BIO 348: Cell

Biology
Chapter 3:
Energy, Catalysis, and Biosynthesis

Energy
Definition: The Capacity to do

work
Many different types of energy:

Potential: Stored energy, measured as

a capacity to do work. example:

stretched spring
Kinetic: Energy of motion, released
potential energy. example: releasing of a
stretched spring
Thermal: Energy released as heat
Chemical: Potential energy stored in
molecules. Measured as Kilocalories

Why do Cells Need

Energy?
Chemical work, build, rearrange,

tear apart compounds

Metabolism
Mechanical work, move cilia, flex a
muscle
Electrochemical work, nerve
impulses

Energy and
Thermodynamics
Thermodynamics: Study of energy

changes within the universe

1st Law of Thermodynamics: Energy in

the universe remains constant, but it

can change forms

2nd Law of Thermodynamics:

Randomness (entropy) in a closed

system increases, processes proceed
from a state of higher energy to a state
of lower energy

Energy and
Thermodynamics

Figure 3-6 Essential Cell Biology ( Garland Science 2010)

Molecules and Energy

The molecules of a living cell possess energy:
Thermal: vibrations, rotations, and movement
through space (heat)
Chemical: the energy that is stored in the bonds
between individual atoms

Gibbs free energy, G (in kcal/mole), measures

the energy of a molecule that could in

principle be used to do useful work at

Free Energy
Changes in free energy occurring in a reaction

are denoted by G, where indicates a

difference. Thus for the reaction:
A+B

C+D

G = free energy of products (C + D) - free

energy of reactants (A + B)
G measures the amount of disorder caused

by a reaction: the change in order inside the

cell, plus the change in order of the
surroundings caused by the heat released.

Chemical Reactions and

Entropy
Changes of bond energy of the reacting

molecules can cause heat to be released,

which disorders the environment (increases
Entropy)

The reaction can decrease the amount of

order in the reacting moleculesfor example,

by breaking apart a long chain of molecules,
or by disrupting an interaction that prevents
bond rotations (increases Entropy)

Chemical Reactions and Entropy

Figure 3-5 Essential Cell Biology ( Garland Science 2010)

Spontaneous vs. Nonspontaneous

Reactions
NegativeG

PositiveG
Figure 3-4 Essential Cell Biology ( Garland Science 2010)

Spontaneous (Exergonic) reactions

Energeticallyfavorable
Chemicalproductshave

lessfreeenergythanthe
reactantmolecules
Reactionisenergetically
downhill
Spontaneousreaction
Gisnegative

Spontaneous Reactions
From the second law of thermodynamics, we

know that the disorder of the universe can

only increase
G is negative if the disorder of the universe

(reaction plus surroundings) increases

In other words, a chemical reaction that

occurs spontaneously must have a negative

G:
G products G reactants = G < 0

Nonspontaneous (Endergonic)
Reactions
Products store

more free energy

than reactants
Reaction is
energetically uphill
Non-spontaneous
reaction (requires
energy input)
G is positive

Chemical
Reactions and
Free Energy
G

+G

Figure 3-16 Essential Cell Biology ( Garland Science 2010)

Reaction Coupling
How can an non-spontaneous (+ G)

reaction happen?
Reaction coupling: two reactions
occur simultaneously, one with a - G
(exergonic) and one with a + G
(endergonic)
The G reaction fuels the + G
reaction

Reaction
Coupling

Figure 3-17 Essential Cell Biology ( Garland Science 2010)

G vs. G
G

= Free energy; energy available

for work
G = change in free energy
(resulting from chemical reaction)
Go= standard free energy change,
measured at defined concentration
and conditions (1M reactants and
products, 25C, pH 7, & 1 atm)

What is the point of G ?

o

Go is used to predict the outcome of a

reaction
Will it proceed to the left or the right?
At what point will it stop?
This allows us to compare reactions by
keeping conditions standard
Examples:

Equilibrium Constant
Take the reaction:
Y
X
To calculate the rate of the reaction (i.e. how long

will it take for Y to convert into X?), we need to

know when the reaction hits equilibrium
Equilibrium is when the forward & reverse
reactions are equal
This results in a state when the ratio of reactants
to products remains constant:
K= =
[X]
[Products]
[Y] [Reactants]
K is the equilibrium constant, the point at which
there is no net change in free energy (G = 0)

Chemical
Equilibrium

Relationship between
G& K
K=[products]/[reactants]
IfKishigh(e.g.100),reaction

goesgreatlytoproducts

IfKislow,reactiongoes

towardsreactants
AveryhighKvalueindicates
thatthereactantsarevery
unstableandtheyreact
spontaneously

Sequential Reactions and

G
G= +5
Kcal/mol

G= -8 Kcal/mol

G= -13 Kcal/mol

K and Binding
Interactions
K is commonly

employed as a
measure of the
binding
strength
between
molecules
The larger the
K, the stronger
the binding
between

Figure 3-19 Essential Cell Biology ( Garland Science 2010)

Closed vs. Open System

The thermodynamics we have been

discussing where developed using

nonliving closed systems
Cells however are an open system
If reactions in a cell were at equilibrium
the cell could not do any work
The continual flow of material into & out of
a cell allows cellular metabolism to exist in
a steady state
This allows concentrations of reactants &

Closed vs. Open System

An amoeba

constantly takes
in nutrients
allowing ADP/ATP
ratio to be at a
steady state far
from equilibrium

Spontaneous Reactions and Catalysis

A spontaneous reaction is not necessarily

instantaneous: a reaction with a negative freeenergy change (-G) will not necessarily occur
rapidly by itself. Example:

But even this highly favorable reaction may

not occur for centuries unless there are

enzymes to speed up the process
Conversely, enzymes are able to catalyze
reactions and speed up their rate, but they do
not change the G of the reaction

Spontaneous Reactions and Catalysis

Example:
A phosphatase enzyme can catalyze a

reaction in 10 milliseconds
Without the enzyme the reaction would take 1

trillion yrs (1,000,000,000,000)

THIS REACTION IS CONSIDERED

SPONTANEOUS

Activation Energy
Why is catalysis

needed?
Activation energy
(EA) is the energy
needed to get a
reaction started
The energy needed
to overcome the
Transition State

Transition State
When reactants

are at the crest of

the energy hill &
are about to
become converted
into products are
said to be in a
transition state

The transition

state is at a higher
energy level than
either reactants or
products

Biological Catalysts
Enzymes are protein catalysts (ribozymes are

RNA catalysts)
They are required in small amounts
They are not altered permanently by the
reaction
They do not change the thermodynamics of a
reaction
They can only accelerate the rate at which a
favorable reaction proceeds
Enzymes increase the velocity of a reaction
108 to 1012 fold

Catalyzing Reactions

Enzyme Activity
Enzymes convert substrate to product, but

remain unchanged themselves:

Figure 3-15 Essential Cell Biology ( Garland Science 2010)

Enzyme Activity
The reactants in an enzyme

catalyzed reaction are called

substrates
Why does a spontaneous reaction

require an enzyme?
Because reactants must contain

sufficient kinetic energy to overcome

activation energy (EA)

Activation Energy and

catalysis

Figure 3-12 Essential Cell Biology ( Garland Science 2010)

Mechanism of Enzymatic
Catalysis

Figure 4-32 Essential Cell Biology ( Garland Science 2010)

Active Site

Active site

Figure 4-28b Essential Cell Biology ( Garland Science 2010)

Enzyme Activity: Induced

fit

Classes of Enzymes

Table 4-1 Essential Cell Biology ( Garland Science 2010)

Enzyme Kinetics
When substrate concentration is high the

velocity of the reaction is also high

As the substrate concentration increases the
enzyme approaches saturation
The velocity at this theoretical saturation
point is the maximal velocity or Vmax
A more useful value for enzyme kinetics is the

Michaelis constant (KM), which is constant for a

given enzyme
KM is the substrate concentration at which the
reaction velocity is half maximal (Vmax/2)

Enzyme Kinetics

Figure 3-24 Essential Cell Biology ( Garland Science 2010)

Enzyme Inhibitors
Competitive, compete with

substrates for binding to the

active site often binding is
reversible
Noncompetitive, do not
compete for the active site,
but rather bind to a different
site (allosteric site) binding is
reversible
Irreversible, bind very tightly
to the enzyme often forming
covalent bonds

Enzyme Inhibitor Kinetics

Competitive

Inhibition affects
KM
Noncompetitive

Inhibition affects
Vmax/2

Enzyme regulation
Negative Feedback

(feedback inhibition)

Figure 4-34 Essential Cell Biology ( Garland Science 2010)

Allosteric Regulation
Activators

bind to
allosteric site
to stabilize
active form of
enzyme
Inhibitors bind
to allosteric
site to
stabilize
inactive form
of enzyme

Metabolism
Metabolism: the

collection of
biochemical reactions
& pathways within a
cell; a combination of
catabolism &
anabolism
Catabolism: tearing
apart of complex
molecules
Anabolism: building

Figure 3-2 Essential Cell Biology ( Garland Science 2010)

Metabolism
Energy is

released via
catabolism &
stored in
activated
carrier
molecules,
which can later
be used to fuel
anabolic
reactions

Figure 3-29 Essential Cell Biology ( Garland Science 2010)

Oxidation-Reduction Reactions
(REDOX Reactions)
Involve the movement of electrons (e-)
When an atom loses electrons it becomes

oxidized
If an atom gains electrons is becomes
reduced
(LEO the lion says GER)
A reducing agent is a compound that loses
electrons
An oxidizing agent is one the gains
electrons

Oxidation-Reduction
Reactions
Many biologically important redox

reactions involve the removal or the

addition of hydrogen atoms (protons plus
electrons) rather than the transfer of
isolated electrons

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=mcb.figgrp.355

Oxidation-Reduction
Reactions
In an organic molecule the oxidation state

of carbon atoms provide a measure of a

molecules free energy

This because in a C-H bond carbon has the

strongest pull on the electrons, this is the

reduced state of carbon
In a C-O bond oxygen has the stronger pull
on the electrons causing carbon to be
oxidized
Thus, the amount of hydrogen a molecule

contains dictates its redox potential & the

Oxidation-Reduction
Reactions

Oxidation-Reduction
Reactions

Figure 3-11b Essential Cell Biology ( Garland Science 2010)

Activated Carriers
Molecules that can pick up hydrogen atoms or

functional groups during catabolic reactions,

and then break down to release those atoms
or groups to fuel or aid in biosynthetic
reactions
Activated carriers may bind to either high-

energy phosphates (e.g. ATP), high-energy

electrons (e.g. NADH), or other common
functional groups (e.g. Acetyl-CoA)

Examples of Activated Carrier

Molecules

Adenosine Triphosphate
(ATP)
The most common activated carrier in the cell
Acts as energy currency for the cell
ATP hydrolysis is energetically favorable (G 0 =

-7.3 kcal/mol) and is coupled with unfavorable

reactions
Examples:
Active transport
Muscle contractions
Anabolic reactions

Adenosine Triphosphate
(ATP)

Figure 3-31 Essential Cell Biology ( Garland Science 2010)

Adenosine Triphosphate
(ATP)
ATP can be

used to
phosphorylate
other
molecules to
drive anabolic
reactions by
increasing the
free energy
stored in the
reactants of
the reaction
Figure 3-32 Essential Cell Biology ( Garland Science 2010)

ATP and Phosphorylation

Phosphorylation is when phosphate group is

added onto a molecule

Example:
ADP +Pi ATP
(ADP becomes phosphorylated to ATP)
ATP can transfer its phosphate group to other
molecules:
ATP + X ADP + X-P
Phosphorylated molecules contain more
energy that their unphosphosphorylated
counterparts

ATP in Action
ATP can be

used to
phosphorylate
other
molecules to
drive
biosynthetic
reactions by
increasing the
free energy
stored in the
reactants
of Science 2010)
Figure 3-33a
Essential Cell Biology ( Garland

ATP in Action
Example:

Figure 3-33b Essential Cell Biology ( Garland Science 2010)

NADH and NADPH

Activated carriers that participate in Redox reactions
Can readily carry and release high energy electrons

and protons (Hydrogen atoms)

NADH: Nicotinamide adenine dinucleotide
NADPH: Nicotinamide adenine dinucleotide
phosphate
NAD+ + 2e- + H+ NADH
NADP+ + 2e- + H+ NADPH
(2e- + H+ = Hydride ion = H-)

NADPH in Action

Figure 3-34b Essential Cell Biology ( Garland Science 2010)

NADPH in Action

Figure 3-35 Essential Cell Biology ( Garland Science 2010)

Other Activated Carriers

Example:

Acetyl
Coenzyme A
(Acetyl-CoA)
can carry and
transfer 2Carbon acetyl
units in
various
different
reactions
Figure 3-36 Essential Cell Biology ( Garland Science 2010)