protein structure

Question 1

which way round is a D isomer of an AA

Answer 1

looking down H - αC bond, from H reads corn ANTICLOCKWISE

Question 2

which way round is an AA L isomer

Answer 2

looking down H - αC bond, reads corn CLOCKWISE

Question 3

which direction isomer are AAs in living organisms tho

Answer 3

L FORM

Question 4

which kind of aa make up bacterial cell walls

Answer 4

D-AA residues make up cell walls and are often used in therapeutics

Question 5

what gives polypeptides their structural polarity

Answer 5

n and c termini

Question 6

what do you call a unit of a polypeptide chain

Answer 6

residue

Question 7

what is the normal structural arrangement of an R chain

Answer 7

trans conformation; cis less energetically favourable

Question 8

what shape is a peptide bond

Answer 8

planar - rotational freedom around αC, 2xH in glycine allows greater flexibility around peptide backbone

Question 9

what does rotational freedom allow

Answer 9

formation of α helices and β pleated sheets

Question 10

how are AAs categorised

Answer 10

structural and chemical properties

Question 11

how are charged AAs subdivided

Answer 11

acidic/basic/ /+ve/-ve

Question 12

what AA group are COO-/carboxyl in

Answer 12

charged or acidic

Question 13

what AA group are NH3+/amine in

Answer 13

charged or basic

Question 14

2º amine & carbonyl are in which group

Answer 14

polar

Question 15

what group does an aa with a hydroxyl side chain go into

Answer 15

polar

Question 16

what aa group does a hydrocarbon r chain go into

Answer 16

non polar hydrophobic

Question 17

what do polypeptides adopt their structure based on

Answer 17

Energy minimalisation - minimisation of the free energy of a molecule G determines the most favourable conformation

Question 18

what is greek for the change in free energy upon folding

Answer 18

ΔG

Question 19

what three things affect G

Answer 19

1. Aq/lipid membrane
2. other proteins or molecules incl salts
3. change in environment can induce further conformational change eg receptor binding to a ligand

Question 20

how much weaker are other bonds than non covalent bonds

Answer 20

1/20 of the strength of covalent ones

Question 21

where do disuphide bonds form

Answer 21

between 2 cysteine residues

Question 22

what reaction makes a disulphide bond

Answer 22

oxidation between SH groups forms crosslink ☛➭➪distant in sequence but adj in 3D structure

Question 23

what defines the categories aa’s go in

Answer 23

their structural and chemical properties

Question 24

what determines the properties of AAs

Answer 24

the R chain

Question 25

why does folding occur

Answer 25

minimise the free energy of a molecule and form structure with the lowest free energy

Question 26

what confers the structural behaviour of a polypeptide chain

Answer 26

the chemical composition of the constituent AAs