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Biochemistry semester 1 > Molecular building blocks of life > Flashcards

Molecular building blocks of life Flashcards

1
Q

primary protein structure

A

sequence of nucleotides joined by peptide bonds in condensation reactions

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2
Q

amino acid structure

A

positive amino end N-terminus
negative carboxyl C-terminus
zwitterion
only L isomers found in proteins

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3
Q

zwitterion

A

having one of each charge but no net charge

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4
Q

amino acid isomers found in proteins

A

L
(L=living)

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5
Q

law for L isomers

A

CORN going clockwise

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6
Q

peptide bonds

A

rigid
partial double bond character
can undergo cis-trans isomerisation

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7
Q

trans vs cis frequency in proteins

A

trans 1000* more common than cis

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8
Q

chloramphenicol

A

antibiotic for eye infections/ penicillin-resistant meningitis.
prevents peptide bond formation by binding to bacterial ribosome

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9
Q

chloramphenicol acetyl transferase

A

enzyme used by resistant bacteria to prevent chloramphenicol ribosome-binding

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10
Q

negatively charged amino acids

A

carboxylate side chains
aspartate (D/Asp)
glutamate (E/Glu)

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11
Q

positively charged amino acids

A

primary amino groups
arginine (R/Arg)
lysine (K/Lys)

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12
Q

hydrophobic amino acids

A

proline (P/Pro)
leucine (L/Leu)
valine (V/Val)
isoleucine (I/Ile)
phenylalanine (F/Phe)
methionine (M/Met)
tryptophan (W/Trp)

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13
Q

aromatic amino acids

A

tryptophan (W/Trp)
phenylalanine (F/Phe)
tyrosine (Y/Tyr)

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14
Q

small amino acids

A

glycine (G/Gly)
alanine (A/Ala)
serine (S/Ser)
cysteine (C/Cys)

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15
Q

smallest amino acid

A

glycine (G/Gly)

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16
Q

charged/ polar amino acids

A

aspartate (D/Asp)
asparagine (N/Asn)
glutamate (E/Glu)
glutamine (Q/Gln)
arginine (R/Arg)
histidine (H/His)

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17
Q

glycine

A

2 hydrogens attached to a carbon
no D/L form
found in flexible regions of protein
neurotransmitter

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18
Q

Cysteine

A

thiol group (H lost more easily)
binds to other cysteine via disulfide bonds
binds to metal in proteins

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19
Q

disulfide bonds characteristics

A

increase stability of proteins

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20
Q

histidine

A

acts as a base> not strongly charged in body
can bind metals as well

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21
Q

aromatic amino acids characteristics

A

largest
hydrophobic
found in protein core
absorb light (used in spectroscopy)
required for diet of humans

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22
Q

phenylketoneuria

A

inability to break down excess phenylalanine > aspartame avoided

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23
Q

residue

A

each amino acid in a sequence

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24
Q

peptide backbone

A

w exposed carbonyls and amides
rigid planar peptide due to partial double bond w resonating electrons

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25
Q

secondary protein structure

A

structure of a protein molecule resulting from regular coiling/ folding of amino acid chain

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26
Q

alpha-helix

A

H bonding between oxygen of carbonyl group of one N on amino acid and hydrogen of NH group of another amino acid 4 places ahead (3.6 residues)
successive side-chains point 100 degrees apart
exist singly/ grouped/ in coils

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27
Q

beta pleated sheet

A

looser/ straighter alpha helix
parallel/ antiparallel
depend on H bonds/ L amino acid/ rigidity of peptide bond
side chains alternate 180 degrees up/ down
2 res repeat

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28
Q

hydrogen bond

A

intermolecular interaction between hydrogen atom bonded to atom more eneg and another atom in another molecule (usually O/N/F)

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29
Q

H bond strength compared to covalent

A

H 1/10 strength of covalent

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30
Q

eneg series

A

O>N>C=H

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31
Q

electronegativity

A

tendency of an atom to attract a bonding pair of electrons

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32
Q

parallel vs antiparallel frequency

A

parallel less common due to poor H-bonding

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33
Q

myoglobin structure

A

tertiary
1 unit

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34
Q

haemoglobin structure

A

tertiary/ quarternary
4 units > 2 alpha 2 beta

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35
Q

myoglobin function

A

binds haem group

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36
Q

haem group

A

contains iron
red pigment
binds oxygen in muscle

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37
Q

haemoglobin

A

binds oxygen in lungs and releases in tissue
acts cooperatively to deliver oxygen to tissues
multiple interacting sites
structure changes upon binding

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38
Q

myoglobin at normal oxygen delivery

A

high saturation

39
Q

myoglobin at low oxygen supply to tissues

A

low saturation

40
Q

haemoglobin graph shape
saturation at lungs/ tissues?

A

sigmoidal
high sat in lungs
low sat in tissues

41
Q

sickle cell anaemia

A

low oxygen structure polymerizes Hb
E6>V mutation in beta sub-unit
blockages in peripheral blood vessels
homozygous recessive
SC trait > malaria resistant

42
Q

mad cow disease

A

bovine spongiform encephalopathy
beef carcasses heat treated and fed back to cattle
brain damage
human variant developed

43
Q

mad cow disease propagation

A

2 beta sheets sticking together

44
Q

prion protein transformation diseases

A

GSS
Alzheimers
CJD
F-F insomnia

45
Q

prion protein transformation

A

alpha-helix stable
exposed H-bonds on beta provide sticky ends

46
Q

amyloid disease

A

uncontrolled protein growth
- can be controlled by single atom changes

47
Q

diseases caused by missing protein

A

cystic fibrosis (missing CF transmembrane regulator protein)
muscular dystrophy (missing dystrophia)
phenylketoneuria (phenylalanine hydroxylase missing)
haemophilia (missing blood clotting factor proteins)
cancer (missing tumour suppressor genes)
type 1 diabetes (insulin-producing cell destruction)

48
Q

TPP2 protein

A

glycine500 > aspartate
G500D mutation
complex quarternary structure

49
Q

insulin action mechanism

A

present as hexamer at high conc in pancreas, dissociates in blood to form single monomer active in blood
bind to receptor
influence cell metabolic activity

50
Q

novonordisk insulin replacement

A

insulin aspart
weaker hexamers due to proline> aspartate mutation

51
Q

binding site for taxol

A

kinesins

52
Q

microtubules

A

tubulin proteins form helix w 13 vertical filaments around hollow core

53
Q

filamentous actin

A

polymer of globular proteins assembling to form long polymers

54
Q

titin

A

largest protein preventing muscles over-stretching
30,000 amino acid residues

55
Q

silk beta pleated sheet design

A

ala/ gly residues interlocking
rigid/ inextensible structure

56
Q

A-keratin

A

coil of alpha helices
stretchy/ flexible w few disulfide bridges

57
Q

collagen

A

coiled coil of three strands
gly-pro-pro sequence
100 res long
e.g. cartilage/ teeth/ skin/ bone

58
Q

enzyme function

A

structure
contractile
defence
catalytic
regulatory
transport
storage

59
Q

enzyme inhiibtor examples

A

tamiflu
penicillin
aspirin
statins/sarin
microcystin

60
Q

tamiflu/ relenza

A

neuraminidase inhibitors
remove neuramic acid residues from host cell surface, easing virus life cycle release stage

61
Q

tamiflu resistance

A

lysine to arginine mutation

62
Q

penicillin mechanism

A

binds to enzymes producing bacterial cell wall

63
Q

equilibrium constant

A

[C][D]/[A][B]
proportional to energy released by reaction

64
Q

change in Gibbs free energy

A

-RT(LnKeq)

65
Q

gas constant

A

8.314

66
Q

catalysis mechanisms

A

proximity
orientation
strain (on bond)
acid-base catalysis (donation/ acceptance of protons)
covalent

67
Q

active site specificity

A

3D shape
H-bonding

68
Q

2 specificity mechanisms

A

lock and key (binding site complementary to substrate)
induced fit (binding site and substrate contact induces active site shape change)

69
Q

specificity types

A

absolute
bond
group
stereo

70
Q

enzyme reaction types

A

oxidation/ reduction
transferase
hydrolases
lyases
isomerases
ligases/ synthases

71
Q

catalysis constant

A

(turnover number)
no. substrate molecules that can be converted to product by one enzyme in 1 second

72
Q

equipment for measuring activity

A

spectrophotometer

73
Q

activity measurement

A

product appearance
reactants disappearance
initial rate

74
Q

rate at specified substrate concentration

A

Vmax[S]/(Km+[S])

75
Q

michaelis constant

A

indicates affinity of an enzyme for a substrate as well as ES-complex stability

76
Q

high Km

A

low affinity

77
Q

low Km

A

high affinity

78
Q

Km

A

[S] at Vmax/2

79
Q

Vmax calculation

A

(only found at infinite [S])
1. line of best fit from least squares fitting programme
2. use linewaver-burk plot (double reciprocal)

80
Q

types of enzyme inhibitors

A

irreversible
reversible: competitive, non-competitive, uncompetitive

81
Q

irreversible enzyme inhibitor

A

irreversible binding of enzyme via covalent bonding to amino acid side chain (ser/cys) at/ near active site
permanent enzyme inactivation/ substrate binding inhibition

82
Q

sarin

A

nerve gas covalently binding to ser residue on AChesterase (no ACh breakdown)

83
Q

irreversible inhibitors examples

A

aspirin
penicillin
beta lactamase

84
Q

aspirin

A

inhibition of cyclooxygenase I/II and therefore prostaglandin H2 synthase via acetyl group transfer to S530

85
Q

penicillin

A

Ser res binding in glycopeptide transpeptidase, preventing peptidoglycan synthesis

86
Q

Beta lactam

A

irreversible inhibition of bacterial cell wall enzymes

87
Q

beta lactams resistance

A

beta lactamase
resistant bacteria product breaking down beta lactams

88
Q

augmentin

A

amoxycillin/ beta lactamase combo

89
Q

competitive inhibitors

A

compete w substrate active site
similar structure to substrate
overcome by [S]^ until outcompeted

90
Q

competitive inhibition Vmax

A

unchanged

91
Q

drugs as competitive inhibition

A

tamiflu (flu)
acarbose (T2 diabetes)
statins (hepatocytes rather than HMG-CoA reductase, reduces mevalomic acid as cholesterol precursor)

92
Q

non-competitive inhibition

A

binds away from active site w same affinity, modifying reaction rate
influences catalysis capacity

93
Q

non-competitive inhibition Km/Vmax

A

both decrease

94
Q

when does pH affect enzyme activity

A

alteration of 3D active site structure
substrate binding group changes charge

Biochemistry semester 1 (7 decks)

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