Lecture Set 4

Question 1

Describe the 4 levels of protein organization

Answer 1

1) amino acid sequence (dictates other levels) –> peptide bonding
2) local folding –> H-bonds btwn backbone
3) long-range folding –> noncovalent interactions between R-groups, covalent too (disulfide bonds)
4) association of peptide units –> noncovalent/covalent interactions

Question 2

Why are protein properties different than free amino acid properties?

Answer 2

Usually exist freely as zwitterions, loss of charge when in peptide chain

Question 3

What are the 4 components that determine stability?

Answer 3

1) electrostatic repulsion of adjacent charged R-groups
2) bulkiness of adjacent R-groups
3) Interactions between R groups 3/4 nucleotides apart
4) amount of proline/glycine aas

Question 4

Describe alpha helix and beta sheet

Answer 4

Alpha helix –> each turn ~3.6 residues, R-groups project outwards
Beta sheet –> can be parallel or antiparallel
Beta turn –> has proline and glycine in it, 4 aa’s

Question 5

Describe motifs and domains

Answer 5

motifs = common, stable secondary structure elements (suprasecondary structures)
have common functions, but can be made of different a.a sequences
Domains = polypeptide chain folding into stable structure with specific function

Question 6

Difference between fibrous and globular proteins?

Answer 6

fibrous = mostly for structure, globular = functional diversity

Question 7

How are proteins modified?

Answer 7

glycosylated, phosphorylated, hydroxylated, cleaved

Question 8

How are protein levels regulated

Answer 8

rate of synthesis/degradation, can be degraded with lysosomes, proteasomes