Chapter 6: Metabolism

Catabolism

Breaking down larger molecules to obtain energy

and smaller precursors

Anabolism

Use of smaller precursor molecules and energy

from catabolism to build macromolecular cell components

An enzyme’s active site….

binds specific substrates and helps to

convert them to products

Gibbs Free Energy

Energy released

An energy-yielding reaction is exergonic (release of energy)

a negative ΔG°'

An energy-absorbing reaction is endergonic (absorbed energy)

a positive ΔG°'

The rate at which the reaction will occur is determined by its

activation energy

activation energy (EA)

How do enzymes work?

Enzymes jump-start

reactions by lowering their

EA, placing substrates in a

more optimal

arrangement

ATP

Energy currency of the cell

Glycolysis

Catabolic breakdown of glucose

into two 3-carbon pyruvate

molecules.

• Process requires input of energy

(burning two ATP molecules) to

obtain greater output of ATP

(four ATP molecules). Net 2 ATPs

electron transport chain

Electrons are passed through here…it generates a proton gradient….and this drives ATP synthase

Oxidation reaction

Oxidation results in loss

of an electron

Reduction Reactions

Reduction results in gain

of an electron

Common electron carrier molecules

Nicotinamide adenine

dinucleotide (NAD+)

What happens to make NAD to NADH

You add electrons

TCA Cycle (Tricarboxylic)

works to oxidize the remnants from glycolysis and generates electron carriers

Glycolysis

metabolic pathway that breaks down glucose into pyruvate, producing ATP and NADH, and occurs in the cytoplasm without requiring oxygen.

Embden Meyerhof Parnas (EMP) pathway

found in all three domains

Divided into 2 phases

o 6-carbon phase

o 3-carbon phase

• Produces ATP

• Produces small

precursor molecules for

biosynthetic reactions

Entner‒Duodoroff pathway

Produces less ATP than the

EMP pathway

Useful for catabolism of

carbohydrates that can’t be

processed by EMP

Has been found in several

aerobic and anaerobic

bacterial species

Pentose phosphate pathway

Doesn’t produce pyruvate

• Produces carbon precursors

for other pathways

• Produces NADPH electron

carriers for later use

• Found in most microbial

organisms

Fermentation

As cells are converted to NADH, they must be recycled for

glycolytic pathways to continue

Fermentation uses organic molecules to get rid of the electrons

carried by NADH.

Lactic acid fermentation

Pyruvate is reduced to

Lactic Acid

Respiration

Electrons of NADH are passed to an electron transport system

and on to an inorganic acceptor.

NADH pushes through respiration through TCA cycle to become NAD+

electrons generated by glycolysis and

the TCA cycle?

As they pass through the electron transport system, they are

used to create a proton gradient.

o This proton gradient can be used for ATP production.

• They are eventually passed to terminal electron acceptors.

o O2 is used in aerobic respiration.

o Other electron acceptors (inorganic molecules) are used in

anaerobic respiration.

proton motive force

protons are pumped

across the membrane and can be used:

• To produce ATP

ATP synthase

The enzyme used to produce

ATP.

o As protons move through it,

they cause the gamma (γ)

subunit to rotate, changing

active site conformation.

o This facilitates addition of Pi

to ADP to form ATP

Proteins and amino acids

Proteases break

polypeptides into individual

amino acids.

Lipids

The β-oxidation pathway then cleaves the fatty acid into small

carbon chunks that can be sent into the TCA cycle individually

for processing.

Photophosphorylation

ATP synthesis

and the “light” reactions

• Photosynthesis combines

phototrophy and carbon fixation to

produce carbon compounds.

• Light reactions capture light energy

and use it to create a proton motive

force (to synthesize ATP).

• In eukarya, the site of light capture

is the photosystem in specialized

thylakoid structures

Photosystem I

Photosystem II

Ultimately produces NADPH and

ATP

The Calvin cycle and carbon fixation: The “dark” reactions

The ATP and NADPH produced in the “light” reactions are

used in the “dark” reactions (aka the Calvin cycle) to produce

carbon compounds (glucose).

o These carbon compounds are then consumed to produce

much more energy through the “standard” catabolic

reactions.

Nitrogen fixation

Plenty of N2 around, but it’s hard to use!

o The nitrogenase enzyme can help, but

• The process is very energy intensive.

• The enzyme is very sensitive to oxygen and requires protection (see

the heterocyst structure in Anabaena).

• Cysts in roots of legume plants also provide protection from oxygen

Lipid Synthesis

Fatty acid formation takes place in the cytoplasm.

• Consists of small multicarbon units added sequentially.

• Carrier proteins shuttle the units to the growing polymer.