Biochem Notes

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Biochemistry 3511Introduction to Metabolism (Chapter 14, Sections 1-3)

1. Overview of Metabolism• Metabolic pathways consist of a series of enzymatic

reactions• Thermodynamics dictates the direction and regulatory

capacity of metabolic flux• Metabolic flux must be controlled

2.“High Energy” Compounds (ATP)• Phosphoryl group-transfer potential and how it can be

coupled to drive endergonic reactions

3.Oxidation-Reduction Reactions (NAD+, NADH, FAD, FADH2)• NAD+ and FAD are electron carriers• Nernst equation describes oxidation-reduction reactions• Favorableness of a reaction can be determined by

measuring reduction potential differences

MetabolismSeries of biochemical reactions

by which material substance(food) is broken down into simpleproducts, which are then used for

the synthesis of complexcompounds (e.g. DNA).

Metabolism

MetabolismSeries of biochemical reactions

by which material substance(food) is broken down into simpleproducts, which are then used for

the synthesis of complexcompounds (e.g. DNA).

Metabolism

Approximately 4,000 knownreactions, and thus 4,000

known enzymes!

The overall process through which living organisms acquire free energy (fromfood) and utilize the free energy to construct complex molecules (e.g. DNA).

Living organisms do not operate at equilibrium but require a constant influx of nutrients.

Degradation of compounds intocommon building blocks

Construction of complexmolecules required for life

Metabolism: Catabolism & Anabolism

Metabolism: Nutrition

• Autotrophs– Chemolithotrophs– Photoautotrophs

• Heterotrophs

• Anaerobes– Obligate anaerobes– Facultative anaerobes

• Aerobes– We are obligate aerobes!

CatabolismFood is converted into common

intermediates (glucose, pyruvate,Acetyl-CoA, NH3, CO2) via two

processes: glycolysis and the citricacid cycle.

Catabolism

Glycolysis and the Citric Acid Cycleconvert:

1. ADP → ATP2. NAD+ → NADH3. FAD → FADH2

•Catabolism will use the free energygenerated by the breakdown of foodinto driving ATP generation (ourenergy currency).

•Catabolism will store the electronsreleased by the breakdown of food inNADH and FADH2 (electroncarriers).

Catabolism

Obtain free energy from food (sugar) by carrying out its stepwise oxidation andtransferring the released energy and electrons to carrier molecules (ATP, NADH, etc.).

Catabolism

The final step in catabolism involvesconverting the electron carriers(NADH, FADH2) into our energy

currency (ATP) via oxidativephosphorylation.

The final electron acceptor is oxygenwhich is converted into water.

Catabolism

Catabolismfull catabolic pathway

Catabolism (degradation) generates NADPH (in addition to NADH, FADH2), ATP andsimple products.

Anabolism uses the NADPH, ATP and simple products to generate complexmetabolites, NADP+ and ADP.

Catabolism & Anabolism:Connected Pathways

Vitamins: present functionality lacking in an organism’s proteins/enzymes,and cannot be synthesized by that organism. Most water-soluble vitamins

are converted to coenzymes.

Rickets

Many Metabolic Reactions Require Vitamins

Vitamins: present functionality lacking in an organism’s proteins, andcannot be synthesized by that organism. Most water-soluble vitamins are

converted to coenzymes.

Rickets

Many Metabolic Reactions Require Vitamins

Pellagra Symptoms1. Diarrhea2. Dermatitis3. Dementia

Vitamins: how to get functionality not present in proteins, and not able to be synthesized by the organism.

Vitamins: Niacin

Obtained by eating fish, chicken, turkey,pork, peanuts, avocados, mushrooms...

Vitamins: how to get functionality not present in proteins, and not able tobe synthesized by the organism.→ Are incorporated in the biosynthesis of key metabolites.

pantothenic acid“vitamin B5”

Obtained by eatingmushrooms,cheese, oily fish,avocados...

Vitamins: Pantothenic Acid

cobalamin“vitamin B12”

vitamin B12 deficiency → vitiligo, psoriasis

Vitamins: Cobalamin (B12)Vitamins: how to get functionality not present in proteins, and not able to be synthesized by the organism.

Obtain by eating shellfish, oily fish, cereals,soy products, beef, milk, cheese, eggs...

Minerals also Assist Metabolic Reactions

(signal transduction,bones, teeth)

(reactions involving ATPand other nucleotides,in synthesis of DNA, RNA,and proteins)

(hemes)

(enzymatic cofactors)

MetabolismWith up to 4,000 possible

reactions in a host of pathways,how does the cell manage all of

these processes???

Metabolism

MetabolismWith up to 4,000 possible

reactions in a host of pathways,how does the cell manage all of

these processes???

Compartmentation!

Metabolism

Different Metabolic Pathways Occur inDifferent Cellular Compartments

Compartmentation in multicellular organisms also occurs on the tissue and organ levels.

Directing Metabolic Information Flow (Flux)

• The majority of metabolicreactions are near-equilibrium.

∆G ≈ 0 Reactions can be easily

reversed by changing thesubstrate/product ratio.

• Some reactions are far fromequilibrium.

∆G << 0 Reactions difficult to reverse

by changing thesubstrate/product ratio.

• How does metabolism controlwhat path a compound shouldtake?

Metabolism: Routing Information Flow (Flux)

Metabolic flux: the rate of flow of metabolites through a series oftransformations (metabolic pathway).

Flux = J = v f " vr

Jeq = 0 so v f = vr

When far fromequilibrium... J " v f

Use an irreversible enzymaticstep to commit the substrate

down a given pathway.

Metabolism:Routing Information Flow (Flux) ⇒ 3 Ways

Use an irreversible enzymaticstep at the end of the pathway,

making the entire pathwayirreversible.

P2The catabolic and anabolic pathway differ.

Use an irreversible enzymaticstep to commit the substrate

down a given pathway.

Use an irreversible enzymaticstep at the end of the pathway,

making the entire pathwayirreversible.

P2The catabolic and anabolic pathway differ.

Mechanisms to Control Metabolic Flux

Flux Control Mechanisms

1. Allosteric regulation and feedback control

2. Regulation by covalent modification

3. Independent control of interconversions (substrate cycling)

4. Genetic regulation

allosteric regulation and feedback

Metabolic Flux Control:Allosteric Regulation

Effectors are often substrates,products, or cofactors of the pathway.

allosteric regulation and feedback

Metabolic Flux Control:Allosteric Regulation

covalent modification(phosphorylation & dephosphorylation)

“Off” “On”

Metabolic Flux Control:Covalent Modification

covalent modification(phosphorylation & dephosphorylation)

Metabolic Flux Control:Covalent Modification

glycogen phosphorylase

independent control of interconversions

Rates of forward andreverse reactions can bevaried independently.

Flux = J = v f " vr

Metabolic Flux Control:Independent Control of Interconversions

Metabolic Flux Control:Genetic Regulation

genetic regulation (products stop enzyme transcription)

Reaction Energetics

ΔGo' = +13.8 kJ/mol

Glycolysis

Is this conversionfavorable or unfavorable?

Reaction Energetics

The energy stored inphosphoryl groups is

used to drivethermodynamically

unfavorable reactions.

These phosphatehydrolysis reactions are

thermodynamicallyfavorable reactions,but kinetically stable

(very slow).

Reaction EnergeticsCoupled reactions can drive unfavorable processes!

What else can we couple this reaction with?

Reaction Energetics

Because the phosphate is not coming from ATP,this is called “substrate-level phosphorylation”.

Another example

Oxidation-Reduction (Redox) Reactions• The reduction potential (E ) describes the tendency for an oxidized compoundto gain electrons (become reduced); these values can be looked up.

• The change in reduction potential (∆E ) for a reaction describes the tendencyfor a given oxidized compound to accept electrons from a given reducedcompound. ∆E is the electromotive force.

• The greater the reduction potential, the more negative the free energyand the more favorable the reaction.

∆G = -nF ∆E

Oxidation-Reduction (Redox) Reactions• Redox reactions generate force/energy.

The more positive the standard reductionpotential, the higher its affinity for

electrons.The more positive the standard reduction

potential, the more negative ∆G.

Arrange the equation to obtain a positivestandard reduction potential.

Fe → Fe2+ + 2e - 0.44 VCu2+ + 2e- → Cu 0.34 V--------------------------------Fe + Cu2+ → Fe2+ + Cu 0.78 V

In this case, the reaction will oxidize Feand reduce Cu2+.

Oxidation-Reduction (Redox) Reactions• Redox reactions generate force/energy.

electrons.The more positive the standard reduction

potential, the more negative ∆G.

Arrange the equation to obtain a positivestandard reduction potential.

Fe → Fe2+ + 2e - 0.44 VCu2+ + 2e- → Cu 0.34 V--------------------------------Fe + Cu2+ → Fe2+ + Cu 0.78 V

In this case, the reaction will oxidize Feand reduce Cu.

Which metal will be oxidized,silver or sodium?

Oxidation-Reduction (Redox) Reactions: Alternative Mode of Calculation

∆E = E (e-acceptor) - E (e-

donor )E = standard reduction potential

∆E = 0.34 – (-0.44) = 0.78

⇒ Once you know which metal accepts theelectrons, you can just plug in the standard

reduction potentials.

Remember: you want to have a positivestandard reduction potential (ΔE ) to get a

negative ∆G.

electrons.

Oxidation-Reduction (Redox) Reactions

Radicals (species with unpairedelectrons) are stabilized byconjugation with adjacent multiplebonds (resonance forms).Addition of H• is really the paired (orstepwise) addition of an electron anda proton.

• NAD+ and FAD are electron carriers:they accept electrons from metabolitesand transfer them to other compounds.

You can also use half reactions for biological reactions!

Which compoundgets oxidized,

oxygenor lactate?

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