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biochem > Q4 > Flashcards

Q4 Flashcards

1
Q

what are membrane proteins?

A

metabolic enzymes and receptors

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2
Q

what do membrane proteins do

A

move polar molecules across the hydrophobic membrane

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3
Q

name and describe a passive membrane protein

A

gramicidin A, an antibiotic polypeptide
allows Na+ and K+ to leak out of bacteria cells, which causes the cell to die

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4
Q

describe portions

A

beta-barrel proteins
alternating hydrophobic and hydrophilic residues
homotrimers and selective

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5
Q

what do helices form

A

substrate-selective channels

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6
Q

what is an example of a membrane transport protein

A

K+ channel protein

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7
Q

describe aquaporins

A

passive transport of H2O
allows 1 water to pass at a time

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8
Q

define tetramers

A

each subunit transports billions of water/sec

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9
Q

define selectivity

A

dual-helix hourglass breaks the water hydrogen bond

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10
Q

describe active transporters

A

require energy
low to high concentration

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11
Q

define primary active transport

A

moves ions from low to high gradient
uses ATP directly

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12
Q

describe secondary active transport

A

coupled with primary
can move in and out or in or out
ATP can create a high gradient

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13
Q

describe NaK ATPase Membrane Protein

A

creates membrane potential important for neurons
ATP hydrolysis drives protein conformational shift

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14
Q

what is the input/output of NaK ATPase

A

3 Na+ out = 2 K+ in

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15
Q

describe NaI symporter

A

essential for thyroid hormone biosynthesis
coupled with NaK ATPase

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16
Q

what is the input/output of NaI symporter

A

1I and 2K+ enter the cell

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17
Q

define SERCA

A

sacro/endoplasmic reticulum Ca2= ATPase

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18
Q

describe SERCA

A

contains increased Ca2+
found in muscle cells
primary active transporters
promotes muscle relaxation
uses ATP
adrenaline activates PKA

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19
Q

list the four steps of SERCA

A
  1. ATP hydrolysis and phosphorylation of Asp 351 releases H+ and binds Ca2+ in the transmembrane helices
  2. ADP dissociates and M2 opens toward the lumenal side and releases Ca2+
  3. ATP binding repositions M2 to trap H+
  4. Asp351 dephosphorylates
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20
Q

describe muscle contraction

A

myosin filaments pull actin filaments together

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21
Q

what make up muslces

A

large fused cells (myoblasts)

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22
Q

what do muscle cells contain

A

nuclei, sarcolemma, and fiber

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23
Q

define myofibrils

A

myosin+actin, which create thick and thin filament

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24
Q

what are the length of sacromers

A

Z-disk to Z-disk

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25
Q

define myocin

A

thick filaments
fibrous tails and globular heads

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26
Q

define actin

A

thin, self-assembled filaments
associated with tropomyosin

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27
Q

what does actin and tropomyosin create

A

troponin

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28
Q

define z-disk

A

the end of the muscle

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29
Q

define titin

A

spring to relax/contract muscle

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30
Q

define I bond

A

z-disk at start of myosin

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31
Q

deifne A-bond

A

myosin stretch

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32
Q

describe the three steps of muscle contraction

A

in relaxed muscles, myosin binding sites on actin are blocked by tropomyosin
2. Ca2+ binds to TnC and induces a conformational change in troponin and tropomyosin which uncover myosin
3. myosin head binds to actin and initiates muscle contractions

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33
Q

describe Ca2+ control and contractions

A
  1. Ca binds to tropomin and uncovers myosin binding sites on actin
  2. Pi release induces power stroke, which pulls actin about 70Å toward the center
  3. ADP binding causes myosin to dissociate from actin
  4. ATP binding causes myosin to dissociate from actin
  5. ATP hydrolysis induces the recovery conformation
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34
Q

what are the 2 types of enzyme mechanisms

A

lock and key
induced fit

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35
Q

define active site

A

area inside enzymes where reaction happens

36
Q

define substrate

A

reactant that binds to enzyme (ligand)

37
Q

define rate

A

reactions/unit

38
Q

define rate entiancement

A

catalyzed rate/uncatalyzed rate

39
Q

define temperature

A

conformational selection and diffustion

40
Q

define concentration

A

shift equilibrium

41
Q

define catalyst

A

lowers activation energy

42
Q

define enzymes

A

biological catalysts

43
Q

what do enzymes bind with

A

high affinity and selectivity

44
Q

what does substrate binding change

A

the enzyme’s conformation

45
Q

what do new conformations favor

A

product formation

46
Q

define transition state

A

high energy intermediate state is formed during the conversion of substrate to product

47
Q

ΔG+=

A

activation energy

48
Q

define spontaneous

A

reactants will have higher G than products

49
Q

what aids reactions

A

aa side chains
cofactors (aid catalysis)
coenzymes (organic components)
prosthetic group (heme, biotin)

50
Q

define hexokinase

A

adds phosphate to a hexose sugar

51
Q

name and describe class 1 of IUBMB

A

oxidoreductase
oxidation or reduction/transfer of O/H atoms

52
Q

name and describe class 2 of IUBMB

A

transferase
trasfers functional gorups

53
Q

name and describe class 3 of IUBMB

A

hydrolase
forms 2 products via hydrolyzing substrate

54
Q

name and describe class 4 of IUBMB

A

lyase
cleaves C-C, C-O, C-N, and similar bonds

55
Q

name and describe class 5 of IUBMB

A

isomerase
intramolecular rearranges transfer groups in molecules

56
Q

name and describe class 6 of IUBMB

A

ligase
forms C-C, C-O, C-N, or C-S using ATP cleavage

57
Q

describe the steps of catalysis

A
  1. stabilize transition state
  2. provide alternative path for product formation
  3. orient substrates for reactions to occur
58
Q

what is needed for the active site microenvironment

A

geometric fit
charged residues
exclusion of solvent

59
Q

describe adolase

A

glyceraldehyde-3-phosphate+dihydroxyacetone phosphate<—-> fructose 1,6-bisphosphate

60
Q

describe the steps of adolase

A
  1. intermediate is formed in enzyme activation site
  2. glyceraldehyde-3-phosphate binds to the activation site
  3. condenstation in activation site forms fructose 1,6-bisphosphate
  4. enzyme releases fructose 1,6-bisphosphate
61
Q

which aminos are used in acid-base catalysis

A

his
asp
glu
ser
thr
tyr
cys
lys
arg

62
Q

why is histidine a good aa

A

pKa=7
can be acidic or basic
can be a donor or acceptor

63
Q

define nucleophile

A

donates e- to form a bond

64
Q

define electrophile

A

accepts e- pair

65
Q

describe covalent catalysis

A

involves forming a transient covalent bond between emzyme and substrate, which forms an unstable intermediate

66
Q

what aa’s are used for covalent catalysis

A

ser
tyr
cys
lys
his

67
Q

describe metal ion catalysis

A

positively charged metal ions stabilize negative intermediates
metal activated emzymes loosely bind to metal ions

68
Q

define metalloenzymes

A

tightly bound metal ions

69
Q

what aa’s are used for metal ion catalysis

A

cys
his

70
Q

what makes up the catalytic triad

A

asp102, his57, and ser195

71
Q

which residue cuts peptide bonds

A

ser

72
Q

define chymotrypsin

A

serine protease that degrades proteins

73
Q

define chymotrypsin

A

serine protease that degrades proteins

74
Q

what are the 3 structural features of chymotrypsin

A

hydrophobic substrate specificity pocket
oxyanion hole
active site (catalytic triad)

75
Q

what is the catalytic triad held together by

A

an H-bond network

76
Q

what is the catalytic triad held together by

A

an H-bond network

77
Q

describe asp102

A

makes a good base and negatively charged protonated state

78
Q

describe asp102

A

makes a good base and negatively charged protonated state

79
Q

describe ser197

A

covalently attaches to substrates and performs the cut

80
Q

describe the mechanism of chymotrypsin

A

6 peptide cleavages
enzyme will fully regenerate
geometric and chemical specificity
acid-base and covalent catalyst

81
Q

describe the steps of the mechanism

A
  1. polypeptide binds to activation site and R-groups binds to substrate specifity pocket
  2. his57 would then donate a proton to the amino group, causing the carboxyl terminal fragment to cleave
  3. water enters, and his57 acts as a general base and deprotonates it. resulting OH will act as a nucleoside and attack the carbonyl carbon.
  4. his57 donates a proton to ser195, causing acyl-enzyme intermediate to cleave.
  5. amino terminal fragment is released, and catalytic triad is regenerated.
  6. catalytic triad is generated in the enzyme activation site.
82
Q

define chymotrypsin

A

large substrate binding pocket accommodates aromatic residues

83
Q

define trypsin

A

binding pocket with negative residues at the bottom to accommodate positive residues

84
Q

define trypsin

A

binding pocket with negative residues at the bottom to accommodate positive residues

85
Q

define elastase

A

thr and val resides close off binding pocket so only small residues are accommodated

biochem (11 decks)

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