2610 E3 Microbe Metabolism

What organic molecules are needed by every microbe?

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur

What are Essential Nutrients?

Materials that organisms are unable to synthesize, but are required for building macromolecules and sustaining life

TRUE or FALSE — Cells must import and assimilate nutrients

TRUE !

Why do nutrients vary between cells?

They vary based on cell needs and molecular machinery (ability to break down certain molecules)

What are the two classifications for how cells acquire energy?

Phototroph and Chemotroph

What are the two classifications for how cells acquire electrons?

Organotroph and Lithotroph

What are the two classifications for how cells acquire Carbon?

Heterotroph and Autotroph

What are Phototrophs?

Microbes that acquire energy from light

What are Chemotrophs?

Microbes that acquire energy from organic a/o inorganic compounds

What are Organotrophs?

Microbes that acquire electrons from organic molecules

What are Lithotrophs?

Microbes that acquire/remove electrons from inorganic molecules

What are Heterotrophs?

Microbes that acquire carbon from pre-existing organic molecules

What are Autotrophs?

Microbes that acquire carbon from inorganic sources

What is a Chemoorganoheterotroph

Inorganic energy source, Organic electron source, acquires C from organic precursors

What is a Chemolithoheterotroph

Inorganic energy source, inorganic electron source, acquires C from organic precursors

What is a Chemolithoautotroph?

Inorganic energy source, inorganic electron source, inorganic C source

What is a Photoorganoheterotroph?

Light source for energy, organic electron source, acquires C from organic precursors

What is a Photolithoheterotroph?

Light source for energy, inorganic electron source, acquires C from organic precursors

What is a Photolithoautotroph?

Light source for energy, inorganic electron source, inorganic C source

What is metabolism?

The building up and breaking down of nutrients within a cell

What is anabolic metabolism?

MAKE - create one from many (+ energy)

What is catabolic metabolism?

BREAK - create many (+ energy) from one

What are enzymes?

Specialized proteins / Biological catalysts

TRUE or FALSE — Catalysts are used up in reactions

FALSE — Catalysts are regenerated!

TRUE or FALSE — Catabolic reactions can provide energy for Anabolic reactions

TRUE !

What is the first law of Thermodynamics?

Energy cannot be created or destroyed

What is the second law of Thermodynamics?

Energy will spontaneously flow from order/stability to disorder/instability

What is entropy?

A measure of randomness/chaos

What is free energy? (G)

The energy available to do work

What is Gibbs free energy?

The amount of free energy released in a chemical reaction

What can Gibbs free energy tell us about a reaction?

The conditions under which it occurs (pressure, temp, etc.), spontinaety, speed

Define exergonic

Energy is released (-∆G)

Define endergonic

Energy is absorbed (+∆G)

What is Activation Energy (Ea)

The rate of the reaction

TRUE or FALSE — The higher the Ea, the slower the reaction

TRUE !

TRUE or FALSE — If the Ea is very negative, a reaction will occur spontaneously

FALSE !

How do enzymes/catalysts work?

They lower the activation energy (Ea)

What are three ways enzymes lower the Ea?

1. Stabilize the transition state / create a favorable environment

2. By orienting enzymes and substrates

3. Providing chemical groups to participate in rxn’s (acids/bases)

What is a substrate?

The molecule an enzyme acts upon

What is the active site?

The site where the substrate binds the enzyme

TRUE or FALSE — The interaction between a substrate and the active site is specific

TRUE !

What are the steps to enzyme-substrate reactions?

1. Substrate contacts active site

2. Substrate/Enzyme complex forms

3. Substrate is transformed into product

4. Product released / Unchanged enzyme

What are the two theoretical methods for enzyme-substrate interactions?

Lock and Key /// Induced Fit

Describe the lock/key method?

The enzyme is a fixed shape that matches the substrate

Describe the induced fit method?

The active site changes conformation to better attach itself to the substrate

Which method is more accurate? (Lock/Key VS Induced Fit)

Induced Fit

What is a cofactor?

A non-protein component that activates an enzyme

TRUE or FALSE — Coenzymes can be organic or inorganic

TRUE !

What is an apoenzyme?

An inactive enzyme without an attached cofactor

What is a holoenzyme?

An active enzyme with an attached cofactor

What is a coenzyme?

An organic cofactor (derived from vitamins / regulates enzymes)

TRUE or FALSE — Humans need 18 dietary vitamins

FALSE — Humans only need 13, but we synthesize most of those

What are some important coenzymes/electron carriers in energy synthesis?

NAD- , NADH, FAD, and Coenzyme A

What are the two kinds of enzymatic inhibition?

Competitive VS Allosteric

How do competitive inhibitors work?

They compete with the substrate for access to the active site

How do allosteric inhibitors work?

They bind to the allosteric site, triggering a conformational change in the active site, preventing the substrate from binding

TRUE or FALSE — Enzymes can be controlled by negative feedback loops

TRUE !

Where does cellular energy come from?

Energy comes from nutrient breakdown in steps by enzymes

TRUE or FALSE — ATP is gained anabolically (make) and spent catabolically (break)?

FALSE — ATP is gained catabolically (break) and spent anabolically (make)

What happens to coenzymes that aid in energy creation? (sorry)

They’re reduced and GAIN electrons

What are two methods for recharging ADP?

1. Substrate-Level Phosphorylation

2. Oxidative Phosphorylation

How does substrate-level phosphorylation work?

Direct phosphate transfer to ADP — Glycolysis/Fermentation — Small ATP payout, happens in cytoplasm

How does oxidative phosphorylation work?

Electrons are stripped form a food source and used in the Electron Transport Chain — Large ATP payout — In eukaryotic mitochondria OR prokaryotic cytoplasm

TRUE or FALSE — Photophosphorylation happens in photosynthetic cells

TRUE!

What are some details about catabolic pathways?

They’re sets of enzyme catalyzed reactions, product A becomes substrate B, provides materials for biosynthesis, Amphibolic pathway (both cata and ana -bolic)

What is fermentation?

The partial degredation of sugars under anaerobic conditions

What is cellular respiration?

Anaerobic and Aerobic respiration

What is aerobic cellular respiration?

Degredation of sugars/organic substances with O2

What is anaerobic cellular respiration?

Degredations of sugars, but it substitutes oxygen with other substances

Where does cellular respiration occur? (E VS P)

Eukaryotes — Cytoplasm (glycolysis) + Mitochondria (ETC)

Prokaryotes — Cytoplasm

What are the three main phases of Cellular Respiration?

1. Glycolysis

2. Intermediate Step (PV acid to Acetyl CoA)

3. Krebs Cycle

4. Electron Transport Chain

Is Glycolysis Substrate-level or Oxidative Phosphorylation?

Substrate-Level Phosphorylation

Is the Krebs Cycle Substrate-level or Oxidative Phosphorylation?

Substrate-level Phosphorylation?

Is the Electron Transport Chain Substrate-level or Oxidative Phosphorylation?

Oxidative Phosphorylation?

What is another name for Glycolysis?

Embden-Meyerhof Pathway (EMP)

What are the three ways for Glycolysis to happen?

EMP — Embden-Meyerhof Pathway

PPP — Pentose Phosphate Pathway

ED — Entner Duodoroff

What’s important about the PPP? (Pentose Phosphate Pathway)

• Alternative to glycolysis, important for biosynthesis

• Uses pentose and glucose

• Yields precursor metabolites and NADPH

What does PPP (Pentose Phosphate Pathway) yield?

1 ATP, Ribose sugars, phosphate backbone, nucelotides, steroids, fatty acids, and NADPH

What’s important about the ED? (Entner Doudoroff Pathway)

Prokaryotes use this pathway in place of glycolysis/EMP

What does the ED (Entner Doudoroff Pathway) yield?

It yields 1 ATP, 1 NAD, 1 NADH, and 1 NADPH

What are the two phases of the EMP (Embden-Meyerhof Pathway)?

Energy investment phase

Energy payout phase

What happens during the Energy Investment Phase?

6 Carbon Glucose combines with 2 ATP to form 2 ADP and Phosphates

What happens during the Energy Payoff Phase?

4 ADP and 4 Phosphates form 4 ATP

2NAD+, 4 electrons, and 4 H form 2 NADH and 2 H

Glucose forms 2 Pyruvate molecules and 2 H2O molecules

What is the net payoff from the EMP (Embden-Meyerhof Pathway)

1 Glucose —> 2 Pyruvate, 2 H₂O

4 ATP formed - 2 ATP used —> Net gain of 2 ATP

2 NAD+ + 4e- + 4H —> 2 NADH, 2 H+

What intermediate step happens after glycolysis?

Pyruvate is transformed into Acetyl CoA

What enzyme turns pyruvate into Acetyl CoA?

Pyruvate dehydrogenase

What are the three names for the Krebs Cycle?

Krebs Cycle (lol)

Citric Acid Cycle

Tricarboxylic Acid Cycle

TRUE or FALSE — Prokaryotes do NOT utilize the Krebs cycle

FALSE — Bacteria and Archaea participate along with Eukaryotes (yeast, protozoa, algae, fungi)

Where does the Cirtic Acid Cycle occur in eukaryotes?

The mitochondria

How many electron carriers are generated per 1 glucose? (TAC/CAC/Krebs)

2 FADH₂, 6 NADH

How much ATP is produced per1 glucose? (TAC/CAC/Krebs)

2 ATP

What other byproducts are formed from the Citric Acid Cycle? (TAC/Krebs)

4 CO₂

TRUE or FALSE — Substrate-level phosphorylation occurs during the Krebs cycle?

TRUE !

How much ATP is generated from Glycolysis and the Krebs Cycle?

4 ATP - 2 from G, 2 from Krebs (GTP, not ATP)

How many NAD+ molecules are reduced from Glycolysis, Intermediate step, and Krebs?

2 NADH from G ///// 2 NADH from Intermediate ///// 6 NADH from Krebs Cycle

How many FAD+ molecules are reduced from Glycolysis, Intermediate step, and Krebs?

2 FADH₂ molecules are produced from the Krebs Cycle

Does Oxidative Phosphorylation or Substrate-Level Phosphorylation occur during the Electron Transport Chain step?

Oxidative Phosphorylation

How do the anaerobic and aerobic respiratory chains differ?

Aerobic — Require O2 as final e- acceptor, NEEDS O₂

Anaerobic — Uses inorganic molecules (NO₃^- , SO₄ ^2- )in place of O₂ as the final e- acceptor

Where does the oxidative phosphorylation step happen in Pro- vs Eu-karyotes?

P — Plasma membrane

E — Mitochondria

How does ATP Synthase work?

A proton gradient is formed and as protons move through ATP-Synthase, the gamma subunit rotates, changing the beta subunit / active site’s conformation, changing ADP to ATP