in the citrate cycle produce CO2?

3 and 4; isocitrate DH and a-ketoglutarate DH

The stop codons in mRNA are UAA, UAG, and UGA. considering only the 3rd position of the codon, how many others are subject to sustaining a nonsense mutation that would lead to one of these?

4 (UAU UAC UGU UGC)

A chiral center is an atom with

4 different functional groups and lacks a plane of symmetry

If the Ka of an acid is 1.5x10^-7, what is the pKa?

6.82

Use the O2 binding curve to calculate the approximate O2% that is released from hemoglobin as pO2 changes from 13 kPa to 4 kPa

60%

If the concentration of aspartate in a cell decreases, what is the predicted outcome. (This has a picture)

A decrease in the concentration of fumarate

A double helix that crosses itself in a right hand coil is referred to as what?

A negative supercoil

A ligand binds to a transmembrane protein. This causes a conformational change in the protein that is detected by an intracellular protein. The intracellular protein is an enzyme that adds a phosphate group to the target proteins. The phosphorylated proteins cause a physiological change within the cell. This is an example of

A signal transduction pathway

Which of the following statements are true?

ATCase is regulated by feedback inhibition

You learned about the importance of hydrophobic interactions; considering this, which of the following might you consider to be true statements about their importance?

All of the above; they guide 3D folding of polypeptides, they're important for membrane formation, they guide enzyme-substrate interactions, they guide interactions between receptors and ligands

The catalytic triad of chymotrypsin is composed of His57, Ser195, and

Asp102

Consider a mutation in procaspase 3 that changes Asp28 to an amino acid that is no longer a substrate of autocleavage. This mutant would

Be partially activated

Refer to the reaction coordinate diagram below. The change in the activation energy of the reaction because of an enzyme is illustrated by the energy of

C- where the middle of the graph is lowered

Place the following steps of the apoptotic pathway in the proper order. A. CASP3 cleavage of cellular proteins B. Cleavage of procaspase 8 C. Cleavage of procaspase 3 D. Assembly of DD and DE protein complexes

D, B, C, A

What is the peptide sequence Asp-Gln-Gly-Ser using 1 letter abbreviations?

DQGS

If a metabolic enzyme ___ the energy of activation of a reaction, the rate of product formation will ___

Decrease;increase

Calculate the delta G for the reaction given: delta H= 25.4 kJ/mol and delta S= 1.0 J/K at 298K. Is the reaction spontaneous in the forward direction?

Delta G= (25.4 kJ/mol) -((298K)(1.0x10^-3 kJ/K)) -> -25.102 kJ/mol and the reaction is spontaneous in the forward direction.

Ovaries produce estrogen. A western blot analysis of expression of estrogen receptors in ovarian tissues at different times of the estrous cycle showed approx. 4x greater protein levels at day 2 than with day 10 of the cycle. Which of the following may be true given these data?

Estrogen is acting as auto rinse signal in ovaries

Fructose-1,6BP is cleaves by aldolase. What is required for the reaction to proceed?

Formation of a Schiff-base intermediate

Which reaction in glycolysis is a redox reaction?

Glyceraldehyde-3P -> 1,3-BPG

Which of the following macromolecules would yield only one type of monomer after complete hydrolysis?

Glycogen

If PKA is activated in a liver cell in response to glucagon binding to B2-adrenergic receptor, which of the following will result?

Glycogen degradation will be turned on

Levels of DAG increase in cell upon the binding of a ligand to a taste receptor. Which trimeric G protein subunit is most likely bound to GTP?

Gqa

Which of the following proteins contain an SH3 domain?

Growth factor receptor-bound 2 (GRB2)

The peptide bond

Has a mix of single and double bond characters

To produce 4 ATP requires 122 kJ/mol. Which reactions in glycolysis produce enough energy to overcome this deficit?

Hexokinase, PFK1, and pyruvate kinase

All of the following are stabilizing forces in maintaining a stable protein tertiary structure, except

High temperature

Vitamin C is required for prolyl hydrolase to function. Prolyl hydrolase enzyme activity is necessary for proper biosynthesis of collagen. Which of the following might result from a vitamin C deficiency?

Higher risk of bone breakage

If an enzyme carried out acid-base catalysis, which of the following amino acids could act as a general acid?

Histidine

Protein secondary structures such as a-helices and B-sheets are stabilized mainly by

Hydrogen bond formation

What are the chemical bonds that stabilize the alpha helix called?

Hydrogen bonds

A molecule is found to be able to diffuse across a membrane. Which of the following characteristics would best describe this molecule?

Hydrophobic

The 3 general categories of enzyme-mediated reactions, which are determined on the basis of the work they accomplish, include all except

Hydrophobic collapse reactions

Acetylcholinesterase is an important enzyme in the nervous system. Acetylcholinesterase activity is blocked by the nerve agent sarin gas, which forms a covalent bond with the sarin active site. Sarin has is an

Irreversible inhibitor

According to delta G, which of the following exerginic reactions is considered to be the rate limiting step of the citrate cycle?

Isocitrate DH reaction

When ATP is bound to myosin,

It cannot interact with actin

Which of the following is true of induced-fit model of enzyme catalysis but not of the lock and key model?

It involves a conformational change of the enzyme

A cell with a membrane potential of -70 mV that contains functioning NaK ATPase membrane transport proteins will maiming am extracellular ___ concentration that is ___ to the intracellular ___ concentration

K+; lower; K+

Shared intermediated are used so effectively in coupled reactions because they

Limit product diffusion and allow intermediated to channel from one enzyme to the next

Which coenzyme is required to convert glyceraldehye-3P into 1,3-BPG?

NAD+

Which of the following is a way that an enzyme can increase the reaction rate in a cell?

Orienting substrates appropriately for the reaction to occur

Classify the reaction that occurs in the step 4 schematic of pyruvate DH

Oxidation reduction

The first reaction of glycolysis that produces high-energy compound is catalyzed by

PFK1

What type of transport is depicted in the figure below?

Passive transport of molecules down a concentration gradient

Which of the following peptides would elude last using gel filtration?

Peptide A (smallest MW and -2 charge)

In a reversible covalent modification reaction involving phosphorylation of a target protein, which of the following amino acids is least likely to be modified with a phosphate group

Phenylalanine

Which class of protein structure does this protein shown below fit into?

Predominantly Beta-sheet

What is the potential metabolic rate of pyruvate under aerobic conditions?

Produce CO2 and H2O

What is the potential metabolic date of pyruvate during strenuous exercise?

Produce lactate

Which of the following statements is true of the data shown below?

Protein A+ Protein B bind to the same ligand

Cyclic pathways contain several metabolites that regenerate during each turn of the cycle. Another way to describe a metabolite is that it functions as a

Reactant or product

On insulin binding to the insulin receptor, MAP kinase signaling proteins are activated. Which of the following proteins are part of this signaling pathway?

Shc

A genetic analysis of an unknown infectious agent reveals that it contains only the nucleotides G, A, U, C in proportions 30%, 50%, 15%, and 20% respectively. Based on this info, the infectious agent is most likely a:

Single-stranded RNA virus

The sarcomere lengths of isolated heart myoblasts can be measured over time in a lab. Myoblasts are maintained in a buffer during the experiment. In a control experiment, Ca2+ and ATP are added to the buffer and change in sarcomere length is analyzed. If EDTA, a chelating agent that sequesters Ca2+, was included in the buffer, the length of change in sarcomere length would be ___ compared to the control.

Smaller

Using the figure below describing monoclonal antibody generation, identify the step where B cells are fused with tumor cells

Step 4

Muscle relaxation in response to NO would be decreased if a ___ was present

Stimulator of cGMP phosphodiesterase

Which of the following do you think most likely influences the lower limit of van der waals radii?

The electron clouds begin to repel each other

Where do citrate cycle reactions take place in eukaryotic cells?

The mitochondrial matrix

Osmosis is

The movement of water across a membrane

Below are 5 biological reactions, which one is most likely to proceed in the direction as written?

The reaction with the lowest delta G

Which scenario would allow B-arrestin to bind to GPCR?

The receptor is phosphorylated

A requirement for a covalent bond to form is that

There are unpaired electrons on each atom

Consider an oxygen binding curve of hemoglobin at pH 7.4 the binding curve would shift ___ if the pH is reduced to 7.2

To the right

Ligand binding causes which of the following to form trimers?

Tumor necrosis factor receptors

A lineweaver-Burk plot displays parallel lines for an enzyme in the absence and present of the increased amount of inhibitor. The inhibitor in the this experiment is

Uncompetitive

Both the substrate and the tetrahedral intermediate, when associated with chymotrypsin

Undergo a nucleophilic attack

The amino acid with the most hydrophobic side chain is

Valine

Rank the following terms of increasing order (weakest 1st, strongest 4th)

Van der Waals, hydrogen bonds, ionic bond, covalent bond

Which of the following have the greatest entropy?

Water vapor

Considering the following interaction between protein and ligand: [P] + [L] <-> [PL]

[P][L]/[PL]

Which enzyme of the citrate cycle catalyzes oxidative decarboxylation reaction that produces CO2, NADH, and succinyl-CoA?

a-ketoglutarate DH