Proteins Flashcards
Protein Structures
primary =
secondary =
tertiary =
quaternary =
- amino acid sequence
- a-helicies or b-sheets
- 3d folding of the protein (1chain)
- complex folding of the protein (many chains)
Cysteines Specifically
undergo ________ chemistry
reduced form =
oxidized form =
redox chemistry
cysteine + cysteine (SH + SH)
disulphide bond (S—–S)
what rxn breaks peptide bonds
hydrolysis
what rxn makes peptide bonds
condensation
what seconday structure has a dipole
a helix since all amides are on one side and all carbonyls are on the other side
phi angle
bond angle between N——Calpha
psi angle
bond angle between Calpha——Carbonyl C
what are the two forms of B-sheets
parallel and antiparallel
antiparallel B-sheets
both sheets run in opposite directions and H bonding is vertical/straight between amide and carbonyl
parallel B-sheets
both sheets run in the same direction and H bonding is diagonal between amide and carbonyl
salt bridge and example
electrostatic interaction between opposite charges
ex. Lys (+) ——— (-) Glutamate
non polar residues =
charged residues =
polar residues =
inside of the portein (core)
surface of the protein
outside of the protein (periphery)
stabilizing forces of proteins
electrostatic int, h bonding, wan ders wals forces, hydrophobic effects
B-sheets
right handed twists result in ______ loops
left handed twists result in ________ loops
shorter
longer
example of B-sheets
TIM barrel
- 8 stand B-barrel with right handed twists
example of a-helicies
Leucine Zippers
- dimerization of 2 a-helicies with Leu repeats every 7 amino acids
Bacteriorhodopsin
protein domains
independantly folded regions on a protein
example of protein-carbohydrate complexes
Lectins
-functions in cell-cell recognition
- polyvalent affinity for polysaccharides not monosaccharides
what are the 4 classes of proteins
- all a helical
- all b sheets
- mixed a/b
- mixed a+b
mixed a/b proteins and example
have both a helicies and b sheets in the same domain
ex. Ricin (2 domains, a+b and another one)
mixed a+b proteins and examples
have a helicies and b sheets in different domains
ex. Type 4 Pilin (2 domains, a helical (N term) and B sheets (C term))
how many residues are there per turn in the a-helix
3.6 residues
what atoms make up the phi angle
carboxyl C - amide N - alpha C - carboxyl C
what atoms make up the psi angle
amide N - alpha C - carboxyl C - amide N
what are helical wheels
a diagram that shows the arrangement/properties of amino acids in a a-helix and how it would look like in a protien
each carbonyl is H-bonded to a amide _____ residues away
4 residues away
n+4
what does the Ramacharan Plot show
shows the sterically allowed/not allowed conformations of the protein backbone through its phi and psi dihedral angles
