Bke2 Biochemistry Exercises

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Group exercise: Protein structure and function

Name four types of functions proteins can have in cells, and outside them. Think of at least one example for each case.
On the ribosome, amino acids are covalently linked together to form a polypeptide chain. Draw a tripeptide, and label the important parts (C-alpha, main chain, side chain, peptide bond, termini). Indicate which bonds are free to rotate. What determines the sequence of amino acid residues found? Why is this sequence important?
During or after synthesis, a polypeptide folds to form a functional protein. What do we mean by the term "folding"? Give a short description of the process, and the forces that make it happen.
List the amino acid side chains most frequently found in the cores of folded protein. What do they have in common? What types of amino acids are most often found on the surface? What features do they have in common?
Compare the interactions (hydrogen bonding, van der Waals, etc.) that are found in a completely unfolded protein (in water) to those of a correctly folded protein. What does this suggest about the basis of the stability of folded proteins?
Name the most common kinds of secondary structural elements, and describe how they are held together. Define the terms tertiary structure and quaternary structure. How are these held together? Why are these things important?
Many cosmetic creams claim to contain collagen as an active ingredient. What does collagen look like? What would be the technical problems of actually including collagen in such a cream? Would it be likely to help your skin?
Which of the following would be expected to stabilize the structure of a protein? Why?
a) introduction of disulfide bonds
b) substitution of a pair of amino acid residues that are hydrogen bonded to each other with a pair of glycine residues
c) replacement of a small amino acid in the crowded hydrophobic core of a protein with Trp
d) decrease in the number of Pro and hydroxy-Pro residues in a collagen molecule
Think of a way you might measure the extent of the change in stability.
You have isolated a protein that binds and acts on a negatively-charged substrate, and determined by peptide mapping that the key part falls somewhere in the following portion of the sequence:
ALMSQRTWNGKCP
Which residue or residues would you test first, if you were going to make mutants of the protein?
Why do our cells use proteins that bind heme for oxygen transport, rather than just using heme directly? What aspects of the proteins are most important in making the protein-heme partnership work?
What does the term "allostery" mean? What are the general roles of allostery in the function of hemoglobin and myoglobin? What general features of a protein are needed for allostery to work?
A fetus is absolutely dependent on its mother for oxygen. How do you think the properties of a fetus' hemoglobin will differ from that of its mother?
Why is the pH relatively low in the capillaries? What consequences does that have for oxygen transport? When you get out of breath during strenuous excercise, lactic acid builds up in the muscles. What effect would that have on your oxygen supply?

Reading material: Horton Chapters 3 and 4.

Lectures:
Amino acids, peptides, proteins
Protein chemistry, structure and function I
Protein chemistry, structure and function II

Links:
Suggested answers

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