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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
define myocin
thick filaments fibrous tails and globular heads
26
define actin
thin, self-assembled filaments associated with tropomyosin
27
what does actin and tropomyosin create
troponin
28
define z-disk
the end of the muscle
29
define titin
spring to relax/contract muscle
30
define I bond
z-disk at start of myosin
31
deifne A-bond
myosin stretch
32
describe the three steps of muscle contraction
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
33
describe Ca2+ control and contractions
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
34
what are the 2 types of enzyme mechanisms
lock and key induced fit
35
define active site
area inside enzymes where reaction happens
36
define substrate
reactant that binds to enzyme (ligand)
37
define rate
reactions/unit
38
define rate entiancement
catalyzed rate/uncatalyzed rate
39
define temperature
conformational selection and diffustion
40
define concentration
shift equilibrium
41
define catalyst
lowers activation energy
42
define enzymes
biological catalysts
43
what do enzymes bind with
high affinity and selectivity
44
what does substrate binding change
the enzyme's conformation
45
what do new conformations favor
product formation
46
define transition state
high energy intermediate state is formed during the conversion of substrate to product
47
ΔG+=
activation energy
48
define spontaneous
reactants will have higher G than products
49
what aids reactions
aa side chains cofactors (aid catalysis) coenzymes (organic components) prosthetic group (heme, biotin)
50
define hexokinase
adds phosphate to a hexose sugar
51
name and describe class 1 of IUBMB
oxidoreductase oxidation or reduction/transfer of O/H atoms
52
name and describe class 2 of IUBMB
transferase trasfers functional gorups
53
name and describe class 3 of IUBMB
hydrolase forms 2 products via hydrolyzing substrate
54
name and describe class 4 of IUBMB
lyase cleaves C-C, C-O, C-N, and similar bonds
55
name and describe class 5 of IUBMB
isomerase intramolecular rearranges transfer groups in molecules
56
name and describe class 6 of IUBMB
ligase forms C-C, C-O, C-N, or C-S using ATP cleavage
57
describe the steps of catalysis
1. stabilize transition state 2. provide alternative path for product formation 3. orient substrates for reactions to occur
58
what is needed for the active site microenvironment
geometric fit charged residues exclusion of solvent
59
describe adolase
glyceraldehyde-3-phosphate+dihydroxyacetone phosphate<----> fructose 1,6-bisphosphate
60
describe the steps of adolase
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
which aminos are used in acid-base catalysis
his asp glu ser thr tyr cys lys arg
62
why is histidine a good aa
pKa=7 can be acidic or basic can be a donor or acceptor
63
define nucleophile
donates e- to form a bond
64
define electrophile
accepts e- pair
65
describe covalent catalysis
involves forming a transient covalent bond between emzyme and substrate, which forms an unstable intermediate
66
what aa's are used for covalent catalysis
ser tyr cys lys his
67
describe metal ion catalysis
positively charged metal ions stabilize negative intermediates metal activated emzymes loosely bind to metal ions
68
define metalloenzymes
tightly bound metal ions
69
what aa's are used for metal ion catalysis
cys his
70
what makes up the catalytic triad
asp102, his57, and ser195
71
which residue cuts peptide bonds
ser
72
define chymotrypsin
serine protease that degrades proteins
73
define chymotrypsin
serine protease that degrades proteins
74
what are the 3 structural features of chymotrypsin
hydrophobic substrate specificity pocket oxyanion hole active site (catalytic triad)
75
what is the catalytic triad held together by
an H-bond network
76
what is the catalytic triad held together by
an H-bond network
77
describe asp102
makes a good base and negatively charged protonated state
78
describe asp102
makes a good base and negatively charged protonated state
79
describe ser197
covalently attaches to substrates and performs the cut
80
describe the mechanism of chymotrypsin
6 peptide cleavages enzyme will fully regenerate geometric and chemical specificity acid-base and covalent catalyst
81
describe the steps of the mechanism
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
define chymotrypsin
large substrate binding pocket accommodates aromatic residues
83
define trypsin
binding pocket with negative residues at the bottom to accommodate positive residues
84
define trypsin
binding pocket with negative residues at the bottom to accommodate positive residues
85
define elastase
thr and val resides close off binding pocket so only small residues are accommodated

biochem (11 decks)

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