The amino acid sequence of a protein is always presented and read in the:

A. N to C direction

B. C to N direction

C. 5' to 3' direction

D. 3' to 5' direction

A. N to C direction

Which of the following does NOT stabilize the folded structure of a protein:

A. Covalent bonds

B. Backbone to backbone hydrogen bonds

C. Side chain to side chain hydrogen bonds

D. Disulfide bonds

E. Van der Waals attractions

F.  All of the above contribute to protein structure

F.  All of the above contribute to protein structure

When exposed to high concentrations of urea, proteins become denatured.  Which of the following is NOT true regarding protein denaturation using urea?

A. Urea is a small molecule

B. Urea acts as both a hydrogen bond acceptor (via -NH₂ groups) and a hydrogen bond donor (via -C=O group) to destabilize hydrogen bonds

C. Urea does NOT destabilize covalent bonds within a protein structure

D. Urea, at high concentrations, destabilizes the hydrogen bonded network of water molecules thus diminishing hydrophobic forces within a protein structure

E. All of the above are true

B. Urea acts as both a hydrogen bond acceptor (via -NH₂ groups) and a hydrogen bond donor (via -C=O group) to destabilize hydrogen bonds

The two regular folding patterns in proteins are the alpha helix and beta sheet, both of which result from hydrogen bonds forming between backbone amine and carbonyl groups.

A. True

B. False

A. True

In an alpha helix, a hydrogen bond is formed between every ____ amino acid, and the helix completes a turn every ____ amino acids.

A. Third; 3.6

B.Third; 4

C. Fourth; 3.6

D. Fourth; 4

E. None of the above

C. Fourth; 3.6

Some protein molecules contain an assembly of two different subunits.  Hemoglobin contains two copies of alpha globin and two copies of beta globin.  The complete structure is called the_____.

A. Primary structure

B. Secondary structure

C. Tertiary structure

D. Quaternary structure

E. Quinary structure

D. Quaternary structure

In theory, a polypeptide chain with n residues has ___ different possible sequences and ____ of the sequences adopt a single, stable conformation.

A. 20ⁿ; nearly all

B. 20ⁿ; very few

C. n²⁰; nearly all

D. n²⁰; very few

E. 20*n; nearly all

F. 20*n; very few

B. 20ⁿ; very few

What is the name of the enzyme class responsible for catalyzing the rearrangement of bonds within a single molecule?

A. Nuclease

B. Protease

C. Isomerase

D. Synthase

E. Oxido-reductase

C. Isomerase

Which of the following statements regarding antibodies is NOT true?

A. An antibody is a protein ligand that binds a target protein with high affinity

B. Antibodies contain two identical binding sites, a result of two identical light chains and two identical heavy chains

C. Antibodies are produced by T cells

D. Antibodies can be coupled to fluorescent dyes for fluorescence microscopy or to gold particles for elctron microscopy

E. Some assays require antibodies that bind to other antibodies

F. All of the above are true

C. Antibodies are produced by T cells

Most drugs work by inhibiting enzymes

A. True

B. False

A. True

Hemoglobin binds four oxygen molecules.  Suppose oxygen binding to the heme group (the subunit within hemoglobin) facilitates further oxygen binding.  This is an example of:

A. Ligand binding

B. Allosteric regulation

C. Feedback inhibition

D. A & B

E. A, B, & C

D. A & B

Proteins are phosphorylated via the enzyme ____, and the addition of a phosphate group results in the addition of ____.

A. Protein kinase; two negative charges

B. Protein phosphatase; two negative charges

C. Protein kinase; two positive charges

D. Protein phosphatase; two positive charges

E. None of the above

A. Protein kinase; two negative charges

The attachment or removal of modifying groups to a protein can control what aspects of the protein?

A. Its behavior or activity

B. Its stability or its binding partners

C. Its location inside the cell

D. A & B

E. A & C

F. A, B & C

F. A, B & C

How do most motor proteins make their movements unidirectional (i.e., irreversible)?

A. They couple a conformational change to a thermodynamically unfavorable reaction.

B. They couple a conformational change to the hydrolysis of an ATP molecule.

C. They couple a conformational change to the formation of an ATP molecule from ADP and P_i.

D. They couple a conformational change to the formation of a GTP molecule from GDp and P_i.

B. They couple a conformational change to the hydrolysis of an ATP molecule.

Using mass spectrometry, proteins are selectively digested (using trypsin digestion, for example) and then separated based on their:

A. Mass to length ration

B. Mass to charge ratio

C. Mass to hydrophobicity ratio

D. Mass to structure ratio

E. Radial distribution function

B. Mass to charge ratio

The large scale study of cellular proteins (studying the activities or structures of many proteins) is called what?

A. Proteomics

B. Genomics

C. Metabolomics

D. Bioinformatics

E. Electrophoresis

A. Proteomics

A cell homogenate (or cell extract) contains large and small molecules as well as membrane enclosed organelles.  Which of the following is NOT used for homogenization of cells or tissues?

A. High frequency sound

B. Mild detergents

C. High pressure

D. Shearing cells

E. Centrifugation

E. Centrifugation

Density gradient centrifugation is used to separate cell components on the basis of their ____.

A. Primary amino acid sequence

B. Mass and charge

C. Buoyant density

D. Sucrose content

E. Radial distribution function

C. Buoyant density

In gel electrophoresis, what is the purpose of adding SDS to samples?

A. Solubilization of proteins

B. Breaking disulfide bonds

C. Covering proteins with the negatively charged detergent

D. A & C

E. B & C

F. A,B & C

D. A & C