11/24/2009Biochemistry: Metabolism I General Metabolism I Andy Howard Introductory Biochemistry 24 November 2009

11/24/2009Biochemistry: Metabolism I

General Metabolism I

Andy HowardIntroductory Biochemistry

24 November 2009


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Metabolism:the core of biochem All of biology 402 will concern itself with the specific pathways of metabolism

Our purpose here is to arm you with the necessary weaponry


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What we’ll discuss

Metabolism Definitions Pathways Control

Metabolism, cont’d Feedback Phosphorylation


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Metabolism Almost ready to start the specifics(chapter 18)

Define it!Metabolism is the network of chemical reactions that occur in biological systems, including the ways in which they are controlled.

So it covers most of what we do here!


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Intermediary Metabolism

Metabolism involving small molecules

Describing it this way is a matter of perspective:Do the small molecules exist to give the proteins something to do, or do the proteins exist to get the metabolites interconverted?


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How similar are pathways in various organisms? Enormous degree of similarity in the general metabolic approaches all the way from E.coli to elephants

Glycolysis arose prior to oxygenation of the atmosphere

This is considered strong evidence that all living organisms are derived from a common ancestor


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Anabolism and catabolism Anabolism: synthesis of complex molecules from simpler ones Generally energy-requiring Involved in making small molecules and macromolecules

Catabolism: degradation of large molecules into simpler ones Generally energy-yielding All the sources had to come from somewhere


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Common metabolic themes

Maintenance of internal concentrations of ions, metabolites, & (? enzymes)

Extraction of energy from external sources

Pathways specified genetically Organisms & cells interact with their environment

Constant degradation & synthesis of metabolites and macromolecules to produce steady state


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Metabolism and energy


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Metabolic classifications

Carbon sources Autotrophs vs. heterotrophs Atmospheric CO2 as a C source vs. otherwise-derived C sources

Energy sources Phototrophs vs. chemotrophs (Sun)light as source of energy vs. reduced organic compounds as a source of energy


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Fourway divisions (table 17.2)

Energy/Carbon Phototrophs:Energy from light

Chemotrophs:Energy from reduced organic molecules

Autotrophs:Carbon from atmospheric CO2

Photoautotrophs:Green plants, cyanobacteria, …

Chemoautotrophs:Nitrifying bacteria, H, S, Fe bacteria

Heterotrophs:Carbon from other [organic] sources

Photoheterotrophs:Nonsulfur purple bacteria

Chemoheterotrophs:Animals, many microorganisms, . . .


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Another distinction: the organism and oxygen Aerobes: use O2 as the ultimate electron acceptor in oxidation-reduction reactions

Anaerobes: don’t depend on O2

Obligate: poisoned by O2

Facultative: can switch hit


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Flow of energy

Sun is ultimate source of energy Photoautotrophs drive synthesis of [reduced] organic compounds from atmospheric CO2 and water

Chemoheterotrophs use those compounds as energy sources & carbon; CO2 returned to atmosphere


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How to anabolism & catabolism interact? Sometimes anabolism & catabolism occur simultaneously.

How do cells avoid futile cycling? Just-in-time metabolism Compartmentalization:

Anabolism often cytosolic Catabolism often mitochondrial


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Pathway A sequence of reactions such that the product of one is the substrate for the next

Similar to an organic synthesis scheme(but with better yields!)

May be: Unbranched Branched Circular


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Catabolism stages

Stage 1: big nutrient macromolecules hydrolyzed into their building blocks

Stage 2: Building blocks degraded into limited set of simpler intermediates, notably acetyl CoA

Stage 3: Simple intermediates are fed to TCA cycle and oxidative phosphorylation


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Anabolism stages

Short list ofsimple precursors

These are elaboratedin characteristic ways to build monomerse.g.: transamination of -ketoacids to make -amino acids

Those are then polymerized to form proteins, polysaccharides, polynucleotides, etc.


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Some intermediates play two roles Some metabolites play roles in both kinds of pathways

We describe them as amphibolic Just recall that:catabolism is many down to few, anabolism is few up to many


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Differences between catabolic and anabolic pathways Often they share many reactions, notably the ones that are nearly isoergic (G ~ 0)

Reactions with G < -20 kJ mol-1 are not reversible as is

Those must be replaced by (de)coupled reactions so that the oppositely-signed reactions aren’t unfeasible


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Other differences involve regulation Generally control mechanisms

influence catalysis in both directions

Therefore a controlling influence(e.g. an allosteric effector)will up- or down-regulate both directions

If that’s not what the cell needs, it will need asymmetric pathways or pathways involving different enzymes in the two directions


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ATP’s role We’ve discussedits significance asan energy currency

It’s one of two energy-rich products of the conversion of light energy into chemical energy in phototrophs

ATP then provides drivers for almost everything else other than redox


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NAD’s role

NAD acts as asan electronacceptor via nettransfer of hydride ions,H:-, in catabolic reactions

Reduced substrates get oxidized in the process, and their reducing power ends up in NADH

Energy implied by that is used to make ATP (3.5 ATP/NAD) in oxidative phosphorylation

QuickTime™ and a decompressor

are needed to see this picture.

Image courtesy Michigan Tech Biological Sciences


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NADPH’s role

Involved inanabolic redoxreactions

Reducing power in NADPH NADP used to reduce some organic molecule

Involves hydride transfers again NADPH regenerated in phototrophs via light-dependent reactions that pull electrons from water


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How do we study pathways?

Inhibitor studies Mutagenesis Isotopic traces (radio- or not) NMR Disruption of cells to examine which reactions take place in which organelle


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Why multistep pathways?

Limited reaction specificity of enzymes

Control of energy input and output: Break big inputs into ATP-sized inputs

Break energy output into pieces that can be readily used elsewhere


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iClicker quiz question 1

A reaction A+B C+D proceeds from left to right in the cytosol and from right to left in the mitochondrion. As written, it is probably

(a) a catabolic reaction (b) an anabolic reaction (c) an amphibolic reaction (d) we don’t have enough information to answer.


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iClicker quiz question 2 An asymmetry between stage 1 of catabolism (C1) and the final stage of anabolism (A3) is (a) A3 always requires light energy; C1 doesn’t

(b) A3 never produces nucleotides;C1 can involve nucleotide breakdown

(c) A3 adds one building block at a time to the end of the growing polymer;C1 can involve hydrolysis in the middle of the polymer

(d) There are no asymmetries between A3 and C1


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iClicker quiz question 3

Could dAMP, derived from degradation of DNA, serve as a building block to make NADP? (a) Yes. (b) Probably not: the energetics wouldn’t allow it.

(c) Probably not: the missing 2’-OH would make it difficult to build NADP

(d) No: dAMP is never present in the cell


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Regulation Organisms respond to change

Fastest: small ions move in msec Metabolites: 0.1-5 sec Enzymes: minutes to days

Flow of metabolites is flux: steady state is like a leaky bucket

Addition of new material replaces the material that leaks out the bottom


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Metabolic flux, illustrated Courtesy Jeremy Zucker’s wiki

http://bio.freelogy.org/wiki/User:JeremyZucker#Metabolic_Engineering_tutorial


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Feedback and Feed-forward

Mechanisms by which the concentration of a metabolite that is involved in one reaction influences the rate of some other reaction in the same pathway


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Feedback realities Control usually exerted at first committed step (i.e., the first reaction that is unique to the pathway)

Controlling element is usually the last element in the path

Often the controlled reaction has a large negative Go’.


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Feed-forward

Early metabolite activates a reaction farther down the pathway

Has the potential for instabilities, just as in electrical feed-forward

Usually modulated by feedback


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Activation and inactivation by post-translational modification Most common:covalent phosphorylation of protein

usually S, T, Y, sometimes H Kinases add phosphateProtein-OH + ATP Protein-O-P + ADP… ATP is source of energy and Pi

Phosphatases hydrolyze phosphoester:Protein-O-P +H2O Protein-OH + Pi

… no external energy source required


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Phosphorylation’s effects

Phosphorylation of an enzyme can either activate it or deactivate it

Usually catabolic enzymes are activated by phosphorylation and anabolic enzymes are inactivated

Example:glycogen phosphorylase is activated by phosphorylation; it’s a catabolic enzyme


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Glycogen phosphorylase

Reaction: extracts 1 glucose unit from non-reducing end of glycogen & phosphorylates it:(glycogen)n + Pi (glycogen)n-1 + glucose-1-P

Activated by phosphorylationvia phosphorylase kinase

Deactivated by dephosphorylation byphosphorylase phosphatase

Documents

11/24/2009Biochemistry: Metabolism I General Metabolism I Andy Howard Introductory Biochemistry 24 November 2009