Bennet's Lecture Flashcards
What are the uses of glucose?
synthesis of structural polymers
storage
oxidation via PPP
oxidation via glycolysis
what are the properties of glucose
rich in potential energy
versatile percursor
in animals and vascular plants glucose has 4 main fates
what are the different uses of glucose between plants and people?
plants use glucose to form cell wall polysaccharides and extracellular matrix
what are the 2 phases of glycolysis
preparatory phase and payoff phase
describe the preparatory phase.
5 enzyme catalyzed reactions (first 5 steps), utilize the energy 2 ATP molecules to generate 2 phosphorylated; 3 carbon high energy molecules
describe the payoff phase.
5 enzyme catalyzed reactions (last 5 steps)
4 ATP molecules are generated
two hydride ions transferred to NAD+ to produce 2 molecules of pyruvate (3C)
what is the net reaction of glycolysis
glucose + 2 NAD+ + 2 ADP + 2Pi -> 2 pyruvate + 2 NADH + 2H+ + 2H2O
what is glycolysis
break down of glucose to pyruvate
what is the first step of glycolysis? glucose -> what? via what?
glucose is converted to glucose 6 phosphate;
via hexokinase; irreversible; uses ATP
requires Mg2+
what is the second step of glycolysis? glucose 6-phosphate -> what? via what?
glucose 6-phosphate is converted to fructose 6-phosphate
via phosphohexase isomerase; reversible; Mg 2+
what is the third step of glycolysis? fructose 6-phosphate -> what? via what?
fructose 6-phosphate to fructose 1,6- bisphosphate
via phosphofructokinase-1 (PFK-1); irreversible using ATP; Mg2+; commitment step/ important regulation step since using energy
what is the fourth step of glycolysis? fructose 1,6 - bisphosphate -> what? via what?
fructose 1,6 - bisphosphate to glyceraldehyde 3-phosphate AND dihydroxyacetone phosphate
via aldolase; reversible
what is the fifth step of glycolysis? glyceraldehyde 3-phosphate AND dihydroxyacetone phosphate -> what? via what?
dihydroxyacetone phosphate is converted to glyceraldehyde 3-phosphate (one step later)
via triose phosphate isomerase (TPI); reversible
what is the sixth step of glycolysis? glyceraldehyde 3-phosphate -> what? via what?
glyceraldehyde 3-phosphate (& NAD+) to 1,3 bisphosphoglycerate and NADH
via glyceraldehyde 3-phosphate dehydrogenase; reversible
oxidative phosphorylation process
what is the seventh step of glycolysis? 1,3-bisphosphoglycerate to -> what? via what?
1,3-bisphosphoglycerate to 3- phosphoglycerate AND ATP
reversible via phosphoglycerate kinase; Mg2+
what is the eighth step of glycolysis? 3- phosphoglycerate to -> what? via what?
3- phosphoglycerate to 2-phosphoglycerate
via phosphoglycerate mutase; reversible; Mg2+
what is the ninth step of glycolysis? 2- phosphoglycerate to -> what? via what?
2- phosphoglycerate is converted to phosphoenolpyruvate and produces water
via enolase; reversible; Mg 2+
moving the phosphate
what is the tenth step of glycolysis? phosphoenolpyruvate to -> what? via what?
phosphoenolpyruvate is converted to pyruvate and ATP
via pyruvate kinase; irreversible; Mg2+ and K+
where does NAD+ come from? what reactions are NAD+ involved in?
vitamin a; player in glycolysis
what occurs when there is no oxygen in skeletal muscles at the end of glycolysis
pyruvate and NADH gets converted to l-lactate and NAD+ (which is slightly acidic)
via lactate dehydrogenase
describe gluconeogenesis
synthesis of glucose from things pyruvate, lactate, or glycerol to produce intermediates and energy supply
2 pyruvate + 4 ATP + 2 GTP+ 2 NADH + 2 H+ + 4H2O -> glucose + 4 ADP + 2 GDP + 6 Pi + 2 NAD+
describe the lactate cori cycle?
glycogen releases energy and forms lactate in the muscle which goes to the blood and into the liver to use amp and make glucose which cycles back into the blood and to form glycogen in the muscles
describe the glucose-alanine cycle.
muscles use glucose to form pyruvate which transaminate glutamate to alpha ketoglutarate and form alanine which goes into the blood but then into the liver to reform glutamate and pyruvate, goes through glucose which goes into the blood and then back to the muscle
what are the bypass reactions between gluconeogenesis and glycolysis
hexokinase (breakdown glucose) -> glucose 6 phosphatase (breakdown glucose 6-phosphate) - in hepatocytes
PFK-1 (from F 1,6-BP) -> fructose 1,6-bisphosphate (F 1,6-PB to F 6-P) - irreversible
pyruvate kinase (forming pyruvate) -> pyruvate carboxylase and PEP carboxykinase (breakdown pyruvate)
discuss pyruvate carboxylase
pyruvate goes into the mitochondria from the cytosol; using coenzyme biotin and activated by acetyl coA; biotin moves CO2 from bicarbonate to oxaloacetate
discuss phosphoenolypyruvate carboxykine (PEP CK)
requires Mg2+ and GTP; produces phosphoenolpyruvate (PEP); alanine precursor moves NADH from mitochondria to cytosol
how is glycolysis hormonally regulated?
high glucagon -> blocks glycolysis
epinephrine -> stimulates glycogen
how is glycolysis allosterically regulated
hexokinase
PFK-1 -> inhibited via ATP and citrate, activated via ACP and F 2,6-BP
F 1,6BP (enzyme)
pyruvate kinase
how is gluconeogenesis hormonally regulated?
glucagon -> stimulates gluconeogenesis
insulin -> inhibits gluconeogenesis
how is glycogen breakdown hormonally regulated
stimulated by epinephrine and glucagon
how is glycogenesis hormonally regulated
inhibited by epinephrine and glucagon
stimulated by insulin
how are hexokinases/ glucokinase in glycolysis allosterically regulated
hexokinase 1-3 are ubiquitous and carry out the phosphorylation of glucose to g 6-p quickly; it is inhibited by high levels of product (g 6-p) because it has a high affinity and low capacity
hexokinase 4 or glucokinase located only in the liver and are NOT product inhibited because it has a low affinity and high capacity
how is PFK-1 regulated
inhibited by high ATP and citrate; activated AMP, ADP, or fructose 2,6-bisphosphate
what occurs in the liver regarding regulation of glycolysis
glucagon (hormone) and ATP activate PKA which phospharylates pyruvate kinase L (the INACTIVE form of PK)
water and protein phosphatase dephosphorylates pryruvate kinase L into its ACTIVE form Pyruvate kinase L/M
how is insulin related to the reulation of glycolysis in the liver forming pyruvate?
insulin activates the dephosphorylation/ activation of pyruvate kinase in order to form more pyruvate; insulin wants to get glucose out of the blood making sense why it would continue glycolysis;
DECREASES gluconeogenesis and glycogen breakdown; INCREASES glycogen synthesis and glycolysis
what does glucagon serve to do
glucagon is a hormone that is secreted to encourage the reformation of glucose from glycogen by
INCREASING gluconeogenesis and glycogen breakdown while DECREASING glycolysis and glycogen synthesis
what is glycogens main purpose
glycogen is the storage form for glucose; mainly in liver
why does glucose need to be stored as glycogen
glucose is polar due to its reducing and nonreducing ends; glycogen has linear connects 1-4 and branches 1-6 cutting off the reducing end in order to store as a stable product
describe glycogenolysis
forming glucose by breaking down glycogen; 3 steps
describe the first step of glycogenolysis
glyocgen phosphoylase a/b cleaves the nonreducing ends of glycogen chains by using a pyridoxal phosphate repeatedly until 4 residues away from the branch point (1->6); produces glucose 1-phosphate
what is glucose 1 phosphate used for
describe step 2 of glycogenolysis
utilizing the debranching enzyme, it transfers branches the first 3 residues to 1-4 link with the branch (transferase) and releases the residue (glucosidase) on the 1 side of the 1-6 bond as free glucose; products: free glucose and an unbranched 1-4 strand
describe step 3 of glycogenolysis
utilizing phosphoglucomutase, glucose 1-phosphate is converted to glucose 6-phosphate which enters glycolysis in muscle but in liver/kidney it is converted to glucose to replenish blood glucose
how is glucose released into the blood from the liver
GLUT2 transporter releases glucose into the blood
describe glycogen synthesis
2 steps; forming glycogen from an activates sugar molecule
describe step 1 of glycogen synthesis
glucose 1 phosphate + UTP through the UDP glucose pyrophosphorylase yields UDP-glucose and pyrophosphate
describe step 2 of glycogen synthesis
using glycogen synthase a/b, glucose is transferred to the nonreducing end of a glycogen molecule elongating an already established chain
what is an unofficial step of glycogen synthesis
for branching to occur, the glycogen branching enzyme is used to branch a molecule 4 residues away to form a 1-6 branching point
describe the regulation of glycogen phosphorylase a/b
glycogen phosphylase a is the active PHOSPHORYLATED form while phosphorylase b is the less active DEphosphorylated form
to phosphorylate (b->a) PKA activates PBK (phosphoylase b kinase) which uses 2 ATP
to dephosphorylate (a->b), phophoprotein phosphotase 1 (PP1) pulls off 2 Pi and replaces with OH (using 2 H2O)
what are the activators/ inhibitors of PP1?
activated by insulin (and G6P in glycogen synthesis)
inhibited by glucagon and epinephrine
what are the activators/ inhibitors of Phosphorylase B Kinase?
activated by glucagon in the liver and epinephrine, Ca2+, high AMP and low ATP in the muscles
describe glycogen synthase a/b regulation.
glycogen synthase a is active and DEPHOSPHORYLATED while synthase b is PHOSPHORYLATED and inactive unless in the presence of G6P
PP1 dephosphorylates (b->a)
glycogen synthase kinase 3 (GSK3) phosphorylates (a->b) using 3 ATP
what symptoms/ organs are affected by a disease influencing glycogen synthase?
symptoms will include low blood glucose, high ketone bodies, and early death
what symptoms/ organs are affected by a disease influencing debranching enzyme?
symptoms: enlarged liver in infants, myopathy
organs: liver, skeletal and cardiac muscle
what symptoms/ organs are affected by a disease influencing branching enzyme
enlarged liver and spleen, myoglobin in urine
organs: liver, skeletal muscle
what symptoms/ organs are affected by a disease influencing muscle phosphorylase
symptoms: exercise induced cramps and pain; myoglobin in urine
organs: skeletal muscle
how does regulation of carbohydrate metabolism differ in the liver and muscle
the liver is signaled by glucagon OR epinephrine to use the stored glycogen increase blood glucose by increasing glycogenolysis and gluconeogenesis while decreasing glycolysis
the muscle is signaled by epinephrine and converts glycogen to pyruvate via increased glycogenolysis and glycolysis, no effect to gluconeogenesis (lacks the enzymes)
scenario: you haven’t eaten in six hours and you are late to class, so you are running. what is the metabolic state of yuor liver and your leg muscles?
Liver: increased glucagon to increase breakdown of glycogen and increase blood glucose; inhibited glycolysis so glucose can get sent to the muscles that need it increased gluconeogenesis
Muscles: increased epinephrine to increase glycolysis and glycogen breakdown to provide immediate energy for the muscle cells
describe the pentose phosphate pathway and its important goal
goal: generate NADPH
oxidizes glucose 6-phosphate to produce pentose phosphates
what biosynthetic pathways require NADPH
fatty acid synthesis
cholesterol and bile acid synthesis
steroid hormone synthesis
cytochrome P-450 dependent detoxification
maintaining glutathione in reduced state
generate superoxide to kill bacteria
what determines the pathway of g 6-P
relative concentrations of NADP+ and NADPH
high NADPH will send g 6p to glycolysis while high NAD+ will send it to pentose phosphate pathway
why is NADPH important
NADPH is important to prevent hydroxyl free radicals that can be produced from hydrogen peroxide and instead NADPH supplies extra H to produce water and inhibit damage
what is the overall equation for pentose phosphate pathway
g 6-P + 2NAD+ + H2O -> ribose 5-phosphate + CO2 + 2NADPH + 2 H+
describe the steps of cellular respiration and where they occur
pre: glycolysis = cytosol
1. pyruvate oxidation = mitochondrion
2. citric acid cycle = mitochondrion
3. oxidative phosphorylation = mitochondrion
describe stage 1 of cellular respiration?
reversible production of acetyl coa via pyruvate oxidation; uses three enzymes and 5 coenzymes
what is E1 of pyruvate oxidation
e1 pyruvate dehydrogenase with coenzyme thiamine pyrophosphate (TPP); TPP stabilizes pyruvate and pulls CH3CO off/ releases CO2
what is E2 of pyruvate oxidation
dihydrolipoyl transacetylase and coenzymes Lipoate and coenzyme A (CoA, CoA-SH), center/ core of pyruvate oxidation
lipase is recused by the CH2OHCH3 from E1 and then transfers it to a CoASH forming acetyl CoA
what is E3 of pyruvate oxidation
FAD (irreversible bound to E3) oxidizes lipoate and transfers the electrons to NAD+(free to move in mitochondria) forms NADH
what is the ATP equivalent of NADH and FADH2?
FADH2 = 1.5 ATP while NADH forms 2.5 ATP
describe the pyruvate dehydrogenase complex
made up of an E2 core with surrounding E1 and E3
responsible form pyruvate oxidation to form acetyl coa
how is PDC (pyruvate dehydrogenase complex) allosterically regulated?
allosterically based on energy status - high energy = off (including high fatty acids, acetyl CoA, ATP, and NAPD); on when need acetyl coa
how is PDC covalently regulated
PDH Kinase inhibits PDH complex by phosphorylation
PDH phosphatase activates PDH complex when ATP low
what are the names of the second stage in cellular respiration
Krebs cycle/ Tricarboxylic acid Cycle/ Citric Acid Cycle
major energy producing pathway that requires oxygen
occurs in mitochondria
generates key intermediates and biomolecules
8 small steps
describe the first step of the CAC that forms citrate
using citrate synthase, acetyl CoA (2C) and oxaloacetate (4C) react with the help of water to produce citrate (6C) and CoA-SH; highly exergonic, irreversible and tightly regulated by induced fit so that when oxaloacetate binds, it creates a binding site for acetyl CoA
describe the second important step of the CAC that forms alpha ketoglutarate (5C)
citrate is dehydrated and rehydrated to form isocitrate to move the -OH group to the fourth carbon on the main chain and produce NADH; reversible, pulled forward due to low [isocitrate]
it is then decarboxylated via isocitrate dehydrogenase to form a-KG (5C) and release CO2 and NADH
describe the third important step of the CAC that forms succinate (4C)
a-KG is decarboxylated using a-KG dehydrogenase complex and CoASH to form succinyl-CoA; highly exergonic, tightly regulated, irreversible
which is then broken to provide energy to phosphorylate GDP-> GTP and forms Succinate via succinylcholine synthetase; slightly reversible but pulled forward with low [succinate]
describe the fourth important part of the CAC that forms oxaloacetate
succinate is dehydrogenated via succinate dehydrogenase and releases FADH2 and forms fumarate
which is hydrated to form L-malate (stereospecific)
which is dehydrogenated via L-malate dehydrogenase to form oxaloacetate and release NADH and start the cycle over
what do pyruvate dehydrogenase complex and a-ketoglutarate dehydrogenase complex have in common?
they use CoA-SH and NAD+ with their substrate to decarboxylate it (release CO2), form NADH, and add S-CoA
what are the important products of the citric acid cycle
(3 NADH, 1 FADH2, 1 ATP, 2 CO2) *2 for every glucose since it’ll start with 2 pyruvate and cycle goes twice
how is the citric acid cycle regulated
- energy status: high fatty acids, acetyl-CoA, ATP, citrate, NADH inhibits cycle; high ADP/NAD+ activate cycle
- (for muscle cells): Ca2+ activates PDH/ isocitrate dehydrogenase/ a-KG complex
compare the inner and outer membrane of the mitochondria
outer membrane is freely permeable while inner membrane that is not permeable and uses transporters;
compare the inner and outer membrane of the mitochondria
outer membrane is freely permeable while inner membrane that is not permeable and uses transporters;
describe the electron transport chain in the mitochondria
there are 4 complexes that act to allow transport of electrons through the chain and pumping protons into intermembrane space
energy generated here is used to generate a proton gradient that converts ADP to ATP
NADH is used to reduce molecules
10 electrons pumpped
describe complex 1 of ETC
electrons are transported from NADH to ubiquinone;
complex 1 is an integral membrane protein with N side on matrix and P side because positive charges on outside;
exergonic transfer of H- from NADH and proton from matrix to ubiquinone
endergonic transfer of 4 protons from N side to P side with energy taken from electron transport
describe complex 2 of ETC
aka succinate dehydrogenase; no proton pumping electrons are transported from succinate to ubiquinone to continue ETC AND from succinate to fumarate to continue citric acid cycle
describe complex 3 of ETC
dimer with each monomer having 11 subunits; 2 electrons are transported from ubiquinol to cytochrome c using iron centers/ heme groups
4 protons to intermembrane space
cytochrome c can more in intermembrane space
describe complex 4 of ETC
final oxidation! electrons are transported from cytochrome c to O2; 3 subunits; iron copper center to copper center in subunit 2; 4 hydrogen pumped through complex into P side
what are the products/ reactants of the electron transport chain
substrates come from citric acid cycle
(3 NADH and 1 FADH2 = 4 pairs of electrons)
what is ATP synthase
integral membrane protein on inner membrane of mitochondria
describe the thermodynamics of electrons
electrons flow from the low affinity molecule to a higher affinity molecule ex. pyruvate to NAD+ to form NADH and oxidized pyruvate
negative reducing potential to more positive reducing potential
describe the relative electron affinity of copper versus hydrogen
copper has a higher affinity for electrons, as shown by a positive voltage in redox reaction; increasingly positive voltage related to greater electron affinity
delta g =?
-nFE
what inhibits complex 1
rotenone
what inhibits complex 3
antimycin A
what inhibits complex 4
Cn- or CO
what is the importance of cytochromes
proteins containing heme; heterocyclic containing single iron which can be reduced to facilitate electron transport
can bind to hydrophobic pocket or other associates
what is the importance of ubiquinone
lipid soluble; coenzyme Q; can accept 2 electrons which acts as junction for a molecule that can only move one at a time
what is the importance of iron salter centers
1-4 iron molecules; with sulfur and iron, electron transport can be facilitated
how many protons are required for one ATP to be produced in ATP synthetase
4 H+
describe the proton motive force and its 2 parts
the energy stored in an electrochemical gradient of protons
chemical energy: difference in concentration of protons across the membrane
electrical energy: separation of charge across a membrane
describe how to calculate the available energy from the electrochemical gradient
delta g = RTln(C2/C1) + ZF(deltapsi)
C1: losing protons
C2 receiving protons
proton gradient conserves 200 kJ that is released by 1 mol of NADH
delta G = 19 kJ/mol for each mol of proton
2 electrons from NADH to O2 results in 10 protons
describe the chemiosmotic model
by Peter Mitchell, describes what is needed to generate energy for synthesis of ATP, knew it had to be a molecule with a high group transfer
- electrons flow through ETC, energy released creates a proton gradient
- dissipation of energy in gradient drives the synthesis of ATP
describe the experiment that proved oxidation and phosphorylation are coupled
adding CN- stops oxidation so when the experiment showed that adding CN- also stopped phosphorylation, coupling proved, DNP stops coupling and allows for oxidation to occur without phosphorylation
describe the experiment that found the role of the proton gradient in ATP Synthesis
creating a fake proton gradient by lowering the pH and getting K+ to move via ionophores caused ATP synthesis to occur, showing the crucial role proton gradients hold
describe the enzyme ATP synthase
aka Complex V, FoF1ATPase
has 2 subunits made of alpha, beta, and gamma parts
describe the F1subunit of ATP synthase
a hexameter with 3 alpha and 3 beta parts; a gamma stalk that rotates; a peripheral stalk that anchors F1
in the mitochondrial matrix (N side)
Beta part is where ATP synthesis occurs
describe the Fo subunit of ATP Synthase
integral membrane protein complex
powers ATP synthesis in the beta parts of F1
has 9-11c hydrophobic parts, each with a proton binding site
1 a part which acts as proton channels
2 b parts
describe binding-change model
3 conformations of the beta parts that change as gamma stalk rotates
1. loose configuration where ADP and Pi can bind to prevent ATP binding
2. central shaft moves and tight binds ATP
3. ATP moved to empty position
3 ATP generated per turn bc 3 beta parts
how does the gamma shaft turn
when there is no proton flow, the empty binding site which contains an arginine interacts with aspartate and glutamate
c part interacts with histidine and kicks out arginine to move protons between aspartate and glutamate which powers the gamma shaft turning
describe the malate aspartate shuttle
indirectly convey electrons from cytosol NADH to mitochondria by converting oxaloacetate to malate by adding 2 protons (one coming from NADH) and forming malate which can be transported into the mitochondria via the malate alpha KG transporter
malate dehydrogenase converts oxaloacetate to malate and back
compound can leave the mitochondria by being converted to aspartate, glutamate, or a-KG via transamination
important because there is no transporter into the mitochondria for NADH or oxaloacetate
describe the glycerol 3-phosphate shuttle
indirect transfer of electrons used by high respiring cells; FAD+ in complex 2 of the ETC can pick up H+ from NADH and move it to quinone and continues ETC
how is ATP production regulated
- energy charge (proton gradient existence)
- substrate availability (ADP, Pi, O2, e source
NO hormone or allosteric regulation
high affinity, low capacity enzymes and
describe shuttle regulation and when to use each
high NADH (in liver or kidney) uses aspartic-malate shuttle
low NADH (skeletal or muscle) uses glycerol 3-phosphate shuttle
