primary protein structure

Question 1

what is contained in primary structure

Answer 1

covalent polypeptide sequence and other details such as location of S=S and prosthetic groups

Question 2

what AAs are hydrophobic

Answer 2

glycine, alanine, valine, leucine, isoleucine, methianine, phenylalanine, proline and tryptophan

Question 3

which AAs are acidic

Answer 3

aspartate and glutamate

Question 4

which AAs are basic

Answer 4

lysine, arginine and histidine

Question 5

which enantiomer of amino acids are biologically active, how can you tell which enantiomer it is

Answer 5

L enantiomer, if looking at the alpha carbon, carboxyl group is to the left, R group is above and amide group to the right

Question 6

what possible configurations steriochemically to AA side chains have

Answer 6

either eclippsed or staggered, eclipsed is when bond directions match staggered is when they don’t

Question 7

which rotamers are favoured biologically

Answer 7

staggered amino acids, the right rotamer is needed for tight packing of protein

Question 8

what is a torsion angle

Answer 8

the torsion angle about bond B-C in a series of bonded atoms A-B-C-D is defined as the angle of rotation needed to make the projection of the line A-B coincide with C-D when viewed along the B-C direction

Question 9

what is the alpha carbon and beta carbon torsion angle called?

Answer 9

chi-1, which is the same as psi

Question 10

what is the standard torsion angle for rows of CH2 groups and why

Answer 10

180 degrees, groups are staggered since it is energetically favourable

Question 11

is the peptide bond loose or rigid, describe the nature

Answer 11

in the peptide chain between R groups there are 3 bonds; one C-C bond and 2 N-Cs, the N-C bond of the carbonyl carbon (the one joining residues) is a partial double bond and so cannot rotate, making the peptide bond rigid, the other 2 bonds can rotate.

Question 12

what leads to alpha helices and beta sheets

Answer 12

regular repeats of bond rotations

Question 13

what does it mean if a peptide bond is cis/trans

Answer 13

between amino acids in the polypeptide chain if the H coming of the N is on the same side as the carbonyl O then it is described as cis, if they are on other sides it is described as trans, most peptide bonds are in trans conformation due to steric interactions of R groups

Question 14

when are cis peptide bonds not uncommon

Answer 14

when one of the R groups is proline, since there is no N-H bonds since it is an imino acid

Question 15

what values do phi and psi and omega represent

Answer 15

the two torsion angles either side of an AA r group; psi is also chi 1, the torsion angle between alpha and beta carbons, phi is between alpha carbon and amide nitrogen

omega is torsion angle between beta carbon and adjacent peptide nitrogen (peptide bond that joins residues)

Question 16

what is the omega value for a peptide bond

Answer 16

w= 180 degrees (for trans)

Question 17

what is a ramachandran plot

Answer 17

a plot containing phi and psi angle values for an protein

phi is plotted on x axis, psi on y axis

Question 18

which secondary structures appear where in the ramachandran plot?

Answer 18

beta strands:top left hand corner
alpha helices: just below centre of left hand side
loops and left handed alpha helices: centre of top right square

Question 19

which AA is best left out of a ramachandran plot and why?

Answer 19

glycine, small R group means torsion angles are very variable and so values do not cluster

Question 20

in metal binding proteins which AAs does iron bind to and zinc

Answer 20

iron: aspartate and glutamate, histidine may also be present
zinc: 2 cysteines 1 histidine

Question 21

what AAs make disulphide bonds, how are they made and where are they found

Answer 21

cysteine, two free cysteine residues are oxidised (a H atom from each SH group removed) creating S=S, in intracellular proteins cysteines are usually free, S=S is common in secreted and extracellular proteins