Microbiology Chapter 5

Metabolism

• The collection of controlled biochemical reactions that takes place within a microbe

• * ultimate function of an organism’s metabolism is to reproduce the organism

What eight statements are metabolic processes guided by?

1. Every cell acquires nutrients

2. metabolism requires energy from light or catabolism of nutrients

3. energy is stored in ATP

4. cells catabolize nutrients to form precursor metabolites

5. precursor metabolites, energy from ATP, and enzymes are used in anabolic reactions

6. enzymes plus ATP form macromolecules

7. cells grow by assembling macromolecules

8. cells reproduce once they have doubled in size

What are the two major classes of metabolic reactions?

catabolism & anabolism

Pathway

a series of reactions

Catabolic pathways

Break larger molecules into smaller products

• exergonic (releases energy → as heat or stored in ATP bonds)

• bond must be destabilized before it will break

Anabolic pathways

synthesize larger molecules from smaller ones

• endergonic (requires energy → from ATP)

• reactants collide with sufficient energy

• increasing concentration of reactants or ambient temperatures increases the number of collisions & produces more chemical reactions → NOT in living organisms

Redox reactions (oxidation-reduction reactions)

Electrons are transferred from an electron donor to an electron acceptor.

• electrons have stored energy

True or false: when an electron acceptor receives electrons, it is said to be reduced

TRUE → electrons are negative

Oxidation (dehydrogenation) reaction

Molecules that lose electrons because their electrons are often donated to oxygen atoms.

• Three ways: losing a simple electron, losing a hydrogen atom, gaining an oxygen atom

True or false: oxidation and reduction reactions occur simultaneously

TRUE

True or false: electrons are gathered from freely moving in the air

FALSE - electron carriers (in H atoms)

What are three important electron carriers?

• nicotinamide adenine dinucleotide (NAD+) → carries one H (NADH)

• nicotinamide adenine dinucleotide phosphate (NADP+) —> carries one H (NADPH)

• flavin adenine dinucleotide (FAD) → carries two H (FADH2)

ATP production and energy storage

organisms release energy from nutrients that can be concentrated and stored in high-energy phosphate bonds (ATP)

Phosphorylation

inorganic phosphate (PO43-) are added to a substrate

• ex: ADP → ATP

Why is ATP well suited to serve as the primary short-term energy carrier in metabolic pathways?

• multifunctional as a ribonucleotide (synthesizes RNA)

• highly water soluble & can accumulate to high concentrations in cells with no ill effects

• 2 different levels of energy donation (ATP → ADP or ATP → AMP)

• ATP can also serve as a phosphate donor

In what 3 ways do cells phosphorylate ADP to form ATP?

1. substrate-level phosphorylation

2. oxidative phosphorylation

3. photophosphorylation

Substrate-level phosphorylation

involves the transfer of phosphate to ADP from another phosphorylated organic compound

Oxidative phosphorylation

energy from redox reactions of respiration is used to attach inorganic phosphate to ADP

Photophosphorylation

light energy is used to phosphorylate ADP with inorganic phosphate

How do anabolic pathways use ATP?

by breaking a phosphate bond (becomes ADP again)

Catalysts

chemicals that increase the likelihood of a reaction but are not permanently changed in the process

• enzymes = organic catalysts

Substrate

the molecule the enzyme acts on

Hydrolases

main role = hydrolysis

Isomerases

rearrange atoms within a molecule (exchange)

Ligases (polymerases)

anabolic → join molecules together

Lyase

catabolic → split molecules WITHOUT water

Oxidoreductases

transfer of electrons or hydrogen atoms from one molecule to another

Transferase

moving a functional group from one molecule to another

Apoenzymes

the protein portion of protein enzymes that is inactive unless bound to one or more nonprotein cofactors

Cofactors

inorganic ions or organic molecules (coenzymes) that are essential for enzyme action

Coenzymes

organic cofactors

• vitamins or containing vitamins

Holoenzyme

binding of an apoenzyme and its cofactor forms an active enzyme

the place where a specific substrate binds to the enzyme

active site

Examples of common cofactors

inorganic = magnesium

organic (coenzymes) = NAD+, NADP+, FAD, coenzyme A, tetrahydrofolate, coenzyme A, pyridoxal phosphate, thiamine phosphate

True or false: all enzymes are proteins

FALSE → ribozymes (remove sections of RNA and splice them together; functional core of a ribosome)

Activation energy

the amount of energy needed to trigger a chemical reaction

• enzymes lower activation energy

Active Site

functional site of an enzyme, the shape of which is complementary to the shape of the substrate.

Induced-fit model

the way an enzymes changes its shape slightly after binding to its substrate as to bind to it more tightly

How does substrate-enzyme interaction work?

enzyme associates with specific substrate molecule → binds to form temporary enzyme-substrate complex in an induced-fit model → bonds within substrate are broken (catabolic) → enzyme dissociates from new products → enzyme resumes its original configuration and is ready to associate with another substrate molecule

What factors influence the rate of enzymatic reactions?

• temperature (high temp = faster reactions; too high = enzyme denatured)

• pH

• enzyme and substrate concentrations (more substrate concentrations = more enzyme activity)

• presence of inhibitors

Allosteric site

a site located away from the active site → enzyme’s active site changes shape

Activators

some enzymes are activated when a cofactor binds to a site other than the active site

Inhibitors

substances that block an enzyme’s activity

• competitive or noncompetitive inhibitors

Competitive inhibitors

inhibitory substances that block enzyme activity by blocking active sites

• permanent or reversible

• reversible → overcome by increase in substrate molecules

Noncompetitive inhibitors

inhibitory substances that block enzyme activity by binding to an allosteric site on the enzyme, changing the shape of the active site.

Feedback inhibition

method of controlling the action of enzymes in which the end product of a series of reactions inhibits an enzyme in an earlier part of the pathway

What are the two ways glucose is catabolized?

• cellular respiration

• fermentation

Cellular respiration

a process that results in the complete breakdown of glucose to carbon dioxide and water

• glycolysis → citric acid cycle & electron transport chain → significant amount of ATP production

Fermentation

results in organic waste products

• glycolysis → conversion of pyruvic acid into other organic compounds → much less ATP

True or false: many organisms oxidize carbohydrates as the primary energy source for anabolic reactions

TRUE

What is the most common carbohydrate used?

glucose

What are the four steps in overall process of cellular respiration?

1. glycolysis

2. pyruvate oxidation (transition step)

3. kreb’s cycle

4. oxidation phosphorylation: ETC and chemiosmosis

Glycolysis

• follows embden-meyerhop-parnas (EMP) pathway

• involves the splitting of a six-carbon glucose molecule into two three-carbon sugar molecules (pyruvate)

• occurs in the cytoplasm of most cells

What are the 3 stages of glycolysis?

1. energy-investment stage = cell invests energy in 2 molecules of ATP by phosphorylating a 6-carbon glucose & rearranging atoms to form fructose

2. lysis stage = fructose to glyceraldehyde & dihydroxyacetone phosphate → G3P

3. energy-conserving stage = 2 molecules of G3P to pyruvic acid → 2 ATP molecules from each oxidation

Substrate-level phosphorylation

direct transfer of phosphate between 2 substrates

What are the products of glycolysis?

net gain of 2 ATP molecules, 2 NADH molecules, 2 pyruvic acid molecules

Cellular respiration (aerobic respiration)

a metabolic process that involves the complete oxidation of pyruvate and then production of ATP by a series of redox reaction

What are the 3 stages of cellular respiration?

1. synthesis of acetyl-CoA

2. citric acid cycle

3. electron transport chain (electrons → chemical)

Synthesis of Acetyl-CoA

• occurs as pyruvate through the mitochondrial membrane into the matrix

• known as “transition step” or “bridge step”

• results in 2 acetyl-CoA molecules, 2 CO2 molecules, 2 NADH molecules

Citric acid cycle (Krebs cycle or TCA cycle)

a “circular” series of 8 enzymatically catalyzed reactions that transfer much of this stored energy in acetyl-CoA via electrons to the coenzymes NAD+ and FAD

• occurs in the cytosol of prokaryotes & matrix of mitochondria in eukaryotes

What are the 6 types of reactions in the citric acid cycle?

• anabolism

• isomerization

• redox reactions

• decarboxylations

• substrate-level phosphorylation

• hydration

What are the end products of the krebs cycle?

2 molecules of ATP, 2 molecules of FADH2, 6 molecules of NADH, 4 molecules of CO2

Electron Transport Chain

Series of carrier molecules that pass electrons from one to another to a final electron acceptor

• most production of ATP

• energy from electrons are used to pump protons (H+) across the membrane, establishing a proton gradient

• located in inner mitochondrial membrane of eukaryotes and in cytoplasmic membrane of prokaryotes

What are the four categories of carriers in the ETC?

• flavoproteins → integral; FAD is a coenzyme

• ubiquinones → lipid-soluble, nonprotein carriers

• metal-containing proteins → copper proteins are only found in ETC involving photosynthesis

• cytochromes → integral; heme

Aerobic respiration

oxygen serves as final electron acceptor

Anaerobic respiration

molecule other than oxygen serves as final electron acceptor

Chemiosmosis

• production of ATP by diffusion of H+ ions through ATP synthase

• cells use energy released in redox reactions of ETC to create proton gradient

• protons flow down electrochemical gradient through ATP synthases that phosphorylate ADP to ATP

• oxidative phosphorylation bc proton gradient is created by oxidation of components

• final electron acceptor = O2; combines with 2 H+ to form H2O

What are the products of chemiosmosis (ETC)?

34 ATP molecules from 1 molecule of glucose, 0 of everything else (38 ATP in prokaryotes?)

Entner-Doudoroff (ED) pathway

• some bacteria substitute this pathway for the EMP pathway

• only found in prokaryotes

• produces 1 ATP, 1 NADH, & 1 NADPH

Pentose phosphate pathway

• alternative to glycolysis

• less energy efficient than glycolysis

• produces precursor metabolites & NADPH; makes DNA nucleotides, steroids, fatty acids

Fermentation

• sometimes cells cannot completely oxidize glucose by cellular respiration

• cells require a constant source of NAD+ → must be recycled bc it cannot be obtained simply by using glycolysis/Krebs cycle

• fermentation is an alternative source of NAD+

• partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as final electron acceptor

• 2 ATP produced

True or false: lipids and proteins contain energy in their chemical bonds

TRUE → can be converted into precursor metabolites; serve as substrates in glycolysis & Krebs

• can generate 129 ATP (in C palmitate fatty acid)

Triglyceride (Lipid) catabolism

1. lipases hydrolyze bonds attaching glycerol to fatty acid

2. catabolize glycerol & fatty acid

3. glycerol → DHAP (pyruvic acid)

4. beta-oxidation = enzymes repeatedly split off pairs of the carbon atoms that make up a fatty acid and join each pair to coenzyme A to form acetyl-CoA; glycerol → DHAP

5. generates NADH and FADH2

6. located in cytosol of prokaryotes & mitochondria of eukaryotes

7. fat is most common

Protein Catabolism

• only when glucose & fats aren’t available

• prokaryotes secrete proteases (enzymes that split proteins into amino acids) → move into cell where enzymes split off amino groups (deamination) → enter citric acid cycle

Photosynthesis

process in which light energy is captured by chlorophylls and transferred to ATP and metabolites

• many organisms synthesize their own organic molecules from inorganic carbon dioxide

Light-dependent reactions overview

convert light energy into chemical energy, forming ATP & NADPH

Light-independent reactions overview

synthesize glucose from CO2 and water

Chlorophylls

• important to organisms that capture light energy with pigment molecules

• composed of hydrocarbon tail attached to light-absorbing active site centered on magnesium ion

• active sites are structurally similar to cytochrome molecules in ETC

• structural differences cause absorption at different wavelengths

Photosystem

an arrangement of numerous chlorophyll and other pigments within a protein matrix on thylakoids to form light-harvesting matrices

• embedded in thylakoid (in prokaryotes = infolding of cytoplasmic membrane; in eukaryotes = formed from inner membrane of chloroplasts)

• arranged in stacks called grana

• stroma is the space between the outer membrane of grana and thylakoid membrane

absorb light energy & use redox reactions to store energy in the form of ATP and NADPH

Reaction center chlorophyll

in a photosystem, a chlorophyll molecule in which electrons excited by light energy are passed to an acceptor molecule that is the initial carrier of an ETC

Where does photosynthesis in eukaryotes occur?

takes place in the chloroplasts, which contain thylakoids stacked into grana

Where does photosynthesis occur in prokaryotes?

takes place in the infolded regions of the plasma membrane that function like thylakoids

Light-dependent reactions in-depth

chlorophyll passes excited electrons to reaction center → electrons move down ETC → pump protons across the membrane → proton motive force (in prokaryotes = out of cell; in eukaryotes = pumped from stroma to thylakoid space)

• photophosphorylation uses proton motive force to generate ATP; cyclic or non-cyclic

• cyclic photophosphorylation = return of electrons to original reaction center of a photosystem after passing down the ETC (ex: PS I → ETC → PS I)

• noncyclic photophosphorylation = light energy excites electrons of PS II → PS I → ETC; generates oxygen

Light-independent reactions in-depth

• do not require light directly

• use ATP & NADPH generated by light-dependent reactions

• Calvin-Benson cycle

Calvin-Benson cycle

carbon fixation = the attachment of CO2 to molecules of 5-carbon RuBP

• very endergonic

• all life on Earth depends on this cycle

• occurs in the cytoplasm of photosynthetic bacteria or inner stroma of chloroplasts in Eukaryotes

What are the steps of the Calvin-Benson cycle?

1. Fixation of CO2 = enzyme attaches 3 carbon to 3 molecules of RuBP → 3-phosphoglyceric acid

2. Reduction = molecules of NADPH reduce 3-phosphoglyceric acid to form 6 glyceraldehyde 3-phosphate (G3P); REQUIRES 6 ATP & 6 NADPH

3. Regeneration of RuBP = regenerates 3 RuBP from 5 G3P; glyceraldehyde 3-phosphate remaining synthesizes glucose through reverse glycolysis

Anabolic Pathways Overview

anabolic reactions are synthesis reactions requiring energy and a source of precursor metabolites

• use energy derived from ATP from catabolic reactions

• many anabolic pathways are the reverse of catabolic pathways

Amphibolic reactions

a reversible metabolic reaction; it can be catabolic OR anabolic

Gluconeogenesis

ability to synthesize sugars from noncarbohydrate precursors (glucose from fats or proteins)

• amphibolic reactions

• highly endergonic

• can ONLY occur when there is an adequate supply of energy

Lipid Biosynthesis

• most energy-efficient = triglycerides

• most common generated in cells = phospholipids

• carotenoids = reddish pigments that are lipids

• fats are synthesized in anabolic reactions; glycerol is derived from Calvin-Benson G3P; fatty acids from linkage of acetyl-CoA

Amino Acid Biosynthesis

cells synthesize amino acids from precursor metabolites produced by glycolysis, citric acid cycle, pentose phosphate pathway

• essential amino acids = must be acquired in diet

• amination = when amine group comes from ammonia and converts precursor metabolites to amino acids

• transamination = amine group is moved from one amino acid to a metabolite; producing a different amino acid; most common; pyridoxal phosphate

Nucleotide Biosynthesis

produced from precursor metabolites of glycolysis and the citric acid cycle

• ribose in RNA and deoxyribose in DNA are derived from ribose 5-phosphate from pentose phosphate pathway

• the phosphate group is derived from ATP

How cells regulate metabolism

• synthesize or degrade channel & transport proteins

• synthesize enzymes only when their substrate is available

• cells catabolize the more energy-efficient choice if 2 energy sources are available

• cells synthesize metabolites they need but stop if they are available

• eukaryotic cells isolate enzymes to maintain different metabolic processes

• cells use inhibitory & excitatory allosteric sites

• feedback inhibition slows or stops anabolic pathways if product is in abundance

• cells regulate amphibolic pathways by requiring different coenzymes for each pathway

What are the two types of regulatory mechanisms?

control of gene expression = cells control the amount and timing of protein (enzyme) production

control of metabolic expression = cells control activity of proteins (enzymes) once produced