Study Unit 9: Making Life Work

Dr. Rebamang Mosa

Department of Biochemistry, Genetics and Microbiology
Agricultural Science Building, Office Number: 3-5
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E-mail: rebamang.mosa@up.ac.za
 Lecture 1: Learning Outcomes (LO)

1. Describe the ways that organisms obtain energy and carbon from the
environment.
2. Define metabolism and distinguish between catabolic and anabolic
reactions.
3. Differentiate between kinetic and potential energy.
4. Discuss the central role of ATP in the overall energy metabolism of the cell
and explain how its chemical structure allows it to perform its role.
5. State the first and second laws of thermodynamics and discuss the
implications of these laws as they relate to living organisms

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LO 1&2
Requirements of the Cell
Cells require:
• a membrane separating the
inside of the cell from the
outside
• a way to encode/transmit
information
• energy to do the work of the
cell: move, grow, pump
ions, and perform reactions
necessary for cellular
function, among other
things
LO 1&2
Metabolic Classification
LO 1&2
Metabolism: An Overview

Anabolism is Catabolism is
the building of the breakdown
molecules of molecules
from smaller into smaller
units, requiring units,
an input of producing
energy (ATP). energy (ATP).

Metabolism is the building and breakdown of carbon sources

to harness or release energy.
LO 3
Forms of Energy: Potential and Kinetic Energy

• Potential energy: energy that is not associated with movement

but rather is stored.
• Kinetic energy: the energy of motion.
LO 3
Energy transformation
Living organisms have an ability to transform energy from
one form into another

• Energy from sunlight is stored as potential energy in covalent

bonds between atoms in sugars
• Breaking bonds between atoms requires energy; energy
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stored in chemical bonds may be used to make new bonds
LO 4 Adenosine Triphosphate (ATP):
the energy currency of the cell

• Cells use the energy

stored in chemical
bonds, like ATP, as
needed.
• By converting one form
of chemical energy into
another form of
chemical energy, cells
are able to utilize the
energy in the bonds of
ATP to fuel cellular
reactions.
LO 4
Potential Energy: Chemical Energy

• Strong bonds have less

potential energy than weak
bonds.
• ATP releases a lot of
energy when the terminal
phosphate bonds (weak)
are broken
• The high energy bonds of
ATP are unstable due
electrostatic repulsion
between the –ve charges
of the phosphate groups
LO 5
First Law of Thermodynamics

• Energy cannot be created or destroyed; it can only be

transformed.
• An example of potential energy can be seen when a ball
rolls down stairs.
• When electrons move from a higher energy level to a lower
energy level, energy is released as heat or light.
• The total amount of energy does not change.
LO 5
Second Law of Thermodynamics

• Energy transformations are not 100% efficient.

• As energy in the cell is transformed, the energy available to
do work in the cell decreases.
• Much of the work of the cell is to combat increases in
entropy, which requires energy.
 Lecture 2: Learning Outcomes (LO)

6. Discuss how changes in free energy in a reaction are related to changes in

entropy and enthalpy.
7. Distinguish between exergonic and endergonic reactions
8. Discuss the importance of energetic (reaction) coupling in linking
biochemical reactions.

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LO 6 Gibbs Free energy (G)

Total energy (H) = energy available to do work (G) + energy lost to

entropy (S, or disorder).

Free energy (Gibbs Free energy, G)- Energy of a system

available to do work
G is expressed as

G = H - TS
Where G- Gibbs free energy
H- Enthalpy (energy contained in chemical bonds)
S- Entropy (randomness/disorderliness, unavailable energy)
T- Absolute temperature (K), K = °C + 273

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LO 6 Free energy change (ΔG )
During a biological process or chemical reaction, there is a change
in the free energy (ΔG)

Consider the reaction

A+B↔C+D
at constant pressure and temperature, ΔG is given by

ΔG = ΔH -TΔS
Where ΔG- change in free energy (predicts whether a reaction is favourable)
ΔH- change in enthalpy (Energy content of reaction)
ΔS- change in entropy (measure of disorderliness)
T- Absolute temperature (K), K = °C + 273

Δ = Change = Final State – Initial State

Negative ΔG (-ΔG) - reaction is thermodynamically favourable

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Positive ΔG (+ΔG)- reaction is thermodynamically unfavourable
LO 7 Endergonic reactions: require energy input

Consider the reaction: A + B ↔ C + D

Products have more free energy than

reactants
• ΔG is positive (+)
• Reaction cannot occur
spontaneously
• Reaction proceeds in the reverse
direction (←)

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LO 7 Exergonic reactions: releases of energy

Consider the reaction: A + B ↔ C + D

Reactants have more free energy than

products
• ΔG is negative (-)
• Reaction can occur spontaneously
(may not be instantaneous)
• Reaction proceeds in the forward
direction (→)

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LO 7
ATP Hydrolysis

• Hydrolysis of ATP is an exergonic (spontaneous) reaction

and releases energy (−ΔG).
• The phosphate groups of ATP are negatively charged at
physiological pH and repel each other.
• ADP has two phosphate groups, so it has a lower potential
energy than ATP, which has three phosphate groups.
LO 8
Energetic coupling links reactions in biology
Thermodynamically unfavourable (endergonic) reaction
can be “driven” in the forward direction by coupling it to a
thermodynamically favourable (highly exergonic) reaction
through a common intermediate.

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LO 8
Significance of ΔG for ATP hydrolysis in the Cell
LO 6-8
ΔG in Anabolic and Catabolic Reactions

Low entropy

High entropy
 Practice questions

Indicate which of the following statements is TRUE or FALSE; if FALSE explain why
1. An exergonic reaction has the following properties
A. +ΔG and the reaction is spontaneous
B. +ΔG and the reaction is not spontaneous
C. -ΔG and the reaction is spontaneous
D. -ΔG and the reaction is not spontaneous

2. Assume ATP hydrolysis has a ΔG of -7.4 Kcal/mol. Can an endergonic reaction with a ΔG
of +12 Kcal/mol be “driven” forward by being coupled to ATP hydrolysis?

A. No, the overall ΔG would still be positive

B. Yes, the overall ΔG would now be negative

C. Yes, but only if an enzyme is used to lower ΔG

D. No, overall ΔG would now be negative

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 Lecture 3: Learning Outcomes (LO)

9. Discuss equilibrium reactions

10. Explain how activation energy and catalysts (enzymes) influence the rate of
spontaneous reactions.
11. Describe the general structure (active site and allosteric site) and the
catalytic cycle of an enzyme.

12. Describe the principle of catalysis performed by enzymes.

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LO 9 Equilibrium reactions
• Many chemical reactions in nature are reversible.
• The point at which the forward and reverse reaction rates are
equal is called chemical equilibrium.
• Every chemical equilibrium can be characterized by an equilibrium
constant (Keq).
Keq
aA + bB cC + dD Keq = [C]c[D]d
[A]a[B]b

When
Keq > 1 then equilibrium favours the products (far to the right)
Keq = 1 the reaction is at equilibrium (forward and reverse reaction rates are equal)
Keq < 1 then equilibrium favours the reactants (far to the left)
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LO 9 Equilibrium reactions
• At equilibrium (Keq = 1), forward and reverse reactions are
balanced (there is no net synthesis of products )-
When Keq = 1, ΔG is zero
Consider the reaction
A+B C+D
The direction of the reaction at equilibrium can be changed by
✓ increasing [A] or decreasing [C]
reaction will proceed to the right (A + B → C + D); ΔG is -ve
✓ decreasing [A] or increasing [C]
reaction will proceed to the left (A + B ← C + D); ΔG is +ve
When
Keq >1 then equilibrium favours products; ΔG is -ve
Keq = 1 the reaction is at equilibrium; ΔG is zero
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Keq <1 then equilibrium favours the reactants; ΔG is +ve
LO 10
Activation Energy and Catalysts

Activation energy: amount of energy needed to initiate a

chemical reaction

• The rate of exergonic reactions depends on the activation

energy
➢ The larger the activation energy of a reaction, the slower
the reaction rate and vice versa

• Reaction rate can be increased by:

1. increasing the energy of reacting molecules- heating up
the reactants
2. lowering activation energy: catalysis (enzyme-catalyzed
reactions)

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LO 10
Activation Energy (EA) and Catalysts

• The higher the

activation
energy, the
slower the
rate of
reaction.

Lowering the activation energy increases the rate of the

reaction but does not change the free energy of the reaction. 26
LO 11
Enzymes: Proteins with catalytic activity

Enzymes:
• mostly proteins except for ribozymes (RNA molecules with
catalytic activity)
• biological catalysts- more efficient than inorganic catalysts
• highly specific for their substrates
• affect reaction kinetics and NOT thermodynamics
• actions (activities) are regulated
• Some exist as multi-enzyme complexes to catalyze reaction
sequences
• most enzymes contain non-protein part (co-factor) which
aids in catalysis
• not changed or consumed in the reaction- needed in small
amounts
• Localized in cytoplasm, cell membranes and organelles
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LO 11
General structure of an enzyme: Active site

Active site: crevice or pocket on the surface of the enzyme (E)

• It is made up of a set of amino acid residues that lie close to
each other in the 3D structure of the protein, but far apart in
the linear polypeptide chain (primary structure)
• It is where the substrate (S) binds, forming the enzyme-
substrate (ES) complex

E+S ES P

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LO 11

Active Site Formation

LO 12
Enzymes: Principles of catalysis

For efficient catalysis:

• Substrates have to be brought together in close proximity
and correctly oriented
• Particular chemical bonds of a substrate needs to stressed
(bond strain)- lowers the activation energy for new bonds
to form

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LO 12
Enzyme-Catalyzed Reactions
 Lecture 4: Learning Outcomes (LO)

13. List factors that influence the rate of enzyme reactions (e.g. temperature,
pH, and inhibitors)
14. Discuss how temperature, pH, and inhibitors affect the rate of enzyme
reactions
15. Differentiate between competitive and noncompetitive inhibitors of enzymes
16. Discuss the regulation of biochemical (metabolic) pathways by negative
feedback

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LO 13 Factors affecting rate of enzyme reactions

Factors

Temp. pH [Enzyme]
[Cofactors]
Inhibitors &
[Substrate] activators

[Substrate]- Substrate concentration

[Enzyme]- Enzyme concentration

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LO 13&14 Enzyme activity can be altered by temperature and pH
changes

• Enzymes are sensitive to

temperature and pH changes
− Have optimum activity in
their natural environment

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LO 13&14
Cofactors: inorganic or small organic molecules

Many enzymes require an additional small molecules, known

as cofactors to aid with catalytic activity.

• Cofactors can either be

- inorganic molecules (metal ions, eg. Mg2+, )
or
- small organic molecules (coenzymes, eg. vitamin Bs).

• Cofactors bind to the active site of the enzyme and

participate in catalysis but are not considered substrates of
the enzymes.

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LO 13&14
Enzyme activity can be altered by inhibitors or activators

Inhibitor: substance that binds to an enzyme and decreases its

activity
Activator: substance that binds to an enzyme and increases its
activity

Enzyme inhibition can be

– competitive or noncompetitive
– reversible or irreversible
LO 15 Competitive and noncompetitive inhibitors
LO 16
Regulation of Biochemical Pathways

• Many metabolic pathways are regulated

because biochemical reactions require
energy.
• In the case of the pathway shown, the
end product inhibits the enzyme that
catalyzes an earlier reaction.
• The process in which the final product
inhibits an earlier step of a biochemical
pathway is known as negative feedback
(Feedback inhibition).
• Negative feedback is important in
helping the cell to conserve energy.
 LO 16
Metabolic or Enzyme regulation: Feedback inhibition

E4 E4
* * E3 E3
E1 E2 E1 E2
E5 E
E6 * 5 E6

E4
E3
E1 E2
E5
E6

Concerted feedback inhibition

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E1-6- Enzymes; *- committed step
 Practice questions

Indicate which of the following statements is TRUE or FALSE; if FALSE explain why
1. Consider the following statements about enzyme inhibition
i. A competitive inhibition is seen when a substrate and inhibitor competes with an enzyme for
binding to an inhibitor protein
ii. Competitive inhibition is seen when the substrate and inhibitor competes for the active site of the
enzyme
iii. Noncompetitive inhibition of an enzyme cannot be overcome by adding large amounts of substrate
iv. Competitive inhibitors are often similar in structure to the substrate of the inhibited enzyme

2. In feedback inhibition, when the end-product binds at an allosteric site on the regulatory enzyme,
i. the active site.
ii. this blocks the substrate from binding at this allosteric site.
iii. this blocks the substrate from binding at another allosteric site.
iv. the enzyme undergoes a conformational change which blocks its active site.
v. the enzyme is covalently modified by the product.
vi. the product blocks

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