Metabolism

Metabolism builds up Catabolism breaks down

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Anabolic pathways take products from catabolic pathways and builds up

KEGG pathway sum total of metabolic pathways (map) Glucose isnt just used for energy Can break down and use for energy Build up make starch/glycogen/sucrose (depending on organism) for storage Extracellular matrix and cell wall polysaccharides o Synthesis of structural polymers Oxidation via pentose phosphate pathway (Ribose 5 phosphate) Oxidation via glycolysis (pyruvate)

Glycolysis occurs in the cytoplasm Whats happening and Why? EXAM QUESTION** Is the sequence of reactions that metabolizes one molecule of glucose to two molecules of pyruvate with the net production of two molecules of ATP o Anaerobic o It evolved before the accumulation of hight amts of oxygen in the atm Pyruvate o Can be further processed anaerobically (fermented) to lactate (lactic acid fermentation) or ethanol o MORE GO INTO SLIDES

In Eukaryotes Glycolysis occurs in the cytoplasm and pyruvate can then be transported into the *mitochondria?*

Invest 2 ATPs rearrange and get a payoff of 4 ATPs ****Study from overview of glycolysis page in slides!!!!!***** ***How could something evolve that requires oxygen that evolved before there were significant amounts of oxygen in the atmosphere??? Glycolysis dont need oxygen What about the Krebs Cycle??? Steps of Glycolysis: 1. Phosphorylation of glucose adding a phosphate Hexokinase Pay attention to the delta G = -16.7 kJ/mol (what is the significance of negative? going to proceed energetically very favorable) Why Phosphorylate? o Prevents glucose from passing through the cell membrane (negatively charged cannot leave the cell) o Phosphate group activates the molecule for other rxns some of the energy frot eh ATP has been transferred to glucose o Many enzymes can bind to the phosphate easily Hexokinase o Found in al cells o High affinity for sugar, but not highly specific for glucose o Inhibited by glucose 6 phosphate o Highly exothermic reaction (essentially irreversible)

2. Isomerization rearrange molecule delta G = 1.7kJ/mol (close to zero)

3. second phosphorylation second investment fo energy highly exothermic rxn (essentially irreversible) 4. cleaves six carbon sugar into two three-carbon fragment

reversible

5. The other product fo step 4 (4, dihydroxyacetone phosphate) is isomerized to the other (glyceraldehyde 3-phsophate) ENDS PREPERATORY PHASE delta G = 7.5 kJ/mol 6. Add an inorganic phosphate how is this different?? o Not attached to carbon, not attached to anything (other phosphates were attached to ATP o Delta G = 6.3 kJ/mol o Energy pay off begins 7. remove a phosphate, place on ADP why is the enzyme that does this called a kinase? o Kinases add phosphates-this is removing one o Named backwards o Can catalyze forward or reverse rxns? 8. move the phosphate 9. make double bond (rearrange to get more energy out of it) 10. creating pyruvate (different amts of energy required for each step) conclusion use 2 ATP in preparation phase used 2 molecules of inorganic phosphate gained 4 ATP from payoff phase gained .. MORE!!! MANY GLYCOLYTIC ENZYMES OCCUR IN MULTIPROTEIN COMPLEXES

Why? - will help products go from one enzyme to the other dont want one step of glycolysis to occur and be too far away from the next molecule reverse glycolysis gluconeogenesis

Krebs Cycle

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memorize different steps. memorize Enzymes substrates each stepwhats occurring and why is it occurring? Know how many carbons are present at each stage!! Occurs in the inner part of the mitochondriawhat is the advantage of this? Why is it a cycle and not linear? What are the advantages/disadvantages of a cycle? o Disadvantagedependent on the products of the cycle to function o Advantageeach product functions in the cycle but also to build other things. Dont have to have complete cycle for other things. (see diagram in slides) Krebs initial model was missing something. Pyruvateacetyl CoA Puruvate dehydrogenase takes PYRUATE and attaches to acetyl CoA Condensation adds water removes CoA-SH. Catalyzed by citrate synthase. Before the common ancestor of everything living today, there was the krebs cycle. Very shortly after the origin of life A reverse krebs cycle? some steps can reverse, some cannot (energetically it is unfavorable to go in the opposite direction for some of them) How would a reverse krebs cycle function? kelvin cycle similar to photosynthesis gluconeogenesis how could the cycle precede life? THINK ABOUT THIS!*** How can you have a series of rxns without the enzymes?

More catalysts than just enzymes. Inorganic catalysts Experiment was able to reproduce 3 steps with inorganic catalysts.

Not just for synthesizing energy Can be compared to miler experiment can drive the krebs cycle in reverse at least in reverse just using sunlight. Might have been crucial for the origin of life May not have been driven abiotically by sunlight, but may have been ..

Catabolism driven by oxidation (loe) Anabolism driven by reduction (goe) Oxidation needs to b carefully controlled Electrons move from one pathway to another (glycolysis, krebs, etc) Electron carriers molecules that can safelyc ary electrons FAD usually bound to specific enzymes o Disadvantage In a long line of reactions some delta Gs will move rxn forward/backwards. Need to take into account the concentrations of each step. A pathway that is going to wok will level out.

The Cori cycle recycling lactate. Sent to liver made back into glucose. Liver has high NAD+/NADH ratio, readily produces glucose **know what this cycle is exam question citric acid cycle is ancient how likely to create new enzymes with same function? one of the enzyes replaced in de novo was one used in the krebs cycle (citrate synthase) there is more than one way to enter or exit the krebs cycle

4 anaplerotic reactions replenish the krebs cycle ****partial krebs cycleprovide building blocks for other molecules why do we see this in parasites all the time> o theyre using resources from their hostnot a big need for all their own materials o cant actually convert our fatty acids to glucose through the krebs cycle. Why? 2 carbons enter krebs cycle go through krebs cycle back up to phosphoenolypyruvate. o No net increase in carbons from the fatty acids. Cant convert.

Glyoxylate cycle similar to krebs take fats and build glucose Entering the cycle with another acetyl-CoA Acetyl Co-A enters the cycle in 2 places! Succinate is a product, nto intermediate HUMANS CANNOT DO THIS o Convert fat to glucose COMPARE THIS TO THE KREBS CYCLEWHAT IS DIFFERENT, ETC.

POTENTIAL EXAM QUESTION: humans cannot directly convert fat into clucose, but the carbn from fat can end up as part of gucose. Expain how/why this is possible. How do we go into slides!

Regulating Metabolism

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Regulating glycolysis/gluconeogenesis: need to be able to turn one on and one off abundance of ATP ADP and AMP, has an effect on enzymes that turn one on or off. o why does this make sense?? o a lot of AMP need more ATP o a lot of ATP will slow down glycolysis o citrate feeding into the krebs cycle. Will turn down Go over slides and think how would this be regulated? the first three steps are important in regulation NAD, NADH different ways of cell sensing and adjusting krebs cycle accordingly

Regulation of glyoxylate cycle GO TO SLIDES!

E. Coli dont have mitochondriahow can they do this> mitochondria evolved from bacteriaalready have ability to do it

Mitochondria: inner part matrix gererate a lot of possible dangerous materials can create reactive oxygen secies if they werent contained in the mitochondria, it could be a problem. It could react with DNA and damage it al the extra membraneincreased surface area o proteins of electron transport chain is in the inner membrane o increase the surface area of the inner mitochondria o

2 membranes where from? Origin inner probably from bacteria, outer membrane-from engulfing the cell (host) outer membrane-more permeable inner membrane o impermeable, full of proteins o electron t c o ATP synthase matrix o innermost space pyruvate dehydrogenase o (most) citric acid cycle enzymes o NAD/NADH o mitochondrial genome (usually) o not a lot of genesonly what is necessary. Most of what used to be there is already in the cells DNA.

**Whats the pupose of fermentation (regenerate NAD) to proceed with glycolysis? No amount of fermentation is going to allow the krebs cycle to proceed why not??? NAD cant enter the mitochondria. Must be in the mitochondria to effect the krebs cycle. Inner membrane is very impermeable

CHEMIOSMOSIS energy derived from electron transport rxns is temporarily stored as a transmembrane difference in charge and pH, which subsequently drives the formation of ATP in oxidative phosphorylation and photophosphorylation setting up a gradient that wil turn a turbine the electro chemical proton gradient and ATP synthase

at the inner mitochondrial membrane, a high energy electron is passed along the etc the energy released pumps hydrogen out of the matrix space the gradient

Electron Transport Chain Q, complex 1,3,4 iron sulfur complexes help electrons move through the chain genes for proteins in the mitochondria mutatemitochondria has high mutation ratecan change quickly 2 - succinate fumarate (part of the krebs cycle)

oxidation of formic acid in some present day baceria donated protons COMPLEX 1 a series of iron-sulfur centers chanel the electrons through the comples 4 protons are pumped out of the mitochondrial matrix protons are obund to the complex, as elecrons pass, the proton binding site is exposed to the intermembrane space and released 2 electrons are passed off to Q

COMPLES 2 succinate dehydrogenase! also has chain of iron-sulfur centers to channel electrosn contains FAD takes electrons from succinate passes electrons along in the chain no proton pumping

COMPEX 3 a dimer comples (dimer of identical monomers)

two routes for electron flow 2 eectrons come in, and are divided, and passed on individually protons are released, not pumped

COMPLEX 4 three subunits iron-copper centers bind electrons (stable) oxygen takes electrons and produce water protons are pumped

Electron Transport Chain

Electron Transport Chain Electrons move from one metabolic pathway to another

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establishes a proton gradient essentially spins a turbine and generates ATP on the inner mitochondrial membrane protons I higher concentration on one side bound to turbine causes it to spin 3 states open empty loose ADP Tight ATP Binding-change model for ATP synthase One beta site binds to ATP tightly Another has loose binding to ADP Third site is empty The proton-motive force causes rotation of the central shaft GO INTO SLIDES AND READ!

ATP builds up in the mitochondriamembrane bound proteins facilitate the movement out costs 1 proton Inner membrane is not permeable to NAD or NADH. Fermentationgenerate NAD. What happens to NADH produced in glycolysis? Cant transfer NADH into the mitochondria, but we can exchange the electrons! Glycerol 3-phosphate shuttle Malate alpha-ketoglutarate transporter. o Take nadh convert oxaloacetate to malate, converting NADH to NAD, move malate into mitochondria then do the reverse and get back the NADH

Other proton gradients Photophosphorylation Electrons are excited by photons and directed through an electron transport chain which establishes a proton gradient