Lecture 8: Protein Structure

Question 1

Structure of an amino acid.

Answer 1

- Amino acids are the monomers of proteins
Each has:
- Amino group
- alpha carbon
- Carboxyl group
- R group (side chain)

Question 2

Know how amino acids are classified based on the structure and atomic makeup of their R group.

Answer 2

Grouped based on :
i. how they interact with water (hydrophillic or hydrophobic)
ii. whether they are basic or acidic
iii. whether they are polar or nonpolar

Question 3

Compare hydrophobic and hydrophilic amino acids to one another.

Answer 3

Hydrophobic:
- Located in the interior of folded proteins in order to be kept away from water.

Hydrophilic:
- Polar side chains: hydrophilic and tend to form hydrogen bonds with one another or with water molecules
Basic and acidic amino acids are strongly polar and hydrophilic.
Basic amino acids: positively charged • Acidic amino acids: negatively
charged
The charged groups can form ionic bonds with one another and with other charged molecules

Question 4

Know the three special amino acids and describe the effect these amino acids have on the proteins that incorporate them

Answer 4

Glycine
• R group is hydrogen: symmetric
Nonpolar and small: the hydrogen side chain allows for freer rotation around the C-N bond
Glycine increases the flexibility of the polypeptide backbone

Proline
• R group is linked back to the amino group:
i. restricts rotation of the C-N bond
ii. puts constraints on protein folding in proline’s vicinity

Cysteine
• contains a –SH (sulfhydryl) group
• Two cysteines together can form S-S disulfide bonds: bridges that can connect different parts of the same protein or different proteins

Question 5

Know the properties of peptide bond formation

Answer 5

• The carboxyl group of one amino acid reacts with the amino group of another amino acid releasing a molecule of water
• The C=O group in the peptide bond is known as a carbonyl group and the N- H group is an amide group
• The free amino group is at the amino end of the peptide, and the carboxyl group is at the carboxyl end
• A polymer of amino acids connected by peptide bonds is a polypeptide

Question 6

Know and compare the four levels of protein structure

Answer 6

1°: Primary structure: sequence of amino acids
2°: Secondary structure: interactions between stretches of nearby amino acids
3°: Tertiary structure: 3D shape of a protein
4°: Quaternary structure: protein subunits interacting with one another

Question 7

Describe the processes of protein denaturation and renaturation

Answer 7

• Proteins can be denatured (unfolded) by chemical treatment or high temperatures and lose their function
• If the optimal conditions are returned, the protein can refold and regain its function

Question 8

Know the functional role of chaperone proteins in the folding of polypeptides

Answer 8

Aid in the folding of slow-folding proteins
• Chaperones shield hydrophobic groups to prevent aggregation until the protein attains its three-dimensional shape
• Chaperones give a protein time to find its correct shape