BoC proteins Flashcards
Give eg of amino acid with hydrophobic sidechain?
Valine (see notes for diagram)
R is CH(CH2)2
No sidechain amino acid
Glycine (non-chiral)
positive sidechain
lysine (see notes for diagram)
R is C4H8NH2
negative sidechain
aspartate (see notes for diagram)
R is ethanoate
polar sidechain
Asparagine (has amide group where N is polar)
R is CH2CONH2
sulphur-containing sidechain
cysteine (can form disulphide bridges)
(see notes for diagram)
R is CH2SH
Amino acid with non-ionisable sidechain titration curve explain
see notes
How many times more readily do amino acids lose a proton than acetic acid, and why?
300, because neighbouring positively charged amino group withdraws electrons from carbonyl stabilising carboxyl form
If R contains an ionisable group…
Titration curve has a third PKa
Which enantiomers of amino acids are found in natural proteins
L
Draw L and D amino acid
see notes
L based on…
similarity to glyceraldehyde again
By convention amino acids in a polypeptide chain are written…
N to C terminus
How much double bond character does a peptide bond have?
40%, is a resonance hybrid
Is peptide bond usually cis or trans and why?
Trans with alpha carbons on opposite sides because if it were cis side chains on adjacent residues would clash
Why are disulphide bridges rare in intracellular proteins?
Because of reducing cytoplasmic environment
Proteins that bind to DNA likely to be…
Rich in positively charged amino acids like lysine to bind to negatively charged phosphate backbone
What are phi and psi?
see notes
What are phi and psi restricted by? Why does glycine have less restrictions?
steric hindrance between main chain and side chains of adjacent residues, therefore as glycine sidechain is just H more combinations allowed
Draw a ramachandran plot
see notes
H bond donors and acceptors in interior of proteins…
bond each other
In exterior H bonds are with…
Water
What are 4 criteria for secondary structures?
1) peptide bond planar with favourable length and angle, 2) each carbonyl O and amide N involved in H bonds, 3) H-bonded atom in straight line, 4) sidechains project out with minimum steric inteference
Describe and draw alpha-helix
see notes
H bonds between i and i+4
3.6 residues per 360 degree turn
Draw and describe beta sheet
see notes
Beta strands connected by ladders of H bonds to other strands
Antiparallel = strands run in opposite directions
In both sheet types sidechains alternately project
Describe reverse beta turn
Puts secondary structure elements together
Allows polypeptide chain to reverse direction
Turn is min of 4 residues
Glycine and proline commonly occur in the turn
