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Medical Biochemistry > Enzymes > Flashcards

Enzymes Flashcards

(64 cards)

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1
Q

Oxioreductases

A

catalyze oxidation-reduction reactions; transfer e-

- need NAD+ cofactor

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2
Q

Transferases

A

catalyze transfer of C, N, or P- containing groups

- need THF cofactor

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3
Q

Hydrolases

A

catalyze cleavage of bonds by addition of water

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4
Q

Lyases

A

catalyze cleavage of CDC, CDS and certain CDN bonds

- no H2O

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5
Q

Isomerases

A

catalyze racemization of optical or geometric isomers

- transfer within the same molecule

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6
Q

Ligases

A

catalyze formation of bonds between C and O, S, N coupled to hydrolysis of high energy phosphates

  • makes new bonds
  • ONLY makes something bigger
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7
Q

Cofactor

A

metal ions

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8
Q

Coenzymes

A

small organic molecules, mostly derived from vitamins

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9
Q

holoenzyme

A

apoenzyme + cofactor/coenzyme = holoenzyme

  • apoenzymes without cofactors are inactive
  • most cofactors are regenerated at the end of the reaction
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10
Q

Enzymes

A
  • biological catalysts
  • highly specific
  • extremely fast
  • activity can be regulated
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11
Q

Enzymatic Reactions Multistep

A

1) enzyme binds to substrate
2) ES->EP
3) dissociation of EP to P and regeneration of E

E + S ES E + P

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12
Q

Catalyst

A
  • REGENERATED at the end of reaction
  • accelerates reaction
  • does not change spontaneity
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13
Q

Catalytic Amino Acids/Active Site

A

scaffold creating active site; amino acids close together in tertiary structure but not in primary structure
- NEED to maintain structure to maintain active site

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14
Q

Enzyme Active Site

A
  • substrates and products bind reversibly through weak noncovalent interactions; numerous weak interactions lead to tight enzyme substrate bonding
  • small volume compared to all of enzyme
  • generally nonpolar (helps increase interactions)

Non covalent Interactions:

  • electrostatic: ionic, dipole-dipole
  • Hbonds
  • Hydrophobic
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15
Q

Denature Proteins

A

via high temperature and acid; unfolds proteins and effects active sites

  • optimal temperature; change in rate is a bell curve
  • optimal pH functionally specific
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16
Q

pH’s effect on enzymes

A
  • at extremes of pH: irreversible denaturation

- at moderate pH: change of charge of enzyme functional groups can affect activity; this is reversible

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17
Q

Glucokinase/Hexokinase

A

precise active site conformation explains specific binding and reaction of ATP with GLUCOSE but NOT galactose

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18
Q

Lock and Key Inadequacies

A
  • according to lock and key the active site should be able to accommodate smaller substrates, this is not the case
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19
Q

Induced Fit Model

A

FLEXIBLE active site; conformational change stabilizes active conformation to substrate after binding
- explains REGULATION and COOPERATIVE effects

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20
Q

Enzyme rate increases

A

10^6-10^17 fold

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21
Q

Relationship of reaction rate and activation energy

A

reaction rate is inversely proportional to activation energy

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22
Q

How do enzymes increase reaction rate

A

decrease the activation barrier by stabilizing the transition state

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23
Q

How do enzymes lower the transition state energy?

A

tighter binding of the active site amino acid residues to the transition state

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24
Q

Exergonic Reaction

A

spontaneous reaction

G<0 (negative)

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25
Endergonic reaction
non spontaneous reaction | G>0 (positive)
26
Catalytic Strategies
- Proximity (ALL) - Transition state stabilization (ALL) - Covalent catalysis or nucleophilic catalysis (some) - general acid-base catalyst (most) - metal ion catalyst (many)
27
Proximity Effect
PROXIMITY AND ORIENTATION | increases the effective concentration of substrates; corrects orientation of substrates for efficient reaction
28
Protease enzyme
1) Active site- general acid-base catalysis 2) transition state stabilization (oxyanion hole) 3) covalent catalysis
29
Chymotrypsin
Active site - catalytic triad - serine, histidine, and aspartate (all serine proteases have catalytic triad) - His accepts proton from serine to become HisH+ - serine becomes negatively charged - a potent nucleophile - enzyme stabilizes negative charges in transition state b/c serine becomes oxyanion hole; activation energy decreased
30
Enzyme Active Site is Complementary to
the transition state structure rather than the substrate
31
Oxyanion hole
space in the enzyme active site ready to bind a negatively charged group - serine stabilizes transition state
32
Enzyme Regulation with Extracellular Signaling
V Slow
33
Enzyme regulation
- feedback inhibitors, enzyme inhibitors, product inhibition, feedback activation - enzyme CONCENTRATION changes-- synthesis (trascrip, translat) and degradation - compartmentation - post-translational modifications - regulatory proteins to activate or inhibit
34
Most common post-translational modification
phosphorylation
35
Phosphorylation of these amino acids can activate or inhibit an enzyme
ser, thr, tyr
36
Zymogens
inactive form of enzyme; regulated by specific protein clevage; irreversibly turn on, degraded when finished
37
Enzymes 3 main affects
- how tightly substrates bind - how fast/what rate - how regulated
38
kcat
rate product is made - turnover number - effected by pH and temp rate S -> P
39
Km
equilibrium constant - how tightly substrate is bound to enzyme - [S] at 1/2 Vmax * ** Km big = weaker affinity, bound and fell off; Km small = stronger affinity/tighter binding
40
Vmax=
total output; ~ complete saturation Vmax=kcat x [E]
41
How do we measure initial velocity?
SLOPE!
42
Michaelis-Menten Equation
v= Vmax [S] / Km + [S]
43
Lineweaver-Burk Plot intercepts
x intercept = -1/Km y intercept = 1/Vmax Slope = Km/Vmax
44
What changes Km values
change with reaction conditions; pH or temp
45
Vmax is linearly dependent on
enzyme concentration - more enzyme, higher rates - is affected by pH and temp
46
kcat equation
kcat = Vmax/[E] - kcat is normalized to [E] - how fast EACH enzyme is producing output - PER ENZYME
47
kcat Vmax equation
kcat x [E] = Vmax
48
Catalytic Efficiency
kcat/Km - ratio of enzyme's kcat and Km calues - shows 1) enzyme's substrate preference 2) enzyme's catalytic efficiency 3) high the kcat/Km, the better the substrate and better the catalytic efficiency of the enzyme
49
Enzyme Inhibition
depends on active site | *** molecules that resemble substrate or transition state structures without reacting are potential drugs ***
50
2 types of inhibitors
``` Irreversible inhibitors (covalent drugs): molecules bind covalently to enzyme to inhibit activity Reversible inhibitors: molecules that bind reversibly to inhibit enzyme activity ```
51
Competitive Inhibitors
bind to same active site; competes with substrate binding; generally look alike ***Km increased, Vmax unchanged***
52
Noncompetitive Inhibitors
bind to a separate site from the active site; does not compete with substrate binding ***Vmax decreased, Km unchanged***
53
As lines move towards zero on a LWB plot
denominator gets bigger
54
Transition state analogs
competitive inhibitors | - stable molecules with geometric and/or electronic features of the highly unstable transition state
55
Feedback regulation
non-competitive
56
Allosteric Enzymes
- have an active site and an allosteric site - oligomeric - active site binds S and allosteric binds E - ALLOSTERIC MOLECULES DO NOT RESEMBLE THE SUBSTRATE
57
Allosteric Enzyme kinetics
cooperative binding - S shaped kinetics curve - hard for first to bind, easy for following to bind
58
R-state vs T-state
- cooperative binding equilibrium conformations - R: active; binds S better and has high catalytic activity - T: inactive
59
Allosteric Activator
- stabilizes the R-state; increases S binding/activity - shifts kinetics chart left - both Km and Vmax are affected
60
Allosteric Inhibitor
- stabilizes the inactive T-state; decreased S binding/activity - shifts kinetics curve right - both Km and Vmax are affected
61
Allosteric vs Noncompetative
Noncompetitive: synthetic drug Allosteric: actual molecule in cell
62
Aspartate Transcarbamylase
conformationally changes and cooperative binding
63
Isozymes
- have different primary structures of AA sequence, but catalyze the same chemical reaction and act upon the same substrates - distinct expression in different tissues of the body - allow find tuning of metabolism to meet the needs of a given tissue or developing stage - have different kcat and Km values and different temperature and pH dependencies - thought to have evolved from gene duplication and divergence
64
Biomarkers
measurement of isozyme levels helps in diagnosis

Medical Biochemistry (7 decks)

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