micro exam 2 focus questions & more

How can microbes be categorized according to their metabolism?

carbon source, energy source, electron source

What makes a chemical reaction energetically favorable?

When it is exergonic (releases free energy and has a - ΔG). This energy can be used to power cellular processes

How do energy carriers "make change" of exergonic reactions?

These energy carriers carry energy in the form of electrons like NADPH, NADH, and FADH2 and break down large energy sources like glucose into smaller energy sources like ATP and GTP.

What are the key steps of glucose catabolism?

1. Glycolysis: Glucose is broken down into 2 pyruvate, 2 ATP, 2 NADH. It can then enter the TCA cycle or fermentation

2. TCA cycle: Pyruvate is converted to acetyl coA, which is a key building block in anabolic pathways. This is further oxidized to produce CO2, NADH, FADH2, and ATP. These electron carriers then feed electrons into the ETS.

--> More energy can be extracted from pyruvate if a strong final electron acceptor like O2 is available

What does 1 cycle of glucose catabolism produce

1 ATP, 4 NADH, 1 FADH2, and a bunch of electron carriers that carry electrons to the ETS where they will be eventually dumped onto O2

What is the major entry point for glucose catabolism?

Acetyl-coA; pyruvate is converted into this so it can enter the TCA cycle

Can other molecules enter catabolism?

Yes - proteins, lipids, peptides and more! they can be converted into intermediates like acetyl-coA to enter other pathways (like TCA cycle)

What are lipids, aromatic rings, etc converted into when entering catabolism?

acetyl coA or another central metabolic intermediate. Then it can be fed into the TCA cycle

What are the two alternative pathways to glycolysis? When are they used?

1. Entner-Doudoroff (ED): Common in enteric bacteria on your gut and can feed off sugar acids. Enteric bacteria "farm" those sugars to generate 1 pyruvate, 1 ATP, and electron carriers (NADH and NADPH)

2. PPP - precursor for biosynthesis. Breaks down glucose into organic molecules building blocks that can be fed into anabolic pathways for the cell to enter biosynthesis to produce NADPH

How are cellular respiration and fermentation different? What about anaerobic respiration?

Cellular respiration uses an ETS, has a final electron acceptor of O2, and generates a lot of ATP.

Anaerobic respiration still has an ETS, but runs when oxygen is not present, and final electron acceptors are not as strong - nitrate, sulfate, etc.

Fermentation - occurs when no strong final electron acceptor is available and without oxygen as a final electron acceptor. It does not have en ETS and instead transfers electrons to oganic molecules. The goal is to regenerate NAD+ so glycolysis can continue so that NADH does not continue to build up.

How do ETS generate proton motive force (Δp)? How does it do work/generate energy?

ETS proteins pass electrons through a series of redox reactions and pump protons out of the cell which creates a proton gradient. This drives ATP synthesis, can be used in symporters and antiporters, and drives flagellar rotation.

- Δp is used to synthesize ATP through oxidative phosphorylation

Where is the ETS located in bacteria? In mitochondria?

Bacteria = cell membrane/plasma membrane

Mitochondria in eukaryotic cells = inner mitochondria membrane; cristae

What are the key features of a bacterial ETS? How are ETS in bacteria similar/different to mitochondria?

Bacteria ETS has oxidoreductases, quinones/quinols, and a terminal oxidoreductase that transfers electrons to a final electron acceptor.

Mitochondria have 4 diff complexes in their inner membrane, greater proton motive force, and are in controlled conditions.

In both - O2 is the best electron acceptor and protons are pumped across a membrane which drives ATP synthase

What Δp used to synthesize?

Synthesizes ATP via oxidative phosphorylation

Why are photosynthesis stages separated into light reactions and light-independent reactions?

Light reactions run in the presence of light ONLY and light-independent reactions can run without light.

Light reactions and what's the name of one?

Use energy from the sun to split electrons from water (photolysis) or other molecules for their ETS. Oxygenic Z!

Oxygenic Z pathway

Used by cyanobacteria and chloroplasts!

1. Antenna complex (made up of pigments that absorb light energy) transfers photo energy to a pigment called PSII.

2. Excitation of that chlorophyll P680 yields energy for photolysis of H20, generating electrons for ETS that are transferred to quinols to be transferred throughout the membrane

3. An ETS relays electrons and contributes to proton motive force by pumping protons out of the cell

4. Energy boost from chlorophyll P700 excitation in PSI transfers electrons to NADPH (production of electron carriers)

What does 1 cycle of the oxygenic Z pathway produce?

2 NADPH (electron carriers) and proton motive force to generate 3 ATP through oxidative phosphorylation

Where does all biomass on earth ultimately come from?

CO2 in the atmosphere that was fixed by autotrophs!

Mainly because of Rubisco, an enzyme that catalyzes the CO2 fixation step in the Calvin Cycle

Key steps of the Calvin Cycle

1. Rubisco incorporates CO2 into ribulose 1,5-bis-phosphate, producing PGA.

2. PGA is reduced using NADPH and ATP to G3P.

3. 2 G3P molecules may condense in a C-C bond to synthesize glucose in biosynthesis OR it can be rearranged to generate RuBP or other metabolic intermediates to synthesize other stuff

*3x turns of the Calvin Cycle = 1 G3P for biosynthesis

Key steps of the Nitrogen Cycle

1. Nitrogen-fixing bacteria like Rhizobium in plant root nodules fix atmospheric N2 to ammonia (NH3).

2. Chemolithoautotrophs like nitrifers oxidize ammonia and nitrite for electrons

3. Denitrifiers use anaerobic respiration to convert nitrate back to N2 gas. They have an alternative final electron acceptor besides O2 at the end of the ETS.

How do Thiomargarita magnifica overcome challenges of large cells

Has a large central vacuole that reduces cytoplasmic space, there are more than 737,000 copies of the genome (polyploid) which allows for their pepin organelles to synthesize proteins across the whole cell so that the cell doesn't have to worry about slow diffusion across the whole cell, pepins contain DNA and ribosomes, and are surrounded by membranes producing ATP through ATP synthase so energy can be produced throughout the cell

Rubisco

Catalyzes the CO2 fixation step in the Calvin Cycle; most abundant enzyme on Earth

Carboxysomes

During photosynthesis, CO2 is converted to bicarbonate in the cytoplasm, which allows the cell to transport and concentrate carbon inside carboxysomes.

What is an alternative pathway to fix Co2?

Reverse TCA cycle

Reverse TCA cycle

Fixes CO2 anabolically to generate acetyl-coA and then build sugars. Anaerobic process

nitrogenous base

DNA or RNA

If nitrogen gas makes up over 75% of the atmosphere, why can't we use it?

2 nitrogen molecules have a triple bond that is super hard to break, so it has to be fixed first

Nitrogenase

an enzyme of nitrogen-fixing bacteria that reduces N2 into 2 molecules of ammonia (NH3)

How do autotrophs play a role in allowing lignin and peptides to go into catabolism?

They assemble carbon and nitrogen into acetyl coA

Antibiotics

Compounds produced by 1 species of microbe that kill or inhibit growth of other microbes

Many soil microbes have biosynthetic pathways to produce antibiotics. Why?

They live in a crowded environment in the soil, and must compete w/ other microbes for nutrients and resources in the soil. Producing antibiotics is an adaptation that allows them to inhibit or kill nearby competing bacteria or fungi to give them a survival advantage. Over time, other microbes have evolved resistance to these antibiotics, so they are continually developing new antibiotics and resistance mechanisms.

anabolism

Assemble organic compounds into complex macromolecules needed for life

What is NADPH's role?

It is an electron carrier used in biosynthesis, energy in the form of a reduction agent

What does anabolism require?

1. Energy (ATP) and NADPH

2. Carbon (and other essential nutrients like Nitrogen)

What is the source of electrons for their ETS in photoorganoheterotrophs?

Photolysis

What is the source of electrons for their ETS in chemoorganoheterotrophs?

Oxidizing organic compounds like glucose

What is the source of electrons for their ETS in photoautotrophs?

Photolysis uses light energy to split electrons from H20 or other molecules

What is the source of electrons for their ETS in chemolithoautotrophs?

Oxidizing inorganic compounds like H2, NH4+

What do anaerobes do with extra unusused light? In what type of bacteria does this take place in?

- Takes place in purple and green non-sulfur bacteria; anoxygenic phototrophs

- Unused light energy/wavelengths can be captured through PSI, where they pass through ETS to generate ATP and proton motive force, and then cycle back to the rxn center

Bacteriachlorophylls

Photosynthetic pigment used by purple and green bacteria and can absorb longer wavelengths of infrared light.

What type of microbe is a bacteriachlorophyll?

Photoorganoheterotroph b/c they don't yield a ton of energy but can oxidize organic compounds too

How does A. ferrooxidans obtain energy from Fe²⁺ oxidation in acidic mine drainage environments, and why does the reaction still proceed even though Fe²⁺ is a weak electron donor?

It obtains energy by oxidizing Fe²⁺ and transferring the e- to the ETS, generating proton motive force for ATP synthase. Although Fe²⁺ is a weak electron donor, the rxn proceeds because the acidic environment consumes H+ ions and the high concentration of reactants drives the reaction forward

Tell me about cable bacteria and how they survive

aka "natural batteries"; they are chains of cells that oxidize sulfur in deeper sediment and transfer the e- along the filament to cells near the oxygen-rich surface.

What does nitrogenase do

Fixes atmospheric nitrogen to ammonia

Methanogens

oxidize H2 gas to yield methane, a MAIN greenhouse gas. Primarily done by archae, not bacteria

Photoautotrophs

Gain energy by absorbing light and obtain carbon by fixing Co2 from atmosphere

Chlorophylls a and b

pigments that absorb primarily blue and red pigments

thylakoid

pigments are housed here. They use proton motive force to generate ATP through ATP synthase!

What form of acquiring organic compounds is unique to microbes?

Chemolithoautotrophy! Iron, sulfur, nitrogen, hydrogen, and carbon monoxide oxidizing bacteria

How do photoautotrophs obtain their carbon?

They fix CO2 themselves from the atmosphere

How do chemolithoautotrophs get their energy and carbon?

They oxidize inorganic compounds like sulfur and obtain carbon by using energy from photolysis to fix CO2

What is CO2 fixation

The reduction and incorporation of Co2 into an organic compound

In the _____, CO2 is incorporated into a precursor of glucose called ____

Calvin Cycle, G3P

Who uses the oxygenic Z pathway

Chloroplasts, cyanobacteria