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Home , Anabolism, Catabolism, Reducing agent

: All the chemical processes carried out by living things Chapter 5 : reactions that require to Metabolism: Overview synthesize complex from simpler ones

Lecture Exam #1 is Monday. Bring Scantron 882 form! See website for review. You will only be tested on material covered in lecture. X + Y + energy X—Y endergonic reaction Dr. Amy Rogers Fall 2006 • Needed for growth, reproduction, repair, Lectures: MW Noon movement, transport, etc. Office Hours: Mon. & Wed. 9-10 AM • Where does the energy come from? Sequoia 530

Catabolism Metabolism

• Reactions that release energy by breaking …as a cycle of synthesis (anabolism) and degradation complex molecules into simpler ones (), 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)

Obtaining Energy & Carbon sources • Auto- (self) – get carbon from CO to synthesize organic molecules • All living things need energy 2 • All living things need Carbon • Hetero- (other) – Why? To synthesize all organic molecules – get carbon from pre-made organic sources

Microbes are extremely versatile in the ways Obtaining Energy in which they acquire energy & carbon. •Photo- •capture the energy of light {Some bug somewhere can eat just about anything: see this week’s news articles!} •Chemo- •capture energy from chemicals

1 Metabolism: Photoautotrophs Categories of energy capturing • Do not generally cause disease • Many perform

Cyanobacteria, algae, plants light energy

6 CO2 + 6 H2O C6H12O6 + 6 O2 Carbon chlorophyll dioxide

•Energy from sunlight •Produce organic energy source (glucose) •Carbon from inorganic •Oxygen gas is a waste product

Photoautotrophs: Green & Purple Sulfur Chemoheterotrophs • Nearly all pathogenic microbes • use a more primitive form of photosynthesis, evolved when the earth’s atmosphere did not • 3 principle pathways for catabolizing food contain free O2 (but was rich in gas) • Strict anaerobes (glucose): 1. Do not require oxygen • Use H2S instead of H2O 2. • Produce elemental S or sulfuric acid instead of 3. Aerobic respiration Oxygen required oxygen gas

Photosynthesis & Respiration Chemoheterotrophs form a cycle

Complete oxidation of glucose by glycolysis & aerobic respiration:

C6H12O6 + 6 O2 6 CO2 + 6 H2O + energy Glucose oxygen carbon water dioxide

•Energy from organic compound •Energy for anabolism is produced •Carbon from organic compound •Carbon dioxide is a waste product

2 Note that photosynthetic organisms (whether Metabolic Pathways microbes or plants) • Chemical transformations like do consume chemical energy photosynthesis & glycolysis occur in a series of chemical reactions in much the same way as heterochemotrophs. • Such a chain of reactions is called a They just make it for themselves first.

(i.e., they metabolize glucose by glycolysis, etc. to A B C D E make ATP and synthesize other organic ) A is the initial substrate; B,C,D are intermediates; and E is the final product

Enzyme : Activation Energy

• (usually) that catalyze reactions • Exergonic / exothermic reactions are, in theory, spontaneous as the products of such reactions are at a • catalysts: lower energy state than the original reactant(s) •Are themselves unchanged by the reaction • Speed up reactions (tremendously) • However, the rate at which many such reactions occur •Lower activation energy spontaneously is SLOW • Are exquisitely specific • Activity can be regulated • One way to increase reaction rates is to increase the temperature • Often named by substrate + ase • Not an option for living things (not viable at higher temps) • For example, Proteases break down proteins; Lipases degrade • Another way? Activation Energy!

How do enzymes 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”

3 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 • Many are synthesized from vitamins – Often this is the reason why a certain nutrient is essential

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

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

Factors affecting enzyme activity Inhibition of enzyme activity

• Sometimes, it is important to reduce catalytic activity • When a better substrate is available NOTE: • When enough product has been made While the shapes of these curves will recur, various species • Competitive inhibition: of bacteria will • A molecule similar enough to the enzyme’s true have peaks at a substrate that it can bind to the active site, but the variety of temperatures enzyme doesn’t affect it and pH’s • The true substrate can’t get in…the site is occupied • The enzyme’s activity stops / slows

4 Noncompetitive (allosteric) Competitive Inhibition 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., , 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 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.

5 BCP- 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.

In metabolism, the energy carrier is often electrons, moving through + for sugar fermentation + for sugar -- for sugar reactions. + for H2 gas production fermentation fermentation

Reduction: Redox reactions • net charge is reduced (made more negative) because • Oxidation & reduction reactions are always coupled so electrons are gained we call them redox • Energy is gained (reduced compound has more In redox reactions, energy) • Electrons are transferred from one atom/molecule to • Often, hydrogen is gained, oxygen is lost another – Simultaneously 2 reactions: red/ox: electron gain/electron loss

• The electrons carry energy (so redox reactions are For example, think: Hydrocarbons. energy transfers) • Totally reduced • In a chain of reactions, the electrons must have a final • Saturated with hydrogen resting place (a terminal ). • No oxygen • Often, this is oxygen. • Lots of energy stored Propane

Oxidation:

• Electrons are lost • Energy is lost • Often, the electrons are transferred to oxygen If it has , it likely can • Oxygen is NOT the only electron acceptor around be oxidized as an energy source • There must always be an electron acceptor and an in redox reactions (coupled) (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

6 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 = • The atom or molecule that is reduced Electron donor • It causes something else to be oxidized (oxidizing 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: One reason why so much energy is released by of the 2nd and 3rd phosphate •is a (yes, the same one that goes into DNA!) groups: •Has 3 phosphate groups attached (tri-) •The distal, third phosphate group can be hydrolyzed to Electrostatic repulsion release a significant amount of energy: ATP ADP + P + energy Each phosphate group is negatively i charged; binding them together takes a lot Where ADP = 3- of energy Pi = inorganic phosphate (PO4 ) {The “first” phosphate, attached to the adenosine, can also be cleaved •Release of the next phosphate group also releases a lot off but the energy release is not impressive: of energy (ADP AMP + Pi + energy) no repulsion from other phosphates!} •This process is not used as much by living things

7 ATP as global energy currency ATP ADP + Pi + energy

• This reaction is reversible – i.e., an input of energy (such as the energy • The energy of ATP hydrolysis can be derived from glucose) can be used to make captured to perform the work of the cell ATP from ADP & Pi

• ATP is like money that can “buy” almost • of ADP to make ATP is any energy-requiring activity 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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