amino acid/peptide/protein

Question 1

structure of a.a.

Answer 1

NH2 + COOH + H + R group

Question 2

alpha carbon

Answer 2

carbon bonded to all groups

Question 3

alpha prefix

Answer 3

extinguish alpha functional groups from side chains

Question 4

zwitter ionic form

Answer 4

NH2 - gain H+ (cations) and COOH lose H+ (anion)

Question 5

Acidic a.a function and example

Answer 5

more hydrophilic in protein - polar
aspartic and glutamic acid
side chain exposed to aq media

Question 6

basic a.a.

Answer 6

lysine - pKa=9 - normal amine for protonation
arginine - pKa=14 - resonance stabilised guanidinium group - v. basic
histidine - pKa=6.8 - aromatic imidazole side chain - protonates = conjugate acid

Question 7

functionalised a.a

Answer 7

H bonds of side chains when protein bind to molecules
Asparagine, Glutamine, Serine, Methionine, Threonine
Cysteine - form disulphide bond = rigid structure

Question 8

hydrophobic a.a.

Answer 8

lipophilic side chains - bind for HP groups and recognition and binding event
Glycerine, Alanine, Valine, Leucine, Isoleucine, Proline

Question 9

Aromatic a.a.

Answer 9

bulky and HP - interior of protein
Phenylalanine, Tryptophan - HP
Tyrosine - form H bonds

Question 10

stereochemistry nomenclature

Answer 10

D- and L- - all alpha a.a in protein has L-

Question 11

D- a.a.

Answer 11

found in peptidoglycan components of bacterial cell wall

Question 12

D/L - rotatioin

Answer 12

different from R/S

uses CORN rule

Question 13

CORN rule

Answer 13

• H placed below plane

- priority - C=O then R group then NH2

Question 14

clockwise - CORN rule

Answer 14

D a.a.

Question 15

anti-clockwise CORN rule

Answer 15

L a.a.

Question 16

stereochem 1 - implication of a.a.

Answer 16

one form of a.a. exist - asymmetric and chiral - recognised by one stereochemistry - has specificity and selectivity

Question 17

stereochem 2 - implication of a.a.

Answer 17

E-catalysed reaction - stereoselective - chirality

Question 18

alpha NH2 - electronic properties of a.a. pKa

Answer 18

its pKa < aliphatic amines
negativity of alpha-carbon effect acidity and basicity
N is highly electronegative - intensifies acidity of COOH

Question 19

alpha COOH - electronic properties of a.a.

Answer 19

pKa < aliphatic COOH (4-5)
O2 in COOH - v. electronegative - weaken basicity of amine
2 O pull e- from amine - less available

Question 20

conc of +ve and -ve charge

Answer 20

depend on pKa value at certain pH therefore amount of -ve and +ve charge
balance = net charge 0

Question 21

isoelectric point (Pi)

Answer 21

at net change

standard chemical property

Question 22

all a.a has own Pi means

Answer 22

each protein has certain pH value

net charge=0 - problem has unique pi value

Question 23

Pi

Answer 23

measure by titration

or calculated by applying Henderson-Hasselbalch equation

Question 24

planar bond

Answer 24

sp2 - because of resonance = bond v. stable and hard to hydrolyse

Question 25

chemical synthesis

Answer 25

protecting group needed standardised

Question 26

directionality

Answer 26

a.a. sequence

Question 27

biological

Answer 27

DNA -> RNA -> peptide | occur in ribosome

Question 28

primary protein structure

Answer 28

linear a.a. sequence define down structure = similar properties e.g. short hexapeptide

Question 29

secondary protein structure

Answer 29

localised repeating rigid structure various interaction - H bonding and HP interaction alpha helix coiled and beta sheet - collection of multiple extended linear structure of H/HP interaction

Question 30

tertiary protein structure

Answer 30

secondary peptide and flexible chains fold into 3D domain | similar primary = similar tertiary

Question 31

quaternary protein structure

Answer 31

spatial arrangement of individual polypeptide chain subunit | collection of tertiary - large protein contain multiple domain

Question 32

relationship of protein structure

Answer 32

primary - Lys act as B and Ser has OH on side chain therefore Nu- Nu catalysed by B but are far apart at primary - can't interact alpha helix formed and folded to tertiary therefore Lys and Ser - closer together - chemical reaction can be catalysed efficiently by groups tertiary - not from same peptide chain - closer and interact between other a.a. side chains - quaternary

Question 33

B in relationship of protein structure

Answer 33

base