Micro exam

Metabolism

The sum of all total chemical reactions that occur in a cell

Catabolic reactions (aka catabolic pathways)

energy releasing, exergonic, metabolic reactions

anabolic reactions

energy requiring, endergonic, metabolic reactions that consume energy

Microbial metabolism knowledge is based on

study of laboratory cultures

Nutrients

supply of monomers (or precursors) required by cells for growth

Macronutrients

Nutrients required in large amounts

Micronutrients

Nutrients required in trace amounts

Examples of Macronutrients

Carbon, oxygen, Nitrogen, Hydrogen, phosphorus, Sulphur, potassium, magnesium, sodium, calcium, iron

Examples of micronutrients

trace metals and growth factors

What major element is used in ALL classes of macromolecules

carbon

A typical _______ cell is 50% carbon

bacterial

most microbes (heterotrophs) use organic __________ and most autotrophs use ___________

carbon; carbon dioxide

Where is the bulk of nitrogen found in nature

ammonia (NH3), nitrate (NO3-), or nitrogen gas (N2)

Nitrogen includes

proteins, nucleic acids, and other cell constituents

Nearly all microbes can use _____ as their nitrogen source yet ____ is more abundant

ammonia; N2

Nitrogen gas is the most abundant form of nitrogen but it is limiting how

it is trapped in the atmosphere

Phosphorus is required by the cell why

for the synthesis of nucleic acids and phospholipids

phosphorus is found where

in proteins and amino acids

Sulfur plays a structural role in which amino acids

the S-containing amino acids (cysteine and methionine)

Where is sulfur found

in several vitamins (ex. thiamine, biotin, lipoic acid) and coenzyme A

What is required by enzymes for activity

potassium

What does magnesium stabilize

ribosomes, membranes, and nucleic acids

calcium helps stabilize

cell walls in microbes

calcium plays a key role in heat stability of

endospores

sodium is required by

some microbes (ex. marine microbes)

Growth factors are inorganic or organic compounds

organic compounds

Growth factors are

organic compounds required in small amounts by certain organisms

examples of growth factors

vitamins, amino acids, purines, pyrimidines

vitamins are the most commonly required

growth factors

most vitamins function as

coenzymes

trace metals (metallic compounds) are

tightly bound and (ex. iron) plays a major role in cellular respiration (key component of cytochromes and Fe-S proteins involved in electron transport)

Acquisition of Iron

Bacteria have evolved ways of acquiring iron from their hosts including

1. Siderophore systems

2. Surface ferric reductases

3. Haemolysins and cytotoxins

Siderophores in human blood

large protein molecules

siderophores in bacteria

small compounds with extremely high-affinity for iron (iron-chelating compounds)

Siderophore systems

Bacterial siderophores bind to the iron in the human body by outcompeting the binding through a TonB process (basically an iron piracy by the bacteria)

Part of our immune system is responsible for taking away iron from

the microbes

Surface ferric reductases

proteins on the surface of bacteria that reduce free ferric ion to ferrous which can be taken up by the cell to be used

Iron can only be used in the ferric state which is what ionization

3+

Hemolysins and cytotoxins

Hemolysins breaks down hemoglobin releasing iron for uptake by bacteria, cytotoxins can damage and rupture cells freeing up intercellular iron as well. This is another way to acquire iron.

Micronutrients (trace elements and growth factors) needed by microbes

Trace elements: Boron, cobalt, copper, iron, manganese, molybdenum, nickel, selenium, tungsten, vanadium, zinc

Growth factors: PABA, folic acid, biotin, B12, B1, B6, nicotinic acid, B2, pantothenic acid, lipoic acid, vitamin K, coenzymes M and B, F420 and F430

Two broad classes of media

chemically defined media and complex media

chemically defined media

precise chemical composition is known

complex media

composed of digests of chemically undefined substances (ex. yeasts and meat extracts)

Selective media

media that selects for a specific type of microbe (ex. a salt-loving bacteria will thrive by growing on salt-based media)

A selective media is great at doing what specifically

suppressing unwanted microbes and encouraging desired microbes

Differential media

makes it easy to distinguish colonies of different microbes (often contains an indicator dye)

Three classes of active transport (found on the inner membrane of gram positive and negative cells)

simple transport

group translocation

ABC system

The three classes of active transport are composed of what

12 alpha-helical membrane spanning regions

Where does the energy come from for active transport for bacteria

proton motive force, ATP, and energy-rich compounds

Simple active transport is driven by what type of energy

proton motive force

Group translocation active transport is driven by what

It is chemical modification of the transported substance because it is driven by the phosphoenolpyruvate

ABC transporter active transport is driven by what type of energy

ATP

What is an example of simple transport

Lac permease (lactose molecule) it is a symporter and is co-transported with a H+ ion in

Energy is considered through the formation of what bonds

Phosphate or sulfur bonds

what releases the energy to drive endergonic reactions

hydrolysis

Eukaryotic energy storage

Starch and simple fats

Prokaryotic energy storage

Glycogen, poly beta hydroxybutyrate, sulfur

Transfer of a high energy PO4- to ADP

Substrate-level phosphorylation

Energized by the proton motive force, dissipates some of the energy in the formation of ATP from ADP + Pi

Oxidative phosphorylation

Light causes chlorophyll to give up electrons, energy release from the transfer (oxidation) is used to generate ATP

Photophosphorylation

Organisms that oxidize carbohydrates as the primary energy source to drive ATP synthesis

chemoorganotrophs

Most common carbohydrates used in catabolism

glucose

Transfer of electrons to oxygen (final electrons acceptor) or to some external compound

Cellular respiration

Anaerobic organic compounds are catabolized (electron donors) and internal organic compounds serve as the final electrons acceptors

fermentation

Glycolysis stage 1

Preparatory reactions (no redos changes)

Glycolysis stage 2

Redbox reactions (energy rich compounds using group transport)

Net gain in glycolysis stage 2

2 ATP and 2 NADH

Net gain in Glycolysis stage 3

2 ATP and two NAD+ regenerated

Glycolysis stage 3

Fermentation reactions (redos balance)

Overview of the three stages of glycolysis

Stage 1; preparatory - form key intermediates

Stage 2; redos

Stage 3; (fermentation) redox balance

End result: two ATPs produced

Differences in fermentation are the products formed by the

Pyruvate

Fermentation

Respiration switch based on energetic benefit

When O2 is available, microbes use what

respiration

In anoxic conditions, microbes use what

respiration

During cellular respiration pyruvate is fully oxidized to

CO2

Aerobic respiration

They final electrons acceptor in the electron transport chain is molecular oxygen

Anaerobic respiration

The final electron acceptor in the electron transport chain is not oxygen.

Acetyl-CoA + oxaloacetate forms

Citric acid

For every 2 pyruvate oxidized in preparatory stage and in the citric acid cycle

6 CO2, 8 NADH, 2 FADH2 and oxaloacetate are regenerated

Electron transport systems have many different functions including

• They are membrane associated

• They mediate electron transportation

• They conserve energy releases during transport and use it to synthesize ATP (proton motive force)

• They utilize many redox enzymes and quinones

Quinones: non-protein electron carriers

Anaerobic respiration

Used electron acceptors other than oxygen

Examples include No3-, Fe3+, So4 2-, Co3 2-, ad certain organic compounds

Dependent on electron transport, generation of a proton motive force, and ATPase activity

Heterotrophic (uses organic compounds as carbon source)

Anaerobic respiration vs aerobic respiration energy release

Anaerobic respiration releases less energy than aerobic respiration

Chemolithotrophy

Uses inorganic chemicals as electron donors (energy source)

Examples include H2s, H2, Fe2+, NH3

Begins with oxidation of inorganic electron donors

Uses electron transport chain and proton motive force

Autotrophic uses CO2 as carbon source

phototrophy

Uses light as energy source

photophosphorylation

Light-mediated ATP synthesis

photoautotrophss

Uses ATP + CO2 for biosynthessis

photoheterotrophs

Use ATP + organic carbon for biosynthesis

Autotrophs

CO2 sole or principal biosynthetic carbon source

Heterotrophs

Reduced, preformed, organic molecules from other organisms

phototrophs

light

lithotrophs

Reduced inorganic molecules

organotrophs

Organic molecules

Group translocation

Substance transported is chemically modified

Energy-rich organic compound (not proton-motive force) drives transport

Multiple proteins including a membrane spanning transporter

Energy derived from phosphoenolpyruvate

ABC (ATP-binding cassette) systems

• ATP drives uptake

• Has a high substrate binding affinity

• Requires transmembrane and ATP-hydrolyzing proteins plus

  • Gram-negative employ periplasmic binding proteins

  • Gram-positive and archaea employ substrate binding proteins on external surface of cytoplasmic membrane

cofactor

Bonds tightly to enzymes, usually covalently and permanently

Coenzymes

Loosely bind to enzymes, they are mostly derivatives of vitamins

Factors influencing enzyme activity

Temperature, pH, substrate concentration, competitive inhibition, noncompetitive inhibition, and feedback inhibitionre

Reduction potential

Tendency to donate electrons

(Reduced substance of a redox couple with a more negative reduction potential donates electrons to the oxidized substance of a redox couple with a more positive reduction potential)

Redox tower

Represents the range of possible reduction potential

(Substances towards the top (reduced) prefer to donate electrons, substances towards the bottom (oxidized) prefer to accept electrons)

The farther the electrons “drop” the greater the amount of energy releases

Oxygen is the strongest significant natural electron acceptor

Facilitates redox reactions without being consumed; they are recycled

NAD+ and NADH