lec8

Question 1

What are the five levels of protein structure, and what bonds are involved in each?

Answer 1

Primary structure: Linear sequence of amino acids; peptide bonds.

Secondary structure: α-helices and β-sheets; hydrogen bonds.

Tertiary structure: 3D shape of a single polypeptide chain; hydrogen bonds, ionic bonds, hydrophobic interactions, Van der Waals forces, disulfide bonds.

Quaternary structure: Assembly of multiple polypeptide chains; hydrogen bonds, ionic bonds, hydrophobic interactions, Van der Waals forces, disulfide bonds.

Question 2

aminos with smallest side chains:

Answer 2

alanine/ala/A (R=methyl)
glycine/gly/G (R=hydrogen-2 H’s therefore achiral)

-moderately hydrophobic
-gly imparts flexibility

Question 3

aliphatic (hydrophobic, nonpolar) side chains

Answer 3

7 total
-glycine, alanine, proline, valine, leucine, isoleucine, methionine
-chains of (uncharged duh) carbon
-expected to be in the middle of the protein chain, away from water or on the surface of membranes interacting with the lipid bilayer because they have some hydrophobic character

Question 4

How is proline different from other aliphatic amino acids?

Answer 4

Proline has a unique cyclic structure, where its side chain bonds back to the amine group, forming a pyrrolidine ring.
This ring structure restricts flexibility, making proline a rigid amino acid.
Unlike other amino acids, proline lacks a free amine (-NH₂) group; instead, it has a secondary amine (-NH).
Because of its rigidity, proline often disrupts alpha-helices and is commonly found in turns and loops of proteins.
(aka helix breaker)

Question 5

aromatic side chains

Answer 5

phenylalanine F, tyrosine Y, tryptophan W
“fuck u water”–hydrophobic
–bulky and f is more hydrophobic then other two bc it has no en atoms
-Can stack via pi-pi interactions within proteins.
-Often found inside soluble proteins (away from water) or on the membrane-exposed surface of membrane proteins.

Question 6

What are disulfide bonds and how do they form?
Where do disulfide bonds play a crucial role in proteins?

Answer 6

Disulfide bonds are covalent bonds formed between two cysteine residues via their thiol (–SH) groups. When two cysteine molecules undergo oxidation, their thiol groups form a bond (–S–S–).
Disulfide bonds stabilize protein structure by locking the protein into its correct three-dimensional shape. They are essential in extracellular proteins or proteins secreted from cells.
Fun Facts:

Found in keratin (hair, feathers) and stabilize their structure.
Disulfide bonds are formed in oxidizing environments like the lumen of the rough endoplasmic reticulum or extracellular spaces.