Proteins II Flashcards
Levels of Protein Structures
Primary (1°) Secondary (2°) Tertiary (3°) Quaternary (4°)
“Supersecondary” structure between
2º and 3º
the linear sequence of amino acids, and the disulfide bonding pattern, in a polypeptide chain written from N-terminus to C-terminus going left to right. E.g. Met-Asn-Pro is a tripeptide.
1° structure:
Proteins can evolve via
genetic mutation
Nucleotide replacements can be ________ (e.g., leu to ile) or __________
conservative, non-conservative
forms when all the phi and psi dihedral angles of a contiguous stretch of polypeptide adopt the same set of values
2° structure
Regular local folding of a short stretch of polypeptide into one of several specific structural forms of secondary proteins:
- Various helices
- Various pleated sheets
- Reverse turns
- Loops (do not have regular, repeating structure)
Side chains radiate outward from helix axis Minimizes steric hindrance; allows for protein-protein and protein-ligand interactions (contains hydrogen bonds
The alpha-helix
The b-strands are not stable by themselves, but only when incorporated into
sheets
Strands can align in either a _____ or an ______manner; mixed sheets are also common
parallel, antiparallel
In alpha helix - n (# residues/turn) = ____ p (pitch) = _____ rise/residue = _____
3.6 5.4 Å 1.5 Å
In beta strands and beta sheets: n = _______ p = _____
n = 2 residues/unit p = 6.8 Å
Silk fibroin
400 kDa protein that has an extensive antiparallel beta sheet structure.
REVERSE TURNS
allow a long polypeptide chain to fold back on itself
Nearly ___of residues in globular proteins are involved in reverse turns.
1/3
What is the most common reverse turn?
the beta-turn
Number of residues required to complete a turn in a beta turn
four
1st residue hydrogen-bonds to _____ in a beta turn
the 4th
common in b-turns but tend to disrupt the a-helix
Gly & Pro
the folding of a continuous sequence of 2° elements into a specific and unique three-dimensional architecture.
Protein Tertiary Structure
Only about 30 residues long. Uses side chains of 2 His and 2 Cys (or 4 Cys) residues residues to coordinate Zn2+ ion
The Zinc-Finger DNA Binding Motif Occur via H-bonds, salt-bridges and hydrophobic interactions.
A feature of some transcription factors (eg., MyoD) that bind DNA and direct transcription, especially during development Forms dimers: 2nd helix involved in dimerization Some similarities to leucine zipper motif
The Helix-Loop-Helix Motif(a type of “supersecondary” structure)
How many Ig domains are present with the antibody (Ig) molecule with each domain containing an Ig fold?
12
Fold consists of a ___layer sandwich of _____ antiparallel beta-strands arranged in two beta-sheets with a ______ topology
2, 7-9, Greek key
