Q4 Flashcards
what are membrane proteins?
metabolic enzymes and receptors
what do membrane proteins do
move polar molecules across the hydrophobic membrane
name and describe a passive membrane protein
gramicidin A, an antibiotic polypeptide
allows Na+ and K+ to leak out of bacteria cells, which causes the cell to die
describe portions
beta-barrel proteins
alternating hydrophobic and hydrophilic residues
homotrimers and selective
what do helices form
substrate-selective channels
what is an example of a membrane transport protein
K+ channel protein
describe aquaporins
passive transport of H2O
allows 1 water to pass at a time
define tetramers
each subunit transports billions of water/sec
define selectivity
dual-helix hourglass breaks the water hydrogen bond
describe active transporters
require energy
low to high concentration
define primary active transport
moves ions from low to high gradient
uses ATP directly
describe secondary active transport
coupled with primary
can move in and out or in or out
ATP can create a high gradient
describe NaK ATPase Membrane Protein
creates membrane potential important for neurons
ATP hydrolysis drives protein conformational shift
what is the input/output of NaK ATPase
3 Na+ out = 2 K+ in
describe NaI symporter
essential for thyroid hormone biosynthesis
coupled with NaK ATPase
what is the input/output of NaI symporter
1I and 2K+ enter the cell
define SERCA
sacro/endoplasmic reticulum Ca2= ATPase
describe SERCA
contains increased Ca2+
found in muscle cells
primary active transporters
promotes muscle relaxation
uses ATP
adrenaline activates PKA
list the four steps of SERCA
- ATP hydrolysis and phosphorylation of Asp 351 releases H+ and binds Ca2+ in the transmembrane helices
- ADP dissociates and M2 opens toward the lumenal side and releases Ca2+
- ATP binding repositions M2 to trap H+
- Asp351 dephosphorylates
describe muscle contraction
myosin filaments pull actin filaments together
what make up muslces
large fused cells (myoblasts)
what do muscle cells contain
nuclei, sarcolemma, and fiber
define myofibrils
myosin+actin, which create thick and thin filament
what are the length of sacromers
Z-disk to Z-disk
define myocin
thick filaments
fibrous tails and globular heads
define actin
thin, self-assembled filaments
associated with tropomyosin
what does actin and tropomyosin create
troponin
define z-disk
the end of the muscle
define titin
spring to relax/contract muscle
define I bond
z-disk at start of myosin
deifne A-bond
myosin stretch
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
describe Ca2+ control and contractions
- Ca binds to tropomin and uncovers myosin binding sites on actin
- Pi release induces power stroke, which pulls actin about 70Å toward the center
- ADP binding causes myosin to dissociate from actin
- ATP binding causes myosin to dissociate from actin
- ATP hydrolysis induces the recovery conformation
what are the 2 types of enzyme mechanisms
lock and key
induced fit
define active site
area inside enzymes where reaction happens
define substrate
reactant that binds to enzyme (ligand)
define rate
reactions/unit
define rate entiancement
catalyzed rate/uncatalyzed rate
define temperature
conformational selection and diffustion
define concentration
shift equilibrium
define catalyst
lowers activation energy
define enzymes
biological catalysts
what do enzymes bind with
high affinity and selectivity
what does substrate binding change
the enzyme’s conformation
what do new conformations favor
product formation
define transition state
high energy intermediate state is formed during the conversion of substrate to product
ΔG+=
activation energy
define spontaneous
reactants will have higher G than products
what aids reactions
aa side chains
cofactors (aid catalysis)
coenzymes (organic components)
prosthetic group (heme, biotin)
define hexokinase
adds phosphate to a hexose sugar
name and describe class 1 of IUBMB
oxidoreductase
oxidation or reduction/transfer of O/H atoms
name and describe class 2 of IUBMB
transferase
trasfers functional gorups
name and describe class 3 of IUBMB
hydrolase
forms 2 products via hydrolyzing substrate
name and describe class 4 of IUBMB
lyase
cleaves C-C, C-O, C-N, and similar bonds
name and describe class 5 of IUBMB
isomerase
intramolecular rearranges transfer groups in molecules
name and describe class 6 of IUBMB
ligase
forms C-C, C-O, C-N, or C-S using ATP cleavage
describe the steps of catalysis
- stabilize transition state
- provide alternative path for product formation
- orient substrates for reactions to occur
what is needed for the active site microenvironment
geometric fit
charged residues
exclusion of solvent
describe adolase
glyceraldehyde-3-phosphate+dihydroxyacetone phosphate<—-> fructose 1,6-bisphosphate
describe the steps of adolase
- intermediate is formed in enzyme activation site
- glyceraldehyde-3-phosphate binds to the activation site
- condenstation in activation site forms fructose 1,6-bisphosphate
- enzyme releases fructose 1,6-bisphosphate
which aminos are used in acid-base catalysis
his
asp
glu
ser
thr
tyr
cys
lys
arg
why is histidine a good aa
pKa=7
can be acidic or basic
can be a donor or acceptor
define nucleophile
donates e- to form a bond
define electrophile
accepts e- pair
describe covalent catalysis
involves forming a transient covalent bond between emzyme and substrate, which forms an unstable intermediate
what aa’s are used for covalent catalysis
ser
tyr
cys
lys
his
describe metal ion catalysis
positively charged metal ions stabilize negative intermediates
metal activated emzymes loosely bind to metal ions
define metalloenzymes
tightly bound metal ions
what aa’s are used for metal ion catalysis
cys
his
what makes up the catalytic triad
asp102, his57, and ser195
which residue cuts peptide bonds
ser
define chymotrypsin
serine protease that degrades proteins
define chymotrypsin
serine protease that degrades proteins
what are the 3 structural features of chymotrypsin
hydrophobic substrate specificity pocket
oxyanion hole
active site (catalytic triad)
what is the catalytic triad held together by
an H-bond network
what is the catalytic triad held together by
an H-bond network
describe asp102
makes a good base and negatively charged protonated state
describe asp102
makes a good base and negatively charged protonated state
describe ser197
covalently attaches to substrates and performs the cut
describe the mechanism of chymotrypsin
6 peptide cleavages
enzyme will fully regenerate
geometric and chemical specificity
acid-base and covalent catalyst
describe the steps of the mechanism
- polypeptide binds to activation site and R-groups binds to substrate specifity pocket
- his57 would then donate a proton to the amino group, causing the carboxyl terminal fragment to cleave
- water enters, and his57 acts as a general base and deprotonates it. resulting OH will act as a nucleoside and attack the carbonyl carbon.
- his57 donates a proton to ser195, causing acyl-enzyme intermediate to cleave.
- amino terminal fragment is released, and catalytic triad is regenerated.
- catalytic triad is generated in the enzyme activation site.
define chymotrypsin
large substrate binding pocket accommodates aromatic residues
define trypsin
binding pocket with negative residues at the bottom to accommodate positive residues
define trypsin
binding pocket with negative residues at the bottom to accommodate positive residues
define elastase
thr and val resides close off binding pocket so only small residues are accommodated
