L02:

CELL CHEMISTRY
and
BIOENERGETICS

*The presenter invokes the principle of fair use for

the use of copyrighted materials in this presentation.
Theme 3: Living things obey chemical and physical laws.
Theme 3: Living things obey chemical and physical laws.

• cell chemistry is more complex than any other chemical

system known

• life is based on carbon compounds incorporated into

enormous polymeric molecules

• the unique properties of these macromolecules enable cells

and organisms to exhibit the characteristics of life

• cells are 70% water allowing an array of chemical reactions

that depend largely on aqueous environment to proceed
 3.1 Cells are made from a few types of atoms

• matter is made up of elements or their combinations

• atoms are _______

• properties of living things depend on the way their atoms are

linked together to form molecules

• C, H, O, N make up 96.5% of the organism’s weight

3.2 The outermost electrons determine how atoms
interact
3.3 Noncovalent attractions help bring molecules
together in cells

• individually weak but can create an effective force between

molecules when together
• electrostatic attractions (ionic bonds)
• attractive forces between oppositely charged atoms
• hydrogen bonds
• polar interaction in which an electropositive hydrogen atom is
partially shared by two electronegative atoms
• van der Waals forces
• force produced by a flickering dipole due to fluctuations in the
electron cloud
• hydrophobic force
• pushing of nonpolar surfaces out of the H-bonded water
network
3.4 Water is the most abundant substance in cells

• high specific heat capacity

• versatile solvent (polarity)
• high surface tension
• cohesion and adhesion
3.5 Cells contain four major families of small organic
molecules

• disregarding water and inorganic ions, nearly all the

molecules in a cell are based on carbon

• cells contain sugars, fatty acids, amino acids, nucleotides

• carbon-based, 100-1000 molecular weight, 30 or so
carbon atoms
• some serve as monomers to macromolecules
• some serve as energy source
3.6 Macromolecules are polymers built from
monomers
3.6 Macromolecules are polymers built from
monomers
 Polysaccharides
Polymer Basic Unit Function Types/Examples
(Monomer)
CARBOHYDRATE Simple sugar Serve as fuel in the cell Monosaccharide
(polysaccharide) (monosaccharide) and as source of carbon (glucose, fructose, galactose)
atoms to form other
small organic molecules Disaccharide
(sucrose, maltose, lactose)

Polysaccharide
(storage - glycogen, starch; structural -cellulose, chitin)
 Lipids
Polymer Basic Unit (Monomer) Function Types/Examples

LIPID None Energy storage; Fats

protection, support, and (glycerol + 3 fatty acids)
--- lipids are a diverse regulation; precursors of
group of hydrophobic important molecules Phospholipids
molecules (phosphate + glycerol + 2 fatty acids)

Steroids
(a carbon skeleton composed of 4
fused rings)
 Polypeptides
Polymer Basic Unit (Monomer) Function Types/Examples

PROTEIN Amino acid Catalyst; storage; Enzymes

(polypeptide) coordination; movement; Storage proteins
protection; transport; Hormones
reception; support Contractile and motor proteins
Defensive proteins
Transport proteins
Receptor proteins
Structural proteins

• Primary structure • Tertiary structure

• sequence of aa • hydrophobic interactions between aa R
groups
• Secondary structure • van der Waals hold nonpolar R groups
• H-bonds between • disulfide bridges
atoms of polypeptide
backbone • Quaternary structure
• helices and sheets • association of polypeptides
 Polynucleotides

Polymer NUCLEIC ACID

(polynucleotide)
Basic Unit Nucleotide
(Monomer)
Function Controls gene
expression
Types/Examples DNA
RNA
Theme 4: Cells create and maintain order through a never-
ending stream of chemical reactions.
Theme 4: Cells create and maintain order through a never-ending stream
of chemical reactions.
Theme 4: Cells create and maintain order through a never-ending stream
of chemical reactions.

• Metabolism is the totality of an organism’s chemical

reactions

• Metabolism is an emergent property of life that arises from

interactions between molecules within the cell
 4.1 Cell metabolism is organized by enzymes

• A metabolic pathway begins with a specific molecule and

ends with a product

• Each step is catalyzed by a specific enzyme

Enzyme 1 Enzyme 2 Enzyme 3

A B C D
Reaction 1 Reaction 2 Reaction 3
Starting Product
molecule
4.1 Cell metabolism is
organized by enzymes
 4.1 Cell metabolism is organized by enzymes

• Catabolic pathways release energy

to break down complex molecules
into simpler compounds

• Anabolic pathways consume

energy to synthesize complex
molecules from simpler ones

• Bioenergetics is the study of how

organisms manage their energy
resources
Energy and Living Systems

• Energy is the capacity to cause change

• Energy exists in various forms, some of which can perform
work
• Kinetic energy is energy associated with motion
• Heat is kinetic energy associated with random
movement of atoms or molecules
• Potential energy is energy that matter possesses because
of its location or structure
• Chemical energy is potential energy available for
release in a chemical reaction
• Energy can be converted from one form to another
A diver has more potential Diving converts
energy on the platform potential energy to
than in the water. kinetic energy.

Climbing up converts the kinetic A diver has less potential

energy of muscle movement energy in the water
to potential energy. than on the platform.
Laws of Thermodynamics

• Energy can be converted from one form to another

• Thermodynamics is the study of energy transformations

• A closed system, such as that approximated by liquid in a

thermos, is isolated from its surroundings

• In an open system, energy and matter can be transferred

between the system and its surroundings

• Organisms are open systems

Laws of Thermodynamics

• According to the first law of thermodynamics, the energy of

the universe is constant

• Energy can be transferred and transformed, but it cannot

be created or destroyed

• During every energy transfer or transformation, some

energy is unusable, and is often lost as heat

• According to the second law of thermodynamics

• Every energy transfer or transformation increases the
entropy (disorder) of the universe
 Heat

Chemical
energy

(a) First law of thermodynamics (b) Second law of thermodynamics

 4.2 Biological order is made possible by the release of
heat energy from cells

• Living things unavoidably

convert organized forms
of energy to heat

• Spontaneous processes
occur without energy
input; they can happen
quickly or slowly

• For a process to occur

without energy input, it
must increase the entropy
of the universe
4.2 Biological order is made possible by the release of
heat energy from cells

• Cells create ordered structures from less ordered materials

• Organisms also replace ordered forms of matter and energy with

less ordered forms

• Energy flows into an ecosystem in the form of light and exits in

the form of heat
4.3 The free-energy change of a reaction tells us
whether the reaction occurs spontaneously

• The change in free energy (∆G) during a process is related to

the change in enthalpy, or change in total energy (∆H),
change in entropy (∆S), and temperature in Kelvin (T)

• Free Energy = Total Energy – Unusable Energy

• Only processes with a negative ∆G are spontaneous
• Spontaneous processes can be harnessed to perform work
Free Energy, Stability, and Equilibrium

• Free energy is a measure of a system’s instability, its

tendency to change to a more stable state

• During a spontaneous change, free energy decreases

and the stability of a system increases

• Equilibrium is a state of maximum stability

• A process is spontaneous and can perform work only

when it is moving toward equilibrium
Free Energy, Stability, and Equilibrium
Free Energy, Stability, and Equilibrium
Free Energy, Stability, and Equilibrium

• Reactions in a closed system eventually reach equilibrium

and then do no work

• Cells are not in equilibrium; they are open systems

experiencing a constant flow of materials

• A defining feature of life is that metabolism is never at

equilibrium

• A catabolic pathway in a cell releases free energy in a series

of reactions
 4.4 Free-energy changes in exergonic and endergonic
reactions

• Exergonic reaction --- ΔG is

negative; net release of
energy; spontaneous

• Endergonic reaction --- ΔG is

positive; absorbs energy;
nonspontaneous
4.5 ATP powers cellular work by coupling exergonic
reactions to endergonic reactions

• A cell does three main kinds of work --- chemical, transport,

mechanical

• Many cellular reactions are endergonic

• To do work, cells manage energy resources by energy

coupling, the use of an exergonic process to drive an
endergonic one

• Most energy coupling in cells is mediated by ATP

Adenosine Triphosphate

• ATP is a high-energy molecule that serves as the cell’s main

energy shuttle

• ATP is composed of ribose (a sugar), adenine (a nitrogenous

base), and three phosphate groups

• The hydrolysis of ATP releases phosphate in a strongly

exergonic reaction that drives endergonic reactions to
completion
 Adenine

Phosphate groups
Ribose

(a) The structure of ATP

Adenosine triphosphate (ATP)

Energy

Inorganic Adenosine diphosphate (ADP)

phosphate

(b) The hydrolysis of ATP ΔG = -7.3 kcal/mol

Phosphorylation

• ATP drives endergonic reactions by phosphorylation,

transferring a phosphate group to some other molecule
(e.g., reactant)

• The recipient molecule is now called a phosphorylated

intermediate
(a) Glutamic acid
conversion NH3 NH2
Glu Glu
 GGlu = +3.4 kcal/mol
to glutamine
Glutamic Ammonia Glutamine
acid

(b) Conversion NH3

reaction
coupled P 2
1 NH2
with ATP ADP ADP Pi
hydrolysis Glu ATP Glu Glu

Glutamic Phosphorylated Glutamine

acid intermediate

 GGlu = +3.4 kcal/mol

(c) Free-energy
change for NH3 NH2
ATP ADP Pi
coupled Glu Glu
reaction
GGlu = +3.4 kcal/mol
GATP = −7.3 kcal/mol
+ GATP = −7.3 kcal/mol

Net G = −3.9 kcal/mol

 Transport protein Solute

ATP ADP Pi

P Pi

Solute transported
(a) Transport work: ATP phosphorylates transport proteins.

Vesicle Cytoskeletal track

ATP ADP Pi
ATP

Motor protein Protein and

vesicle moved
(b) Mechanical work: ATP binds noncovalently to motor
proteins and then is hydrolyzed.
 Regeneration of ATP
• ATP is a renewable resource that is regenerated by addition
of a phosphate group to adenosine diphosphate (ADP)

• The energy to phosphorylate ADP comes from catabolic

reactions in the cell

ATP H2O

Energy from catabolism Energy for cellular work

(exergonic, energy-releasing (endergonic, energy-
processes) consuming processes)
ADP Pi
4.6 Enzymes speed up metabolic reactions by lowering
energy barriers

• A catalyst is a chemical agent that speeds up a reaction

without being consumed by the reaction

• An enzyme is a catalytic protein

• exhibits great specificity for the reaction catalyzed and
the molecules acted on

Sucrase

Sucrose Glucose Fructose

(C12H22O11) (C6H12O6) (C6H12O6)
Activation Energy

• Every chemical reaction between molecules involves bond

breaking and bond forming

• The initial energy needed to start a chemical reaction is

called the free energy of activation, or activation energy
(EA)

• Activation energy is often supplied in the form of thermal

energy that the reactant molecules absorb from their
surroundings
Activation Energy

• Enzymes catalyze reactions by lowering the EA barrier

• Enzymes do not affect the change in free energy (∆G);

instead, they hasten reactions that would occur eventually
 Course of
reaction EA
without without
enzyme EA with
enzyme
enzyme
is lower
Free energy

Reactants

Course of G is unaffected
reaction by enzyme
with enzyme

Products

Progress of the reaction

Substrate Specificity

• The reactant that an enzyme acts on is called the substrate

• The enzyme binds to its substrate, forming an enzyme-substrate

(ES) complex

• The active site is the region on the enzyme where the substrate
binds

• The lock-and-key model portrays an enzyme as

conformationally rigid and able to bond only to substrates that
exactly fit the active site

• Induced fit of a substrate brings chemical groups of the active

site into positions that enhance their ability to catalyze
(flexibility) the reaction
 Substrate

Active site

Enzyme Enzyme-substrate
complex
(a) (b)
Catalysis in the Enzyme’s Active Site

• In an enzymatic reaction, the substrate binds to the active

site of the enzyme

• The active site can lower an EA barrier by

• Orienting substrates correctly
• Straining substrate bonds
• Providing a favorable microenvironment
• Covalently bonding to the substrate
 1 Substrates enter active site.
2 Substrates are held
in active site by weak
interactions.

Substrates
Enzyme-substrate
complex 3 Active site can
lower EA and speed
up a reaction.
6 Active
site is
available
for two new
substrate
molecules.
Enzyme

5 Products are 4 Substrates are

released. converted to
products.
Products
Effect of Local Conditions on Enzyme Activity

• An enzyme’s activity can be affected by

• General environmental factors, e.g., temperature and pH
• Chemicals that specifically influence the enzyme

• Optimal conditions favor the most active shape for the

enzyme molecule
Effect of Local Conditions on Enzyme Activity

• Temperature
• collision between enzyme and substrate
• low temperature --- low collision
• high temperature --- enzyme denaturation

• pH
• causes denaturation of enzymes
• optimum enzyme action at pH 6-8
 Optimal temperature for Optimal temperature for
typical human enzyme (37°C) enzyme of thermophilic
(heat-tolerant)

Rate of reaction
bacteria (77°C)

0 20
60 80 40 100 120
Temperature (°C)
(a) Optimal temperature for two enzymes

Optimal pH for pepsin Optimal pH for trypsin

(stomach (intestinal
enzyme) enzyme)
Rate of reaction

0 1 5 2 3 4 6 7 8 9 10
pH
(b) Optimal pH for two enzymes
Effect of Local Conditions on Enzyme Activity

• Substrate concentration
• low substrate concentration --- slow reaction
• high substrate concentration --- faster reaction

• Cofactors
• cofactors are nonprotein enzyme helpers
• cofactors may be inorganic (such as a metal in ionic form)
or organic
• an organic cofactor is called a coenzyme, e.g., vitamins
Effect of Local Conditions on Enzyme Activity

• Enzyme inhibitors

• Competitive inhibitors bind to the active site of an enzyme,

competing with the substrate; usually resemble normal
substrates but cannot form products

• Noncompetitive inhibitors bind to another part of an enzyme,

causing the enzyme to change shape and making the active site
less effective

• Examples of inhibitors include toxins, poisons, pesticides, and

antibiotics
Evolution of Enzymes

• Enzymes are proteins encoded by genes

• Changes (mutations) in genes lead to changes in amino acid

composition of an enzyme

• Altered amino acids in enzymes may alter their substrate

specificity

• Under new environmental conditions a novel form of an

enzyme might be favored
4.7 Regulation of enzyme activity helps control
metabolism

• Chemical chaos would result if a cell’s metabolic pathways

were not tightly regulated

• A cell does this by switching on or off the genes that encode

specific enzymes or by regulating the activity of enzymes
• Allosteric regulation
may either inhibit or
stimulate an
enzyme’s activity

• Allosteric regulation
occurs when a
regulatory molecule
binds to a protein at
one site and affects
the protein’s function
at another site
• Cooperativity is a form
of allosteric regulation
that can amplify
enzyme activity
• One substrate
molecule primes an
enzyme to act on
additional substrate
molecules more
readily
• In feedback
inhibition, the end
product of a metabolic
pathway shuts down
the pathway

• Feedback inhibition
prevents a cell from
wasting chemical
resources by
synthesizing more
product than is
needed
BREAK!