Biochem- AA and Proteins

How many unique dipeptides ( made from linking two amino acids) can be synthesized using only alanine and glycine residues?

4 (G-G, A-G, A-A, G-A)

At pH 6.0 between the pKas of the ammonium and carboxyl groups what will be the charge on a molecule of glycine? A) 0 B) 1 C) -1 D) -2

A

Disruption of a protein's shape without breaking the peptide bond is called? A) Denaturation B) Association C) Dissociation D) Nonfunctional

A

Enzymes alter A) Rate of reaction B) Energy of Reaction C) Delta G D) Both A&B

A

No matter how much substrate you add, the inhibitor will not be displaced from its side of action when ti comes to which inhibitor? A) Noncompetitive B) Competitive C) Uncompetative inhibiton D) Mixed-type inhibition

A

Which level of protein folding is known for its linear ordering of amino acids? A) Primary B) Secondary C) Tertiary D) Quaternary

A

Which of the following will be true of the Lineweaver-Burk plot of an enzyme in the presence of increasing concentrations of a competitive inhibitor? A) It will be a series of lines that intersect along the y-axis B) It will be a series of lines that intersect along the x-axis C) It will be a series of parallel lines D) It will be a series of lines that will intersect, but neither on the y-axis or x-axis

A

What is the favorable reaction that the cell can use to drive unfavorable reaction?

ATP hydrolysis

If a single polypeptide folds once and forms a Beta pleated sheet with itself, would this be a parallel or antiparallel Beta Pleated sheet?

Antiparallel

For a given enzyme concentration at a low substrate concentration, how does reaction rate change as the substrate concentration increases? A) Logarithmically B) Linearly C) Exponentially D) Indirectly

B

Ribonuclease has eight cysteines that form four disulfide bonds. What effect would a reducing agent have on its tertiary structure? A) No effect B) Break the disulfide bridges C) Make new disulfide bridges D) Make tertiary structure more stable

B

Some enzymes can modify their substrate and by this means to regulate its activity. In many instances, these modifications are not permanent since other enzymes can reverse them. Which of the following category of enzymes will irreversibly modify their substrate? A) A kinase B) A protease C) A phosphatase D) An acetylase

B

Some inhibitors bind irreversibly to enzymes by covalent attachment. Would the kinetics seen under these conditions be similar to those seen with a reversible noncompetitive inhibitor? A) Yes, because it would reduce the Km of the reaction B) Yes, because the net effect would be a loss of active enzyme available for the reaction C) No, because if enough substrate binds to the active site the reaction will reach Vmax D) No, because Km will increase and Vmax will stay the same, similar to competitive inhibition

B

Which level of amino acid folding includes Beta-pleated sheets and alpha pleated sheets? A) Primary B) Secondary C) Tertiary D) Quaternary

B

Which of the following would have the LEAST effect on the ability of an enzyme to bind its substrate? A) Placing an enzyme that optimally functions at pH 7 in a pH 5 solution B) Increasing the temperature of the enzyme's surroundings C) Mutating the Glu and Asp residues in the active site to Lys and HIs D) Changing the substrate from a tripeptide to a disaccharide

B

Which structure level is primarily based off of hydrophilic and hydrophobic interactions? A) Primary B) Secondary C) Tertiary D) Quaternary

B

Which of the following amino acids has the largest pKa? A) Lysine B)Arginine C) HIstadine

B (Lys= 10, Arg+12, His= 6.5)

When the pH of the solution is greater than the pKa of an acidic group the acidic group will most likely...

Be in its deprotonated form

Glycine is the simplest amino acid, with only hydrogen as its R-group. Its only functional groups are the backbone groups discussed above (amino and carboxyl). What will be the net charge on a glycine molecule at pH 12? A) 0 B) 1 C) -1 D) -2

C

The transition state for a reaction possesses a transient negative charge. The active site for an enzyme catalyzing this reaction contains a His residue to stabilize the intermediate. If the His residue at the active site is replaced by glutamate that is negatively charged at pH 7.0, what effect will this have on the reaction, assuming that the reactants are present in excess compared to the enzyme? A) THe repulsion caused by the negative charge in the glutamate at the altered active site will increase the activation energy and make the reaction proceeded more slowly than it would in a solution without enzyme B) The rate of catalysis will be unaffected, but the equilibrium ratio of products and reactants will change, favoring reactants. C) The transition state intermediate will not be stabilized as effectively by the altered enzymes, lowering the rate relative to the rate without catalysis by the normal enzyme D) The rate of catalysis will decrease, the equilibrium constant will change

C

When calculating an isoelectric point of an amino acid you want to ___ the pKas, functional groups A) subtract B) add C) average D) divide

C

Which of the following amino acids is most likely to be found on the exterior of a protein at pH 7.0? A) Leucine B) Alanine C) Serine D) Isoleucine

C

Which amino acid never appears in an alpha helix? A) Glutmaine B) Glycine C) Proline D) Histadine

C ( Because it eliminates the only hydrogen atom on the nitrogen atom of proline and it forces a kink in the peptide chain

Which functional group of amino acids has a stronger tendency to donate protons: A Carboxyl group (pKa= 2.0) or ammonium group (pKa=9)?

Carboxyl (?)

What is the name for an oxidized cysteine?( When two cysteines have formed a disulfide bridge)

Cystine

Both hemoglobin and myoglobin are proteins that carry oxygen in the human body. Hemoglobin exhibits cooperativity and is found in red blood cells, whereas myoglobin is not cooperative and is found in muscle cells. Which of the following is likely try regarding these oxygen-carrying proteins? A) The O2 situation curve will be sigmoidal for myoglobin, but not hemoglobin. B) Hemoglobin has a lower binding affinity for oxygen than myoglobin. C) Hemoglobin is used to tightly bind oxygen in the body, while myoglobin is used to deliver oxygen to body cells. D) Hemoglobin most likely consists of multiple protein subunits, whereas myoglobin may or may not consist of multiple protein subunits

D

If pure B is put into solution in the presence of an enzyme that catalyzes the reaction between A and B, which one of the following will be true? Keq= [B]/[A]=1,000 A) All the B will be converted into A, until there is 1,000 times more A than B B) All of the B will remain as B, since B is favored at equilibrium C) The enzyme will have no effect, since enzymes act on the transition state and the is no transition state present. D) The reaction that produces A will predominate until delta G=0.

D

If the disulfides serve only to lock into place a tertiary protein structure that forms first on its own, then what effect would the reducing agent have on correct protein folding? A) No effect B) Make tertiary structure more stable C) Denature protein D) Make tertiary structure less stable

D

Which of the following amino acids has important consequences for protein folding? A) Arginine B) Aspartic Acid C) Glycine D) Proline

D

If a mutation changed an Arg residue in the protein interior to a Leu residue, what would be the likely effect on the delta G protein folding? A) Delta G would become more positive B) Delta G would become more negative C) Delta G would remain unchanged D) The effect on delta G cannot be determine without additional information

D ( We need to know what's on the inside)

What protein level would a molecule that disrupts hydrogen bonding, such as urea, NOT affect? I. Primary II.Secondary III. Tertiary IV. Quaternary A) I B) II C) II, III, IV D) III and IV

I

Which fo the following may be considered an example of tertiary protein structure? I. van der Waals interactions between two Phe R-groups located far apart on a polypeptide II. Hydrogen bonds between backbone amino and carboxyl groups III. Covalent disulfide bonds between cysteine residues located far apart on a polypeptide

I and III

Carbon dioxide is an allosteric inhibitor of hemoglobin. It dissociates easily when Hb passes through the lungs, where the CO2 can be exhaled. Carbon monoxide, on the other hand, binds at the oxygen-binding site with an affinity 300 times greater than oxygen; it can be displaced by oxygen, but only when there is much more O2 than CO in the environment. Which of the following is/are correct? I. Carbon monoxide is an irreversible inhibitor II. CO2 is a reversible inhibitor III. CO2 is a noncompetitive inhibitor

II and III

What is the name at which the pH at which a molecule is unchanged?

Isoelectric point

I the oligopeptide Phe-Glu-Gly-Ser-Ala, state the number of acid and base functional groups which residue has a free alpha- amino group and which residue has a free alpha- carboxyl group.

Phe has the alpha amino and Ala has the alpha carboxyl. This peptide has 3 acid/base functional groups (Glu and the two terminals)

Assuming a pKa of 2, will a carboxylate group be protonated or deprotonated at pH 1?

Protonated

Will the amino group (pKa=9) be protonated or deprotonated at pH 1?

Protonated

What is the difference between a disulfide bridge involved in the quaternary structure and one involved in tertiary structure?

Quaternary disulfides are bonds that form between chains that aren't linked by peptide bonds. Tertiary disulfides are bonds that form between residues in the same polypeptide.

When the pH of the solution is less than the pKa of an acidic group...

The acidic group will most likely be in its protonated form

Lineweaver-Burk Plot

Vmax= rate of rxn Km= how easily the enzyme is saturated

Would a protein end up folded normally if you (1) first put it in a reducing environment, (2) then denatured it by adding urea, (3) next removed the reducing agent, allowing disulfide bridges to reform, and (4) finally removed the denaturing agent?

Yes