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BIOL1026/28 Chemistry of Life > amino acid/peptide/protein > Flashcards

amino acid/peptide/protein Flashcards

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1
Q

structure of a.a.

A

NH2 + COOH + H + R group

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2
Q

alpha carbon

A

carbon bonded to all groups

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3
Q

alpha prefix

A

extinguish alpha functional groups from side chains

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4
Q

zwitter ionic form

A

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

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5
Q

Acidic a.a function and example

A

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

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6
Q

basic a.a.

A

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

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7
Q

functionalised a.a

A

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

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8
Q

hydrophobic a.a.

A

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

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9
Q

Aromatic a.a.

A

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

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10
Q

stereochemistry nomenclature

A

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

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11
Q

D- a.a.

A

found in peptidoglycan components of bacterial cell wall

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12
Q

D/L - rotatioin

A

different from R/S

uses CORN rule

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13
Q

CORN rule

A
  • H placed below plane

- priority - C=O then R group then NH2

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14
Q

clockwise - CORN rule

A

D a.a.

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15
Q

anti-clockwise CORN rule

A

L a.a.

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16
Q

stereochem 1 - implication of a.a.

A

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

17
Q

stereochem 2 - implication of a.a.

A

E-catalysed reaction - stereoselective - chirality

18
Q

alpha NH2 - electronic properties of a.a. pKa

A

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

19
Q

alpha COOH - electronic properties of a.a.

A

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

20
Q

conc of +ve and -ve charge

A

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

21
Q

isoelectric point (Pi)

A

at net change

standard chemical property

22
Q

all a.a has own Pi means

A

each protein has certain pH value

net charge=0 - problem has unique pi value

23
Q

Pi

A

measure by titration

or calculated by applying Henderson-Hasselbalch equation

24
Q

planar bond

A

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

25
Q

chemical synthesis

A

protecting group needed standardised

26
Q

directionality

A

a.a. sequence

27
Q

biological

A

DNA -> RNA -> peptide

occur in ribosome

28
Q

primary protein structure

A

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

29
Q

secondary protein structure

A

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

30
Q

tertiary protein structure

A

secondary peptide and flexible chains fold into 3D domain

similar primary = similar tertiary

31
Q

quaternary protein structure

A

spatial arrangement of individual polypeptide chain subunit

collection of tertiary - large protein contain multiple domain

32
Q

relationship of protein structure

A

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

33
Q

B in relationship of protein structure

A

base

BIOL1026/28 Chemistry of Life (20 decks)

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