Metabolism: Catabolism. Metabolism. Energy & Carbon sources. Chapter 5 Metabolism: Overview. Obtaining Carbon. Obtaining Energy

Metabolism: All the chemical processes carried out by living things Chapter 5 Metabolism: Overview Lecture Exam #1 is Monday. Bring Scantron 882 form...
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Metabolism: All the chemical processes carried out by living things

Chapter 5 Metabolism: Overview Lecture Exam #1 is Monday. Bring Scantron 882 form! See website for review. You will only be tested on material covered in lecture.

Dr. Amy Rogers Fall 2006 Lectures: MW Noon Office Hours: Mon. & Wed. 9-10 AM Sequoia 530

Anabolism:

reactions that require energy to synthesize complex molecules from simpler ones

X + Y + energy X—Y endergonic reaction • Needed for growth, reproduction, repair, movement, transport, etc. • Where does the energy come from?

Catabolism • Reactions that release energy by breaking complex molecules into simpler ones

Metabolism …as a cycle of synthesis (anabolism) and degradation (catabolism), with energy tranferred & consumed along the way

X—Y X + Y + energy exergonic reaction • Energy is captured / stored in high energy bonds of ATP & similar molecules • Involves electron transfer (oxidation-reduction)

Energy & Carbon sources • All living things need energy • All living things need Carbon – Why? To synthesize all organic molecules Microbes are extremely versatile in the ways in which they acquire energy & carbon. {Some bug somewhere can eat just about anything: see this week’s news articles!}

Obtaining Carbon • Auto- (self) – get carbon from CO2 to synthesize organic molecules

• Hetero- (other) – get carbon from pre-made organic sources

Obtaining Energy •Photo•capture the energy of light •Chemo•capture energy from chemicals

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Metabolism: Categories of energy capturing

Photoautotrophs • Do not generally cause disease • Many perform photosynthesis Cyanobacteria, algae, plants light energy

6 CO2 + 6 H2O Carbon dioxide

•Energy from sunlight •Carbon from inorganic carbon dioxide

Photoautotrophs:

• Use H2S instead of H2O • Produce elemental S or sulfuric acid instead of oxygen gas

Chemoheterotrophs

glucose

oxygen

•Produce organic energy source (glucose) •Oxygen gas is a waste product

Chemoheterotrophs

Green & Purple Sulfur Bacteria • use a more primitive form of photosynthesis, evolved when the earth’s atmosphere did not contain free O2 (but was rich in hydrogen gas) • Strict anaerobes

C6H12O6 + 6 O2

water chlorophyll



Nearly all pathogenic microbes



3 principle pathways for catabolizing food (glucose): 1. Glycolysis 2. Fermentation 3. Aerobic respiration

Do not require oxygen Oxygen required

Photosynthesis & Respiration form a cycle

Complete oxidation of glucose by glycolysis & aerobic respiration:

C6H12O6 + 6 O2

6 CO2 + 6 H2O + energy

Glucose

carbon dioxide

oxygen

•Energy from organic compound •Carbon from organic compound

water

•Energy for anabolism is produced •Carbon dioxide is a waste product

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Metabolic Pathways

Note that photosynthetic organisms (whether microbes or plants) do consume chemical energy in much the same way as heterochemotrophs. They just make it for themselves first. (i.e., they metabolize glucose by glycolysis, etc. to make ATP and synthesize other organic macromolecules)

Enzymes • Proteins (usually) that catalyze reactions • Enzyme catalysts: • • • • •

Are themselves unchanged by the reaction Speed up reactions (tremendously) Lower activation energy Are exquisitely specific Activity can be regulated

• Often named by substrate + ase • For example, Proteases break down proteins; Lipases degrade lipid

• Chemical transformations like photosynthesis & glycolysis occur in a series of chemical reactions • Such a chain of reactions is called a metabolic pathway A

B

C

D

E

A is the initial substrate; B,C,D are intermediates; and E is the final product

Enzyme catalysis:

Activation Energy • Exergonic / exothermic reactions are, in theory, spontaneous as the products of such reactions are at a lower energy state than the original reactant(s) • However, the rate at which many such reactions occur spontaneously is SLOW • One way to increase reaction rates is to increase the temperature • Not an option for living things (not viable at higher temps)

• Another way?

How do enzymes

Activation Energy!

activation energy?

• Precise 3-D conformation (shape) • Active site • Location where enzyme binds its substrate • Substrate(s) bind in a way that resembles the transition state (a kind of halfway point in the reaction) Analogies:

Rock resting in a depression at the top of a hill Charcoal waiting to be lit

Activation energy as “a hurdle over which molecules must be raised to get a reaction started”

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Specificity • An exact match of the shape of the active site with its substrate is critical • Each enzyme catalyzes only one type of reaction, often only on one particular substrate (with single atom changes, or changes in chiralty, often ruining the fit)

• Often, an additional chemical is needed at the active site to make the substrate fit, or to aid catalysis: coenzymes & cofactors

Coenzymes & Cofactors • Coenzyme: • A nonprotein organic molecule • Many are synthesized from vitamins – Often this is the reason why a certain nutrient is essential

• Niacin is used to make NAD – nicotinamide adenine dinucleotide – Critical reagent for energy production by aerobic respiration

• Cofactor • Inorganic, often a metal ion (Mg, Zn, etc.)

Factors affecting enzyme activity

NOTE: While the shapes of these curves will recur, various species of bacteria will have peaks at a variety of temperatures and pH’s

Inhibition of enzyme activity • Sometimes, it is important to reduce catalytic activity • When a better substrate is available • When enough product has been made

• Competitive inhibition: • A molecule similar enough to the enzyme’s true substrate that it can bind to the active site, but the enzyme doesn’t affect it • The true substrate can’t get in…the site is occupied • The enzyme’s activity stops / slows

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Competitive Inhibition

Noncompetitive (allosteric) Inhibition • A molecule binds to the enzyme outside of the active site • “Allosteric site” • This binding alters the enzyme’s shape so that the active site no longer functions

• Feedback inhibition often is allosteric • When “enough” of the enzyme’s product is present, the product binds to an allosteric site and slows / stops production of any more

Noncompetitive / Allosteric Inhibition

Inhibition & Drugs/Toxins Many drugs and poisons act by disrupting vital enzyme activity. Such inhibition can be temporary, depending on how long the drug/toxin stays around (reversible inhibitors) or permanent (irreversible inhibitors) e.g., lead, mercury

Our study of bacterial metabolism will focus on energy acquisition: • What is food for bacteria? • The various biochemical pathways available for catabolism of glucose • The impact of these metabolic pathways on cell growth • The role of oxygen • The conversion of the chemical energy of food into the chemical energy of ATP • The end products of metabolism In lab, you will learn how unknown bacterial isolates can be identified on the basis of what they can eat, how they eat it, and what trash they leave behind when they’re done.

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BCP-carbohydrate broths: Lab 13 “Eating” is all about taking the energy stored in the chemical bonds of food, and transferring that energy to a form directly usable by the cell.

+ for sugar fermentation + for H2 gas production

+ for sugar fermentation

In metabolism, the energy carrier is often electrons, moving through redox reactions.

-- for sugar fermentation

Reduction:

Redox reactions • Oxidation & reduction reactions are always coupled so we call them redox In redox reactions, • Electrons are transferred from one atom/molecule to another

• net charge is reduced (made more negative) because electrons are gained • Energy is gained (reduced compound has more energy) • Often, hydrogen is gained, oxygen is lost

– Simultaneously 2 reactions: red/ox: electron gain/electron loss

• The electrons carry energy (so redox reactions are energy transfers) • In a chain of reactions, the electrons must have a final resting place (a terminal electron acceptor). • Often, this is oxygen.

For example, think: Hydrocarbons. • • • •

Totally reduced Saturated with hydrogen No oxygen Lots of energy stored

Propane

Oxidation: • Electrons are lost • Energy is lost • Often, the electrons are transferred to oxygen • Oxygen is NOT the only electron acceptor around • There must always be an electron acceptor and an electron donor in redox reactions (coupled)

If it has hydrogens, it likely can be oxidized as an energy source (food) by some type of bacteria!

For example, think: Hydrocarbons burning •The molecule gains oxygen/loses hydrogen (yielding CO2 & H2O) •Energy is released (heat) •Oxygen is the electron acceptor

Propane

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Redox terms • Electron donor = reducing agent • The atom or molecule that is oxidized • It causes something else to be reduced (hence the name reducing agent)

• Electron acceptor = oxidizing agent • The atom or molecule that is reduced • It causes something else to be oxidized (oxidizing

Electron donor

agent)

Electron acceptor

Electron Carriers in metabolism

Electron carriers NAD+ & FAD

• NAD (nicotinamide adenine dinucleotide) • Derived from vitamin niacin

• FAD (flavin adenine dinucleotide) • Derived from vitamin riboflavin

Both carriers cycle between oxidized (NAD+, FAD) and reduced states (NADH, FADH2)

ATP: Adenosine triphosphate •is a nucleotide (yes, the same one that goes into DNA!)

One reason why so much energy is released by hydrolysis of the 2nd and 3rd phosphate groups:

•Has 3 phosphate groups attached (tri-) •The distal, third phosphate group can be hydrolyzed to release a significant amount of energy:

ATP

ADP + Pi + energy

Where ADP = adenosine diphosphate Pi = inorganic phosphate (PO43-) •Release of the next phosphate group also releases a lot of energy (ADP AMP + Pi + energy)

Electrostatic repulsion Each phosphate group is negatively charged; binding them together takes a lot of energy {The “first” phosphate, attached to the adenosine, can also be cleaved off but the energy release is not impressive: no repulsion from other phosphates!}

•This process is not used as much by living things

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ATP as global energy currency

ATP

ADP + Pi + energy

• This reaction is reversible • The energy of ATP hydrolysis can be captured to perform the work of the cell • ATP is like money that can “buy” almost any energy-requiring activity

– i.e., an input of energy (such as the energy derived from glucose) can be used to make ATP from ADP & Pi

• Phosphorylation of ADP to make ATP is a key feature of metabolism

Relevant reading in Black’s Microbiology: (pages from 6th edition)

• Ch. 5: p.112-120; 132-134

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