Microbiology - Metabolism

Definitions

• Metabolism — the sum of all chemical reactions in a cell that sustain life.

• Catabolism — metabolic reactions that break down molecules to release energy.

• Anabolism — metabolic reactions that build complex molecules using energy.

• Enzyme — a protein catalyst that speeds up biochemical reactions by lowering activation energy.

• Coenzyme — a small organic molecule that assists enzymes by carrying electrons or chemical groups.

• Apoenzyme — the inactive protein portion of an enzyme that requires a cofactor or coenzyme to function.

• Anaerobic metabolism — energy production that occurs without oxygen, typically yielding less ATP.

• Aerobic metabolism — energy production that requires oxygen and generates large amounts of ATP.

• Adenosine triphosphate (ATP) — the cell’s primary energy currency that stores and releases usable energy.

• Amination — the addition of an amino group to a molecule.

• Deamination — the removal of an amino group from an amino acid or molecule.

• Decarboxylation — the removal of a carboxyl group (CO₂) from an organic molecule.

• Assimilation — the incorporation of nutrients into cellular biomass.

• Beta‑oxidation — the stepwise breakdown of fatty acids into acetyl‑CoA units for energy production.

• Oxidation — the loss of electrons from a molecule.

• Reduction — the gain of electrons by a molecule.

Electron transport chain

• all need to make ATP

mitochondria

• inner and outermembrane folds

• electron transport chain

• proteins in the phospholipid bilayer

• ATP Synthase- Important protein (molecular propeller) located in phospholipid bilayer

• nadh dehydrogenase- enzyme; molecular dumptruck (carries electrons and H)→ electron transport chain → nad

  • from glycolysis or Kreb cycle

  • takes nadh, removes h2O and gains energy

• FADH 2- another molecular dumptruck

  • FADH 2 - >FAD

• Cytochrome x2- cyanide poisoning inhibits atp creation

OIL RIG - electrons

electrons are passed

To make ATP

• ADP gets phosphorylated with P and makes ATP

• Facilitated diffusion- all protons and hydrogen ions that get pumped out create high concentration of H outside and low concentration inside

• atp synthase- LIKE GUMBALL MACHINE

• H join with oxygen to form water

cellular respiration

• (Glucose) CHO + O → carbon dioxide + water

• gives off ATP

chemiosmosis- proton motive force

Dumptrucks

NAD+- nicotinamide adenine dinucleotide (dumptruck) also called Niacin

• why sugarfree energy drinks

FAD- flavin adenine dinucleotide

• NAD+ reduces 2 Hydrogen atoms and carries 2 electrons away represented as NADH (loaded dumptruck)

• final electron acceptor is Oxygen and aerobic respiration

reduced substrate- substrate x gets electrons stuck on it

oxidized substrate- electrons get removed from substrate x

make substrate NAD+

• NAD+ is oxidized

• NADH is reduced (dumptruck)

ATP: 1 ecoli bacteria can consume 2.5 atp

Oxidative phosphorylation

respiration, fermentation, photosynthesis, chemoautotrophy (chemically making own food. maybe how life was made.)

all use when adp+P <-> atp

• chemical work, transport work, and mechanical work

Most ATPs in aerobic organisms are formed during oxidative phosphorylation using ATP synthase

• bringing electron and hydrogen dumptrucks (oxidation) then take adp and add phosphorus (phosphorylation)

• photosynthetic organisms have a system of photophosphorylation using sunlight driven electron transport

• catabolism for chemoheterotrophs have three pathways

  • glycolysis (EMP pathway)

  • Kreb cycle (citric acid cycle, tricarboxylic acid cycle)

  • electron transport chain (respiratory chain, oxidative phosphorylation)

Energy strategies

all living organisms use one or more of these

aerobic respiration: is cellular respiration.

• get glucose + O → make CO2 and water

• also taking 38 ADP and taking 38 Pi and making 38 ADP

• can use glucose, fructose, galactose, fatty acid subunits can all be used as reactants

• glycolysis converts glucose into pyruvic acid (pyruvate)

  • synthesizes a small amount of ATP to release NADH

anaerobic respiration

fermentation

Glycolysis

takes glucose (C-C-C-C-C-C) and splits it evenly into 2 halves

• each half (C-C-C) is called pyruvic acid

In process

• NAD+ turns to NADH for both halves → ETC

• ADP is phosphorylated into ATP (4 atp made but 2 of the atp are used to make it) net atp is 2

• then pyruvate goes to the Kreb’s cycle

about 9 different steps processed

just need to know big picture

loading up dumptrucks and making some atp

make a tiny bit of atp and each pyruvate give 8 nadh and 2 fadh2

What are the starting and end products of glycolysis? Where does glycolysis occur? How many ATP (net) are produced as a result of glycolysis?

• Start: Glucose

• End: 2 pyruvate + 2 NADH + 2 ATP (net)

• Location: Cytoplasm

• Purpose: Break glucose in half and generate small amounts of ATP + NADH for later steps

Kreb Cycle

2 pyruvates from glycolysis

• before enter Kreb, have to be converted to acetyl coA

  • one carbon given off at NAD+ → NADh

  • another is given off

• each pyruvate goes through 8 diff chem reactions

then FAD to Fadh2

all give off atp

Identify the series of reactions known as the Kreb's cycle. What waste products are generated in this cycle? How many ATP are generated in this cycle? Which and how many coenzymes are reduced in the Kreb's cycle? Identify starting and end products of the Kreb's cycle.

• Cycle purpose: Strip electrons from Acetyl‑CoA to load NADH & FADH₂

• Waste: CO₂

• ATP yield: 1 ATP per turn (2 per glucose)

• Reduced coenzymes: 3 NADH + 1 FADH₂ per turn

• Start: Acetyl‑CoA

• End: Oxaloacetate regenerated + CO₂ + NADH + FADH₂ + ATP

Aerobic Respiration

• o2 is the final electron acceptor

• max theoretical ATP yield= 38

Aerobic Net transport

• FADH2 → 2 ATP in ETC

• NADH2 → 3 ATP in ETC

Glycolysis : 6 ATP

• 2ATP

• 2 NADH

• 2 Pyruvate

Transition Step: 6 ATP

• 2 NADH

• 2 CO2

Kreb’s Cycle: 18 ATP+ 4ATP

• 4 CO2

• 6 NADH

• 2 ATP

• 2 FADH2

ETC + Oxidative Phosphorylation

• 34 ATP

Anaerobic respiration

• nonoxygen electron

• acceptors ex. So34 NO-3 CO 2-3

• possible ATP varies with microbes

Fermentation

• an organic molecule is the final electron acceptor

• pyruvate. acetaldehyde, etc.

• max atp yield= 2atp

• do it without oxygen, but cannot live off alone

Lose weight?

cellular respiration formula

• use more ATP

• Use more oxygen

• eat less sugars

Where does weight go?

• you exhale weight: CO2

Photosynthesis is opposite

What is the purpose of catabolic degradation of glucose? Identify the 3 pathways required for the total aerobic breakdown of glucose. Where does each occur?

• Purpose of glucose catabolism: Make ATP by extracting electrons and sending them to the ETC

• Three pathways:

  1. Glycolysis — cytoplasm

  2. Kreb’s cycle — mitochondrial matrix

  3. ETC + chemiosmosis — inner mitochondrial membrane

• Your page confirms: NADH, FADH₂, proton gradient, ATP synthase, oxygen → water, and ATP production

Enzymes

Enzymes

• simple enzymes- proteins alone

• holoenzymes- conjugated enzymes contain protein and nonprotein molecules

  • apoenzyme- protein portion

    • temporary enzyme- substrate union occurs (induced fit)

  • cofactors- nonprotein portion

    • metallic cofactors: iron, copper, magnesium

    • coenzymes, organic molecules: vitamins

    • micronutrients are needed as cofactors

    • act as carriers to assist the enzyme in its activity

Exoenzymes

• transported extracellularily, where break down large food molecules or harmful chemicals

• cellulase, amylase, penicillinase

Endoenzymes

• retained intracellularly and function there

  • most enzymes are endoenzymes

Constitutive enzymes

regulated enzymes

enzymes may be active extracellularly

• operate under temp pH and osmotic pressure of organisms habit

• labile: chemically unstable enzyme

• denaturation: weak bonds that maintain shape of apoenzyme are broken

regulation of enzyme action

1. competitive inhibition

2. allosteric inhibition

enzyme repression

• normal protein synthesis

• enzyme produced

• end products block transcription of dna

Energy

Endergonic reactions

exergonic reaction

redox reactions

• electron and proton carriers- facilitate transfer

• gain electrons and hydrogens

ATP made of

bioenergetics- study of mech of cellular energy release

• catabolic and anabolic

Kreb cycle- co2 given off

What are coenzymes? Identify the components from which coenzymes are synthesized. Name and state the function of 3 coenzymes we discussed in class. Are there other coenzymes

Coenzymes are small, organic, non‑protein molecules that bind to enzymes and help them carry out chemical reactions.
They act as carriers—usually of electrons, hydrogen atoms, or functional groups—allowing metabolic reactions to proceed.

They are not enzymes themselves, but they are essential for enzyme function.

From what are coenzymes synthesized?

Most coenzymes are synthesized from vitamins, especially B‑vitamins, combined with other organic components made by the cell.

Examples:

• Niacin (vitamin B₃) → precursor for NAD⁺ / NADH

• Riboflavin (vitamin B₂) → precursor for FAD / FADH₂

• Pantothenic acid (vitamin B₅) → precursor for Coenzyme A

Three coenzymes we discussed in class (with functions)1. NAD⁺ / NADH (Nicotinamide adenine dinucleotide)

Made from: Niacin (vitamin B₃)
Function:

• Electron and hydrogen carrier

• Accepts electrons during glycolysis and the Krebs cycle

• Delivers them to the electron transport chain to help make ATP
  (Your notes call NADH a “molecular dump truck,” which is exactly right.)

2. FAD / FADH₂ (Flavin adenine dinucleotide)

Made from: Riboflavin (vitamin B₂)
Function:

• Electron and hydrogen carrier

• Accepts electrons in the Krebs cycle

• Donates them to the electron transport chain
  (Your notes list FADH₂ as another “molecular dump truck.”)

3. Coenzyme A (CoA)

Made from: Pantothenic acid (vitamin B₅)
Function:

• Transfers acetyl groups

• Forms acetyl‑CoA, the molecule that enters the Krebs cycle

• Essential for carbohydrate, lipid, and amino acid metabolism

Are there other coenzymes?

Yes—many. Some important examples include:

• TPP (Thiamine pyrophosphate) – from vitamin B₁; used in decarboxylation reactions

• Biotin – carries CO₂ in carboxylation reactions

• Pyridoxal phosphate (PLP) – from vitamin B₆; used in amino acid metabolism

• Tetrahydrofolate (THF) – from folate; carries one‑carbon units

• Coenzyme Q (Ubiquinone) – electron carrier in the electron transport chain

• Lipoic acid – involved in pyruvate dehydrogenase complex

What are the many fates of pyruvic acid?

• Aerobic: Pyruvate → Acetyl‑CoA → Krebs cycle → ETC

• Anaerobic: Pyruvate → Lactic acid or Ethanol

• Other fates: Amino acids, oxaloacetate, fatty acid synthesi

What is Coenzyme A? Acetyl Coenzyme A? Succinyl Coenzyme A? What is the importance of this coenzyme?

• CoA: Vitamin‑derived carrier of acyl groups

• Acetyl‑CoA: Entry molecule for Krebs cycle; central metabolic hub

• Succinyl‑CoA: Krebs cycle intermediate that helps generate ATP/GTP

• Importance: Links glycolysis → Krebs → ETC; enables NADH/FADH₂ production → ATP synthesis

Why are the reactions of the electron system termed oxidative phosphorylation? What waste product is generated in the ets?

• Why oxidative? NADH and FADH₂ are oxidized as they pass electrons down the chain.

• Why phosphorylation? ATP synthase uses the proton gradient to phosphorylate ADP → ATP.

• Waste product: Water, formed when oxygen accepts electrons and H⁺

How can oxidation of a substrate proceed without oxygen?

• Oxidation requires NAD⁺.

• Without oxygen, cells regenerate NAD⁺ by:

  • Fermentation (pyruvate or acetaldehyde accepts electrons)

  • Anaerobic respiration (nitrate, sulfate, CO₂, etc. accept electrons)

• This allows glycolysis and other catabolic reactions to continue even when oxygen is absent.

Using the concept of fermentation, describe the microbial mechanisms (biochemical mechanisms) that cause milk to sour

Milk sours because lactic acid bacteria perform lactic acid fermentation:

1. Lactose → glucose + galactose

2. Glycolysis → pyruvate + NADH

3. Pyruvate is reduced to lactic acid, regenerating NAD⁺

4. Lactic acid accumulates → pH drops

5. Acid denatures milk proteins → sour, curdled milk

➡ Fermentation is the biochemical mechanism that allows bacteria to oxidize NADH without oxygen, producing lactic acid that sours milk.

What is the commercial importance of fermentation reactions? Are the products of fermentation limited to alcohol? List at least 3 other products that are produced fermentation reactions.

• Fermentation is commercially important for food preservation, flavor production, industrial chemicals, and biofuels.

• Products are not limited to alcohol.

• Other fermentation products include:

  • Lactic acid

  • Acetic acid

  • Propionic acid

  • Butyric acid

  • Acetone

  • Butanol

  • CO₂

Intermediary products of metabolism are said to be amphibolic. Define Amphibolism. List a few examples of amphibolic compounds. What is produced from these products?

• Fermentation is commercially important for food preservation, flavor production, industrial chemicals, and biofuels.

• Products are not limited to alcohol.

• Other fermentation products include:

  • Lactic acid

  • Acetic acid

  • Propionic acid

  • Butyric acid

  • Acetone

  • Butanol

  • CO₂

Identify the 6 major categories of enzymes and their function

Enzyme Class	What It Does	Easy Memory Cue
Oxidoreductases	Redox reactions; electron transfer	ETC enzymes like NADH dehydrogenase
Transferases	Move functional groups	“Transfers stuff”
Hydrolases	Break bonds with water	Hydrolysis
Lyases	Break/form bonds without water	“Leave or add groups”
Isomerases	Rearrange atoms	Same formula, new shape
Ligases	Join molecules using ATP	“Glue with ATP”

What is the biological importance of fermentation reactions?

Biological importance of fermentation:

• Regenerates NAD⁺ so glycolysis can continue

• Allows ATP production without oxygen

• Supports survival in anaerobic environments

• Produces acids/alcohols that shape microbial communities

• Provides rapid ATP when oxygen is limited

➡ Fermentation keeps cells alive when the electron transport chain cannot function.

Explain how ATP is generated by chemiosmotic coupling on the cristae of the mitochondria. What is proton motive force?

• ETC pumps H⁺ out → creates proton motive force

• H⁺ flows back through ATP synthase (“gumball machine”)

• Flow of protons spins ATP synthase → ATP is made

• Oxygen accepts electrons → water is formed

Cyanide binds irreversible to the cytochromes of the electron transport system. How do organisms die from cyanide poisoning?

Cyanide binds to cytochromes in the ETC, blocking electron transfer to oxygen. This stops proton pumping, collapses the proton motive force, shuts down ATP synthase, and halts ATP production. Cells die from energy failure, causing rapid death of the organism

What is stated in the Heterotroph Hypothesis? How does this hypothesis attempt to explain metabolic evolution?

Heterotroph Hypothesis:

• First life forms were anaerobic heterotrophs that fed on organic molecules in the primordial oceans.

Metabolic evolution according to the hypothesis:

1. Fermentation was the earliest metabolism (no oxygen needed).

2. Organic molecules ran low → pressure to evolve autotrophs.

3. Autotrophs produced oxygen → atmosphere changed.

4. Oxygen allowed evolution of aerobic respiration, the most efficient ATP‑producing pathway.

Compare photosynthesis and respiration. How are these processes similar? Different?

Photosynthesis stores energy in glucose; respiration releases energy from glucose

Similarities

• Both use electron transport chains

• Both create H⁺ gradients to power ATP synthase

• Both involve redox reactions

• Both occur in membrane‑bound organelles

• Both are essential to energy flow in ecosystems

Differences

Feature	Photosynthesis	Respiration
Energy	Requires light	Releases energy
Pathway	Anabolic	Catabolic
Organelle	Chloroplast	Mitochondrion
Reactants	CO₂ + H₂O	Glucose + O₂
Products	Glucose + O₂	CO₂ + H₂O
ETC Location	Thylakoid membrane	Inner mitochondrial membrane
Electron Carrier	NADPH	NADH/FADH₂