Protein Structure

Question 1

Primary

Answer 1

sequence of amino acids from N–>C terminus
everything depends on primary structure
fundamental to the final shape
the alphabet, secondary=words, tertiary= sentences, quaternary= paragraphs

Question 2

Secondary

Answer 2

alpha helices, beta sheets, loops
occurs bc of the plane formed by the peptide bond
makes it so the C-alpha is the only print of flexibility
proline makes a structure less flexible and is kinky
glycine increases flexibility

Question 3

Alpha helix

Answer 3

tight right-handed coil
no real space in middle
one twist is about 3.6 amino acids
carbonyls all point towards C-terminus
Hydrogens all point towards N-terminus
Backbone carbonyls hydrogen bond w/ backbone NH
Residue= smaller part of a longer thing
whole structure linked via hydrogen bonds
solid structure, not wobbly
H-bonds hold the shape
side chains all pointed out and towards N-terminus
Center is packed w/ Van der Waals interactions
Side chains also interact
side chain interacts w/ n+3
won’t find prolines in the middle of alpha helix but others at the front or end (n-cap or c-cap)
don’t usually find glycines in the middle bc they are wobbly and flexible
AA that has 2 C-gammas will unlikely be in the middle of an alpha helix

Question 4

Beta sheet

Answer 4

amino acids are extended or stretched out
linked by backbone hydrogen bonds to form a sheet
H bond between backbone carbonyl and backbone NH
No prolines in beta sheets
side chains are normal to the plane of the sheet
Sheet can be mixture of parallel and antiparallel
Glycine will not show up in beta sheets TOO WOBBLY

Question 5

Loops

Answer 5

most variety of structures
least systematic but still structured
Turn: short amino acid sequence that has a sharp change of direction and an internal H-bond C3-5 amino acids, highly likely to encounter glycines and prolines
Random coils: unspecified length of amino acids, long loops, no determined structure, not a big but can be used in specific situations

Question 6

!

Answer 6

alpha helix, beta sheets, and turns provide structure while random coils provide flexibility

Question 7

Tertiary

Answer 7

alpha keratin is a coiled-coil
made up of 2 alpha helices
inside is hydrophobic outside is hydrophilic
hydrophilic residues help together by hydrophobic amino acids (hydrophobic effect)
disulfide bonds

Question 8

Fibroin

Answer 8

the protein that makes silk and spider webs
strongest tensile strengths
Repeat structure Ser-Gly-Ala-Ser-Gly-Ala…
Stack of beta sheets
Tons of van der Waals interactions
hydrophobic effect