Biochemistry 3511

Introduction to Metabolism (Chapter 14, Sections 1-3)

1. Overview of Metabolism
Metabolic pathways consist of a series of enzymatic
reactions
Thermodynamics dictates the direction and regulatory
capacity of metabolic flux
Metabolic flux must be controlled
2.High Energy Compounds (ATP)
Phosphoryl group-transfer potential and how it can be
coupled to drive endergonic reactions
3.Oxidation-Reduction Reactions (NAD+, NADH, FAD, FADH2)
NAD+ and FAD are electron carriers
Nernst equation describes oxidation-reduction reactions
Favorableness of a reaction can be determined by
measuring reduction potential differences

Metabolism

Metabolism
Series of biochemical reactions
by which material substance
(food) is broken down into simple
products, which are then used for
the synthesis of complex
compounds (e.g. DNA).

Metabolism

Metabolism
Series of biochemical reactions
by which material substance
(food) is broken down into simple
products, which are then used for
the synthesis of complex
compounds (e.g. DNA).

Approximately 4,000 known

reactions, and thus 4,000
known enzymes!

Metabolism: Catabolism & Anabolism

The overall process through which living organisms acquire free energy (from
food) and utilize the free energy to construct complex molecules (e.g. DNA).

Degradation of compounds into

common building blocks

Construction of complex
molecules required for life

Living organisms do not operate at equilibrium but require a constant influx of nutrients.

Metabolism: Nutrition

Autotrophs
Chemolithotrophs
Photoautotrophs

Heterotrophs

Anaerobes
Obligate anaerobes
Facultative anaerobes

Aerobes
We are obligate aerobes!

Catabolism

Catabolism
Food is converted into common
intermediates (glucose, pyruvate,
Acetyl-CoA, NH3, CO2) via two
processes: glycolysis and the citric
acid cycle.

Catabolism
Glycolysis and the Citric Acid Cycle
convert:
1. ADP ATP
2. NAD+ NADH
3. FAD FADH2
Catabolism will use the free energy
generated by the breakdown of food
into driving ATP generation (our
energy currency).
Catabolism will store the electrons
released by the breakdown of food in
NADH and FADH2 (electron
carriers).

Catabolism

Obtain free energy from food (sugar) by carrying out its stepwise oxidation and
transferring the released energy and electrons to carrier molecules (ATP, NADH, etc.).

Catabolism

The final step in catabolism involves

converting the electron carriers
(NADH, FADH2) into our energy
currency (ATP) via oxidative
phosphorylation.
The final electron acceptor is oxygen
which is converted into water.

Catabolism

Catabolism
full catabolic pathway

Catabolism & Anabolism:

Connected Pathways

Catabolism (degradation) generates NADPH (in addition to NADH, FADH2), ATP and
simple products.
Anabolism uses the NADPH, ATP and simple products to generate complex
metabolites, NADP+ and ADP.

Many Metabolic Reactions Require Vitamins

Rickets

Vitamins: present functionality lacking in an organisms proteins/enzymes,

and cannot be synthesized by that organism. Most water-soluble vitamins
are converted to coenzymes.

Many Metabolic Reactions Require Vitamins

Rickets

Vitamins: present functionality lacking in an organisms proteins, and

cannot be synthesized by that organism. Most water-soluble vitamins are
converted to coenzymes.

Vitamins: Niacin
Vitamins: how to get functionality not present in proteins, and not able to
be synthesized by the organism.

Pellagra Symptoms
1. Diarrhea
2. Dermatitis
3. Dementia
Obtained by eating fish, chicken, turkey,
pork, peanuts, avocados, mushrooms...

Vitamins: Pantothenic Acid

Vitamins: how to get functionality not present in proteins, and not able to
be synthesized by the organism.
Are incorporated in the biosynthesis of key metabolites.

pantothenic acid
vitamin B5

Obtained by eating
mushrooms,
cheese, oily fish,
avocados...

Vitamins: Cobalamin (B12)

Vitamins: how to get functionality not present in proteins, and not able to
be synthesized by the organism.

vitamin B12 deficiency vitiligo, psoriasis

cobalamin
vitamin B12

Obtain by eating shellfish, oily fish, cereals,

soy products, beef, milk, cheese, eggs...

Minerals also Assist Metabolic Reactions

Minerals also Assist Metabolic Reactions

(signal
transduction,
bones, teeth)

(reactions
involving ATP
and other nucleotides,
in synthesis of DNA, RNA,
and proteins)

(hemes)

(enzymatic
cofactors)

Metabolism
Metabolism
With up to 4,000 possible
reactions in a host of pathways,
how does the cell manage all of
these processes???

Metabolism
Metabolism
With up to 4,000 possible
reactions in a host of pathways,
how does the cell manage all of
these processes???
Compartmentation!

Different Metabolic Pathways Occur in

Different Cellular Compartments

Compartmentation in multicellular organisms also occurs on the tissue and organ levels.

Directing Metabolic Information Flow (Flux)

The majority of metabolic
reactions are near-equilibrium.
G 0
Reactions can be easily
reversed by changing the
substrate/product ratio.
Some reactions are far from
equilibrium.
G << 0
Reactions difficult to reverse
by changing the
substrate/product ratio.
How does metabolism control
what path a compound should
take?

Metabolism: Routing Information Flow (Flux)

Metabolic flux: the rate of flow of metabolites through a series of
transformations (metabolic pathway).

P3

P1

P2

Flux = J = v f " v r

J eq = 0 so v f = v r
When far from equilibrium... J " v f

Metabolism:
Routing Information Flow (Flux) 3 Ways
P3

P2
Use an irreversible enzymatic
step to commit the substrate
down a given pathway.

P1

Metabolism:
Routing Information Flow (Flux) 3 Ways
P3

P1

P2
Use an irreversible enzymatic
step at the end of the pathway,
making the entire pathway
irreversible.

Metabolism:
Routing Information Flow (Flux) 3 Ways

P2
The catabolic and anabolic pathway differ.

Metabolism:
Routing Information Flow (Flux) 3 Ways
P3

P3

P1

P1

P2

P2

Use an irreversible enzymatic

step to commit the substrate
down a given pathway.

Use an irreversible enzymatic

step at the end of the pathway,
making the entire pathway
irreversible.

P2
The catabolic and anabolic pathway differ.

Mechanisms to Control Metabolic Flux

Flux Control Mechanisms
1. Allosteric regulation and feedback control
2. Regulation by covalent modification
3. Independent control of interconversions (substrate
cycling)
4. Genetic regulation

Metabolic Flux Control:

Allosteric Regulation
allosteric regulation and feedback

Effectors are often substrates,

products, or cofactors of the pathway.

Metabolic Flux Control:

Allosteric Regulation
allosteric regulation and feedback

Metabolic Flux Control:

Covalent Modification
covalent modification
(phosphorylation & dephosphorylation)

Off

On

Metabolic Flux Control:

Covalent Modification
covalent modification
(phosphorylation & dephosphorylation)

glycogen phosphorylase

Metabolic Flux Control:

Independent Control of Interconversions
independent control of
interconversions
Rates of forward and
reverse reactions can be
varied independently.

P2

Flux = J = v f " v r

Metabolic Flux Control:

Genetic Regulation

genetic regulation
(products stop enzyme transcription)

Reaction Energetics
Glycolysis

Go' = +13.8 kJ/mol

Is this conversion
favorable or unfavorable?

Reaction Energetics
The energy stored in
phosphoryl groups is
used to drive
thermodynamically
unfavorable reactions.

These phosphate
hydrolysis reactions are
thermodynamically
favorable reactions,
but kinetically stable
(very slow).

Reaction Energetics
Coupled reactions can drive unfavorable processes!
O

OH
HO
HO

O
OH
OH

HO
HO

OH
OH
O
OH
OH

Go' = +13.8 kJ/mol

Reaction Energetics
Coupled reactions can drive unfavorable processes!
O

OH
HO
HO

O
OH
OH

HO
HO

OH
OH
O
OH
OH

Go' = +13.8 kJ/mol

What else can we couple this reaction with?

Reaction Energetics
Another example

Go' = +30.5 kJ/mol

Because the phosphate is not coming from ATP,

this is called substrate-level phosphorylation.

Oxidation-Reduction (Redox) Reactions

The reduction potential (E ) describes the tendency for an oxidized compound
to gain electrons (become reduced); these values can be looked up.
The change in reduction potential (E ) for a reaction describes the tendency
for a given oxidized compound to accept electrons from a given reduced
compound. E is the electromotive force.

G = -nF E

The greater the reduction potential, the more negative the free energy
and the more favorable the reaction.

Oxidation-Reduction (Redox) Reactions

Redox reactions generate force/energy.

The more positive the standard reduction

potential, the higher its affinity for
electrons.
The more positive the standard reduction
potential, the more negative G.
Arrange the equation to obtain a positive
standard reduction potential.

Fe Fe2+ + 2e - 0.44 V
Cu2+ + 2e- Cu 0.34 V
-------------------------------Fe + Cu2+ Fe2+ + Cu 0.78 V
In this case, the reaction will oxidize Fe
and reduce Cu2+.

Oxidation-Reduction (Redox) Reactions

Redox reactions generate force/energy.

The more positive the standard reduction

potential, the higher its affinity for
electrons.
The more positive the standard reduction
potential, the more negative G.
Arrange the equation to obtain a positive
standard reduction potential.

Fe Fe2+ + 2e - 0.44 V
Cu2+ + 2e- Cu 0.34 V
-------------------------------Fe + Cu2+ Fe2+ + Cu 0.78 V
Which metal will be oxidized,
silver or sodium?

In this case, the reaction will oxidize Fe

and reduce Cu.

Oxidation-Reduction (Redox) Reactions:

Alternative Mode of Calculation
The more positive the standard reduction
potential, the higher its affinity for
electrons.

E = E (e-acceptor) - E (e-donor )
E = standard reduction potential
E = 0.34 (-0.44) = 0.78

Once you know which metal accepts the

electrons, you can just plug in the standard
reduction potentials.
Remember: you want to have a positive
standard reduction potential (E ) to get a
negative G.

Oxidation-Reduction (Redox) Reactions

NAD+ and FAD are electron carriers:
they accept electrons from metabolites
and transfer them to other compounds.

Radicals (species with unpaired

electrons) are stabilized by
conjugation with adjacent multiple
bonds (resonance forms).
Addition of H is really the paired (or
stepwise) addition of an electron and
a proton.

You can also use half reactions for biological reactions!

Which compound
gets oxidized,
oxygen
or lactate?