Metabolic Pathways,

revisited
Importance of ATP
Regulation by inhibition
1

Students will understand how energy is

transformed from chemical or solar
energy into the universal power source
of cells, ATP.
Focus:

Cells use ATP to do work

Regulation of metabolic pathways
2

General principles:
Organic molecules in a cell began with the fixation
of carbon from CO2 during photosynthesis
plant biomass: 10 kg

seed: 0.1 g
pot + dirt: 10 kg

water, CO2,
sunlight, and time
pot + dirt: 10 kg
10.0001 kg

20 kg
3

Overview of respiration and

photosynthesis
PHOTOSYNTHESIS

GLUCOSE:

RESPIRATION

CO2 + H2O

temporary storage

CO2 + H2O

Catabolic
pathways

Anabolic
pathways

ATP

simple monomers and organic

molecules

macromolecules

General principles:
The same molecule can serve many different
functions in the cell.
Amino acids serve as building blocks for more complex molecules
proteins
heme synthesis pathway glycine heme
fruit fly pigment synthesis pathway tyrosine pigments
Nucleic acids can serve as
building blocks for RNA and DNA
energy sources (RNA A and G become ATP and GTP)
signals (GTP is the G of G-proteins and G-protein coupled receptors)
5

ATP: for cellular work

Three negative charges repel each other

Makes the molecule unstable
Unstable = high energy!
6

ATPthe cells TNT!

ATP hydrolysis
ATP

H2O

ADP

Pi

+
Energy release
7

Connections: remember this slide from chapter 8?

Cells drive endergonic reactions by

coupling them to exergonic reactions

Enzymes use up ATP every time they have to catalyze a

thermodynamically unfavorable reaction
Figure 8.9

Cells drive endergonic reactions by

coupling them to exergonic reactions
Energy boost
from Pi

A+
B C

A B+
C

ATP

+A

ADP +

A
P

endergonic

exergonic

A +B C
P

A B+ C
+P
exergonic

Hydrolysis of ATP involves covalently attaching the Pi to another molecule.

If the molecule is a reactant, it boosts the potential energy of the reactant.
9

General principles:
To access/transfer the energy in ATP, one of the
phosphate groups is attached to something else
If its attached to a reactant, it gives the reactant
more free energy (G)
If its attached to a macromolecule,
it will change the 3D shape of that molecule
10

ATP: an on-off switch

Pi from ATP hydrolysis can also be attached to proteins.
This always causes a conformational change that alters protein function.
This is called phosphorylation.
Inactive
enzyme

Active
enzyme

Active
enzyme
P

Sometimes it activates a proteins

function.
Inactive
pump

Sometimes you need to keep

phosphorylating it to keep it
moving.

Inactive
enzyme

Sometimes it turns it off.

Active,
binds ion
P

Pushes
ion across

11

ATP: an on-off switch

Pi from ATP hydrolysis can also be attached to proteins.
This always causes a conformational change that alters protein function.
This is called phosphorylation.
Inactive
enzyme

kinase

Active
enzyme

phosphetase

Active
enzyme
P

kinase

Inactive
enzyme

phosphetase

A whole new sub-category of enzymes:

Kinases add phosphate groups to things (usually proteins).
Phosphetases remove phosphate groups from things (usually proteins).
12

Example: MAPK phosphorylation

13

Why will phosphorylating (adding

ATP to) a protein alter the function
of the protein?
A.
B.
C.
D.

It alters secondary and tertiary structure

It alters primary structure by converting
one amino acid to another
It mutates the gene for the protein
You lost me back at the plant

14

ATP: a multi-purpose signal

There may be multiple phosphorylation sites
each having DIFFERENT effects on the protein.
phosphorylating this
location blocks the
active site of the
enzyme

phosphorylating this
location causes the
enzyme to work faster

active
enzyme

phosphorylating this
location makes the
enzyme associate with
another protein

phosphorylating this
location causes the
cell to degrade the
protein

15

Phosphorylation of the Na+/K+ pump is required for each

cycle of the pump.
Which sentence below best rephrases the above
statement in plain English?
A.

Sodium/potassium ions are attached to phosphate groups as they

are moved across the membrane

B.

The sodium-potassium pump requires ATP electrochemical

gradients to function

C.

Adding a phosphate group to the pump protein creates a

structural change that pushes ions across the membrane; this has
to be done for every cycle

D.

Adding a single phosphate group to the sodium-potassium pump

turns the pump on indefinitely
16

ATP: for cellular work

ADP can be hydrolyzed as well.

H2O

ATP

H2O

ADP

AMP
+ Pi

+ Pi

Cellular processes use up ATP (and ADP if ATP is unavailable)

17

ATP: for cellular work

Pi

ATP
H2O

Pi

ADP

AMP

H2O

The reverse reactions (reconstituting ATP) require a very steep input of

energy
(What kind of reactions are they?)
Respiration and photosynthesis ensure the cell has a steady supply of ATP at
all times.
Both processes produce ATP directly.
Photosynthesis also stores quick fuel for respiration in the form of glucose.
18

General Principle
Metabolic pathways are ALWAYS highly regulated
by the cell.
Mechanisms of regulation:
1. Control whether enzymes are present to begin with
transcription
gene regulation

Youll discuss gene regulation in 160

2. Control existing enzymes

feedback inhibition
phosphorylation
degradation (of enzyme)

also triggered through phosphorylation

19

Feedback Inhibition: allosteric

Metabolic pathway: synthesis of
enz. 1

enz. 2

enz. 3

When we want synthesis on:

high concentrations of substrate
low concentrations of product
When we want it off:
high concentrations of final product

20

General Principle:
There are thousands of any given molecule/enzyme at any time...not just one

Relative concentrations determine rate of metabolic

pathway regulated by feedback inhibition
enz. 1

enz. 2

enz. 3

(this is the symbol for

inhibition)

>

<

rate of synthesis is
high

rate of synthesis is
low

synthesis is
halted

(little inhibition)

(some inhibition)

(mostly inhibited)
21

Inhibition through phosphorylation

glycogen synthase

glucose
monomers

glycogen fibers

22

Hey! what is glycogen and how is it

linked?
A. carbohydrate; peptide bonds
B. protein; ester linkages
C. carbohydrate; -glycosidic linkages
D. protein; peptide bonds
E. phospholipids; not covalently linked
23

Inhibition through phosphorylation

glycogen synthase
kinase (GSK-3)

P
glycogen synthase

glycogen synthase

glycogen synthase
glycogen synthesis active
glucose
monomers

glycogen fibers

24

Inhibition through phosphorylation

glycogen synthase
kinase (GSK-3)

P
glycogen synthase
glycogen synthesis inhibited
glucose
monomers

glycogen fibers

25

Often there are cascades of

phosphorylation
Protein Kinase B (Akt)
P
glycogen synthase
kinase (GSK-3)

GSK-3 inactivated by
phosphorylation

glycogen synthase
glycogen synthesis active
glucose
monomers

glycogen fibers

26

Often there are cascades of

phosphorylation
P
yet another
Kinase

Protein Kinase B (Akt)

Akt activated by
phosphorylation

P
glycogen synthase
kinase (GSK-3)

GSK-3 inactivated by
phosphorylation

glycogen synthase
glycogen synthesis active
glucose
monomers

glycogen fibers

27

Other ways to inhibit an enzyme:

(not generally used by body, though often a
mechanism of action of drugs)
reversible

competitive inhibition

another

molecule competing for active site

can be overcome by adding more substrate
other

covalent modifications

chemicals

or toxins bind to enzyme and

render it inoperative permanently
28

So a ribonucleotide can be used for energy?!

Prediction: other ribonucleotides are also used as energy.
True!! They all provide energy, but ATP is the most commonly
used.

Guanosine triphosphate (GTP) is essential for Gprotein signal transduction

Cytidine triphosphate (CTP) is essential for some

smooth and rough ER enzyme functions

Uridine triphosphate (UTP)s role in extracellular

receptors is still under investigation
29

You should be able to:

Explain how chemicals and molecules in a cell can be used for multiple
functions, and give examples

Explain ATPs relationship to RNA.

Explain what ATP is, and why its so important to ensure a steady supply of
it. Give at least three examples of how it is used in the cell, and describe
the types of reactions that require it.

Explain ATPs high energy levels (what about its structure makes it high
energy and unstable), and explain where the energy to make ATP comes
from (directly and indirectly).

If I tell you an enzyme is a kinase or a phosphorylase, tell me what the

enzyme does (on a general level)

30

You should be able to:

Explain how cells use allosteric feedback

inhibition to turn down synthesis pathways

Explain how cells use phosphorylation to turn

enzymes in metabolic pathways on or off

Interpret a diagram that includes activation and

inhibition cascades (more when we do signal
transduction)
31

You should be able to:

Explain how the metabolic pathways (respiration and

photosynthesis included) as shown in the book relate to metabolic
pathway concepts as presented in lecture.
Explain what arrows mean, what each molecule is, what a metabolic
pathway is
Identify which components are encoded by genes and which are organic
molecules related to glucose, and what would happen if a given gene
were mutated
Identify points of feedback inhibition (allosteric regulation) in the
pathway and how the presence of particular components will affect the
rate of the pathway

Explain how any given chemical in the respiration or photosynthesis

metabolic pathways may have multiple uses in the cell (ex: see
figure 9.3 and 9.4)
32