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Biochemistry > Exam 1 Lectures 11-12 > Flashcards

Exam 1 Lectures 11-12 Flashcards

1
Q

In catalysis, what does the catalyst do and DO NOT do

A

DOES NOT destroy themselves

DO return to original shape at end of rxn (temporary change)

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2
Q

From TD perspective, how do we overcome the AE?

A
  1. Raise the energy of all molecules of the rxn by raising the temp
  2. Use an enzyme to lower energy requirement (transient state)
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3
Q

what is the risk of raising the temp to speed up a rxn?

A

Run the risk of destroying proteins in biological sys. Denaturing DNA/RNA

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4
Q

what is the benefit to using an enzyme to speed up a rxn?

A

Quicker we will have more molecules that get to the barrier and get to products

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5
Q

what is the induced fit model?

A

enzyme changes shape when substrate binds. Substrate is forced into the transition state

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6
Q

catalysis is achieved through: think stabilizing transition state…

A 
substrate orientation
straining 
substrate bonds 
creating favorable microenvironment
and 
covalent and/or noncovalent interactions between enzyme and substrate
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7
Q

what is covalent catalysis?

A

Covalent (temporary bond) transfer e-s to stabilize transition state (not completely stable but more stable)

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8
Q

what is acid-base catalysis?

A

proton transfer

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9
Q

what is approximation?

A

orientated just the right way and close enough

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10
Q

approximation aka and why?

A

entropy reduction bc stuck in 1 conformation and stuck together = decreased entropy and lowering free energy

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11
Q

what is electrostatic catalysis?

A

stabilizes unfavorable chargers on the transition state by polarizable side chains in the enzyme and/or metal ions

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12
Q

magnitude of catalysis describes:

A

we can go from a half life of a rxn (half our reactants) that may take a billion years to complete to being done in a milliseconds bc of an enzyme

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13
Q

why do we need proteases?

A

recycling, regulation, and defense

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14
Q

chymotrypsin active site is an example of a _

A

catalytic triad

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15
Q

what makes up chymotrypsin’s active site?

A

serine: nucleophile
histidine: a base (H+ acceptor)
aspartic acid: an acid (H+ donor)

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16
Q

cysteine protease classic example?

A

papain a meat tenderizer

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17
Q

cysteine protease human example?

A

calpains and caspases; cell death pathway proteins

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18
Q

aspartyl protease classic example?

A

HIV protease cleave precursor proteins

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19
Q

aspartyl protease human examples?

A

renin

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20
Q

metalloproteases classic example?

A

thermolysin

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21
Q

metalloproteases human examples?

A

MMPs and ADH

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22
Q

NAD+ resides in the active site of _

A

ADH and is doin the rxn

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23
Q

_ stabilizes the tetrahedral intermediate (transition state)

A

oxyanion hole

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24
Q

T/F: interactions with amines in side chains not backbone!

A

FALSE. Interactions with amines in BACKBONE not side chains!

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25
Q

what type of side chains can stabilize electrostatic interactions with the aminies in the backbone?

A

small side chains ie S and G

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26
Q

where does chymotrypsin cut?

A

S1 (specificity) pocket

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27
Q

how does chymotrypsin cut?

A

cuts the peptide bond immediately after what ever fits in the specificity pocket

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28
Q

what fits in S1 pocket?

A

small and hydrophobic aas ie van der waals

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29
Q

carbonic anhydrases active site contains? And this coordinates to?

A

a Zn++ ion coordinates to 3 Histidines and a water

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30
Q

how does carbonic anhydrases regulate pH?

A

Acid-base balance is measure of CO2 (an acid) and HCO3 (a base) in blood. dissolved CO2 goes to carbonic acid and lowers the pH (if too much HCO3)

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31
Q

what makes carbonic anhydrases an example of convergent evolution?

A

Conversion of CO2 is very important and thus found in all species

32
Q

how does H20 facilitate the transition state?

A

H20 interacts with Zn++ and lowers pKa of H20 down to 7. pKa is just a bit lower than physiological pH so DEPROTONATED H20. Also approximation via making a charge and putting that charge exactly where it needs to be

33
Q

how does the entry channel for carbonic anhydrase contribute to specificity?

A

It determines size of substrate. Only really small and weakly polar can get in. ie CO2

34
Q

We need to regenerate our enzyme: carbonic anhydrase. How is this done?

A

Regenerate H20. H20 is too polar to fit through channel so we are just shuffling some H+ around ie “gaining H20”

H2O dissociates the OH binds to Zn++ and H+ is released.

35
Q

Always: Low S means High _

A

G

36
Q

substrate-level control acts on a _

A

single rxn

37
Q

feedback control targets a _

A

different step in the pathway

38
Q

T/F: all principles can be combined (use multiple in a pathway)

A

true

39
Q

activators _ more products

A

promote

40
Q

inhibitors _ more products

A

prevent

41
Q

activators are _

A

substrate-level single step

42
Q

how can we regulate the amt of availabilit (on/off switch) or enzymes?

A
  1. temporal control of gene expression
  2. protein degradation
  3. enzyme compartmentalization
  4. substrate availability
43
Q

how can we regulate activity of the enzyme aka volume control?

A
  1. isozymes and isoforms
  2. covalent modifications
  3. allostery
44
Q

temporal control of gene expression means control via:

A

chromatin, regulation of transcription, splicing, is there any repression?

45
Q

protein degradation can be accomplished via:

A

lysosomes with acid hydrolases (nucleases, proteases, etc) and ubiquitination and proteosome

46
Q

enzyme compartmentalization can be accomplished via:

A

protein will only act accordingly in specific locations.

47
Q

substrate availability via:

A
  • Make a rxn irreversible by keeping enzyme in a particular location (1 direction) and away from enzyme that does reversible rxns.
  • Where is the substrate coming from? In a cell or not
48
Q

izoymes and isoforms catalyze the SAME rxn but with

A

DIFFERENT efficiencies

49
Q

compartmentalized izosymes results in

A

tissue specificity

50
Q

temporal expression of isozymes is common in

A

development

51
Q

an isozyme example is _

A

LDH as truly reversible rxn. Also a tetramer (picks up whatever is available)

52
Q

covalent modifications can be reversible bc:

A

it creates nonproteinogenic aas by adding “functional groups” to activate/deactivate the enzyme

53
Q

what are the common additions for covalent modifications?

A

lipids, proteins, nucleic acids, small molecules, and carbohydrates

54
Q

_ is the greatest source of diversity to the proteome

A

carbohydrates

55
Q

the type of lipid covalent modifications?

A

myristolylation and farnesylation

56
Q

the type of nucleic acid covalent modification?

A

ADP ribosylation

57
Q

the type of protein covalent modification?

A

ubiquitination

58
Q

the type of carbohyrdate covalent modification?

A

O-linked (oxygen) or N-linked (nitrogen)

59
Q

the types of small molecules covalent modifications?

A
  1. gamma-carboxylation (refers to where it is being added; happens on carbon)
  2. sulfation (happens on oxygen)
  3. acteylation and methylation (on arginine and lysine ie all on nitrogens)
  4. phosphorylation (happens on hydroxyls)
60
Q

why is phosphorylation activating?

A

TD coupling to exergonic favorable rxn; helps drive the rxn foward

61
Q

shape and charge complimentary: each phosphate adds _ charge and _ H-bonds

A

(-2) charge and (+3) H-bonds

62
Q

kinases add

A

phosphates

63
Q

phosphatases remove

A

phosphates

64
Q

a type of irreversible covalent modification is:

A

proteolytic activation

65
Q

proteases need to be _ to be active

A

cleaved

66
Q

cutting a polypeptide is bad when it ends up

A

degrading it

67
Q

cutting a polypeptide is good when it ends up

A

changing the activity of it

68
Q

zymogens need something _

A

taken away

69
Q

apoenzymes need something _

A

added

70
Q

examples of zymogens:

A

porteases, collagen, blood clotting factors, insulin/hormones

71
Q

why is cleaving important in proteolytic activation?

A

Primary structure is not really active. If we cleave strategically, able to have flexibility with folding aas (need interactions with further away aas) and promote positive interactions and change shape of the active site

72
Q

heteroallostery:

A

causing difference in enzyme activity need external effector that binds at the allosteric site

73
Q

homoallostery:

A

cooperativity ie internal control

74
Q

ATCase is a good example of

A

heteroallostery as needs an effector

75
Q

ATCase has 2 options for binding. #1: binding of CTP prefers the _ state

A

T (pyrimidines)/inactive state; we have enough and do not deed to make any more

76
Q

ATCase has 2 options for binding. #2: binding of ATP prefers the _ state

A

R (purines)/active state

77
Q

Protease is for _ and kinase is where _

A

Proteas is for ACTIVE SITE and kinase is WHERE WE ARE PUTTING THAT PHOSPHATE

Biochemistry (32 decks)

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