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Biomed > BB1702 amino acids > Flashcards

BB1702 amino acids Flashcards

1
Q

what are the main properties of amino acids?

A
  • 20 different amino acids
  • alpha
  • have negative and positive charge
  • alpha carbon
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2
Q

properties of alpha carbon

A
  • acidic carboxyl group
  • basic amino group
  • hydrogen connected to carbon
  • closer to carboxyl group in proteins
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3
Q

what’s the importance of amino acid structure?

A

structure correlates to function

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4
Q

what are GABA amino acids?

A

neurotransmitters in the brain
NH2 attached to y

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5
Q

how can amino acids be organised?

A

stereoisomers
chiral carbon
enantiomers

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6
Q

what is a stereoisomer?

A

same molecular formula and bonding but different 3d oritentation of atoms

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7
Q

what is a chiral carbon atom?

A

carbon with four different groups bonded to it

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8
Q

which amino acid is not chiral?

A

glycine

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9
Q

what is an enantiomer?

A
  • stereoisomers that are non superimposable mirror images
  • can either be L or D
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10
Q

what is an L amino acid?

A
  • consitiuents of proteins
  • more soluble than a racemic mixture of D and L, form crystals
  • more dominant in solution due to solubility difference
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11
Q

what are D amino acids?

A

rare
found in bacteria

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12
Q

what is the ionisation behaviour of amino acids?

A
  • can be placed in five groups due to characteristics, depending on their r group
  • 7/20 amino acids have readily ionisable side chains, able to donate or accept protons to dacilitate reactions and form ionic bonds
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13
Q

how can amino acids be organised?

A
  • nonpolar aliphatic
  • aromatic
  • polar uncharged
  • positively charged
  • negatively charged
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14
Q

properties of non polar aliphatic amino acids?

A
  • R groups consist of hydrocarbon chains, except glycine and methionine
  • side chains are hydrophobic as they cluster together rather than contact water
  • different sizes and shapes of hydrocarbon side chains enable them to pack together to form compact structures with little empty space
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15
Q

examples of nonpolar aliphatic amino acids?

A
  • glycine
  • alanine
  • proline
  • valine
  • leucine
  • isoleucine
  • methionine
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16
Q

methionine

A

contains an aliphatic side chain
includes thioether group

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17
Q

isoleucine

A

side chain includes an additional chiral centre

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18
Q

proline

A

has a pyrrolidine ring structure
side chain bonded to alpha carbon and nitrogen
cycle structure makes it more conformationally restricted

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19
Q

examples of aromatic amino acids?

A

phenylalanine
tyrosine
tryptophan

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20
Q

phenylalanine

A

has a phenyl ring in place of H atom of alanine
purely hydrophobic

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21
Q

tryptophan

A

indole group, two fused rings containing NH group, joined to methylene, a double ring, benzene and nitrogen
less hydrophobic due to side chain NH group

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22
Q

tyrosine

A

version of phenylalanine
hydroxyl group attached to hydrophobic side chain
hydroxyl group makes amino acid more hydrophilic and reactive

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23
Q

examples of polar uncharged amino acids?

A

serine
cysteine
threonine
asparagine
glutamine

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24
Q

serine

A

version of alanine with hydroxyl group attached

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25
Q

cysteine

A

similar to serine
contains sulfhydryl
sulfydryl is more reactive than OH, groups may form disulfide bonds
important for stabilising proteins

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26
Q

threonine

A

contains additional asymmetric centre with one isomer present

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27
Q

asparine and glutamine

A

both contain terminal carboxamide
side chain of glutamine is one methyl group longer

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28
Q

examples of positvely charged amino acids?

A

lysine
arginine
histidine

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29
Q

lysine and arginine

A

long side chains, end with + group at neutral pH
lysine capped by pos amino group
arginine capped by a guanidinium group

30
Q

histidine

A

pos charged aromatic and imidazole group
uncharged or pos at neutral pH
found in enzyme active sites
imidazole binds and releases protons in course of enzymatic reaction

31
Q

examples of negatively charged amino acids

A

aspartate
glutamate

32
Q

properties of negatively charged amino acids

A

side chain lacks a proton at physiological pH
present in acidic form
side chain accepts a proton

33
Q

apartate and glutamate

A

come from aspartic acid/asparagine and glutamic acid/glutamine

34
Q

glutamate vs glutamic acid

A

glutamic acic:
- COOH
- protonated
- donate to form glutamate
glutamate:
- COO-
- lost protons
- acid

35
Q

what are peptide bonds

A

small condensation products of amino acids
smaller than proteins
peptide ends are not the same
have polarity

36
Q

formation of peptide bond

A

COO- + NH3 -> CONH + H2O

37
Q

what is a bronsted lowry acid

A

proton donor

38
Q

what is a bronsted lowry base

A

proton acceptor

39
Q

acid dissociation constant

A

stronger the acid, higher the Ka and lower the pKa - more protons, lower pH
weaker acid, low Ka and high pKa - more OH, higher pH

40
Q

what is a buffer

A

resist pH changes by addition of small amounts of acid or base
mixture of weak acid and conjugate base
narrow pH range
buffer region is flat and steep in equilibrium

41
Q

why is it important that pH is monitored by buffers

A
  • almost every biological processes are pH dependent
  • small changes in pH produce large change in rate
  • cystolic pH near 7, biological molecules in optimal ionic state
42
Q

what are zwitterions

A

contain a pos and negative charge
amino acids can act as acids and bases depending on pH environment

43
Q

how can ionisation state of amino acids vary with pH?

A
  • low pH: lots of H+, fully protonated, acidic, +1 charge, NH3+ and COOH
  • increasing pH: H+ increases, zwitterion, COO-, NH3+, 0 charge (isoelectric point)
  • high pH: alkali, low H+, high OH-, NH2, COO-, -1 charge, deprotonated
44
Q

how to work out isoelectric point?

A

(pK1 + pK2)/2

45
Q

fill in the gaps:
Formation of a peptide bond produces _____ as a byproduct.

A

water

46
Q

fill in the gap
n the following peptide, which amino acid is the N-terminus?
phenylalanine-alanine-glycine-arginine

A

phenylalanine

47
Q

fill in the gap:
Of the 20 standard amino acids, only ___________ is not chiral. The reason is that its side chain _________

A
  1. glycine
  2. a hydrogen atom
48
Q

what do proteins contain?

A

only L amino acids

49
Q

how many of the 20 common amino acids have rings in their structures?

A

5

50
Q

What do leucine, isoleucine and valine have in common?

A

they have nonpolar aliphatic side chains

51
Q

Which amino acids contain a hydroxyl group in their side chain?

A

serine, threonine, tyrosine

52
Q

Which amino acids contain an acid group in their side chain?

A

aspartate, glutamate

53
Q

which amino acids contain an amide group in their side chain?

A

asparagine, glutamine

54
Q

which of the following pairs of amino acids is positively charged at a neutral pH?

A

lysine, arginine

55
Q

Which two amino acids contain a sulfur atom?

A

cysteine, methionine

56
Q

Which of the following tripeptides would be expected to be the most hydrophobic?

A

Gly-Tyr-Ala

57
Q

name aromatic amino acids

A

phenylalanine, tyrosine, tryptophan

58
Q

Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease have shown that:

A

he primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.

59
Q

Protein folding to a native conformation is highly dependent upon:

A
  • rotation about the alpha-carbon, carbon bond in the backbone
  • the polar character of sequences of amino acids
  • the relative size of amino acid R-groups
  • the rotation about the alpha-carbon, nitrogen bond
60
Q

Protein folding to a native conformation is not dependent upon:

A

the rotation about the peptide bond

61
Q

what is the disulphide bond between two cysteine molecules?

A

a covalent bond formed by oxidation

62
Q

The molecular interaction called “hydrophobic effect” is best described as:

A

the tendency of non-polar molecules to avoid interactions with water and thus aggregate.

63
Q

The overall three-dimensional structure of a single polypeptide is referred to as

A

tertiary structure

64
Q

The term “quaternary” with respect to protein structure means

A

a multisubunit structure

65
Q

What important function do molecular chaperones perform?

A

fold proteins into a native conformation

66
Q

What level of protein structure is composed of α helices, β sheets, and turns?

A

secondary

67
Q

which amino acid residue would most likely be buried in the interior of a water-soluble, globular protein?

A

phenylalanine

68
Q

how do you best describe the arrangement of amino acid side chains in an alpha helix?

A

the side chains point outward away from the helical axis

69
Q

which bonds within a peptide backbone show free rotation around both bonds?

A

C α—C and N—C α

70
Q

Most proteins have a molecular mass between:

A

10kDa - 500kDa

71
Q

which sequence best represents the backbone arrangement of two peptide bonds?

A

C a—C—N—C a—C—N

Biomed (59 decks)

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