The next few classes will be about metabolism.

Chapters 11 - 15 (2nd & 3rd edition)

Chapters 9 - 12

Topics are:

(first edition)

Glucose metabolism.
Citric acid cycle.
Oxidative phosphorylation.

Metabolism
Metabolism is all the chemical reactions taking place in an organism
Heterotrophs use organic carbon as food

(example = humans)

Autotrophs use inorganic carbon as food

(examples = ??? )
Two subtypes of metabolism within cell:
Catabolism (complex ==> simple molecules)
Anabolism (simple ==> complex molecules)

One goal of metabolism is to make ATP.

Why would we want to make ATP? Whats it good for?

Useful energy is released when the phosphoanhydride bonds

are cleaved.

Hydrolysis of ATP releases energy.

about 50 kJ/mole

ATP is useful for is driving the conformational changes

in the motor protein myosin.

wiki muscle

Also, active transport requires energy, which may be

provided by ATP hydrolysis.

The Na+/K+ transporter uses

energy released by ATP
hydrolysis to move ions against
a concentration gradient.

Another thing that ATP can be used for:

ATP can be used to drive chemical reactions that would

otherwise be thermodynamically unfavorable.

Illustrate this important point with an example.

Consider a reaction:
R

====>

G = +20 kJ/mol

Consider a reaction:
R

====>

G = +20 kJ/mol

ATP

====>

ADP + Pi

G = -50 kJ/mol

R + ATP

====>

P + ADP + Pi

G = -30 kJ/mol

So the combined or coupled reaction will spontaneously

form product P.

Hopefully, I convinced you that ATP is useful !

How do living things make ATP?

One way to make ATP is through glycolysis.

Glycolysis
What is glycolysis?
A metabolic pathway that converts glucose to pyruvate.
Overall reaction of glycolysis:

Glycolysis is an oxidation-reduction reaction:

Glucose gets oxidized to pyruvate.
Something must get reduced!

NAD+ gets reduced to NADH.

Why is NAD+ needed? To collect electrons.

When glucose gets oxidized to pyruvate, something must get reduced!

NAD+ gets reduced to NADH.

NAD+ is a cofactor

Why do some enzymes require cofactors ???

Amino acids are NOT good at donating electrons and

accepting electrons.

So enzymes that catalyze oxidation/reduction reactions

usually need cofactors that can be easily oxidized or
reduced as needed.

In NAD+, we met a vitamin !

Vitamin B3. Nicotinic acid

(a precursor for NAD+).
Also known as niacin.

nicotinic acid

NAD+ is needed for glycolysis.

Where does glycolysis happen in eukaryotes?

In the cytosol !
Diagram of a eukaryotic cell
cytosol

Where does glycolysis happen? In the cytosol !

Diagram of a prokaryotic cell
cytosol

Glycolysis is an enzyme-catalyzed reaction:

glucose
10 steps in glycolysis (sorry!).
Each step is catalyzed by its
own enzyme.
Generate 2 ATPs for each
glucose consumed.

Why so many steps?

2 pyruvate

Why are there so many steps in glycolysis ?

A) Biochemistry professors want to make you miserable.
B) If there was only one enzyme in glycolysis, biochemistry would
be too easy, and anyone could get into medical school.
C) Lots of steps means that there will be lots of different
intermediates, many of which are useful.
D) Many steps means that there are many opportunities for
regulation, at the individual enzyme catalyzed steps.

Why study glycolysis?

Almost all cells and almost all living things use glycolysis to make ATP
(I think we agree that making ATP is important).
Its the first complex metabolic pathway to be well understood.
Mechanism of glycolysis was figured out between 1860 and 1940!
1860 - Pasteur figures out that microbes are responsible for fermentation.
1897 - Eduard Buchner found that extracts of cells can cause fermention.
1912 to 1940 - Otto Meyerhof (and many others) worked out most details
of the glycolysis pathway (using yeast extracts, and good analytical
chemistry to detect reaction intermediates). Meyerhof got 1922 Nobel in
medicine for his work.

Glycolysis starts with glucose.

Glucose is a carbohydrate with 6 carbons .

Where do we get glucose for glycolysis ?

Carbohydrates in our diet provide glucose monomers, or polymers
that are hydrolyzed to glucose monomers.

glucose
glucose

glucose
10 steps in glycolysis.
Each step is catalyzed
by its own enzyme.

Its time to make a

few comments about
each step.

2 pyruvate

Step 1:
glucose converted to glucose-6-phosphate by hexokinase.

This step uses ATP.

What ???

I thought we were supposed to make ATP !!!

The first 5 steps in glycolysis are sometimes called energy

investment phase.

Last 5 steps in glycolysis are called generation phase or energy

payoff phase.
Our text uses energy payoff phase.

The last 5 steps are where the ATP is made.

Hexokinase catalyzes step 1.

Step 1 releases a lot of energy (therefore is essentially irreversible).

(G = -16.7 kJ/mole)

Step 2. Catalyzed by phosphoglucose isomerase.

G for this step is very small.

The reactant and product are present in similar amounts.

Step 3.

Catalyzed by phosphofructokinase (PFK-1).

Oh no, we just used another ATP! Arent we supposed to be

making ATP? We are still in the preparatory phase.
Notes on step 3: Energetically very favorable, therefore not
reversible.
This is the slowest step in glycolysis, and rate determining step.

Step 4.
Aldolase breaks the 6-carbon sugar into 2 phosphorylated trioses.

Step 5: Triose phosphate isomerase catalyzes the interconversion

of the two 3-carbon sugars.

The glyceraldehyde-3-phosphate proceeds through glycolysis.

This step insures that the dihydroxyacetone phospate is not
wasted!

Step 6. This is an oxidation step. Glyceraldehyde-3-P is oxidized,

and NAD+ gets reduced to NADH.

Step 7.

We finally made some ATP!

This must be in the generation phase.

Step 8. Phosphoglycerate mutase.

Step 9. Enolase.

Step 10.

Pyruvate kinase.

More ATP is produced.

Large negative G (essentially irreversible).

The overall score through the 10 steps is a gain of

2 ATPs per glucose consumed.

We also gain some reduced NADH (useful for other

things, coming soon!).

Nice figure from the glycolysis wikipedia page.

7 of the 10 steps are

reversible.
The 3 irreversible steps
are regulated.

Focus on these:
The 3 regulated steps.
& the overall goal of
glycolysis.

Phosphofructokinase is an example of an enzyme that

undergoes feedback inhibition.

PEP is an inhibitor of
phosphofructokinase.
(PEP)

Feedback inhibition also

regulates glycolysis.
10 steps in glycolysis, each
catalyzed by its own enzyme.
Phosphofructokinase catalyzes
step 3.
Phosphoenolpyruvate (PEP) is
the product of step 9, and it
inhibits the enzyme at step 3.
Product of step 9 inhibiting
the enzyme of an earlier step
(step 3) is an example of
feedback inhibition.

phosphofructokinase

The three regulated enzymes are hexokinase (step 1)

phosphofructokinase (step 3)
pyruvate kinase (step 10)

Hexokinase (there are several isoforms) is inhibited by glucose-6phosphate, also regulated by a binding protein, and transcriptional
regulation.
Phosphofructokinase (step 3) has inhibitors PEP and ATP.
Pyruvate kinase (step 10) is activated by its own substrate, and
inhibited by its product ATP.

PFK-1 (3rd glycolysis enzyme): ATP binds to an allosteric

site on PFK-1 and lowers the affinity of the enzyme for
its substrate fructose-6-P.
So a high level of ATP
inhibits PFK-1.

(this makes sense, since

if there is plenty of
ATP already present,
there is no need to
make more).
PEP (feedback inhibitor)
binds at the active site.

Ribbon diagram showing two

subunits of the PFK-1 tetramer.

Glycolysis produces 2 molecules of pyruvate.

What happens to the pyruvate?

What happens to the pyruvate?

Pyruvate may be converted to lactate:

Why do we make lactate ???

Making lactate regenerates NAD+ that is required for step 6 of glycolysis!

(this can keep glycolysis going until too much lactate builds up).

Other things that can be done with pyruvate:

It can enter the Citric Acid Cycle (coming soon!)
Pyruvate is also a precursor for making alanine.

In yeast, pyruvate is a precursor for ethanol.

In yeast, pyruvate is a precursor for ethanol.

How does making ethanol benefit yeast?

Making ethanol regenerates the NAD+ used in glycolysis.

Summary up to now.
10 steps in glycolysis.
Each step is catalyzed by its
own enzyme.
Glycolysis is regulated at the
irreversible steps.
Generate 2 ATPs.
energy investment phase
where ATP is consumed, and
payoff phase where ATP is
generated.