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bch4024 > Lecture 11-15 > Flashcards

Lecture 11-15 Flashcards

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

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

A

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

24
Q

Primary metabolites

A

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

25
Q

Secondary metabolites

A

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
Q

Pyruvate

A

Alpha-ketoacid of Ala

27
Q

Oxaloacetate (OAA)

A

Alpha-ketoacid of Asp

28
Q

Alpha-ketoglutarate

A

Alpha-ketoacid of Glu

29
Q

Nutritionally essential AAs

A

Phe, Val, Trp, Thr, Ile, Met, His, Leu, Lys

30
Q

Conditionally essential AAs

A

Arg essential for growth (childhood + pregnancy). Tyr essential when Phe is low. Cys essential when Met is low

31
Q

Pepsin

A

Cleaves Phe, Leu, Glu

32
Q

Chymotrypsin

A

Cleaves aromatic AAs

33
Q

Trypsin

A

Cleaves Lys, Arg

34
Q

Carboxypeptidase

A

Cleaves C-terminal AA

35
Q

Elastase

A

Cleaves elastin (highly elastic protein in connective tissue)

36
Q

Zymogen

A 
Inactive form (precursor) of protease
Pepsinogen --> Pepsin
Chymotrypsinogen --> Chymotrypsin
Trypsinogen --> Trypsin
Procarboxypeptidase --> Carboxypeptidase
37
Q

Trypsinogen activation

A

Stored in secretory vesicles with trypsin inhibitor. Enterokinase (ectoprotein on intestinal mucosal wall) converts trypsinogen into trypsin

38
Q

Chymotrypsinogen activation

A

Activated by trypsin (cleaves first) and by chymotrypsin (second cleavage)

39
Q

Pepsinogen activation

A

Autocatalytic. Slow acid-catalyzed activation by stomach pH. As more pepsin accumulates, pepsin catalyzes activation of pepsinogen

40
Q

Lysosomal/phagolysosomal pathway

A

Intracellular protein turnover pathway where lysosome uses acidic compartment to induce isoelectric expansion (partial unfolding). Low pH makes proteins more susceptible to proteolysis

41
Q

Ubiquitin-dependent pathway

A

Intracellular protein turnover pathway that enzymatically joins ubiquitin to poorly folded proteins. Ubiquitinated proteins are degraded in proteasomes

42
Q

Proteasome

A

Barrel-like macromolecular protease complexes

43
Q

Positive nitrogen balance

A

Intake > Excretion. Needed for growth (childhood and pregnancy), healing, convalescence

44
Q

Negative nitrogen balance

A

Excretion > Intake. Occurs during starvation, malnutrition, disease, injury

45
Q

Marasmus

A

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
Q

Kwashiorkor

A

Acute childhood protein malnutrition. Inadequate protein intake but normal caloric intake. Characterized by irritability, enlarged liver, abdominal edema caused by hypoalbuminemia

47
Q

Transamination exceptions

A

Pro, Hyp = have secondary amines that cannot undergo transamination
Lys = would cyclize to form toxic nonmetabolite
Thr = would dimerize to form toxic nonmetabolite

48
Q

Glutamate Dehydrogenase (GDH)

A

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
Q

Glutaminase

A

Catalyzes hydrolysis of glutamine. Widely distributed in mitochondria to avoid futile cycle with glutamine synthetase
Gln + H2O <> Glu + NH3

50
Q

Asparaginase

A

Catalyses hydrolysis of asparagine

Asn + H2O <> Asp + NH3

51
Q

Histindinase

A

Catalyzes deamination of histidine

His <> Urocanate + NH3

52
Q

Glutamine synthetase

A

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
Q

Carbamoyl-Phosphate Synthetase I (CPS-I)

A

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
Q

Carbamoyl-Phosphate Synthetase II (CPS-II)

A

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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