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BCH4024 > Lecture 11-15 > Flashcards

Lecture 11-15 Flashcards

(54 cards)

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1
Q

Chemical rxn rate

A

Always expressed in M/sec

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2
Q

Rate constant

A 
Has units that allow rxn rate to have units on M/sec
E + S  EX  E + P
k1 = M-1 x sec-1
k2 = sec-1
k3 = sec-1
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3
Q

Michaelis-Menten assumptions

A
  1. [S]tot&raquo_space; [E]tot such that [S]tot = ([S]free + [EX]) = [S]free
  2. Conservation of enzyme such that [E]tot = [E]free + [EX]
  3. [P] = 0 throughout measurements such that EX -> E + P is unidirectional
  4. Enzyme remains fully active throughout measurements
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4
Q

Steady state assumption

A

d[EX]/dt = 0. Constant flow through each step

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5
Q

v

A

Initial rate or velocity. v = k3[EX]

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6
Q

Vmax

A

Maximal rate or velocity. Vmax = k3[E]tot

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7
Q

Michaelis-Menten equation

A

v = (Vmax)/(1 + Km/[S])

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8
Q

Km

A

Kinetic parameter that may or may not equal Kd. Km only equals Kd when k2&raquo_space; k3. Gives substrate concentration for rate that is half of Vmax.
Km = (k2+k3)/k1

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9
Q

kcat

A

Turnover number. The number of product molecules formed by each enzyme active site per second. Frequency of catalysis. True constant that represents catalytic efficiency
Vm = kcat[E]tot

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10
Q

Kd

A

Thermodynamic parameter and measure of affinity. Lower Kd means higher affinity
Kd = k2/k1

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11
Q

Ordered ternary complex mechanism

A

Model of how enzymes use two substrates. A binds first and Q leaves last
E + A <> EA + B <> EAB <> EPQ <> EQ + P <> E + Q

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12
Q

Random ternary complex mechanism

A

Model of how enzymes use two substrates. No compulsory order for substrate addition or release. A or B could bind first and P or Q could leave first. Neither path alters EX and overall catalytic mechanism

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13
Q

Ping pong mechanism

A

Model of how enzymes use two substrates. Forms covalent rxn intermediate (E-X). Ex: chymotrypsin
E + A <> EA + P <> E-X + B <> E-XB <> E + Q

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14
Q

Stopped-flow apparatus

A

Designed to use both absorbance and fluorescence detectors to observe multiple rxn intermediates during pre-steady-state phase. Evaluates all rate constants and all “internal” equilibrium constants for a more complete picture of catalysis

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15
Q

Competitive inhibition

A

Reversible form of inhibition. Inhibitor binds in place of substrate at active site. Raising [S] can fully reverse inhibition. Poor drug model

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16
Q

Noncompetitive inhibition

A

Reversible form of inhibition. Inhibitor binds at separate site to substrate. Raising [S] cannot fully revers inhibition. Better model for effective drugs

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17
Q

Uncompetitive inhibition

A

Reversible form of inhibition. Substrate binding creates site for inhibitor binding. Rare inhibitory mode as transition from EX to E+P is fast

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18
Q

Metabolism

A

Totality of cellular processes that make and degrade chemical substances (metabolites), fueling and facilitating vital processes such as meiosis, locomotion, transport, genetics, evolution, etc

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19
Q

Anabolism

A

Pathways that synthesize biomolecules form simpler precursor metabolites

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20
Q

Catabolism

A

Pathways that degrade complex biomolecules yielding energy and/or forming simpler metabolites

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21
Q

Allosteric regulation

A

Reversible binding of regulatory molecules that alter enzyme conformation and activity (µsec-msec). Activators increase substrate binding/kcat. Inhibitors decrease substrate binding/kcat

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22
Q

Reversible covalent modification

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A

Group from donor molecule is transferred to target enzyme to change catalytic activity and can be removed to reverse effects (msec-sec)

23
Q

Induction/Repression

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A

Concentration of enzyme is controlled at the gene and/or mRNA level (1-1000 sec)

24
Q

Primary metabolites

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A

Needed for normal operation of metabolic pathways and main cellular functions. Ex: AAs, nucleotides, RNA, DNA, B vitamins

25
Secondary metabolites
Those organic compounds not needed for cell growth, development, or reproduction. Many ward off pathogens/predators. Others protect against osmotic damage. Many are useful for treating illnesses. Ex: alkaloids, fungal metabolites
26
Pyruvate
Alpha-ketoacid of Ala
27
Oxaloacetate (OAA)
Alpha-ketoacid of Asp
28
Alpha-ketoglutarate
Alpha-ketoacid of Glu
29
Nutritionally essential AAs
Phe, Val, Trp, Thr, Ile, Met, His, Leu, Lys
30
Conditionally essential AAs
Arg essential for growth (childhood + pregnancy). Tyr essential when Phe is low. Cys essential when Met is low
31
Pepsin
Cleaves Phe, Leu, Glu
32
Chymotrypsin
Cleaves aromatic AAs
33
Trypsin
Cleaves Lys, Arg
34
Carboxypeptidase
Cleaves C-terminal AA
35
Elastase
Cleaves elastin (highly elastic protein in connective tissue)
36
Zymogen
``` Inactive form (precursor) of protease Pepsinogen --> Pepsin Chymotrypsinogen --> Chymotrypsin Trypsinogen --> Trypsin Procarboxypeptidase --> Carboxypeptidase ```
37
Trypsinogen activation
Stored in secretory vesicles with trypsin inhibitor. Enterokinase (ectoprotein on intestinal mucosal wall) converts trypsinogen into trypsin
38
Chymotrypsinogen activation
Activated by trypsin (cleaves first) and by chymotrypsin (second cleavage)
39
Pepsinogen activation
Autocatalytic. Slow acid-catalyzed activation by stomach pH. As more pepsin accumulates, pepsin catalyzes activation of pepsinogen
40
Lysosomal/phagolysosomal pathway
Intracellular protein turnover pathway where lysosome uses acidic compartment to induce isoelectric expansion (partial unfolding). Low pH makes proteins more susceptible to proteolysis
41
Ubiquitin-dependent pathway
Intracellular protein turnover pathway that enzymatically joins ubiquitin to poorly folded proteins. Ubiquitinated proteins are degraded in proteasomes
42
Proteasome
Barrel-like macromolecular protease complexes
43
Positive nitrogen balance
Intake > Excretion. Needed for growth (childhood and pregnancy), healing, convalescence
44
Negative nitrogen balance
Excretion > Intake. Occurs during starvation, malnutrition, disease, injury
45
Marasmus
Malnutrition associated with extensive tissue and muscle wasting. Little/no edema. "Protein-energy malfunction" resulting from inadequate intake of protein and calories. Severe deficiency in nearly all nutrients
46
Kwashiorkor
Acute childhood protein malnutrition. Inadequate protein intake but normal caloric intake. Characterized by irritability, enlarged liver, abdominal edema caused by hypoalbuminemia
47
Transamination exceptions
Pro, Hyp = have secondary amines that cannot undergo transamination Lys = would cyclize to form toxic nonmetabolite Thr = would dimerize to form toxic nonmetabolite
48
Glutamate Dehydrogenase (GDH)
Major route for oxidative deamination. Regenerates a-ketoglutarate and provides ammonia. GDH located in mitochondrial matrix. Couples with transaminases. Uses NAD+ to drive deamination. Uses NADPH to drive amination Glu + NAD+ + H2O <> a-KG + NADH + NH3
49
Glutaminase
Catalyzes hydrolysis of glutamine. Widely distributed in mitochondria to avoid futile cycle with glutamine synthetase Gln + H2O <> Glu + NH3
50
Asparaginase
Catalyses hydrolysis of asparagine | Asn + H2O <> Asp + NH3
51
Histindinase
Catalyzes deamination of histidine | His <> Urocanate + NH3
52
Glutamine synthetase
Main way to trap NH3. Formation of Gln provides major inter-organ nitrogen shuttle to avoid direct transfer of NH3. Gln is a major source of nitrogen for many biosynthetic rxns. Uses gamma-glutamyl-P as essential intermediate Glu + ATP + NH3 <> Gln + Pi + ADP + H+
53
Carbamoyl-Phosphate Synthetase I (CPS-I)
Main ammonia-assimilating rxn in mitochondria. Highly energy dependent. First step resembles glutamine synthetase. 2 ATP + HCO3- + NH3 <> 2 ADP + HPO4(2-) + Carbamoyl Phosphate ``` Location: mitochondria Substrate: ammonia Affinity for NH3: high Affinity for Gln: none Pathway: urea cycle Activator: N-acetyl-glutamate ```
54
Carbamoyl-Phosphate Synthetase II (CPS-II)
Uses transfer tunnel to move unprotonated NH3 from glutamine-hydrolysis site to biosynthetic site. Essential -SH group generates a gamma-glutamyl thioester that occupies active site - permitting unprotonated NH3 transfer. ``` Location: cytosol Substrate: glutamine Affinity for NH3: none Affinity for Gln: high Pathway: pyrimidine nucleotide biosynthesis ```

BCH4024 (7 decks)

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