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1st year: Physiology and Metabolism > 1st test - 7 lectures > Flashcards

1st test - 7 lectures Flashcards

1
Q

carbonic anhydrase

A

converts carbon dioxide and water to hydrogencarbonate ions and hydrogen ions
w/o enzyme: 0.1 molecules per sec
w/ : 1000000 s-1 kcat

zinc ion prosthetic group

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2
Q

ribozymes

A

RNA molecules operate as enzymes

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3
Q

kcat

A

catalytic constant
turnover no.
number of molecules of substrate that 1 enzyme molecule can convert in 1 second

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4
Q

BRENDA

A

database of enzymes

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5
Q

difference between enzymes+substrates and receptors+ligands

A

receptors don’t change the ligand but just bind to it

enzymes alter the substrate to a product

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6
Q

cofactor
prosthetic group
coenzyme

A

general term for helping enzymes

cofactor permanently bound by covalent bond

organic, non-protein, bind temporarily, chemically changed

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7
Q

apoenzyme

A

enzyme lacking essential cofactor or coenzyme

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8
Q

holoenzyme

A

complete machinery, enzyme with cofactor

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9
Q

EC 3: hydrolases

A

water cleaves a bond

e.g. glucose-6-phosphatase

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10
Q

EC 4: lyases

A

non-hydrolytic cleavage addition or removal of groups

e.g. carbonic anhydrase

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11
Q

EC 5: isomerases

A

intramolecular rearrangement

triose-phosphate isomerase

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12
Q

EC 6: ligases

A

join 2 molecules

e.g. amino-acyl tRNA synthetases

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13
Q

EC 1: oxidoreductase

A

oxidation/reductions

e.g. lactate dehydrogenase

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14
Q

EC 2: transferase

A

transfer of a group

e.g. hexokinase

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15
Q

when are non-specific enzymes advantageous?

A

for washing products

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16
Q

specific mammalian proteinases (hydrolases)

A

trypsin (hydrolyse peptide binds at C-terminal of lysine or arginine)

chymotrypsin (same but at phenylalanine, tyrosine, tryptophan)

thrombin (hydrolyse arginine-glycine bond)

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17
Q

bonds in ES complex

A

weak non-covalent interactions: electropositive, electronegative, hydrogen bonding

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18
Q

catalytic triad

A

specific residues from different parts of the structure contribute to the catalytic active site

Asp - carboxylic acid group
His - capture electron flow
Ser - OH forms transient covalent bond with substrate

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19
Q

lock and key model

induced fit model

A

active sites are fixed and immobile and exactly fit the substrate

enzymes adjust on binding

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20
Q

active sites bind……

A 
transition states (highest energy state)
ES complex
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21
Q

activation barrier

A

difference in energy between reactants and the transition state (activation energy basically)
enzymes lower activation barrier so speed up reaction, by providing an alternative reaction pathway which stabilises the transition state temporarily

enzymes could have more than 1 activation barrier and transition state

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22
Q

Michaelis complex

A

enzyme-substrate complex

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23
Q

transition complex is

A

temporarily covalent

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24
Q

enzyme’s catalytic mechanisms

A

bring substrates and catalytic groups together
ensure good orientation for reaction
exploit acid/base groups and metal ions
provide protected env.

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25
steady state studies
substrate conc much greater than enzyme conc and v can be measured over a period
26
parameters that can be derived using Michaelis-Menten equation
affinity selectivity inhibitor characteristics - pharmacology
27
rate of enzyme-catalysed reactions....do what over time
rate declines as substrate is depleted so measure rate early while v is constant and the system is in steady-state (rate linear/steady)
28
conc of substrate and v
proportional at lower [S] but v becomes constant at higher [S] because enzyme becomes saturated giving Vmax
29
E+S ES --> E+P | why is the 2nd part only a forward reaction?
the reverse reaction is negligible in initial steady state conditions where [P] is very low
30
equilibrium defined by dissociation constant K = ka kd
[E] [S] / [ES] forward rate constant reverse
31
rate of appearance of ES = disappearance = so K =
``` ES = ka[E][S] ES = kd[ES] ``` K = kd/ka
32
ES --> E+P equation
rate constant is kcat (turnover number) rate of appearance of P=ka2[ES] d[P]/dt = kcat[ES] v=d[P]/dt so v=kcat[ES]
33
Vmax =
kcat*[E.total]
34
[E.total] = so [E] = so [ES] =
[E] + [ES] [E.total] - [ES] [E.total]*[S.total] / (K+[S.total])
35
Michaelis-Menten equation
v = Vmax*[S]/(Km+[S])
36
Km
Michaelis constant | measure of affinity
37
when v is half of Vmax
Km = [S]
38
enzyme efficiency
kcat/Km | units s-1 M-1
39
how do different substrates change values in the Michaelis-Menten equation?
under identical conditions and same [E], Vmax is the same for different substrate but Km may vary because enzyme has diff affinities for diff substrates
40
interpretation of Km values
lower number is a better substrate | works at low conc of substrate
41
how to determine Vmax and Km
Lineweaver-Burk plot plot 1/v (y) against 1/S (x) ``` y-intercept= 1/Vmax x-intercept= -1/Km gradient= Km/Vmax ```
42
Eadie-Hofstee plot
``` v=Vmax - v/[S]*Km so plot v/[S] (x) against v (y) gradient = -Km y-intercept = Vmax x-intercept = Vmax/Km ```
43
Arrhenius equation
K = Ae-^(Ea/RT) logn(k) = logn (A) – Ea/R.(1/T) ``` k = Rate constant A = Pre-exponential factor Ea = Activation energy R = Gas constant T = Absolute temperature, K ``` ``` gradient = -Ea/R y-intercept = ln(A) ```
44
Arrhenius plots
derive activation energies 1/T (x) against lnk (y) ``` gradient = -Ea/R y-intercept = ln(A) ```
45
pH can affect
Km and kcat
46
ACE Aspirin Penicillin
lower blood pressure, stop promotion of blood vessel contraction inhibits enzyme that produces prostaglandin so block inflammatory response inhibits enzymes that help bacteria
47
some enzyme inhibition is...
permanent because bound by covalent bonds
48
structural homologues
similar structure
49
competitive inhibition
same Vmax at very high [S] altered Km (increased) because it's about affinity and Ki is the affinity of enzyme to inhibitor e.g. Oseltamivir inhibits neuraminidase by mimicing substrate acetyl sialic acid
50
non-competitive inhibition
Vmax never reached (decreased) | same Km
51
antitrypsin
``` inhibits elastase (breaks down elastin) by distorting active site protein-protein interactions ```
52
regulatory proteins
proteins mediate control of enzymes by interpreting other signals (calcium) e.g. calcium activates calmodulin which activates proteins and enzymes calcium binding causes helices to twist round so conformational change and exposes hydrophobic patch, finds other hydrophobicity of other proteins
53
reversible covalent modification
enzymes regulated by phosphorylation on free OH group | phosphate can be removed by hydrolysis, catalysed by phosphatase
54
Ras proteins | RAFs
ubiquitous small GTPases | serine/Thr kinases
55
BRAF is found mutated in how many malignant melanomas? RAS mutated in how many human cancers?
80% most in kinase domain 20-25%
56
ubiquitin
bind to protein so it is targeted to proteasome (degrades it)
57
activation by controlled proteolysis chymotrypsin example
some enzymes inactive signal leads to activation by cleavage of peptide bonds e.g. digestive enzymes chymotrypsinogen (inactive) synthesised in pancreas, pi-chymotrypsin (active) --> alpha-chymotrypsin with active site unmasked so fully active
58
Aspartate transcarbamoylase (ATCase)
allosteric regulation catalyses aspartic acid and carbamoyl-phosphate to carbamoyl-aspartate inhibited by end product CTP so affinity decreased shows sigmoidal kinetics of substrate binding like Hb ATP shifts curve to left and reduces co-operativity
59
allosteric regulation
``` T state (tense) add substrate- movement to R state (relaxed, more active) ``` CTP promotes T state to inhibits ATCase
60
Km in R and T state
higher Km in T | lower Km in R
61
where are enzymes for glycogen synthesis and breakdown?
bound to glycogen particles
62
enzymes of the respiratory chain
oligomeric and multi-enzyme complex | in inner mitochondrial matrix
63
ribosomes proteasome
complex multi-component enzyme machine - proteins and RNAse concentric wheels of diff proteases, active sites in tube
64
multi-functional enzymes
diff activities located sequential regions of structure channel intermediate compounds so avoid competitions between branches of pathway, improves efficiency because successive active sites are close
65
applications of enzymes in biotechnology
``` food washing env technology fine chemicals made pharmaceuticals biosensors diagnostic therapeutics ```
66
cheese production
rennet - enzymes from stomach of calves chymosin is a protease that digests casein (milk protein) so milk clots
67
meat, leather textile industry
remove hair and soften skin tenderise meat plant thiol proteinases (e.g. papain, bromelain from pineapple, actinidin from kiwi) cellulases treat denim for stone-washed look
68
starch processing corn starch
starch to glucose (bacterial amylases and amylo-glucosidases) bacterial glucose isomerase high fructose corn syrup made (HFCS) starch slurry to maltose to glucose to HFCS
69
aspartame - artificial sweetener
L-Asp-L-Phe-OMe dipeptide O-methyl ester in diet drinks peptidase thermolysin form dipeptide
70
organic solvents
low-water-content system used to reverse normal equilibrium promote enzyme denaturation thermolysin is thermo-stale so recovery is easy, aspartame crystallizes because insoluble in organic solvent
71
env technologies
``` lipases clear drains bacterial cellulases break plant biomass to fermentable sugars make biofuels degrade waste-water pollutants bioremediation ```
72
acylases
make semisynthetic penicillins
73
biosensors
direct read-out enzyme based device, monitor blood glucose and cholesterol measure turnover of enzyme enzymes immobilised in permeable gel for microelectrode biosensors
74
aptamers
recognise molecules
75
adenosine biosensor
current against time against conc of adenosine
76
therapeutics
tissue plasminogen activator (tPA) clot-buster after heart attacks. initiates breakdown of fibrin in clots
77
what does thermodynamics tell us?
which reactions are spontaneous and how much energy is required/released
78
first law of thermodynamics
total energy of system and its surroundings is constant
79
energy
capacity to carry out a change
80
enthalpy
heat of the system change in E same as change in enthalpy for biochemical reaction deltaH = deltaE + pdeltaV (pressure and volume same)
81
2nd law of thermodynamics
entropy always increasing in isolated system if disorder increases - means that entropy increases and energy shared with all molecules rather than being concentrated tells you which permissible reactions will happen spontaneously (if entropy increased)
82
Gibbs Free energy
amount of energy available to do work ΔG=ΔH-TΔS change in free energy=change in enthalpy - (change in entropy*temp) negative ΔG means reaction is spontaneous
83
negative ΔH
heat is released
84
negative ΔG means entropy...
of universe is increasing | entropy always increasing
85
negative ΔG positive ΔG
spontaneously loss of free energy exergonic (release energy) reaction unfavourable/not spontaneous endergonic (requires energy, product have higher E than reactants) free E depends only on reactants and products
86
ΔG = 0
no free energy change system at equilibrium reactant and product have same energy reacting at same rate forward and back
87
reactions close to equilibrium
glucose-6-phosphate to and from fructose-6-phosphate
88
mass action ratio
q = [C] [D] / [A] [B] | tells you how much reactants or product you have
89
Standard Free Energy
ΔG0 - change in free energy when conc of all reactants and products are 1M at 25C, 1 atm ΔG = ΔG0'+2.3RTlog10q ΔG = ΔG0'+RT lnq (J/mol or kcal/mol)
90
ΔG=0
no free energy change take place | equilibrium
91
at equilibrium.....
``` ΔG=0 q=Keq so 0=ΔG0'+2.303RTlog10Keq Keq=10^(-ΔG0'/1.36) equilibrium constant related to standard free energy in logarithimic manner ```
92
relationship between ΔG0' and Keq
small changes in energy can mean large changes in equilibrium constant
93
adenylate kinase
interconverts ATP ADP AMP | ADP side of equation favoured
94
Keq affected by coupling reactions
add 2 reactions together so add standard free energies | favour right side, shift equilibrium
95
oxidation | reduction
donates electrons | accepts electrons
96
redox potentials
describe propensity to accept electrons high redox potential will readily accept electrons low redox potential don't like to accept electrons unless lots of them (low potential)
97
redox potentials and ΔG0'
ΔG0' = -nFΔE0' (n-no. electrons, F-faraday constant) positive E gives negative G

1st year: Physiology and Metabolism (7 decks)

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