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Medical Biochemistry > Enzymes > Flashcards

Enzymes Flashcards

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USMLE® Step 1 flashcards
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
Q

Endergonic reaction

A

non spontaneous reaction

G>0 (positive)

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26
Q

Catalytic Strategies

A
  • Proximity (ALL)
  • Transition state stabilization (ALL)
  • Covalent catalysis or nucleophilic catalysis (some)
  • general acid-base catalyst (most)
  • metal ion catalyst (many)
27
Q

Proximity Effect

A

PROXIMITY AND ORIENTATION

increases the effective concentration of substrates; corrects orientation of substrates for efficient reaction

28
Q

Protease enzyme

A

1) Active site- general acid-base catalysis
2) transition state stabilization (oxyanion hole)
3) covalent catalysis

29
Q

Chymotrypsin

A

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
Q

Enzyme Active Site is Complementary to

A

the transition state structure rather than the substrate

31
Q

Oxyanion hole

A

space in the enzyme active site ready to bind a negatively charged group
- serine stabilizes transition state

32
Q

Enzyme Regulation with Extracellular Signaling

A

V Slow

33
Q

Enzyme regulation

A
  • 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
Q

Most common post-translational modification

A

phosphorylation

35
Q

Phosphorylation of these amino acids can activate or inhibit an enzyme

A

ser, thr, tyr

36
Q

Zymogens

A

inactive form of enzyme; regulated by specific protein clevage; irreversibly turn on, degraded when finished

37
Q

Enzymes 3 main affects

A
  • how tightly substrates bind
  • how fast/what rate
  • how regulated
38
Q

kcat

A

rate product is made
- turnover number
- effected by pH and temp
rate S -> P

39
Q

Km

A

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
Q

Vmax=

A

total output; ~ complete saturation

Vmax=kcat x [E]

41
Q

How do we measure initial velocity?

A

SLOPE!

42
Q

Michaelis-Menten Equation

A

v= Vmax [S] / Km + [S]

43
Q

Lineweaver-Burk Plot intercepts

A

x intercept = -1/Km
y intercept = 1/Vmax
Slope = Km/Vmax

44
Q

What changes Km values

A

change with reaction conditions; pH or temp

45
Q

Vmax is linearly dependent on

A

enzyme concentration

  • more enzyme, higher rates
  • is affected by pH and temp
46
Q

kcat equation

A

kcat = Vmax/[E]

  • kcat is normalized to [E]
  • how fast EACH enzyme is producing output
  • PER ENZYME
47
Q

kcat Vmax equation

A

kcat x [E] = Vmax

48
Q

Catalytic Efficiency

A

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
Q

Enzyme Inhibition

A

depends on active site

** molecules that resemble substrate or transition state structures without reacting are potential drugs **

50
Q

2 types of inhibitors

A 
Irreversible inhibitors (covalent drugs): molecules bind covalently to enzyme to inhibit activity
Reversible inhibitors: molecules that bind reversibly to inhibit enzyme activity
51
Q

Competitive Inhibitors

A

bind to same active site; competes with substrate binding; generally look alike
Km increased, Vmax unchanged

52
Q

Noncompetitive Inhibitors

A

bind to a separate site from the active site; does not compete with substrate binding
Vmax decreased, Km unchanged

53
Q

As lines move towards zero on a LWB plot

A

denominator gets bigger

54
Q

Transition state analogs

A

competitive inhibitors

- stable molecules with geometric and/or electronic features of the highly unstable transition state

55
Q

Feedback regulation

A

non-competitive

56
Q

Allosteric Enzymes

A
  • 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
Q

Allosteric Enzyme kinetics

A

cooperative binding

  • S shaped kinetics curve
  • hard for first to bind, easy for following to bind
58
Q

R-state vs T-state

A
  • cooperative binding equilibrium conformations
  • R: active; binds S better and has high catalytic activity
  • T: inactive
59
Q

Allosteric Activator

A
  • stabilizes the R-state; increases S binding/activity
  • shifts kinetics chart left
  • both Km and Vmax are affected
60
Q

Allosteric Inhibitor

A
  • stabilizes the inactive T-state; decreased S binding/activity
  • shifts kinetics curve right
  • both Km and Vmax are affected
61
Q

Allosteric vs Noncompetative

A

Noncompetitive: synthetic drug
Allosteric: actual molecule in cell

62
Q

Aspartate Transcarbamylase

A

conformationally changes and cooperative binding

63
Q

Isozymes

A
  • 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
Q

Biomarkers

A

measurement of isozyme levels helps in diagnosis

Medical Biochemistry (7 decks)

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