Biochemistry Exam 1 (Multiple Choice + Formulas)

Approximately what percentage of the human genome encodes for protein?

3%

What pairs of atoms in bases are involved in hydrogen bonds?

A) N-H and O-H

B) N-H and S-H

C) O-H and P-O

D) All of the above

E) None of the above

A) N-H and O-H

The structure of DNA described by Watson and Crick included

A) a double helix

B) the sugar phosphate backbone aligned in the center of the helix

C) the base pairs that are stacked on the inside of the double helix

D) A and B

E) A and C

E) A and C

What two properties of water are important for biological interactions?

The polarity of water

The cohesive properties of water

How many hydrogen bonds are formed between A and T?

2

What gives proteins a dominant role in biochemistry?

Their ability to spontaneously fold into complex three-dimensional structures

Which of the following is considered a noncovalent bond?

A) Electrostatic interactions

B) Hydrogen bonds

C) Van der Waals interactions

D) All of the above

E) None of the above

D) All of the above

The First Law of Thermodynamics states what?

The total energy of a system and its surroundings is constant

The Second Law of Thermodynamics states what?

The total entropy of a system and its surroundings always increases for a spontaneous process

List atoms commonly found in biological molecules that are often hydrogen-bond acceptors.

Oxygen

Nitrogen

What is the [A-]/[HA] ratio when the weak acid is in a solution one pH unit below its pKa?

1:10

If a particular reaction has a negative delta-G (Gibbs Free Energy), is it likely to occur?

Yes, it is spontaneous

What is the [H+] concentration in a urine sample that has a pH of 8?

10^-8 M

What happens to nonpolar molecules in water?

They aggregate together

What type of chiral amino acids is found in proteins?

L

What is another name for dipolar molecules?

Zwitterions

When a peptide bond is formed, what molecule is also made?

Water

Write the name, three letter code, and single letter code for the amino acid for the following:

A) the amino acid with a pKa near neutral pH

B) disulfide bonds are formed by pairs of which amino acid

C) this amino acid residue disrupts the alpha-helix because its side chain contains a unique ring structure that restricts bond rotation

A) Histidine, His, H

B) Cysteine, Cys, C

C) Proline, Pro, P

What determines a protein's function?

Structure

What is the name of the plot that allows one to investigate the likely orientation of certain amino acid pairs?

Ramachandran

What type of structure includes alpha-helices, beta-sheets, and turns?

Secondary structure

What type of protein structure develops when two proteins combine to form one larger protein?

Quaternary structure

What is responsible for the tertiary structure of proteins?

Interactions between amino acid side chains

Which of these agents can denature proteins?

A) Salt

B) Alcohol

C) UV light

D) All of the above

D) All of the above

Combining three amino acids produces what?

A tripeptide + 2 water molecules

Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as _______.

Beta-mercaptoethanol

What type of purification is based on the attraction of the protein for a particular chemical group?

Affinity chromatography

What affects the sedimentation of a particle?

Mass

Shape

Density of the solution

Proteins can be separated from small molecules and ions through a semi-permeable membrane by what process?

Dialysis

In the Edman procedure for peptide sequence, what is used to selectively remove the N-terminal residue as a PTH-derivative.

Phenyl isothiocyanate

The first step in protein purification from a homogenate is usually what?

Isolation by centrifugation

Exclusion gel or gel-filtration chromatography separates molecules on what basis?

Size

Polypeptides can be fragmented into smaller peptides by cleavage with chymotrypsin, which hydrolyzes the peptide bond at the C-terminal side of what amino acid residues?

Phenylalanine

Tyrosine

Tryptophan

What gels are often used as the media for electrophoretic techniques such as SDS-PAGE and isoelectric focusing?

Polyacrylamide

The mobility of proteins in SDS-PAGE is inversely proportional to what?

The log of their masses

What is the advantage of adding SDS to gel electrophoresis?

SDS allows proteins to be separated on the basis of their approximate mass

What are some techniques that can be used to obtain information about protein shape?

X-ray crystallography

NMR spectroscopy

Which are some techniques that can be used for quantitative analysis?

ELISA

Absorbance spectroscopy

What is the information carrying intermediates of translation?

mRNA

Codons that specify the same amino acids are termed what?

Synonyms

Each amino acid residue in a protein is encoded by a set of three bases of mRNA referred to as a ______.

Codon

The enzyme that is capable of synthesizing DNA from an RNA template is _________.

Reverse transcriptase

DNA polymerase reads the template strand in what direction?

3' to 5'

What is the nucleotide sequence on the DNA template strand that yields the CUA codon for leucine?

TAG

How does a nucleotide differ from a nucleoside?

A nucleotide is a nucleoside with a phosphate ester linked to the sugar

The flow of genetic information from DNA to protein is called what?

Gene expression

A three-base codon defines a specific ______.

Amino acid

In DNA and RNA synthesis, the new strand growth is always in what direction?

5' to 3'

The difference in RNA bases compared to DNA bases is what?

RNA contains U instead of T

The nucleoside that is composed of a D-ribose linked to a cytosine base is called ______.

Cytidine

What was the technique used by Franklin and Wilkins to deduce the structure of DNA?

X-ray diffraction

The feature(s) of DNA deduced by Watson and Crick included what?

A) Two antiparallel polynucleotide chains coiled in a helix around a common axis

B) The pyrimidine and purine bases lie on the inside of the helix

C) The bases are nearly perpendicular to the axis

D) All of the above

E) None of the above

D) All of the above

DNA renaturation after melting is called what?

Annealing

What is the Henderson-Hasselbach equation?

pH = pKa + log [A-]/[HA]

What is the equation for determining Ka?

Ka = [H+][A-]/[HA]

Ka = products/reactants

For the reaction A + B -> 2C, give the equation for Q and Keq. Tell the difference.

Q = [C]^2 / [A][B]

Keq = [C]^2 / [A][B]

The difference is that Keq must be the values when the reaction is at equilibrium.

Give the equation for delta-G naught.

delta-G naught = -RT ln(Keq)

What is the value of R and the value of T?

R = 8.314 J/mol x K = 1.987 cal/mol x K

T = 298 K

What is the equation used to determine delta-G when the value of delta-G naught is known?

delta-G = delta-G naught + RT ln(Q)