Ford Review Flashcards
What are the four types of noncovalent interactions?
charge-charge
dipole interactions
van der waals
hydrogen
Example of charge-charge interaction
salt bridges
Example of dipole interaction
selectivity filter of K+ channgel
Example of van Der Waals interactions
nucleotide stacking
Example of hydrogen interactions
nuclei acid and base pairing/protein secondary structure
If pH< pKa what does that mean?
protonated
If pH> pKa what does that mean
deprotonated
If pH=pKa what does that mean?
just as likely to be protonated as deprotonated
what is the equation for pKa?
pKa= -logKa = [H+] [A-] / [HA]
What does Ka mean?
dissociation constant, predicts how likely an acid will donate a proton
What is the Henderson-Hasselbalch equation?
pH= pKa + log [A-] / [HA]
What happens when something is reduced?
gains electrons (H)
What happens when something is oxidized?
loses electrons
What amino acid preforms redox?
cystein (disulfide linkages are reductions)
What are the 3 important electron carriers in cellular metabolism and their reduced and oxidized forms?
NAD+/NADH
FAD/FADH2
FMN/FMNH2
What is equilibrium?
forward rate = reverse rate, no net formation or destruction
How does Le Chatlier fit into cellular metabolism?
it’s how to drive an unfavorable reaction forward
- make pathway/use up products
- couple it to a favorable reaction like ATP hydrolysis
What is the gibs free energy equation?
deltaG= deltaH- TdeltaS
how does thermodynamics relate to protein folding?
change of entropy–protein folds, loses entropy
aqueous environment has more disorder
negative delta H
energy released
postive delta H
energy added
zero delta H
closed system
negative delta S
decrease disorder
positive delta S
increase disorder
zero delta S
no net change in disorder
negative delta G
free energy released
exergonic, favorable
spontaneous reaction
positive delta G
free energy required
endergonic, unfavorable
driven reaction
zero delta G
equilibrium
Give example of cooperative binding
hemoglobin binds oxygen cooperatively
Positive cooperativity definition
binding site affinity for ligand increases with every subsequent binding
negative cooperativity definition
binding site affinity for ligand decreases with every subsequent binding
no cooperativity definition
binding sites are independent, situation can be Michaelis menten enzyme
Km definition
Michaelis constat, [S] where reaction rate is half maximal OR half of the active sites are full
Km= [E] [S] / [ES]
Vmax definiton
maximum rate possible for a give concentration of enzyme
Vmax= Kcat [E]T
Kcat definition
number of substrate molecules concerted per active site per time (first order rate constant)
kcat= K2
Kcat/Km definition
measure of enzyme performance by predicting the fate of E*S, how good an enzyme is
Kcat/Km= Kcat/ k-1 +Kcat
VIEW DIFFERENT TYPES OF INHIBITORS
pictures on slides
similarities between substate level control and feedback control
alters ability of reaction to proceed
differences between substate level control and feedback control
substrate: acts on single reaction
feedback: acts on different reaction pathway
example of substrate level control
G6P and hexokinase
Acetyl-CoA inhibits PDH
example of feedback control
nucleotide de novo synthesis
aa biosynthesis
similarities between activation and inhibition
alters ability of reaction to proceed, can be substrate or feedback
differences between activation and inhibition
activation: adds new or increases existing function
inhibition: decreases or stops existing function
example of activation
dephosphorylation of pyruvate kinase
example of inhibition
phosphorylation of pyruvate kinase
description of reversible covalent modification
+/- small molecule
description of irreversible covalent modification
proteolytic activation
similarities between reversible covalent modification and irreversible covalent modification
reversible: may be activating
irreversible: activating mechanism only
differences between reversible covalent modification and irreversible covalent modification
reversible: may be inhibiting, reversible
irreversible: never inhibiting, irreversible
examples of reversible covalent modification
histone modification
adenylation/uridylation
and glutamine synthetase
phosphorylation
examples of irreversible covalent modification
protease cascade/digestive enzyme
blood clotting factors
insulin
allosteric effector description
binds at unique locations and alters the proteins functionality
competitive effector description
competes with intended substate to bind the active site
allosteric effector and competitive effector similarities
allosteric: may inhibit function
competitive: always inhibits function
allosteric effector and competitive effector differences
allosteric: does not bind active site, may be activating
competitive: binds at active site, can never be activating
allosteric effector examples
ATCase
ribonucleotide reductase
phosphofructokinase
competitive effector examples
methotrexate vs dihydrofolate for dihydrofolate reductase
What does covalent catalysis do?
share electrons
What does acid base catalysis do?
share protons
What does approximation do in catalysis?
orientation and proximity
What does electrostatic catalysis do?
non covalent interactions
oxidoreductases description and example
description: redox, move elections
example: dehydrogenase (oxidizers)
reductases (reducers)
transferases description and example
move a functional group
kinases add phosphate
phosphotases remove phosphate
hydrolases description and example
break a bond by adding water
citrate synthase, lactose
lyases description and example
break a bond without water
aldolase in glycolysis
isomerases description and example
rearrange order of atoms
TPI
ligases description and example
make a covalent bond
aldolase in gluconeogenesis
Describe active transport
requires energy
moves something against/creates a concentration gradient
Describe the P-type ATPase
phosphorylates itself
transports ions
4 domains: transmembrane, actuator, nucleotide, binding, phosphorylation
example: Na/K pump
Describe the ABC transporter
no phosphorylation of self
transport small molecules
dimeric, contains 2 copies of transmembrane domain and aTP binding cassette (ABC)
example: multidrug resistance protein
describe the secondary transport
uses gradient established by primary active transport
moves ion or molecule against its gradient without using energy
example: Na-glucose cotransport
describe passive transport
no energy needed
describe the ion channel
selectivity filter
gate: voltage gated, ligand gated
describe the aquaporin
selectivity filter
no gate
describe the gap junction
no selectivity filter
no gate
review glycolysis, TCA and ox-phos
look at notes
location of glycolysis
cytoplasm
rate limiting enzyme of glycolysis
phosphofructokinase
how does hexokinase regulate in glycolysis
G6P inhibits
how is phosphofructokinase regulated in glycolysis
citrate inhibits
low ATP is activating
how is pyruvate kinase regulated in glycolysis
high ATP is inhibitory
F16BP activates
location of TCA cycle
mitochondrial matrix
rate limiting enzyme of TCA cycle
isocitrate dehydrogenase
how is the pyruvate dehydrogenase complex regulated in the TCA cycle
ATP, acetyl CoA, NADH are inhibitory (kinase/+PO4)
ADP and pyruvate are activating (phosphatase/-PO4)
how is isocitrate dehydrogenase regulated in the TCA cycle
ATP and NADH inhibit
ADP activates
how is alpha-ketoglutarate dehydrogenase complex regulated in TCA cycle
ATP, succinyl CoA and NADH inhibit
location of ox phos
mitochondrial inner membrane and inter membrane space
glycogenolysis location
cytoplasm
glycogenolysis rate limiting enzyme
glycogen phosphorylase
glycogenolysis regulated enzyme
glyogen phosphorylase
- dephosphorylation inhibits
- phosphorylation activates
amino acid catabolism location
cytoplasm and mitochondrial matrix
urea cycle only in liver
beta oxidation location
cytoplasm (activation) mitochondrial matrix (beta oxidation)
rate limiting enzyme of beta oxidation
perilipins
how is perilipins regulated in beta oxidation
phosphorylation promotes TAG release by inhibiting perilipin
location of ketone bodies
only produced in liver, but broken down in non liver cells though
location of gluconeogenesis
cytoplasm (ER in liver and kidney only)
rate limiting enzyme of gluconeogenesis
fructose- 1,6- bisphophate
How is pyruvate carboxylase regulated in gluconeogenesis
ADP inhibits
acetyl CoA is activating
how is PEP carboxykinase regulated in gluconeogenesis
ADP inhibits
how is fructose 1,6 bisphoate regulated in gluconeogenesis
low ATP is inhibitory
citrate activates
location of PPP
cytoplasm
rate limiting enzyme of PPP
glucose 6 phosphate dehydrogenase
how is G6P dehydrogenase regulated in the PPP
monomers inactive, dimers activate
dephosphorylated inactive, phosphorylation activates
insulin activates
location of nucleotide de novo synthesis
cytoplasm (except dihydroorotate dehydrogenase in mitochondria)
what are the regulated in enzymes in nucleotide de novo synthesis
general theme: feedback regulation
ribonucleotide reductase: activity site and specificity site
amino acid biosynthesis location
cytoplasm and mitochondrial matrix
amino acid biosynthesis regulated enzymes
general theme: feedback regulation
glutamine synthetase:
- adenylylation inhibits/deadenylylation actives
- PII is inactivating/ PII-UMP is activating
- feed back inhibition is glutamine
- feed forward activation is alpha ketoglutarate, ATP
fatty acid synthesis location
cytoplasm and mitochondrial matrix
rate limiting enzyme of fatty acid synthesis
acetyl coA carboxylase
how is ATP citrate lyase regulated in fatty acid synthesis
activated by phosphorylation and glucose/insulin
inhibited by PUFAs and leptin
how is acetyl coA carboxylase regulated in fatty acid synthesis
active by citrate, -PO4/ insulin, high carb diet
inhibited by palmitate, +PO4/epinephrine/glucagon/AMP
how is fatty acid synthase regulated in fatty acid synthesis
activated by sugar-PO4, insulin, high carb diet
inhibited by high fat diet, starvation and PUFAs
glycogenesis location
cytoplasm
glycogenesis rate limiting enzyme
glycogen synthase
how is glycogen synthase regulated in glycogenesis
phosphorylation inhibits
dephosphorylation activates
where does TAG synthesis occur
hepatocytes and adipocytes
