Proteins Flashcards
linear polymer formed by linking amino acid residues with peptide bonds
(polypeptide chains)
N to C terminus
Primary (1º) Structure
N to C terminus
Peptide bonds link amino acids to form polypeptides by:
the alpha-carboxyl (COO) group of one amino acid to the alpha-amino group of another (NH3+)
peptide bond characters:
- have double bond character at C-N
- are planar
- uncharged
- are usually trans
amino acid residues are what weight:
110 g/mol
a polypeptide with 50 amino acids weights what?
5500 g/mol
1 AA weights 110 g/mol
Where can disulfide bonds occur?
between the thiols of cysteines (SH + SH) = S-S and 2H+ in a REDOX rxn
vertical bonds, not horizontal like peptide bonds
whats an alpha helix?
a coiled rod-like structure with a tightly coiled backbone; stabilized by intrachain hydrogen bonds (R groups on outside)
Secondary structure
basically a coiled ribbon
Where are the H bonds in an alpha helix?
CO group bonds with the NH group of the amino acid situated 4 residues ahead. all but N and C term. ones bonded
“hotdog fold”
Whats the rise and rotation of each residue
Rise = 1.5 A
Rotation = 100º (3.6 AA’s per turn)
What is a beta sheet made of?
2+ polypeptide chains called beta strands (side by side, linked through H bonds)
Fully extended, beta strands have ____ A between AA’s?
3.5A between amino acids (alpha is 1.5A b/w adjacent AA’s)
The side chains of adjacent amino acids point in ____ direction?
opposite
Describe antiparallel vs parallel
anti = R chains point in opposite directions (N and C terminus line up)
parallel = side chains point in same directions (N and C terminus’s are opposite sides)
can beta sheets be mixed between antiparrallel and parallel?
beta sheets can be parallel, antiparallel, or mixed.
- Usually 5-10+ B strands per sheet
- not flat, but usually twisted
Whats a “motif” / supersecondary structure
specific combinations of secondary structure present in many proteins exhibiting similar functions
EX helix-turn-helix and beta-hairpin
Whats a domain in tertiary protein?
a compact globular region of a protein (30-400 AA)
stability in 3º structure through:
hydrophobic, hydrophillic and other residues (hydrophobic inside b/c no more H bond donors left)
what is quartenary 4º structure?
In proteins containing more than one polypeptide chain, the spatial arrangements of those chains (subunits) and the nature of contacts among them.
Interactions in 4º structire
VDW (side chains)
H bonds (C to N a-helix or b-sheet)
dipole dipole
whats a subunit in 4º structure?
Any of the polypeptide chains in a protein that contains more than one such chain.
Homo vs hetero-oligomer
homo = 2+ identical subunits
hetero = 2+ different subunits
Dimer, Trimer, Teramer refers to:
number of subunits (polypeptides) in a protein
What is denaturation?
When a protein is converted into a randomly coiled peptide without its normal activity (unfolded)
Cleavage of disulfide bonds b/w cystines, for example, into cysteines
Sequence specifies conformation: native confirmation is most thermodynamically stable
the information needed to specify the catalytically active three-dimensional structure of ribonuclease is contained in its amino acid sequence.
