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What makes it possible to build complex structures that are low in entropy Spending energy from the Sun
Catabolism vs anabolismCatabolism: energy producing, breakdown<div>Anabolism: energy consuming, biosynthetic&nbsp;</div>
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How is free energy calculatedΔG = ΔH – TΔS
How do you calculate free energy under standard conditions (1M reactants and products, 298 K, 1 atm, pH=0)ΔG0 = -RTlnKeq
What can make a reaction rate speed up-temp increase<div>-reactant concentration increase</div><div>-product concentration decrease</div><div>-enzyme catalysis</div><div>-ATP activation&nbsp;</div>
What are the conditions of ΔG’0pH = 7<div>[H2O] = 55 M</div>
How can free energy be calculated using concentrations"<img src=""paste-71d126c79a937b3ef36a4be1a81f5451c7d7eb01.png""><br>"
"When K’ eq is &gt; 1, <span style=""-webkit-tap-highlight-color: rgba(0, 0, 0, 0);"">ΔG’0 is&nbsp;</span>"Negative
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When K’ eq is &lt; 1,&nbsp;<span style=""-webkit-tap-highlight-color: rgba(0, 0, 0, 0);"">ΔG’0 is&nbsp;</span>"Positive
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When K’ eq is &nbsp;1,&nbsp;<span style=""-webkit-tap-highlight-color: rgba(0, 0, 0, 0);"">ΔG’0 is&nbsp;</span>"Zero (rxn is at equilibrium)
Catabolic reaction pathways are ___________Exergonic (release energy)
In the cell, are hydrolysis reactions favorable or unfavorableFavorable (bc there’s so much water in the cell, consuming it isn’t a problem)
Molecular oxygen is in the ___________ spin stateTriplet (making it paramagnetic)
What type of bond cleavage generates radicalsHomolytic
Why is ATP such a good activator (why does it want to undergo hydrolysis)-relieve electrostatic repulsion<div>-ADP is resonance-stabilized (and tautomerized)</div><div>-ADP has more entropy than ATP</div><div>-ADP can form better H-bonds with water</div><div><br></div><div>So it has a very negative free energy</div>
What groups can be transferred from ATP, in order to raise energy state of target-AMP<div>-P</div><div>- P-P (pyrophosphate)</div>
Thioesters are _______ stable than oxygen estersLess&nbsp;<div>(Bc its hydrolysis product is more resonance-stabilized)</div>
Is thioester hydrolysis favorable or unfavorable&nbsp;Strongly favorable
What does acetyl-CoA donateAcyl groups in fatty acid biosynthesis
Is ATP involved in redox reactionsNo bc it cant take electrons
What is the most highly oxidized compound in living systemsCO2
What does a high reduction potential (E) indicateHigh affinity for electrons
What must reduction potentials be in order for a reaction to have a negative free energyE of acceptor &gt; E of donor
Why can’t NAD+ immediately give O2 2 electrons (why must it go through the electron transport chain)O2 can’t accept 2 electrons at once&nbsp;
NADH is usually in _________ reactions, while NADPH is usually in _________ reactionsCatabolic, Anabolic
Why is FAD needed when NADH existsFAD can work with homolytic reactions and can transfer EITHER 1 or 2 electrons at a time&nbsp;<div><br></div><div>This allows it to use O2 as the final electron acceptor (1 electron at a time)</div>
In redox reactions, electrons are transferred from a molecule with a __________ to a ___________ reduction potention(E)Lower to higher
What is special about glutamate regarding metabolismIt is the nitrogen storage so you need a lot of it
Describe the thyroid feedback loopHypothalamus releases TRH<div>TRH activates anterior pituitary</div><div>Anterior pituitary releases TSH</div><div>TSH activated thyroid</div><div>Thyroid releases T4 , which becomes T3</div><div>T3 inhibits the anterior pituitary (so no more TSH is made)</div>
Does positive feedforward existYes! Seen in fructose 1,6-bisphosphate that activates pyruvate kinase (which is much more ahead of f16p)
Reaction rates are more sensitive at ______ substrate concentrationsLow&nbsp;<div>(frequency of substrate meeting enzyme matters)</div>
What do enzymes/substrates do in order to have a high responseThey have a Km near the physiological concentration of S&nbsp;
Where in a pathway is regulation bestIn a very favorable step, which ensures rxn goes forward<div><br></div><div>(Key enzymes operate far from equilibrium)&nbsp;</div>
What is the role of insulin (a hormone) in metabolismINCREASES TRANSCRIPTION of many glycolysis enzymes,&nbsp;<div><br></div><div>DECREASES gluconeogenic enzymes</div><div><br></div><div>So overall encourages usage of sugar, not the production of it</div>
What are isozymes"Different enzymes that catalyze SAME RXN with diff kinetics and regulation<div><br></div><div>Ex: hexokinase I (in all tissues)&nbsp;<span style=""background: var(--field-bg);"">and Hexokinase IV (only in liver, can function at higher glucose levels)</span></div>"
Do proteins have a longer or shorter life than DNAShorter
How does the cell know how old a protein isUbiquitination
Does the cell detect ATP or AMPAMP (AMP kinase does this job)
Decreasing ATP will __________ AMPIncrease (by A LOT)
Is ATP or AMP a more potent allosteric regulatorAMP
Describe the effects of AMPK(inase)-decreases fatty acid synthesis<div>-decreases insulin secretion</div><div><br></div><div>-increases fatty acid oxidation and uptake</div><div>-increases food intake (hunger)</div>
What turns on AMPK(inase)High AMP levels<div>Exercise</div><div>SNS activation</div><div>Lectin, adiponectin</div>
What is the role of hexokinaseConverts glucose into glucose-6-phosphate<div><br></div><div>Glucose-6-phosphate allosterically inhibits hexokinase</div>
Describe the committed step in glycolysisPFK-1 catalyses the conversion of fructose-6-phosphate into fructose-1,6-bisphosphate
Glycolysis is only activated when ATP is _____Low &nbsp;(ATP is a substrate and a negative allosteric effector)
Describe the role of PFK-2/FBPase-2It activates glycolysis if AMP is high (PFK-2 domain of enzyme)<div>It activates gluconeogenesis if AMP is low (FBPase-2 domain of enzyme)</div><div><br></div><div>(Forward and reverse reactions)</div>
How is PFK-2/FBPase-2 changed in order to catalyze forward or reverse rxnSerine 32 is phosphorylated to increase glycolysis (uses PFK-2 domain)<div><br></div><div>Serine 32 is dephosphorylated to decrease glycolysis (uses FBPase-2 domain)</div>
Define glycolytic fluxRate of turnover of molecules through glycolysis, best regulated by irreversible steps
Which enzymes are good targets for glycolytic fluxHexokinase and phosphofructokinase-1 bc these catalyze irreversibly&nbsp;
List functions of carbohydrates-Energy source and storage<div>-structural component of cell walls and exoskeletons</div><div>-informational molecules in cell-cell signaling</div><div>-glycoproteins and proteoglycans&nbsp;</div>
What are epimers"Diastereomers that differ at only one carbon<div><img src=""paste-5919b1424ac82e480ef347c2e16843369491e20a.png""><br></div><div><br></div>"
What do pentose sugars become when they cyclizeFuranose
What do hexose sugars become when they become ringsPyranose
Describe intramolecular monosaccharide cyclizationPenultimate carbon’s OH group attacks carbonyl carbon<div>Carbonyl carbon becomes new chiral center (anomeric carbon)</div><div>Former carbonyl oxygen becomes OH group (if CH2OH is on same side as this OH -&gt; cis -&gt; BETA)</div>
Describe the range of molecular weights of carbohydrates90 g/mol (glyceraldehyde) to 200,000,000 g/mol (amylopectin)
Is glucose a ketose or an aldoseAldose w/ 6 carbons
List the “artificial” sugars-saccharin<div>-aspartame</div><div>-acesulfame potassium</div><div>-sucralose</div>
What is the difference between the aspartame epimers"L,L aspartame tastes sweet
D,L aspartame tastes bitter"
Galactose + glucose =Lactose
Fructose + glucose =Sucrose
Which disaccharide is found in insects and drought-resistant plantsTrehalose
What’s a main difference btwn polysaccharides and polypeptides-no template is used to make polysaccharides&nbsp;<div>-no defined molecular weight</div>
Polysaccharides are synthesized/degraded from their many _________________ endsNonreducing
Describe glycogenMain storage polysaccharide in animals<div>Made of branched glucose</div><div>Soluble</div>
Describe starchMain storage polysaccharide in plants<div>Made of branched glucose</div><div>2 forms: amylose (unbranched) and amylopectin (branched, harder for us to get energy from, insoluble)</div>
Describe celluloseUnbranched glucose found in plants<div>H bonds form btwn adjacent monomers and chains</div><div>Tough and insoluble</div><div>We cannot digest it so it is fiber to us</div>
"<img src=""paste-30f7f0ed3c37bcc516defe8444c4709a03a8d476.png"">"Glycogen
"<img src=""paste-f94c97ee63af40c03f2e60e48afbe2d98db1f85a.png"">"Cellulose (fiber)
"<img src=""paste-91e9dccbe1b1e84628ec207e1e19308d12e81578.png"">"Amylose (starch)
"<img src=""paste-e041fcca52a00a98ef562937cb35798e280b19b1.png"">"Amylopectin (starch)
What enzyme would humans need to be able to digest cellulose&nbsp;Cellulase
Describe chitinUnbranched N-acetylglucosamine<div>Hard, flexible, insoluble&nbsp;</div><div>Digested by chitinase (vertebrates dont have this enzyme)</div><div>Found in exoskeleton of insects, spiders, crabs</div><div>Found in mushroom cell walls</div>
Describe agaroseComplex mix of galactose<div>Used in seaweed cell wall</div><div>Thickening agent (in ice cream, cheese, labs)</div>
Describe glycosaminoglycansLinear polymers of repeating disaccharide units (made of neg charged glucosamine and galactosamine)<div><br></div><div>Form connective tissue</div><div><br></div><div>Found in growth factor heparin (inhibits antithrombin/coagulation)&nbsp;</div>
Describe glycoproteinsProtein with small sugar attached via anomeric carbon<div>Help with protein-protein recognition, growth signals, adhesion, etc</div>
Describe the two types of glycoprotein linkageO-linked: sugar linked to Ser or Thr via glycosidic bond<div>N-linked: sugar linked to Asn via N-glycosyl bond</div>
Blood groups are determined by a&nbsp;Glycolipid
Describe proteoglycans"Glycosaminoglycans attached to large rod-shaped protein in cell membrane to form connective tissue<div><br></div><div>Forms extracellular matrix (along with collagen and elastin)</div><div><br></div><div>Keeps cells together</div><div><br></div><div>Lubricated joints</div><div><br></div><div><img src=""paste-443d05bae31f8d5ac072c0ae58436253d4b060bc.png""><br></div>"
How does H. Pylori cause stomach ulcersBy adhering to sugars on stomach cells
How does influenza enter and exit cellsUses lectin (hemagglutinin) to enter cells<div>Uses neuraminidase to trim sugars on host cell for release (this is inhibited by Tamiflu)</div>
What are selectins"Proteins that recognize sugars<div>Mediate the inflammatory response in rheumatoid arthritis, asthma, psoriasis, MS, organ rejection, etc</div><div><br></div><div><img src=""paste-2e58d461a820cad6bc4ba9dd75fae19d9e7a3e02.png""><br></div>"
What is high fructose corn syrupSucrose (glucose + fructose)
What does short term glucose blood test doDetects gluconolactone (drop of blood tells you blood sugar RIGHT NOW)
What does long-term glucose blood test doA1c measures hemoglobin glycation (estimates blood glucose over the past 120 days)<div><br></div><div>Diabetics have A1c at 6.5% or above</div>
What is the first intermediate made by plants in photosynthesis3 Carbon glyceraldehyde-3-phosphate
Describe inputs and outputs of Calvin cycle in plantsEnzyme: rubisco<div><br></div><div>Inputs: 3 CO2, 6 NADPH, 5 H2O, 9 ATP</div><div><br></div><div>Outputs: glyceraldehyde 3-phosphate, 2 H+, 6 NADP+, 9 ADP, 8 Pi</div>
What does oxygen react to form if it acts in the Calvin cycle&nbsp;2-phosphoglycolate, which is a metabolic waste (takes too much energy to change into something useful)
Can plants store lipids and proteins in seeds for energyYes
Can plants turn fats into sugarsYes (glyoxylate cycle, animals dont do this)
Describe ligninIn plant cell walls<div>Very strong</div>
Describe peptidoglycanN-acetlyglucosamine and N-acetylmuramic acid cross-linked<div>In bacteria extracellular tings</div><div>Inhibited by penicillin, cleaved by lysozyme</div>
__________ is found in wrinkled peas due to lack of starch-branching enzymesAmylose&nbsp;
What is the goal of glycolysis&nbsp;Breakdown of glucose into pyruvate
What can bacteria do with glucoseBuild carbon skeleton of all amino acids, membrane lipids, dNTPs, rNTPs, and cofactors needed for metabolism
How does glycogen enter glycolysisGlycogen is cleaved into glucose by glycogen phosphorylase, yielding glucose 1-phosphate, which needs to be converted into glucose 6-phosphate to enter glycolysis
How do disaccharides enter glycolysisThey’re hydrolyzed Into their respective monosaccaride units
Which came first: photosynthesis or glycolysisGlycolysis (atmosphere was still anaerobic)
How did early organisms find out how to free energy from glucose anaerobically (glycolysis)Activate glucose by phosphorylation&nbsp;<div>Collect energy from the high-energy metabolites</div>
Describe the preparatory and payoff phases of glycolysisPrep: 6C glucose turned into two 3C units, with input of 2 ATP&nbsp;<div><br></div><div>Payoff: oxidation of 3C units into pyruvate</div>
Why is the first step of glycolysis so favorableBc phosphorylation traps glucose inside the cell, lowering intracellular glucose concentration to allow further uptake<div><br></div><div>*catalyzed by hexokinase in euk, and glucokinase in prok.&nbsp;</div>
Describe the first committed step of glycolysisFructose 6-phosphate gets phosphorylated (via PFK-1) to become fructose 1,6-bisphosphate<div><br></div><div>This step requires ATP, and further activates glucose (its a phosphorylation)</div>
What occurs in people with phosphofructokinase deficiency&nbsp;RBCs and muscle cells can’t use glucose as energy&nbsp;<div>Results in glycogen deposits, muscle cramping, and hemolytic anemia</div>
Describe the first production of ATP in glycolysis1,3-BPG + ADP get help from a kinase and generates ATP and 3-phosphoglycerate<div><br></div><div>Highly favorable but also reversible bc of coupling to GADPH reaction</div>
Describe the second production of ATPPhosphoenolpyruvate and ADP get help from pyruvate kinase and make an ATP and a pyruvate<div><br></div><div>Pyruvate tautomerizes into keto form&nbsp;</div><div><br></div><div>Highly favorable</div>
What occurs in people with a pyruvate kinase deficiency2,3-BPG builds up, reducing Hb:O2 binding, leading to hemolytic anemia&nbsp;<div><br></div><div>*most common glycolytic disease</div>
What can pyruvate be used forAerobic conditions: becomes acetyl CoA, goes into citric acid cycle, makes CO2 and H2O<div><br></div><div>Anaerobic conditions: fermented into lactate (ethanol in yeast)</div>
What is the net gain of glycolysis2 ATP, 2 NADH, 2 pyruvate
Where is glycogen storedLiver and muscle
Describe glycolysis in cancer patientsTumor cells take up glucose and do glycolysis 10x faster than other cells<div>SO for PET scans they use a glucose that isn’t metabolized to locate cancer metastasis</div>
Describe type I diabetesToo few beta cells in pancreas (that are supposed to release insulin, and get glucose transporter GLUT4 to plasma membrane) and shortage of insulin<div>So cells can’t get transported to surface, so no glucose can enter cell</div><div><br></div><div><br></div><div>This causes hyperglycemia and ketoacidosis</div>
What is the goal of fermentationRegenerates NAD+ for more glycolysis under anaerobic conditions<br><div>Pyruvate is reduced to lactate</div>
What is the cori cycleDuring hard exercise muscles ferment glycogen, lactate builds up, lactate is transported to liver, and converted back to glucose via gluconeogenesis<div>Then this glucose is released to blood and returned to muscles to replenish glycogen stores</div><div><br></div><div>So glucose -&gt; lactate -&gt; glucose</div>
Describe ethanol fermentationIrreversible reduction of pyruvate to ethanol requires thymine pyrophosphate (TPP) cofactor<div><br></div><div>Enzymes: pyruvate decarboxylase, alcohol dehydrogenase</div><div><br></div><div>Humans only have alcohol dehydrogenase for ethanol metabolism</div>
Where in the cell does glycolysis occurCytosol
Describe the regulation observed in the committed step of glycolysisToo much ATP inhibits PFK-1<div><br></div><div>Fructose-2,6-bisphosphate activates PFK-1<br></div><div><br></div><div>Inhibition of oxidative phosphorylation causes NADH to build up and INHIBIT PFK-1</div>
Why is glucose phosphorylated in the first step of glycolysis&nbsp;It traps glucose in the cell
What makes GAPDH special in the first energy-yielding step in glycolysisGAPDH active site cysteine forms a high-energy thioester intermediate, that can be inactivated by oxidative stress&nbsp;
2,3-BPG __________ hemoglobins affinity for oxygenReduces
PEP is ________ in energy than 2-PGHigher
Lactate and pyruvate are a circulating redox buffer that equilibriate the ____________ ratio across tissuesNADH/NAD+
What’s the main goal of gluconeogenesisTo make glucose from pyruvate (and other metabolites)
What can glucose be made from, what can glucose NOT be made fromCan be made from: pyruvate, lactate, oxaloacetate, or proteins (amino acids)<div><br></div><div>Can NOT be made from: fatty acids (acetyl-CoA)</div>
Which steps are different between glycolysis and gluconeogenesisStep 1 and 3 of glycolysis (phosphorylations)<div>Last glycolysis step (loss of phosphate)</div>
Where does gluconeogenesis occurLiver
Where is biotin cofactor used in gluconeogenesisIn first step (carboxylation)
What are the positive regulators of glycolysisFructose-2,6-bisphosphate and AMP
What is the negative regulator of glycolysisATP
What is the positive regulator of gluconeogenesisATP
What are the negative regulators of gluconeogenesisFructose-2,6-bisphosphate and AMP
What enzyme replaces PFK-1 in gluconeogenesisFructose-1,6-bisphosphatase-1
What enzyme replaces hexokinase in gluconeogenesisGlucose-6-phosphatase
What enzymes replace pyruvate kinase in gluconeogenesis&nbsp;Pyruvate carboxylate and PEP carboxykinase
What are the net inputs and outputs of gluconeogenesisInputs: 4 ATP, 2 GTP, 2 NADH<div><br></div><div>Output: 1 glucose</div>
What is the main goal of the pentose phosphate pathwayUse glucose to make NADPH and ribose-5-phosphate
High [NADPH] ________ pentose phosphate pathwayInhibits
What enzyme is essential in the pentose phosphate pathway&nbsp;Glucose 6-phosphate dehydrogenase<div><br></div><div>This produces NADPH to protect against reactive oxygens</div>
Where is glycogen madeLiver and muscles
What protein primes the formation of glycogenGlycogenin
Describe glycogen synthesis (glycogenesis)Glucose reacts with UTP to make energy for synthesis<div>glycogen synthase catalyzes this rxn</div><div>Glycogen-branching enzyme creates more branches</div>
What is the positive regulator of glycogenesisInsulin activates glycogen synthase (which makes glycogen)
What are the negative regulators of glycogenesisGlucagon and epinephrine
Describe glycogenolysisGlycogen phosphorylase removes glucose from glycogen , generating glucose 1-phosphate (which must be isomerized to glucose 6-phosphate)
What do glucagon and epinephrine doLead to glucose 6-phosphate dephosphoylation for transport OUT of the liver, INTO the bloodstream (blood glucose goes up)<br>
Describe the effects of glucagon and epinephrine in the LIVERActivates glycogenolysis<div>Activates gluconeogenesis</div><div>INHIBITS glycolysis</div>
Describe the effects of glucagon and epinephrine in the MUSCLESActivates glycogenolysis&nbsp;<div>Activates gluconeogenesis</div><div>Activates glycolysis</div>
What is observed in people with glucose 6-phosphate dehydrogenase deficiencyReactive oxygens result in jaundice and kidney failure<div><br></div><div>*can be triggered by fava beans (falafel)</div><div>*common in the Mediterranean&nbsp;</div><div>*protective against malaria due to high oxidative stress in RBCs</div>
Describe the role of PFK-2 / FBPase-2Activates glycolysis if AMP is high (serine 32 is not phosphorylated)<div><br><div>Activates gluconeogenesis if AMP is low (serine 32 is phosphorylated)</div></div>
In the first step of gluconeogenesis, pyruvate is carboxylated with CO2 to ____________ (not found in glycolysis), which is then decarboxylated to phospoenolpyruvate (now caught up with glycolysis)Oxaloacetate
What is the goal of cellular respiration-Cell consumes O2 and releases CO2<div>-provides a lot of energy</div><div>-captures energy stored in lipids and amino acids</div>
How efficient is cellular respiration&nbsp;About 40% efficient
What are the three stages in cellular respirationGlycolysis, citric acid cycle, and electron transport chain
Describe the phosphorylation types in the three stages of cellular respiration&nbsp;Glycolysis: substrate-level phos<div>Citric acid cycle: substrate-level phos</div><div>Electron transport chain: oxidative phos</div>
What is substrate-level phosphorylationMake ATP using a substrate (like PEP)
What is oxidative phosphorylation&nbsp;ATP is made using oxygen and electron transport chain
What’s the goal of the central metabolic pathwaysExtract electrons from glucose, give to ETC, and PRODUCE ATP
When was cellular respiration developedAround 2.5 billion years ago… its used by animals, plants, and microorganisms
Describe locations of the 3 stages of cellular respirationGlycolysis: cytoplasm<div><br><div>Citric acid cycle: mitochondrial matrix</div><div>—&gt; except succiante dehydrogenase is in the membrane</div><div><br></div><div>Oxidative phos: mitochondrial inner membrane</div></div>
Why is it difficult to study cellular respiration in lablysing cells dilutes their enzymes 100-1000x , so they have less proteins, causing gaps in knowledge&nbsp;
Describe pyruvate decarboxylation-Step after glycolysis but before citric acid cycle<div>-pyruvate translocase moves pyruvate into the mitochondria<br><div>-pyruvate loses a CO2, and an NADH is made (and the acetal-CoA!!)</div><div>-this is the first carbon of glucose to be fully oxidized!</div><div>-catalyzed by pyruvate dehydrogenase complex</div></div>
Describe pyruvate dehydrogenase complex"<span style=""background: var(--field-bg);"">-has pyruvate dehydrogenase (E1), dihydrolipoyl transacetylase (E2), and dihydrolipoyl dehydrogenase (E3)</span><div><font face=""-apple-system-body""><br></font></div><div>-requires 5 coenzymes<font face=""-apple-system-body""><br></font><div><div>-biological tethers (covalently bound) move intermediates from one active site to the next<br><div>-has TPP, lipoyllysine, and FAD as prosthetic groups</div><div>-cosubstrates are NAD+ and CoA-SH</div></div></div></div>"
Are coenzymes a permanent part of an enzyme’s structureNo, they dissociate after fulfilling their function<div><br></div><div>Ex: coenzyme A accepts and carries acetyl groups&nbsp;</div>
Do prosthetic groups remain attached to enzyme after completing their functionYes. Theyre strongly bound to the protein<div><br></div><div>Ex: lipoic acid is covalently liked to enzyme via lysine&nbsp;</div>
Describe the advantages of multienzyme complexes like pyruvate dehydrogenase-easy regulation of one subunit affects the whole ting<div>-substrate channeling btwn catalytic sites since they’re close in distance</div><div>-channeling minimizes side reactions</div>
What enzyme performs the first decarboxylation of glucosePyruvate dehydrogenase
When is there a C-C bond formed during the citric acid cycleVery first step (rate-limiting step)
Describe aconitaseHas iron-sulfur center which catalyzes water removal and addition (sensitive to oxidative stress)<div><br></div><div>Is used to isomerize citrate into isocitrate</div><div><br></div><div>Binds to its own mRNA to prevent degradation&nbsp;</div><div><br></div><div>*stereospecific so only R-isocitrate is produced&nbsp;</div>
When are the carbons from glucose oxidized to CO2In the citric acid cycle (1 is oxidized in PDC but yea)
Succinate dehyrogenase is part of ___________ and ___________Citric acid cycle and electron transport chain
&nbsp;How many ATP are formed per glucose molecule after glycolysis, citric acid cycle, and ETC30-32 ATP
How many times must one glucose molecule pass through the citric acid cycle to be fully oxidizedTwice
High energy ___________ the citric acid cycleInhibits
List the activators and inhibitors of the citric acid cycleActivators: NAD+ and AMP (low energy)<div>Inhibitors: NADH and ATP (high energy)</div>
What in the citric acid cycle detects the energy levels of the cellPyruvate dehydrogenase phosphorylation
What is citrate synthase inhibited bySuccinyl-CoA (bc alpha ketoglutarate is a big branch point for amino acid metabolism)
Describe the activation and inactivation of pyruvate dehydrogenaseIf ATP phosphorylates E1 —&gt; INACTIVATION<div><br></div><div>If E1 is dephosphorylated —&gt; ACTIVATION (and then pyruvate can become acetyl-CoA)</div>
What’s an anaplerotic reactionA reaction that replenishes intermediates such that citric acid cycle can continue<div><br></div><div>Bring a CO2 in (maybe as HCO3-) to increase the carbon chain of another intermediate</div><div><br></div><div>**requires biotin to grab a CO2 and move it where it needs to go</div>
What is the goal of the electron transport chainTake energy from carbs, lipids, AA, NADH, and FADH2 and make it ATP
What’s the final electron acceptor in the electron transport chain in eukaryotesOxygen
How is ADP phosphorylated in oxidative phos, since this reaction is so unfavorable&nbsp;The phosphorylation isn’t directly through the ADP, but via the flow of protons DOWN the electrochemical gradient
Membranes are ____________ to ionsImpermeable
Describe the structure of the mitochondria<u>Outer membrane</u> is porous, allows metabolites to pass<div><br></div><div><u>Intermembrane space</u> is like cytosol, but lower pH</div><div><br></div><div><u>Inner membrane</u> is impermeable, with proton gradient across it (where ETC happens), has folds (cristae) increase surface area</div><div><br></div><div><u>Matrix</u> is where citric acid cycle happens, some parts of lipid and AA metabolism, high pH</div>
Describe FMN and FAD-initial electron acceptors for complex I and complex II<div>-can carry 2 electrons by transferring ONE AT A TIME</div>
What are the components of the electron transport chain complexes-FMN or FAD<div>-cytochromes a, b, c</div><div>-iron-sulfur cluster</div><div>-NADH dehyrogenase</div><div>-succinate dehydrogenase</div><div>-ubiquinone</div><div>-cytochrome oxidase</div>
What are cytochromesPorphoryin ring derivatives that coordinate iron<div>Transfer electrons ONE AT A TIME<br><div><br></div><div>A, b, and c differ by ring additions (named for absorptions)</div></div>
Describe iron-sulfur clustersCoordinated by cysteines in the protein<div><br></div><div>Carry ONE ELECTRON AT A TIME</div>
Describe ubiquinone and ubiquinolAKA coenzyme Q10<div><br></div><div>Lipid-soluble compound that accepts 2 electrons and 2 protons (one at a time), and is reduced to ubiquinol</div><div><br></div><div>Ubiquinol freely diffuses in the membrane, carries electrons with protons from one side of membrane to the other side</div><div>(Transports electrons from complexes I/II to complex III )</div>
For a negative delta G, you need a ________ delta E (reduction potential)Positive
Which component can NOT use one electron at a timeNADH (can only accept two at a time)
Describe complex IHas over 40 polypeptide chains, and is encoded by BOTH nuclear and mitochondrial genes
Describe NADH and FMN at start of electron transport chainNADH cant cross membrane so it has to be transported into mitochondria by malate-aspartame shuttle<div><br></div><div>NADH (in matrix) gives FMN 2 e-, and sends 1 e- at a time towards oxygen</div><div><br></div><div>Many iron-sulfur clusters pass 1 e- at a time toward ubiquinone</div><div><br></div><div>FOUR PROTONS PUMPED PER NADH via proton wires, ubiquinone picks up 2 protons</div>
What is complex IISuccinate dehydrogenase
What’s the difference btwn complex I and complex IIComplex II does NOT transport any protons
Describe complex II(Succinate dehydrogenase)<div><br></div><div>Uses FAD to accept 2 e- from succinate, which are passed ONE AT A TIME via iron-sulfur clusters to ubiquinone, which becomes ubiquinol&nbsp;</div>
Describe complex IIIHas iron-sulfur clusters, cytochrome b, and cytochrome c<div><br></div><div>Uses 2 electrons from ubiquinol to reduce 2 molecules of cytochrome c</div><div><br></div><div>Does the Q cycle —&gt; 4 extra protons being transported to intermembrane space</div>
How are reactive oxygen species producedWhen electron entry and transfer is mismatched, superoxide radicals are made and partially reduced ubiquinone radical donates an electron to O2<div><br></div><div>This makes a highly reactive hydroxyl free radical (can be removed by enzymes)</div><div><br></div><div>This is the problem with the Q cycle</div>
What’s the first and second mobile electron carrier1st: ubiquinol<div>2nd: cytochrome c</div>
Describe cytochrome cSoluble heme-containing protein in intermembrane space<div><br></div><div>Heme iron Fe3+ is reduced to Fe2+ to carry the electron</div><div><br></div><div>Carries a SINGLE ELECTRON from complex III to complex IV</div><div><br></div><div>Released from mitochondria to form the apoptosome in apoptosis</div>
Describe complex IVHas 13 subunits, 2 heme groups, and copper ions to accept electrons from cytochrome c<div><br></div><div>Copper ions transfer two electrons (from 2 cyt c) to reduce half an O2 into an H2O&nbsp;</div><div><br></div><div>Results in an extra 2 protons to pass through the membrane</div><div><br></div><div>*inhibited by cyanide, which binds to iron in the complex&nbsp;</div>
How much ATP is made from an NADH in the electron transport chain2.5 ATP
How much ATP is made from an FADH2 in the electron transport chain1.5 ATP
Which complex does NOT move protonsComplex II
How is the electrochemical proton gradient created-they transportation of protons across membranes by complex I, III, and IV<div>-the removal of protons from the matrix by reduction of ubiquinone and oxygen</div><div>-the release of protons into intermembrane space (oxidation of QH2)</div>
Describe ATP synthase-has F0 (integral) to transport protons, and F1 to do ATP synthesis<div>-F1 is a hexamer arranged in three alpha-beta dimers, with loose ADP/Pi and tight conformations</div><div>-1 proton rotates it by 36 degrees, so it turns 120 degrees per ATP (bc 3.33 protons are needed to make an ATP)</div><div><br></div><div>-proton translocation (as H+ not H3O+) via a carboxylate causes a rotation of the F0 subunit and the central shaft</div><div><br></div><div>-conformational change in all three alpha-beta pairs promotes condensation of ADP/P into ATP</div>
What is the function of ATP translocaseBinds ATP and takes it out the cell<div>Binds ADP and Pi and transports it into the mitochondria</div>
How is oxidative phos regulated<div>-substrate (NADH, ADP, and Pi) availability</div><div>-during low oxygen and low pH, inhibitor of F1 (IF1) prevents ATP synthase from making ATP</div><div><br></div><div>-inhibiting oxidative phos leads to accumulation of NADH, which causes feedback inhibition of PFK-1 in glycolysis!</div><div><br></div>*oxidative phos can go in reverse
In photosynthetic organisms, light causes a ___________________ btwn a pair of chlorophyll moleculesCharge separation
What is the ultimate electron acceptor in photosynthesis&nbsp;NADP+
What is the byproduct of water oxidation&nbsp;Oxygen
What is the source of electrons in photophosphorylation&nbsp;Water
What do photopigments do in photophosphorylationAbsorb different wavelengths of light
Describe the order of the components in photosynthesisPhotosystem II —&gt; cytochrome —&gt; photosystem I&nbsp;
Describe noncyclic photosynthesisLinear path through two systems that makes both ATP and NADPH
Describe cyclic photosynthesis&nbsp;Cycles through photosystem I and produces more ATP&nbsp;
What is the ratio of ATP to NADPH needed by the cell3:2
What caused the great oxygenation event 2.3 billion years ago (banded iron in rock)The development of photosystem II, oxygen is released there
Describe the Q cycle in the ETC"-Complex III has two binding sites, one for QH2 (ubiquinol) and one for Q (ubiquinone)<div>-with 2 QH2 and 1 Q in the membrane, one Q and one QH2 bind in their sites</div><div>-QH2 loses 2 protons and becomes semiquinone (radical), 2 protons go into intermembrane space</div><div>-electron from semiquinone are transferred to cytochrome c</div><div>-semiquinone’s (now Q) other electron goes to the Q @ other site, making that Q a semiquinone</div><div>-Q is replaced by QH2 bc of binding preferences</div><div>-new QH2 does same thing other QH2 did, giving 2 protons to IM space, and reducing cytochrome c</div><div>-second electron now goes to semiquinone at other binding site, which can now gain 2 protons from <u>matrix</u>, and become QH2</div><div>-QH2 and Q dont match binding preferences and dissociate from complex III</div><div><br></div><div><br></div><div>Overall: 4 protons moved into IM space, 2 reduced cytochrome c can go to complex IV now</div><div><br></div><div><img src=""paste-ff698d5fc630aa0e89676ccea6edfd2691cf7bd2.png""><br></div>"