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MICRO 442 > TA BIOCHEM Review > Flashcards

TA BIOCHEM Review Flashcards

1
Q

isoelectric point (refers to the whole protein)

A

-pH at which the net charge of the amino acid is zero
-ALSO roughly 50% aa’s deprotonated and the other 50% are protonated

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2
Q

when pH below the pl the overall charge of the protein is

A

positive (think H+ acid)

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3
Q

when pH above the pl the overall charge of the protein is

A

negative (think OH-)

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4
Q

(A-/HA)= 10^(+) or value>1

A

DEPROTONATED

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5
Q

(A-/HA)= 10^(-) or value<1

A

PROTONATED

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6
Q

gel filtration chromatography or size exclusion chromatography

A

larger molecules elute first whereas smaller molecules elute later

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7
Q

ion exchange chromatography has 2 types

A

-DEAE (weak anion exchanger)
-CM (weak cation exchanger)

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8
Q

ion exchange chromatography interaction strenght with exchange matrix depends on:

A

-charge density of protein (modulated by pH)
-strength of ions that compete with protein for binding

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9
Q

2 ways to elute

A
  1. modulate pH (start with getting protein with most basic pH a positive charge and wash, repeat to get all of the through)
  2. increase salt concentrations (both +/- interactions) -> will compete for binding and displace bound proteins with smaller overall charge first ie pl closer to the pH e.g. have 3 protein pH’s of 3,5,7 C would wash away first if using a pH of 9
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10
Q

SDS ONLY reducing

A

reduces disulfide bridges so same protein appears as smaller in reducing but as whole size in non-reducing

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11
Q

delta H>0

A

when BREAKING bonds

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12
Q

delta H<0

A

when FORMING bonds

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13
Q

S>0 and H<0

A

spontaneous at ALL temps (G<0)

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14
Q

S<0 and H<0

A

spontaneous at low temps (when TdeltaS is small)

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15
Q

H>0 and S<0

A

spontaneous at high temps (when TdeltaS is large)

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16
Q

S<0 and H>0

A

non-spontaneous at all T (G>0)

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17
Q

hemoglobin and hemoglobin have similar binding sites BUT

A

different quaternanry structures

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18
Q

Fe(II) octahedrally coordinated by four nitrogen groups of poryohrin ring, O2 and His F8

A

Hb

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19
Q

Deoxy-Hb (T-state) -> RELAXED

A

-energetically favored when NO oxygen
-lower pH stabilizes with salt brideges
-BPG binds central cavity and increases favorability to stay in T-state

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20
Q

Oxy-Hb (R-state) -> TIGHT

A

-energetically favored when THERE IS oxygen

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21
Q

Cooperativity in Hb

A

-O2 + Fe(II)
-Fe(II) moves into plane of heme
-HisF8 interacting with Fe(II) pulled up like a lever and moves helix F
-surronding subunits move relative to one another and change pKa of certain amino acids involved in salt bridges needed to stabilize T-state
-protons released in these amino acid groups and T-state salt bridges break (because pH inc.)
-the cavity in the center shrinks but the C2 symmetry remains in the R-state

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22
Q

cooperativity O2

A

favors R-state

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23
Q

cooperativity H+

A

favors T-state (dec. pH) RIGHT shift

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24
Q

cooperativity CO2

A

favors T-state (dec. pH) RIGHT shift

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25
Q

cooperativity BPG

A

favors T-state (high altitudes more tightly bound) RIGHT shift

26
Q

cooperativity CO

A

favors R-state (competitive inhibitor) LEFT shift

27
Q

what type of curve does Hb have?

28
Q

what type of curve does myoglobin have?

A

hyperbolic

29
Q

Hb exhibits what type of cooperativity?

A

positive :D

30
Q

cholera toxin

A

-hetero-hexamer
-C5 cyclical point symmetry
-B-pentamer + A-subunit = AB5

31
Q

globular actin (G-actin)

A

-4-domain subunit
-helical symmetry

32
Q

GroEL.GroES

A

-CHAPERONE
-C7 symmetry in subunits
-NOT D3 symmetry in upper/lower rings because conformational changes
-involves ADP binding

33
Q

ATCase

A

-D3
-12 total chains
-6 regulatory chains (R-chains) -> binding of CTP to R subunits causes R-> T which INHIBITS catalysis
-6 catalytic chains (C-chains) -> binding of substrate to the catalytic subunits causes T->R which causes CATALYSIS

34
Q

ATCase catalyzes the first committed step in

A

pyrimidine synthesis (CTP & UTP)

35
Q

myoglobin

A

-8 alpha helices
-ONE subunit
-Fe in center

36
Q

Hb

A

-4 total subunits
-2 alpha sub units -> C2
-2 beta sub units -> C2
-Fe in center
-cooperativity

37
Q

hemocyanin

A

-D3
-Cu in center
-THE METAL IS OXIDIZED UNLIKE HB

38
Q

calmodulin

A

-Ca2+ dependent conformational change

39
Q

TIM

A

beta-BARREL surrounded by alpha helices

40
Q

chymotrypsin

A

cleaves large hydrophobic chains -> Tyr, Typ, Phe, Leu

41
Q

Trypsin

A

cleaves Lys or Arg

42
Q

elastase

A

cleaves ala, gly, val

43
Q

All (chymotrpysin, trypsin, elastase) cleave

A

peptide bond of amino acids

44
Q

ribonuclease A

A

-BETA protein with FOUR disulfide bonds and four ANTI-PARALLEL strands
-RNA binds 2 His in active sire, Lys residue to stabilize phosphate group
-endonuclease that cleaves single-stranded RNA (P-O bond)
-secreted from pancreas and cleaves in digestive tract, no specific sequence

45
Q

neuramindiase

A

-PROPELLER
-4 beta strands per propeller
-2 Glu in active site
-cleaves sialic acid from cell surface
-facilitates virus release from infected cells

46
Q

keratin

A

-a-b-c-d-e-f-g psuedo pattern
-two right-handed helices form left-handed coiled structure

47
Q

collagen triple helix

A

-2 alpha-1 and alpha-2 chains (NOT related to 2° structure)
-RIGHT handed twist
-Glo-Pro-Hyp (HYDROPHOBIC) repeats

48
Q

k1 -> ES

A

BUILDUP of ES

49
Q

k-1 <- ES -> k2

A

BREAKDOWN of ES

50
Q

Km

A

=micheaelis constant
=[S] at 1/2 Vmax
=(k-1 + k2)/k1

51
Q

the Km/Vmax in the equation 1/Vnaught=Km/Vmax x 1/[S] + 1/Vmax represents

52
Q

the 1/Vmax in the equation 1/Vnaught=Km/Vmax x 1/[S] + 1/Vmax represents

53
Q

Vnaught=

A

Vmax[S] / Km + [S]

54
Q

assumptions of MM

A
  1. only Vnaught is measured
  2. steady-state assumption
  3. [E] &laquo_space;[S]
55
Q

competitive inhibitor

A

-alpha changes in both equations (Lineweaver-burk and MM)
-ONLY Km changes
-inhibitor binds to enzyme before substrate

56
Q

uncompetitve inhibitor

A

-alpha’ changes
-changes BOTH Vmax (lower) and Km
-PARALLEL LINES
-slower rate because binds to allosteric site -> unable to catalyze substrate -> lower Vmax

57
Q

mixed/non-competitive inhibitor

A

-BOTH alpha & alpha’ changes
-slopes, x/y-intercept are ALL different
-x-intercept has both a’ and a contributing to its changes
-Km ONLY unaffected is a=a’

58
Q

Catalytic mechanisms

A
  1. acid-base
  2. metal ion
  3. catalysis via proximity and orientation
  4. covalent catalysis -> nucleophiles and electrophiles
  5. catalysis by preferential TS binding
59
Q

carbonic amhydrase (metal ion catalysis)

A

-Zn2+ polarizes a water molecules which ionizes due to the action of a fourth (not shown) His and becomes OH-
-OH- performs nucleiphillic attack on the C atom of the CO2 substrate
-HCO3- product
-H2O comes in and cycle repeats

60
Q

Serine proteases are a mixture of

A

-covalent catalysis
-concerted acid-base catalysis
-TS stabilization

61
Q

Serine proteases functions and characteristics

A

-Asp102 orients His57
-His57 = general acid/base
-Ser195 forms covalent bond with peptide to be cleaved
-covalent bond formation turns a trigonal C into a tetrahedral C of intermediate
-tetrahedral oxyanion intermediate stabilized by main NHs of Gly193 and Ser195-> OXYANION HOLE

MICRO 442 (25 decks)

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