BIO 208 Unit 2 Review of General Metabolism Concepts

Review - Important Concepts for Lectures over Metabolism

I assume that you have had an introduction to the basics of metabolism in an introductory biology course. The metabolism you learned was probably entirely focused on the types of metabolism that animal (maybe plant) cells carry out --aerobic respiration; perhaps you were exposed to lactic acid fermentation (When muscles are working very hard, they may be temporarily depleted of oxygen, muscle cells can perform lactic acid fermentation for a short period of time. The lactic acid end products are secreted by the muscle cells into your tissues, and you feel the lactic acid as muscle soreness). The microorganisms are tremendously more diverse and complex in metabolic patterns than are Eucarya and I want to spend our time emphasizing what microbes can do, not just covering what you have already had in other courses.

So, if you do not remember the basics of metabolism you will need to review. The following pages should serve as a reminder. If it doesn’t all come back to you then read Chapter 5 in the text. If you have not had chemistry you will also need to read Chapter 2.

Review of oxygen tolerance: Obligate anaerobe – does not require O2. Aerotolerant anaerobe – does not require O2 for . Microaerophile – needs a little O2 for metabolism, but less than amount present

in the atmosphere. Facultative anaerobe – can switch its metabolism based on whether or not O2 is

present. Aerobe (obligate aerobe) – requires O2 for metabolism.

Review of nutritional patterns:Source of energy Source of carbonChemicals CO2 (used by autotrophs)

organic Organic molecules (-C-C-C-) (used by heterotrophs)inorganic

Light

Most common combinations of Energy gaining strategy plus Carbon gaining strategy

Chemoorgano heterotrophsChemolitho autotrophsPhoto autotrophsPhoto heterotrophs

BIO 208 Unit 2 Review of General Metabolism Concepts

You should also knowDefinitions of metabolism, anabolism, and catabolismThat ATP (Adenosine Tri Phosphate) is made to store energy and used to release energy – it is the energy “currency” for the cell.Pyruvate is a key intermediate molecule in many catabolic pathways.

Should understand basics of oxidations - reductionsRemember - A loss of an electron is called an oxidation; a gain of an electron is called a reduction (remember as: LEO the lion says GER).

In biological molecules it is usually the entire H atom (electron and proton) that is lost or gained, but not always. Sometimes the electrons are separated from the proton and only the electrons are lost or gained; and sometimes it may be one H atom + 1 electron (from a second H atom) that are lost or gained.

In any pair of molecules you can distinguish which is the oxidized and which is the reduced:

Oxidized state Reduced state:Contains more oxygen atoms OR Contains fewer oxygen atoms ORfewer hydrogen atoms AND more hydrogen atoms ANDtherefore has fewer electrons and is therefore has more electrons and isless negative or more positive more negative or less positive

Example pairs:

Glucose PyruvateC6H12O6 C3H4O3

NAD+ NADH

Sulfate Hydrogen sulfideSO4 H2S

BIO 208 Unit 2 Review of General Metabolism Concepts

All cells need:

1. A source of carbon for making cellular molecules.

There are two strategies for obtaining carbon:a. Recycle the C already present in some organic (-C-C-) moleculeb. Use CO2 from the atmosphere

2. A source of energy for performing all cellular work (building molecules, transport across the plasma membrane, locomotion, etc.)

Energy is created by harvesting the electrons present in:

a. Organic molecules.

(specifically the electrons in the H atoms in the molecules)

Hydrogen – showing the proton and electron

like a sugar or an amino acid

OR

b. Inorganic molecules.

electrons in molecules like

ammonia hydrogen sulfide

The more electrons a molecule has, the more energy the molecule is capable of yielding – so look at glucose compared to hydrogen sulfide – which molecule should yield the most energy? (glucose – 12 H vs. 2 in H2S)

BIO 208 Unit 2 Review of General Metabolism Concepts

The electrons that are released when bonds are broken have to go somewhere, so they get passed from the donor (the molecule that you started with that had all the electrons) to intermediate electron carriers.

NAD+ is a soluble carrier present in the cytoplasm. It is lacking 1 electron (1 H) and so it can accept 1 electron (1 H). As it accepts the electron, it is reduced to NADH.

Oxidized statefewer H, fewer e-

more positive (NAD+)

Reduced statemore H, more e-

BIO 208 Unit 2 Review of General Metabolism Concepts

pH 8.5

electrochemical gradient - energyFig. 5.16

NAD+ is in limiting quantities in the cell and it must be regenerated if energy production is to continue.

There are 2 ways to regenerate NAD+ from NADH :

1. NADH passes the electron to an organic molecule like pyruvate – this process is called fermentation - as NADH loses the electron it becomes oxidized to NAD+ again. As pyruvate accepts the electron it becomes reduced to acetic acid or to ethanol, etc., which are excreted from the cell, carrying waste electrons with them. Acetic acid, ethanol, etc. still have electrons, so potential energy is lost in the fermentation strategy.

2. NADH travels to the cytoplasmic membrane and passes the electron off to the electron transport chain. This process is called respiration.

(NADH then becomes NAD+ )

BIO 208 Unit 2 Review of General Metabolism Concepts

The electrons are passed along the chain, generating two types of usable energy along the way – electrochemical gradient and ATP - until they reach a final electron acceptor, an inorganic molecule which can be:

a. oxygen (aerobic respiration)

OR

As oxygen accepts electrons it will become

reduced to H2O

b. some other inorganic molecule (anaerobic respiration)

like nitrate or sulfate

becomes reduced to nitrite (NO2)

becomes reduced to hydrogen sulfide (H2S)

Note – fermentation is NOT anaerobic respiration. By definition respiration requires both an electron transport chain and an inorganic terminal electron acceptor. Fermentation does not employ an electron transport chain and the terminal electron acceptor is an organic molecule. Fermentation takes place in the absence of oxygen, it can occur in anoxic and anaerobic environments, but it is not respiration!

BIO 208 Unit 2 Review of General Metabolism Concepts

Comparison of Respiration vs Fermentation in Chemoorganotrophs

Respiration FermentationInitial electron donor: organic molecule organic molecule

examples: carbohydrates, amino acids, lipids carbohydrates, amino acids, lipids

Intermediary electron carrier(s):

NADH, FADH2, carriers in the electron transport chain NADH

Final electron acceptor inorganic molecule organic moleculeexamples: O2 CO2, NO3, SO4 pyruvatefinal electron acceptor reduced to: H2O CH4, NO2, H2S

lactic acid, acetic acid, ethanol, etc.

example organisms Mitochondria, E. coli,

Pseudomonas,S. aureus

Methanogens, E. coli,

Pseudomonas, Sulfate-reducing

bacteria

Bifidobacterium, Lactobacillus, E. coli,

Clostridium, Bacteroides

Potential net ATP yield:

as many as 38 if starting with 1 glucose by aerobic respiration with an electron transport chain containing all the cytochromes – but often far fewer than 38 - but still more than 2.

2

BIO 208 Unit 2 Review of General Metabolism Concepts

Comparison of Respiration in Chemoorganotrophs vs Chemolithotrophs

Chemoorganotroph ChemolithotrophInitial electron donor: organic (-C-C-) molecule inorganic molecule

examples: carbohydrates, amino acids, lipids hydrogen gas, ammonia, nitrate, hydrogen sulfide

Electron donor oxidized to: CO2

water, nitrate, nitrite, sulfuric acid

Final electron acceptor inorganic molecule inorganic molecule

examples: O2 (aerobic respiration)

CO2, NO3, SO4

(anaerobic respiration)

O2 (aerobic respiration)

electron acceptor reduced to: H2O CH4, NO2, H2S H2O

example organisms

Mitochondria, E. coli,

Pseudomonas,S. aureus

Methanogens,E. coli,

Pseudomonas, Sulfate-reducing

bacteria

Alcaligenes, Nitrosomonas, Nitrobacter,

Thiomargarita