Chapter 1: Flashcards
(30 cards)
What category of enzyme does RNA polymerase III fall into?
Haloenzyme - a complete and functional enzymes that is used in catalytic interactions.
Why would the active site of RNA Polymerase III have polar and positively charged side chains?
Because this is where it will interact with DNA, and DNA is a negatively charged molecule. It must be polar and positively charged to help stabilize DNA in the catalytic process.
The active site of RNA polymerase III would be most likely to contain enzymes that have:
a. Non-polar and neutral side chains.
b. Non-polar and positively charged side chains.
c. Polar and negatively charged side chains.
d. Polar and positively charged side chains.
d. Polar and positively charged side chains - because it needs to stabalize the negative charges of DNA.
Primary structure of a protein:
A chain of amino acids linked together by covalent peptide bonds, with a 2D structure. This will have NO non-covalent interactions.
Secondary structure of a protein:
A chain of amino acids bound together by peptide bonds is folded into a-helices and B-pleated sheets, done by hydrogen bonding by neighboring amino acids. Proteins become 3D at this point.
Tertiary structure of a protein:
Further folding of a protein using non-covalent interactions like hydrogen bonding, disulfide bonds, ionic bonds, etc. 3D structure!
Quaternary structure of a protein:
Bonding of multiple tertiary structures by non-covalent interactions, like hydrogen bonding, ionic bonding, disulfide bonding, etc. The interaction of alpha, sigma, and theta subunits.
Which of the following is an example of the allosteric effect?
a. The interaction of alpha, sigma, and theta subunits in a protein by non-covalent interactions.
b. Changes in the structure of DNA polymerase III that happen when DNA is bound to it.
c. A chain of Asp-Gly-Lys-Try bound together by peptide bonds.
d. The folding of a-helices and b-pleated sheets.
b - Changes in the structure of DNA polymerase III that happens when DNA is bound to it.
Which of the following amino acids is least likely to be found in a protein structure that is primarily composed of alpha helices?
a. Proline
b. Alanine.
c. Glycine.
d. Valine.
Proline - because charged or bulky amino acids are not found in alpha helices, and proline has a bulky alpha amino 5-member ring, which causes steric strain and prevents alpha helix formation.
Proinsulin must undergo cleavage by proteases, which results in two smaller subunits of functional insulin. This indicates that proteases act on the:
a. Primary structure.
b. Secondary structure.
c. Tertiary structure.
d. Quaternary structure.
a - primary structure - it is breaking peptide bonds and changing the sequence of amino acids.
What is the PI of aspartic acid given the following pKa values - Amide = 9.4, carboxyl = 4.8, carboxyl side chain = 2.4.
a. 4.8.
b. 3.6.
c. 14.
d. 11.8
When the side chain of an amino acid contains a carboxyl group, PI = pKa(carboxy) + pKa(Side chain)/2
4.8 + 2.4/2 = 3.6 PI
What is the PI of an amino acid?
The pH at which an amino acid will be electrically neutral (no net charge). Uses the equation pKa1 + pKa2 / 2 = PI.
Histidine has the following pKa values, what is its PI? pKa(amide) = 7.2, pKa(carboxy) = 3.5, pKa(side chain) = 5.6.
a. 10.7.
b. 5.35.
c. 4.55.
d. 6.4.
d - 6.4.
Histidine has an amide side chain, and therefore to calculate the PI we will use PI = pKa(amide)+pKa(side chain)/2
(7.2 + 5.6)/2 = 6.4.
Tryptophanase is an enzyme that is used to catabolize the amino acid tryptophan into derivatives. Which of the following amino acids would be least likely to be found on the active site of tryptophanase?
a. Glycine.
b. Proline.
c. Histidine.
d. Threonine.
a. glycine.
Glycine is the only small non-polar amino acid listed. The active site of any enzyme is going to contain polar or charged amino acids, which assist in binding of the substrate. Glycine is hydrophobic and does not participate in non-covalent interactions, and therefore will typically be found in core of a protein. Proline is also non-polar, but makes 5 member ring with its alpha amino - making it bulky
A researcher is interested in the potential impacts of a drug on protein synthesis. Using radioactive sulfur to stain the amino acids of interest. Which of the following amino acids will the research be capable of drawing conclusions about?
a. Valine.
b. Methionine.
c. Cysteine.
d. Aspartic acid.
b. Methionine.
c. Cysteine.
Since we are tracing amino acids based on stained sulfur, we can only trace amino acids that contain sulfur. Methionine and cysteine are the only amino acids containing sulfur.
In the synthesis of proteins BOC protecting groups will often be added to amino acids with amide-containing side chains. The purpose of this is to:
a. Prevent the amino acids from dissociating within the cytosol.
b. To stop the peptide linkage between the amide-amino acid and the previous amino acid in our peptide chain.
c. To prevent the amino acid from reacting with itself, rather than with the polypeptide chain.
d. The BOC group protects the amino group, making the amino acid more reactive.
c - To prevent the amino acid from reacting with itself, rather than with the polypeptide chain.
True or false: Highly reactive side chains on amino acids will never use a BOC protecting group, as it would limit their reactivity.
FALSE: Amino acids with highly reactive side chains will often have Boc groups added to protect them prior to their usage in a polypeptide. This stops the formation of peptide bonds between side chains.
Protecting groups will have:
a. A major effect on the reactivity of a molecule. ‘
b. The ability to prevent any covalent bonds between molecules.
c. Decrease the Gibbs free energy of a chemical reaction.
d. No effect on the reactivity of a molecule.
D. no effect on the reactivity of a molecule.
Consider the structure of lysine. Which of the following explains why a Boc protecting group is a bad idea for lysine?
a. When deprotecting, the amine side chain can interact in peptide bonds with neighboring amino acids.
b. The amine group in the side chain will undergo an SN1 reaction during deprotection.
c. The Boc cannot be removed from an amide side chain.
d. The amide side chain is basic, and therefore would react with the Boc, rendering it inactive.
a - When deprotecting, the amine side chain can interact in peptide bonds with neighboring amino acids - creating unwanted side products.
What type of reaction will be used to remove a Boc protecting group from a tertiary carbocation?
a. SN1.
b. SN2.
c. E1.
d. E2.
E1 - because the methyl groups would hinder the backside attack of a substitution reaction.
True or false: Boc protecting groups are removed from amino acids using trifluoroacetic acid, which will remove all Boc groups by the same mechanism, regardless of the structure of the amino acid.
TRUE!
What is the only amino acid capable of forming disulfide bonds?
a. Valine.
b. Tryptophan.
c. Methionine.
d. Cysteine.
Cysteine.
Which mechanism must the breaking of a covalent bond between valine and isoleucine be done?
a. Redox.
b. Dehydration synthesis.
c. Hydrolysis.
d. Acid-base synthesis.
c - Hydrolysis.
We know that the only amino acid that can form a covalent disulfide bond is cysteine, so valine and isoleucine must be bound together by a peptide bond. Peptide bonds will require the addition of water through hydrolysis to cleave them.
Which of the following mechanisms will most often be used in the synthesis of a long-chain carbohydrate?
a. Redox.
b. Dehydration synthesis.
c. Hydrolysis.
d. Acid-base reactions.
Dehydration synthesis - the removal of H2O to bind together adjacent monomers.
