Biochem Questions 5

When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?

Mostly the hydrophobic effect that results from greater ordering of water molecules around amino acids in the denatured (unfolded) state, followed by stronger electrostatic bonds (H-bonds and slat bridges) due to the lower dielectric constant of the protein core

Two proteins, X and Y, have similar tertiary structures. The quaternary structures of the proteins are indicated by the diagram below. What differences can be expected in the surfaces of the polypeptides X and Y?

The contact surfaces are hydrophobic, while the surfaces that remain exposed to the solvent in the quaternary structure are hydrophilic]

Describe the resonance structure of a peptide bond, and explain why there is no rotation around the C—N bond.

The double bond in the carbonyl group C=O delocalizes to a C=N double bond. As a result, the C-N bond is no longer able to rotate freely

Each of the following reagents or conditions will denature a protein. For each, describe in one or two sentences what the reagent/condition does to destroy native protein structure.

(a) urea [is a chaotropic agent that disrupts H-bonds on the polypeptide backbone] (b) high temperature [High temperature changes the deltaG of folding] (c) detergent [solubilizes nonpolar residues that would otherwise fill the protein core] (d) low pH [alters the state of ionization of acidic and basic groups]

Explain what is meant by motifs in protein structure

A motif is a particular arrangement of elements of secondary structure, mainly -helix and b-sheet within a protein

Describe three of the important features of a sheet polypeptide structure.

chain in extended (zig-zag) conformation, neighboring strands H-bond in parallel or antiparallel configuraitons, R-groups are on alternate sides of the plane defined by neighboring strands

Explain how circular dichroism spectroscopy could be used to measure the denaturation of a protein.

CD measures the difference in specific absorption of UV light with two different directions of polarization. Highly ordered secondary structures within a protein, such as -helix and B-sheet have distinct CD spectra. Denaturation causes the loss of these structures and a change in the CD spectrum of a protein

Pauling and Corey showed that in small peptides, six atoms associated with the peptide bond all lie in a plane. On a dipeptide of two amino acids in trans linkage (side-chains can be shown as —R), which six atoms are part of the planar structure of the peptide bond?

Calpha, C(carboxyl), O(carboxyl), N(amino), H(amino), Calpha

Identify and quantify the secondary structures present in this protein: Look at pic in the PDF

Four -helices and a single, two-stranded, antiparallel b-sheet

Explain (succinctly) the theoretical and/or experimental arguments in support of this statement: "The primary sequence of a protein determines its three-dimensional shape and thus its function."

Given that the 20 amino acids have different propensities to form secondary structures, hydrophobicity etc. different primary sequences should not give rise to identical three-dimensional structures. Loss of function mutations that alter the primary sequence provide one kind of experimental evidence of the same

Why are glycine and proline often found within the Beta turn?

Glycine has the smallest sidechain group reducing the possibility of steric clashes within the turn, and proline has the greatest propensity of all 20 common amino acids to assume a cis peptide bond, which allows it to bend the backbone sharply

Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.

H-bonds (urea), hydrophobic effect (detergent), ionic interactions (pH, detergent), disulfide bridges (pH), metal-ion bridges (pH)

Describe the quaternary structure of hemoglobin

Hemoglobin comprises 2 pairs of and b subunits arranged that so that they alternate around the protein's center

Where are the hydrogen bonds typically found between residues in an alpha helix?

In an alpha helix, the H bonds form between amino acids that are 4 spaces apart on the sequence.

What is typically found in the interior of a water-soluble globular protein?

Non-polar amino acids

Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?

Not every protein can be renatured. Some proteins can be renatured after being denatured under mild conditions, such as with 4-6 M urea. In these cases, renaturation can be achieved by slowly removing the urea through dialysis. The explanation lies in the difficulty to recreate the correct folding pathway for most proteins

What are 2 mechanisms by which "chaperone" proteins assist in the correct folding of polypeptides?

PDI (protein disulfide isomerase) assisted shuffling of disulfide bridges, and ATP-dependent binding to hydrophobic residues

In superhelical proteins, such as collagen, several polypeptide helices are intertwined. What is the function of this superhelical twisting?

To add tensile strength to the structure by close packing of collagen subunits

How can changes in pH alter the conformation of a protein?

pH alters the degree of ionization of acidic and basic groups, possibly disrupting electrostatic bridges within the protein, and its interactions with the solvent

Describe three of the important features of the -helical polypeptide structure predicted by Pauling and Corey

right-handed, a period of 3.6 amino acids per turn, R-groups on the outside face