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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
secondary protein structure
structure of a protein molecule resulting from regular coiling/ folding of amino acid chain
26
alpha-helix
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
27
beta pleated sheet
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
28
hydrogen bond
intermolecular interaction between hydrogen atom bonded to atom more eneg and another atom in another molecule (usually O/N/F)
29
H bond strength compared to covalent
H 1/10 strength of covalent
30
eneg series
O>N>C=H
31
electronegativity
tendency of an atom to attract a bonding pair of electrons
32
parallel vs antiparallel frequency
parallel less common due to poor H-bonding
33
myoglobin structure
tertiary 1 unit
34
haemoglobin structure
tertiary/ quarternary 4 units > 2 alpha 2 beta
35
myoglobin function
binds haem group
36
haem group
contains iron red pigment binds oxygen in muscle
37
haemoglobin
binds oxygen in lungs and releases in tissue acts cooperatively to deliver oxygen to tissues multiple interacting sites structure changes upon binding
38
myoglobin at normal oxygen delivery
high saturation
39
myoglobin at low oxygen supply to tissues
low saturation
40
haemoglobin graph shape saturation at lungs/ tissues?
sigmoidal high sat in lungs low sat in tissues
41
sickle cell anaemia
low oxygen structure polymerizes Hb E6>V mutation in beta sub-unit blockages in peripheral blood vessels homozygous recessive SC trait > malaria resistant
42
mad cow disease
bovine spongiform encephalopathy beef carcasses heat treated and fed back to cattle brain damage human variant developed
43
mad cow disease propagation
2 beta sheets sticking together
44
prion protein transformation diseases
GSS Alzheimers CJD F-F insomnia
45
prion protein transformation
alpha-helix stable exposed H-bonds on beta provide sticky ends
46
amyloid disease
uncontrolled protein growth - can be controlled by single atom changes
47
diseases caused by missing protein
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
TPP2 protein
glycine500 > aspartate G500D mutation complex quarternary structure
49
insulin action mechanism
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
novonordisk insulin replacement
insulin aspart weaker hexamers due to proline> aspartate mutation
51
binding site for taxol
kinesins
52
microtubules
tubulin proteins form helix w 13 vertical filaments around hollow core
53
filamentous actin
polymer of globular proteins assembling to form long polymers
54
titin
largest protein preventing muscles over-stretching 30,000 amino acid residues
55
silk beta pleated sheet design
ala/ gly residues interlocking rigid/ inextensible structure
56
A-keratin
coil of alpha helices stretchy/ flexible w few disulfide bridges
57
collagen
coiled coil of three strands gly-pro-pro sequence 100 res long e.g. cartilage/ teeth/ skin/ bone
58
enzyme function
structure contractile defence catalytic regulatory transport storage
59
enzyme inhiibtor examples
tamiflu penicillin aspirin statins/sarin microcystin
60
tamiflu/ relenza
neuraminidase inhibitors remove neuramic acid residues from host cell surface, easing virus life cycle release stage
61
tamiflu resistance
lysine to arginine mutation
62
penicillin mechanism
binds to enzymes producing bacterial cell wall
63
equilibrium constant
[C][D]/[A][B] proportional to energy released by reaction
64
change in Gibbs free energy
-RT(LnKeq)
65
gas constant
8.314
66
catalysis mechanisms
proximity orientation strain (on bond) acid-base catalysis (donation/ acceptance of protons) covalent
67
active site specificity
3D shape H-bonding
68
2 specificity mechanisms
lock and key (binding site complementary to substrate) induced fit (binding site and substrate contact induces active site shape change)
69
specificity types
absolute bond group stereo
70
enzyme reaction types
oxidation/ reduction transferase hydrolases lyases isomerases ligases/ synthases
71
catalysis constant
(turnover number) no. substrate molecules that can be converted to product by one enzyme in 1 second
72
equipment for measuring activity
spectrophotometer
73
activity measurement
product appearance reactants disappearance initial rate
74
rate at specified substrate concentration
Vmax[S]/(Km+[S])
75
michaelis constant
indicates affinity of an enzyme for a substrate as well as ES-complex stability
76
high Km
low affinity
77
low Km
high affinity
78
Km
[S] at Vmax/2
79
Vmax calculation
(only found at infinite [S]) 1. line of best fit from least squares fitting programme 2. use linewaver-burk plot (double reciprocal)
80
types of enzyme inhibitors
irreversible reversible: competitive, non-competitive, uncompetitive
81
irreversible enzyme inhibitor
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
sarin
nerve gas covalently binding to ser residue on AChesterase (no ACh breakdown)
83
irreversible inhibitors examples
aspirin penicillin beta lactamase
84
aspirin
inhibition of cyclooxygenase I/II and therefore prostaglandin H2 synthase via acetyl group transfer to S530
85
penicillin
Ser res binding in glycopeptide transpeptidase, preventing peptidoglycan synthesis
86
Beta lactam
irreversible inhibition of bacterial cell wall enzymes
87
beta lactams resistance
beta lactamase resistant bacteria product breaking down beta lactams
88
augmentin
amoxycillin/ beta lactamase combo
89
competitive inhibitors
compete w substrate active site similar structure to substrate overcome by [S]^ until outcompeted
90
competitive inhibition Vmax
unchanged
91
drugs as competitive inhibition
tamiflu (flu) acarbose (T2 diabetes) statins (hepatocytes rather than HMG-CoA reductase, reduces mevalomic acid as cholesterol precursor)
92
non-competitive inhibition
binds away from active site w same affinity, modifying reaction rate influences catalysis capacity
93
non-competitive inhibition Km/Vmax
both decrease
94
when does pH affect enzyme activity
alteration of 3D active site structure substrate binding group changes charge

Biochemistry semester 1 (7 decks)

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