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Terms in this set (205)
Are all enzymes proteins?
No - ribozyme acts as a enzyme but is made out of RNA
Is an enzyme chemically altered in a reaction?
enzyme that adds or subtracts electrons
enzyme that transfers small groups like amino, acyl, phosphoryl, one carbon, sugar
enzyme that adds water across bonds to cleave them
enzymes that add the elements of water, ammonia, or CO2 across a double bond (or the reverse reaction)
enzyme that does structural rearrangements
enzyme that joins molecules together
4 mechanisms of catalysis of enzyme reactions
catalysis by proximity - close active sites
catalysis by strain- 3D conformational change of the ES complex strains that target bond to cleave
acid-base catalysis - pepsin
Explain lock and key model of enzyme action
enzymes are very specific - they bind a substrate to the active site
ONLY certain substrates can fit the active site
E+S complex forms and substrate reacts to form product which is then released
Which model of enzyme action occurs more commonly in nature?
induced fit model
What is induced fit model of enzyme action?
enzyme changes shape slightly as substrate binds
What is the difference between cofactors and coenzymes
none - coenzymes are cofactors
2 types of cofactors
non-protein organic and inorganic molecules that are required for or aid in the activity of certain enzymes
helps enzyme be active and do its function
ORGANIC molecules obligatory for enzyme function - they are tightly bound to the enzyme and help in the transfer of functional groups like biotin, heme, NAD, FAD
inorganic molecules not absolutely essential for enyme function - like Zn, Mg, Ni, Mo, Se, Mn (most common)
what is most common coenzyme
enzyme withOUT its cofactor
enzyme with its cofactor
enzyme that has a metal ion as its cofactor
a tightly bound coenzyme that does not dissociate from the enzyme
What do (1) and do not (3) enzymes affect?
Enzymes do not affect deltaG0 or deltaG (free energy or energy released by reaction) or Keq
They DO affect the free energy of activation - Eact or DG or DeltaG dot
What do enzymes do to activation energies?
they decrease the activation energy required for a chemical reaction to proceed
amount of energy present in a substance
free energy G
spontaneous reaction - what is delta G?
it is negative
Change in free energy equation?
deltaG = G(p) - G(s)
change in free energy = free energy of products - free energy of substrate
delta G 0 means what?
standard free energy change -
free energy calculated at fixed concentration of 1M concentration of substrate and product
Michaelis Menten reaction model equation (not actual equation)
what are the rate constants?
E + S <--> ES <--> E + P
K1 and K-1
What is the michaelis menton equation?
V0 = (Vmax [S])/(Km + [S])
what is Km
substrate concentration at 1/2 of Vmax
What is Km's relationship to affinity?
it is inversely proportional
Low Km means what?
high affinity of the enzyme for a given substrate
what does high Km mean?
low affinity of enzyme for given substrate
velocity where all the enzyme is bound to substrate
what does temperature do to enzymes and the Vmax?
generally increases enzyme activity and therefore reaction rate until you reach temp which causes it to denature -- enzymes are proteins
How does pH affect vmax of enzyme?
narrow range of maximum/optimum pH and therefore Vmax - enzyme activity is lost outside of that range
substrate concentration affect on vmax in reaction with enzyme
increasing substrate increases the reaction velocity until you saturate the enzyme -- all available enzyme molecules occupied with substrate -- will plateau
in non-enzymatic reaction, what does substrate concentration do to velocity
the increase in velocity is DIRECTLY PROPORTIONAL to the amount of substrate -- NO PLATEAU because there is no enzyme to saturate
What does enzyme concentration do to the Vmax and Km?
affects Vmax but does not affect Km -- so increases velocity where all enzyme is bound because more enzyme present. but Km does not change
What will changing enzyme concentration look like on a lineweaver burke plot?
X intercept will stay the same while Y intercept will increase or decrease bc only Vmax is changing
what does X intercept mean on a LWB plot?
what does y intercept mean on a LWB plot?
x axis on LWB plot?
Y axis on LWB plot?
y axis is 1/Vo
x axis is 1/S
What is a competitive inhibitor
it has a structure similar to the substrate and occupies the active site
competes with substrate for active site
how do you reverse effect of competitive inhibitor?
increasing substrate concentration to overcome to comp inhibitor
what is a noncompetitive inhibitor?
does NOT have a structure like substrate
binds to the ENZYME but not the active site - changes shape of the enzyme and the active site
What will comp inhib look like on MM plot as it affects reaction?
It will have the same Vmax but a different Km so the plateau will be the same and the starting point at 0 is the same but the line between is taking different route - it is affecting affinity - decreasing it
what will noncomp inhib do to the curve on a MM plot?
it will keep the same Km but change the Vmax so this plotted curve just looks like a lowered version of the normal enzyme curve - the plateau has lowered but kept a very similar shape - still has same affinity for substrate but overall velocity changes
Irreversible inhibition occurs when an inhibitor covalently binds to the enzyme or binds so tightly that it is not released
reversible inhibitor: competitive
what does it look like on a LWB plot?
the Km moves closer to 0 on the X axis as the Vmax on the y axis stays the same - Km is getting bigger so affinity is getting lower
Reversible inhibitor non- comp
what does it look like on a LWB plot?
it has a Km on the x axis that does not change and a Vmax on the Y axis that moves higher which means it is getting lower in value and decreasing the rate of reaction
what can non-comp inhibitor bind in the E + S <--> ES --> E + P equation?
it can bind to free E or ES complex -- it uniquely forms ESI - this does NOT occur in the presence of CI because comp inhib bind to the active site and prevent this
Noncomp inhibitors DO NOT BIND to substrate binding site so they do NOT affect ?
alters conformation of enzyme and affects catalysis but not substrate binding
enzyme quantity is regulated by what
transcription and translation
multiple forms of an enzyme which can differ in physical and chemical properties and catalyze the same reaction as an enzyme
isoenzymes can be separated in 3 ways
electrophoretic techniques (specific)
this type of enzymes have multi-subunits with quaternary structure and have multiple active sites
when you plot an allosteric enzymes what kind of curve does it produce (instead of a hyperbola)
allosteric modulators bind to sites other than the active site
End products of allosteric enzymes are often ? and this is how they participate in?
inhibitors - feedback inhibition
K class effectors - allosteric enzymes - what is affected and what is not?
(Km and Vmax)
Km is affected but Vmax is same
V class effectors - allosteric enzymes - what is affected and what is not?
(Km and Vmax)
Km is not affected but Vmax remains the same
allosteric enzymes have allosteric modulators and these modulators are either ? or ?
inhibitor or activator
With an allosteric activator, the binding of the allosteric activator increases ?
affinity of the enzyme for the substrate
allosteric inhibition - binding of the inhibitor prevents the substrate from efficiently what?
becoming product - very low affinity state
product of enzyme-catalyzed pathway acts as allosteric inhibitor of first inhibitor of the first enzyme in pathway and helps conserve cellular resources
what is this term called?
regulation by feedback inhibition
enzymes can be regulated by chemical modification which often involves what?
reversible addition or removal of phos, methyl, or acetly groups
what are some examples of enzyme regulation via chem modification?
protein kinases ADD PHOS groups to enzymes and protein phosphatases REMOVE PHOS
multiple forms of the same enzyme that catalyze the same reaction and act on the same substrate giving the same product
how do isoenzymes differ?
they differ in molecular weight or structure or charge and can be separated by electrophoresis
originate in proenzyme or inactive forms and become active upon proteolytic cleavage - some modifier is attached to them
2 principal functions of lipids
structural support and cellular protection and signaling
as well as energy storage
ratio of protein to lipids to carbs in membrane tell you what?
gives you idea of function of membrane
if protein is high in the membrane of a cell - what does that indicate?
what is an example?
very active cell type
inner mitochondrial membrane has high protein
non-esterified fatty acids
are all major lipids in circulation
what are the essential FAs?
what are the semi-essential FAs?
linoleic acid -- linoleate
linolenic acid -- linolenate
semi is arachidonic acid
what makes arachidonic acid semi-essential
only essential if linoleic acid is deficienT
most fatty acids have odd or even # of carbon atoms?
4 categories of fatty acids based on # of Cs in length
short chain FA
medium chain FA
long chain FA
very long chain FA
naturally occuring FA are what kind>
they are unbranched - cis (double bonds)
branched fatty acids are found in what
phytanic acid in dairy products and rudiment meat
saturated vs. unsaturated fatty acid
unsaturated has double bonds - cis double bonds
saturated has no double bonds
fxn of triglyceride
fxn of phospholipid like phophatidylcholine
major component of biologic membranes
2 major fxns of sphingolipid
important structural component of cells in CNS and cell surface antigens (blood type determination)
free cholesterol indicates what about a membrane
esterified cholesterol is what
insoluble and found in serum
what is backbone of triglyceride and spingolipid
glycerol and sphingosine
Where does fatty acid biosynthesis occur
in the liver in the cytosol - cytoplasm of hepatocytes
what is required for FA biosynthesis
NADPH and Acetyl CoA
Acetyl CoA can come from what 4 things?
Glycolysis -- pyruvate -- ACoA
Fatty Acid Oxidation -- ACoA
Oxidation of AAs and Ketones -- ACoA
What is produced in HMP shunt
2 molecules of NADPH2 are produced per molecule of glucose that enters this pathway
Mito membrane is impermeable to AcoA so what must happen?
it must leave the mito as citrate
what do you need to begin each successive turn of the cycle of FA synthesis?
1 ACoA and 1 MalCoA
Key enzyme in fatty acid biosynthesis is
acetyl CoA carboxylase ACC
Acetyl CoA Carboxylase is what kind of enzyme (think about cofactor)
ACoA --> MalCoA
in what process does this occur?
what enzyme catalyzes it?
reversible or irreversible
* a different enzyme is required for the reverse rxn
Acetyl CoA carboxylase
How is ACC regulated?
phos or dephos
there is crosstalk between ACC and what
expression of fatty acid synthase complex is stimulated by ?
Fatty acid synthase allow 2 FAs to be synthesized simultaneously
Regulation of FA Biosynthesis - do these things turn on or off?
Does citrate activate FA Biosynthesis or inactivate?
What about palmitoyl CoA?
enzymes that lengthen growing FA chains
enzyme that introduces double bonds
mammals have what desaturases - what does this mean?
4, 5, 6, and 9 - cannot introduce double bonds beyond C9
Where are elongases present? (in regards to FA biosynth)
where are newly synth FAs elongated? what is the carbon donor for these?
where are pre-existing FAs elongated? what is the carbon donor for these?
in mito and ER
in the ER - malonyl CoA
in the mito - Acetyl CoA - these are remnants from FA oxidation
What is in abundance in the mito matrix? Why?
AcoA - pushing it into TCA Cycle
key sites of triglyceride biosynthesis
LIVER AND ADIPOSE TISSUE
Key step 1 of triglyceride biosynthesis is
Key step 2
key step 3
synthesis of glycerol 3 phosphate
fatty acid activation
attachment of FAs to the glycerol backbone
2 things that can make glycerol 3 phos (step 1 of trigly biosynth)
in liver from glucose via DHAP in glycolysis
in adipose cell via DHAP in glycolysis
what does the activation of FA require (step in triglyceride synth)
what does this indicate?
energy - ATP -- indicates we have surplus energy -- can synth to put into savings
beta oxidation -- you are now in fasting state so extracting energy to push toward ?
Key step 1 in triglyceride hydrolysis
hormone sensitive lipase
effects of hormones on triglyceride hydrolysis
aka fasting, stress, exercise
aka fed condition
all top 3 are stimulatory -- need more energy!!
insulin is inhibitory because you already have enough energy
what is the relationship between ACC and HSL
their regulation is the inverse of each other
Fatty Acid Oxidation
Key Step 1
Hormone sensitive lipase
what is the only energy requiring step in FA oxidation
the activation of fatty acids - converting fatty acids via Acyl CoA synthetase to Fatty Acyl CoA
After HSL and FA activation in Fatty acid oxidation, you need to transfer across inner mito membrane
out of SCFA, MCFA, LCFA, and VLCFA -- how do all of these get across inner mito membrane?
SCFA and MCFA go freely
LCFA needs CAT-1
VLCFA goes 1st to peroxisomes
what happens in peroxisomes involving VLCFA
peroximsomal beta-oxidation - 1st step makes H2O2
What inhibits CAT1 from FA biosynthesis
Mitochondrial Beta-oxidation - produces what or what?
acetyl coA for the TCA cycle
Regulation of FA Oxidation
all primary signals for HSL
What happens in MCAD deficiency?
results in many short chain dicarboxylic acids from omega oxidation
what is Zellwegers syndrome
increase in VLCFA
what is Adrenoleukodystrophy
deficiency in peroxisomal acyl CoA synthetase for VLCFA activation
what happens in Refsums disease
alpha hydroxylase deficiency
phytanic acid build up
alpha oxidation involves ?
alpha hydroxylase is required as an additional enzyme
branched chain FA
oxidation of unsaturated FA - double bonds are removed by coordinated sequential action of isomerases, drhydrogenases, and reductases
ingest meal and ? will suppress FA movement into mito matrix
Malonyl CoA - it inhibite CAT 1
in MCAD deficiecy - problem oxidizing fatty acids, so cant undergo traditional beta oxidation - instead what occurs?
bring in omega oxidation - start chopping at omega end
check adipate levels
alpha oxidation helps us actually utilize branch chain fatty acids
Fatty acid oxidation generating a lot of acetyl CoA ad want to push this where
into mito matrix
What is starting material for TCA
PDH is enzyme for which reaction
pyruate --> acetyl CoA
PDH is regulated by what 2 things
Acetyl CoA and NADH
3 acetyl CoA sources
FA or AA oxidation
PDH deficiency is an X linked disorder that results from what?
E1 subunit mutation
Primary Biliary Cirrhosis - what is this and what does it attack?
related to PDH
autoimmune disease against E2 subunit
matrix of mito has high or low pH/proton concentration
low proton and pH high
ATP-ADP translocase helps get ADP back into ? to make more ATP - this is a ? (type of transporter)
this interacts with a symporter called ?
What is inhibited by atractyloside and bongkrekic acid
bongkrekic acid specifically causes what
adenine nucleotide transporter (ATP-ADP translocase)
build up of ATP inside the mito matrix so energy cannot get out to cell
What is purpose of alpha-glycerol phosphate shuttle
what is purpose of malate-aspartate shuttle
What do inhibitors of tricarboxylate transporters do?
reduce fatty acid synthesis
Malate-aspartate shuttle inhibition results in ?
increase in NADH/NAD+ ratio in the cytosol so the key 2 rxns proceed in reverse
Malate-aspartate shuttle inhibition results in decreased pyruvate which leads to
decreased pyruvate and OAA inhibits gluconeo and activate glycolysis
malate aspartate shuttle inhibition results in what effect on lactate?
it increases lactate and increases lactic acidosis
EtOH consumption increases cytosolic ? and reduces availability of ?
What happens to Cori Cycle with EtOH abuse
Individuals that have done severe exercise and then consumed alcohol immediately after then show hypoglycemia, persistent lactic acidosis, muscle cramping, pain, and fainting have had one process has been affected?
cori cycle -- generated lactate taken to liver to be converted to pyruvate for gluconeo
Ethanol abuse impedes what fatty acid involved process
fatty acid oxidation
if you increase the NADH/NAD ratio --
and then you decrease gluconeogenesis and increase glycolysis --
what will result?
severe hypoglycemia and eventual loss of consciousness
if you increase the NADH/NAD ratio --
and then you increase the amount of pyruvate converted to lactate --
what will result?
if you increase the NADH/NAD ratio --
and then decrease fat breakdown and increase synthesis of fat --
what will result?
fatty change of the liver (Steatosis)
ETC is located where specifically>
inner mitochondrial membrane
How many ATP made from ETC with 1 glucose?
process by which the energy stored in the NADH and FADH2 is used to produce ATP
For 1 molecular oxygen to be converted to water, 4H+ are needed -- how many times does ETC have to occur?
Inhibitors of ETC - Match the inhibitor with the Complex
Complex I Antimycin
Complex II Cyanide
Complex III Rotenone
Complex IV MPP
Rotenone, Amytal, MPP - Complex I
Malonate, TTFA- Complex II
Antimycin - Complex III
Cyanide and CO - Complex IV
Which complex in ETC is a NADH dehydrogenase?
Which complex in ETC is succinate dehydrogenase?
how is malonate related to this?
Complex II - malonate is a competitive inhibitor
Which complex in ETC is aka cytochrome b/c1 complex or cytochrome c reductase?
which complex in ETC is aka cytochrome a/a3 complex or cytochrome C oxidase?
in oxidative phosphorylation, how many protons are pumped out per mito NADH electron transfer?
how many are pumped per mito FADH2 electron transfer?
How many protons through ATP Synthase are needed per ATP made?
In the complete oxidation of one molecule of glucose, a total of ? or ? molecules of ATP are produced depending on the use of glycerol 3-phosphate or malate aspartate shuttle respectively ?
30 or 32
ETC and Ox Phos are coupled
what are some uncouplers?
high doses of aspirin
wood preservative - pentacholophenol
norepi -- therminogen in brown fat
Does uncouple serve any useful purpose?
body heat generation
What is the P:O ratio?
number of ATP made/number of O2 atom consumed?
What is the respiratory control ratio and what does it measure?
when is it high and when is it low?
O2 consumption in state 3 (active) /O2 consumption in state 4 (resting - respiration)
this measures the tightness of coupling between oxidation and phosphorylation
ratio is high if process is coupled and is low if uncoupled (uncouplers increase the denominator)
P:O ratio is defined as the number of what generated in ox phos per atom of oxygen
molecules of ATP
In a tightly coupled system, NADH has a P:O ratio of?
where are ketone bodies primarily produced?
where are the enzymes necessary for their synthesis localized?
in the liver
cells and tissue types that CANNOT oxidize FAs and therfore CANNOT use ketone bodies ?
RBCs (b/c no mito) and Brain - cannot use them - it prefers glucose
blood levels of ketone bodies and fatty acids do what during starvation and fasting so BG can be maintained
in uncontrolled diabetes, ESP type ONE (insulin dependent) - blood levels of ketone bodies, fatty acids, and glucose do what?
synthesis of ketone bodes happens initially in ?
what molecule is initially used to form ketone bodies ?
what is the major enzyme?
HMG CO-A synthase and HMG CoA Lyase
what are the major ketone bodies?
beta-hydroxybutyrate and acetoacetate and acetone
which enzyme is absent in the liver that allows for the oxidation of ketone bodies (converted back to Acetyl CoA) by peripheral tissues
what creates sweet breath smell in pt with ketoacidosis
what is checked for in urine test of someone with ketoacidosis
beta hydroxybutyrate levels
Alcohol is a potent inhibitor of ?
leads to what effect on
early stage of sterol synthesis occurs where
late stage of sterol synthesis occurs where
cell membrane component important for membrane fluidity
precursor for bile salts, steroids, and vit D
all of this describes what?
Which molecule is participating in the cytoplasm cholesterol biosynthesis and helps acetyl CoA and acetoacetate to cholesterol
in cholesterol biosynthesis which enzyme is the rate limiting step which also acts as a target of drug therapy for hypercholesterol
HMG CoA Reductase
lipids are transported in the serum in association with ?
free fatty acids are carried bound to ?
cholesterol and phospholipids are transported as ? complexes
lipoproteins contain a hydrophobic core of TGs and cholesterol esters that is surrounded by a layer of phospholipids, free cholesterol, and protein called ?
apolipoproteins are classified based on densities -- largest and lease dense to smallest and most dense:
elimination of cholesterol - is converted into ? and excreted
also converted to other sterols by ? and excreted
biological detergents synthesized from cholesterol in the liver and stored in the gallbladder - help in absorption and digestion of fat and elimination of cholesterol
inborn error of cholesterol biosynthesis - autosomal recessive, caused by def in DHCR7
mild ID, behav problems, lethal malformations
Smith Lemli Opits Syndrome
how do PUFAs lower cholesterol levels?
stimulate cholesterol excretion in bile
stimulate conversion of ch into bile acids
upregulate LDL receptors -- decrease LDL and increase HDL synthesis
cholesterol concentration >15% can result in precipitation of cholesterol in bile and formation of gallstones
what is this?
what kind of things can deficiency of bile salts cause
biliary duct obstruction
PUFAs can decrease and prevent what?
lower Cholesterol level and prevent atherosclerosis
sphingomyelinase deficiency leading to organomegaly and neurodegeneration is what disease
niemann pick disease
Glucose 6 phosphatase deficiency leading to large liver and hypoglycemia
Type 1a Von Gierke's disease
defective apo- B100 LDL receptors leading to xanthomas and hypecholesterolemia is what genetic diseases -- AD
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