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Biochemistry > Proteins > Flashcards

Proteins Flashcards

1
Q

what is the Henderson-Hasselbalch equation

A

pH= pKa +log10 ([A-]/[HA]

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2
Q

features of a peptide bond

A
  • planar bc of delocalised electron pair of the C=O

- resonance restricts the amount of conformations

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3
Q

what is a peptide bond

A

CO-HN

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4
Q

peptide bond and condensation vs hydrollysis

A

condensation:
build up from amino acid to protein
Hydrolysis:
break down protein to amino acid

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5
Q

what is cis

A

successive alpha C are on the same side of the peptide bond

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6
Q

what is trans

A

successive alpha C are on different side of peptide bond

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7
Q

cis or trans, which is more stable?

A

cis is less stable bc of steric interference- non-bonding interaction that affects conformation

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8
Q

how many amino acids

A

9 essential
11 non-essential
20 total

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9
Q

what is the structure of amino acids

A
  • amino group (NH2)
  • R group
  • Carboxyl group (COOH)
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10
Q

how many functional groups does an amino acid have

A

2: amino and carboxyl

- -> acts as a zwitterion

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11
Q

what is a zwitterion

A

a single species that contains both positively and negatively charged regions but has no overall charge

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12
Q

what determines the amino acid properties

A

R group bc it is variable

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13
Q

name the non-polar and no overall charge amino acids (hydrophobic)

A 
glycine
proline
leucine
alanine
phenyalanine
methionine
valine
tryptophan
isoleucine
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14
Q

name amino acids that are polar but uncharged side chains

hydrophilic

A 
serine
threonine
asparagine
cysteine
tyrosine
glutamine
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15
Q

name negatively charged amino acids (hydrophilic)

A

aspartate/ aspartic acid

glutamate/ glutamic acid

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16
Q

name positively charged amino acids

hydrophilic

A

lysine
arginine
histidine

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17
Q

what is the letter for glycine

A

g

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18
Q

letter for alanine

A

a

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19
Q

letter for valine

A

v

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20
Q

letter for leucine

A

l

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21
Q

letter for isoleucine

A

i

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22
Q

letter for phenylalanine

A

f

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23
Q

letter for methionine

A

m

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24
Q

letter for proline

A

p

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25
Q

letter for tryptophan

A

W

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26
Q

letter for serine

A

S

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27
Q

letter for threonine

A

t

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28
Q

letter for tyrosine

A

Y

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29
Q

letter for cysteine

A

C

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30
Q

letter for asparagine

A

n

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31
Q

letter for glutamine

A

q

32
Q

letter for aspartic acid

A

d

33
Q

letter for glutamic acid

A

E

34
Q

letter fr histidine

A

H

35
Q

letter for lysine

A

L

36
Q

letter for arginine

A

r

37
Q

what is a chiral centre

A

molecule with 4 different groups attached

38
Q

what are the properties of a chiral molecule

A
  • lacks plane of symmetry
  • can’t be superimposed on their mirror image
  • rotates planes of light
39
Q

what is the only amino acid that isn’t chiral

A

glycine

40
Q

what are enantiomers

A

pairs of molecules that have the same Mr and the atoms are joined in the same way, but they occupy different spaces
-optical isomers

41
Q

difference between enantiomers

A
  • rotates single plane of light in specific direction

- different properties

42
Q

if only one enantiomer is present in a system, the system has

A

enantiometric specificity and is enantiomerically pure

43
Q

what are diastereoisomers

A

pairs of stereoisomers that are not mirror images

44
Q

how do you distinguish between enantiomers

A

-enantiomers cause optical rotation of light travelling in a single plane

45
Q

what does +/- denote

A

the opposing effects that pain of enantiomers has of the behaviour of light

46
Q

what does d/l refer to

A

the rotation of light direction

47
Q

what is the primary structure of proteins

A
  • basic sequence of amino acids
  • only covalent peptide bonds
  • determined by DNA and base sequence of mRNA
  • N terminus to C terminus
48
Q

define the secondary structure of protein

A
  • local fold in the sequence caused by interaction on the back bone
  • non-covalent bonding e.g hydrogen, Van der Waals and electrostatic forces of attraction
49
Q

what are the 3 non-covalent bonding

A
  • hydrogen
  • van der waal
  • electrostatic forces of attration
50
Q

what structures does secondary have

A
  • alpha helix
  • beta-pleated sheets
  • loop region
51
Q

what are the alpha helices

A
  • narrow bore tube

- 3.6 amino acids per turn and a pitch of 5.4 Å

52
Q

how are alpha helices formed

A

H bonds form btw C=O of amino acid to N-H of another four amino acids

53
Q

why do alpha helices form

A
  • stability bc the side chains are well separated and each peptide link has 2 H bonds
  • dipole bc all H bonds point in the same direction
54
Q

what are the two other types of alpha helix

A

pi:
loose coil with H bond to the 5th residue
3(10):
tight could with H bond to 3rd residue

55
Q

structure of beta-pleated sheets

A
  • /\/\/\/\
  • regular, repeating H bonds
  • can be antiparallel or parallel
  • two residue repeats at a distance of 7Å
56
Q

bonds in beta-pleated sheets

A
  • polypeptide is fully stretched to allow N-H and C=O o point at right angles
  • H bonds form btw carboxyl O and amide ben strands are adjacent
57
Q

describe parallel beta-pleated

A
  • b strands run in the same direction

- less stable bc H bonds are on an angle - weaker

58
Q

describe anti-parallel beta pleated

A

b strands run in same direction

more stable bc H bonds are small and straight

59
Q

which is weaker, parallel or antiparallel

A

parallel

60
Q

what is a loop region

A

connection btw beta-pleated sheets

61
Q

describe structure of loop region

A
  • rich in polat and charged residues
  • makes H bonds with water as they are on the surface
  • made from b-turns or hairpin loops
  • has glycne as second residue
62
Q

where do proteases attack most

A

loop region

63
Q

what are the top 3 amino acids in alpha helices

A

glutamic acid
methionine
alanine

64
Q

what are the top 3 amino acids in b pleated sheets

A

valine
isoleucine
tyrosine

65
Q

what are the top 3 amino acids in b turns

A

glycine
asparagine
proline

66
Q

how are antiparallel sheets connected

A

small loop

67
Q

how are parallel sheets connected

A

extensive crossover

68
Q

what is supersecondary structure

A

compact 3d structure of several adjacent elements of secondary structure or motifs that are smaller than protein domains

69
Q

describe tertiary structure

A
  • 3D structure of the whole chain
  • affected by secondary structure and the atoms conformation
  • consists of two or more layers of 2nd to seal off the hydrophobic core from aqueous environment
70
Q

why has teriary structure stayed the same in evolution

A
  • form stable folding patterns
  • tolerates amino acid deletions, substitutions, and insertions
  • supports biological functions
71
Q

how do the proteins fold

A
  • hydrophobic interations (non-polar substances aggregate)
  • ionic interactions
  • H bonds
  • disulfide bridges
72
Q

desribe ionic interaction

A

some amino acids have an extra COOH and others have extra NH2. fCOOH donated proton to amine

73
Q

describe disulfide bridges

A
  • covalent bond btw 2 thiol groups of 2 adjacent cysteine residues
  • created by the oxidation of sulfhydryl groups
  • formed in the ER
  • stabiliezes protein structure
74
Q

describe Quaternary structure

A

made up of multiple polypeptie subunits

75
Q

what are lots of subunits joined together called

A

supra molecular assemblies

Biochemistry (10 decks)

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