Chapter 4: Cells and

Energy
MS GOSHAN
LEARNING OBJECTIVES
to define what is meant by energy
to describe the difference between potential, kinetic, free and activation energy
To describe the functions of enzymes and enzyme inhibition
WHAT DOES A CELL USE
ENERGY FOR?
Cellular use of energy
Synthesis and breakdown of molecules
Transport of molecules
Ingestion and breakdown of pathogens
Exporting waste and toxic material
Movement of cells
The first law of thermodynamics, also known as Law of
Conservation of Energy, states that energy can neither be
created nor destroyed; energy can only be transferred or
changed from one form to another
Flow of energy through living systems = BIOENERGETICS
METABOLISM = all of the chemical reactions that take place
inside a cell
◦ Including those that release and consume energy
METABOLIC PATHWAYS
Two examples:
ANABOLIC PATHWAYS- creating bonds –
building large molecules from smaller ones
◦ Energy is stored in the bonds 🡪 requires energy

CATABOLIC PATHWAYS- breaking bonds –

breaking down polymers to monomers
◦ Bonds are broken 🡪 energy released

Both processes involve Adenosine

Triphosphate (ATP)
Metabolism of sugar: an example
Photosynthesis:
◦ Plants use sun energy to convert CO2 to sugar molecules (Glucose)

◦ Synthesis of energy storing molecule = requires energy

◦ The energy rich Glucose can also be broken down to release ATP in the
reverse reaction

◦ All metabolic reactions are facilitated or catalyzed by enzymes

ENERGY
DEFINITIONS:
Thermodynamics- the study of energy and energy
transfer involving physical matter
System- all the matter involved in the specific
transfer of energy
◦ Eg/ pot on stove- system includes the stove, the pot, the
water because energy is transferred between those things

Open system- a system where energy can be

exchanged with the surroundings
Closed system- a system where energy cannot be
exchanged with the surroundings
Biological organisms are OPEN system
◦ What does this mean?
ENERGY: defined as the ability to do work
or create some kind of change
Examples of energy?
THERMODYNAMICS
Energy is governed by a number of laws
First law of thermodynamics
◦ Refers to quantity of energy
◦ Total amount of energy in the universe is constant and conserved
◦ Therefore energy is not created or destroyed, it is transferred from place to place, or
transformed from one form of energy to another

All living organisms have the challenge of obtaining energy that in a form that
can be transferred or transformed into energy that can be used for work
Eg/ chemical energy stored in food molecules transformed to ATP through
chemical reactions
THERMODYNAMICS
Second law of thermodynamics
◦ Refers to the quality of energy
◦ It states that as energy is transferred or transformed, more and more of it is wasted (mostly through heat energy
◦ The Second Law also states that there is a natural tendency of any isolated system to degenerate into a more disordered
state.  (increase in entropy)

At a biological level
◦ Organisms are highly organised
◦ Require very large amount of energy to maintain a state of organisation / low entropy
POTENTIAL AND KINETIC ENERGY
Kinetic energy = the energy that a particle possesses due
to its motion
Potential energy = the energy stored within an object, due
to the object's position, arrangement or state.
On a molecular level the formation of bonds requires
energy and braking bonds releases energy
◦ THEREFORE bonds contain potential energy in the form of
CHEMICAL ENERGY
FREE ENERGY
FREE ENERGY –
◦ the energy left after the loss of energy through a reaction
◦ Effectively it’s the usable energy from a metabolic reaction

EXERGONIC REACTIONS (Exothermic)

◦ If a reaction occurs where energy is released, the products will have less free energy than the reactants
◦ Energy is exiting the system
◦ Also referred to as spontaneous reactions (doesn’t mean quick)

ENDERGONIC REACTIONS (Endothermic)

◦ If a reaction occurs where energy is absorbed, products will have more free energy than reactants
◦ Energy is entering the system
◦ Non-spontaneous – reaction wont happen without addition of free energy
ACTIVATION ENERGY
Defined as the amount of energy input required for a
reaction to occur
Exergonic reactions usually have low activation energy
Endergonic reactions have high activation energy

◦ In the graph, is this an endergonic or exergonic reaction?

ENZYMES
CATALYST- substances that help chemical reactions to occur
Biological catalysts – ENZYMES
Enzymes
◦ Mostly proteins
◦ Work by lowering the activation energy of chemical reactions

Most chemical reactions occur too slowly at normal temperatures. Enzymes

speed up the process by binding to reactant molecules and making the bond
making or breaking process easier
Enzymes are NOT used in a reaction, they simply assist reactions
They do not affect free energy, they simply reduce activation energy
Enzymes : how they work
ENZYME INHIBITION
It is not ideal to have all enzymes working at full capacity at all times
◦ Eg, digestive enzymes only need to be at full capacity directly after a meal

By controlling the readiness of enzymes an organism can control the presence or rate of reactions
Enzymes are controlled by
◦ pH
◦ Salt concentration
◦ Temperature
◦ Co-enzymes
◦ INHIBITION
Allosteric inhibition
Allosterically regulated
enzymes have multiple
protein sub-units
◦ Attachment of allosteric
inhibitor means structure of
all activation sites changes
slightly to reduce efficacy
◦ Opposite for allosteric
activators
Recap questions:
What is the difference between anabolic and catabolic reactions
What is the most common energy source for living organisms?
What is the form of energy used by cells?
What is the first and second law of thermodynamics?
What is the difference between Kinetic and Potential energy?
What is the difference between Free and Activation energy?
Define enzyme?
What methods of inhibition of enzymes are there?
Importance of Co-enzymes and Co-factors
Enzymes work most optimally with the aid of other substances
They bond to them with covalent or hydrogen bonds
◦ Bonding creates most optimal structure for the function of the enzyme \

Co-Factors- inorganic ions (Eg, Magnesium and Iron)

Co-enzymes- organic helper molecules comprised of carbon and hydrogen
◦ Like enzymes they are not used up, but recycled
◦ Eg/ Vit C – involved in production of Collagen

Enzyme function is partly regulated by abundance and availability of these co-factors and co-enzymes
Feedback Inhibition
Mechanism for enzyme regulation
Cells have evolved to use the products of a reaction to regulate enzyme activity
ATP- ADENOSINE TRIPHOSPHATE
- Addition of phosphate group
requires high amount of energy –
high energy bond formed
- Phosphate groups –ve charge
repel eachother = molecule is quite
unstable
- Release of one or more phosphate
group = release of energy
- Process called HYDROLYSIS
GLYCOLYSIS
First step towards cellular
respiration to yield ATP
Glucose converted to 2
Pyruvate molecules
Occurs inside the cytoplasm
of all cells
GLYCOLYSIS- Energy requiring half
Step 1: enzyme HEXOKINASE catalyses the phosphorylation of glucose
◦ Process requires ATP (where the phosphate comes from)
◦ Negatively charged phosphate group means glucose molecule is no longer able to exit the cell through the plasma
membrane
GLYCOLYSIS
Step 2: An Isomerase enzyme converts glucose-6-phosphate into an isomer Fructose-6-phosphate
GLYCOLYSIS
Step 3: phosphorylation of Fructose-6-phosphate
◦ Catalysed by PHOSPHOFRUCTOKINASE – rate limiting enzyme (less active at low ADP levels)
◦ Second ATP molecule donates a high energy phosphate = Fructose-1,6-Bisphosphate
GLYCOLYSIS
Step 4: fructose-1,6-bisphosphate is highly unstable because of phosphate group
◦ Aldolase enzyme used to cleave it into 2 3-Carbon isomers

Step 5: Dihydroxyacetone-phosphate is transformed into its isomer glyceraldehyde-3-phsophate with isomerase

enzyme
GLYCOLYSIS- energy releasing half
Step 6: glyceraldehyde-3-
phosphate is oxidized (loss
of hydrogen)
◦ Hydrogen is picked up by
NAD+ =NADH
◦ Sugar is then
phosphorylated (not from
ATP)
Glycolysis
STEP 7: ADP takes the high energy phosphate from the molecule forming an ATP
◦ Left with a 3-phosphoglycerate molecule
Glycolysis
STEP 8: mutase enzyme catalyses the move of the remaining phosphate group from third carbon, to the second
carbon= 2-phosphoglycerate
Glycolysis
STEP 9: Enolase enzyme causes the 2-phosphoglycerate to lose water in dehydration reaction= formation of a
double bond that increases the potential energy in the remaining phosphate bond In the molecule of
phosphoenolpyruvate
Glycolysis
STEP 10:Pyruvate kinase enzyme catalyses the phosphorylation of ADP to ATP with the remaining phosphate
group= formation of pyruvate
Krebs Cycle/ Citric acid cycle
Glycolysis recap:
Re-dox reactions
Reduction reaction – molecule gains an electron
Oxidation reaction – molecule loses an electron

Electrons usually in the form of hydrogen ions

Conversion of pyruvate
In Eukaryotic cells, the pyruvate enters the cell’s
mitochondria
Cellular respiration happens in the
mitochondria
Pyruvate 🡪 2 carbon acetyl group 🡪 picked up by
coenzyme A (CoA) = ACETYL CoA
Acetyl CoA then enters the citric acid cycle
Citric acid cycle
Occurs in the matrix of the
mitochondria
Step 1: Acetyl CoA joins with 4
carbon molecule (Oxaloacetate).
CoA is released and a 6 carbon
molecule formed called CITRATE

STEP 2: Citrate converted to its

isomer Isocitrate. Done in two
steps, first the removal then
addition of water
Citric acid cycle
Step 3: Isocitrate oxidized and
releases a molecule of CO2 - 5
carbon a-ketogluterate left
During this step NAD+ is reduced =
NADH
This step is catalyzed by the
enzyme Isocitrate dehydrogenase
◦ Essential mechanism of regulating
speed of citric acid cycle
 Citric acid cycle
Step 4: a-ketogluterate oxidized
NAD+ 🡪 NADH
CO2 released
Remaining 4 carbon molecule picks
up Coenzyme A = Succinyl CoA
◦ Very unstable compound

This step is catalyzed by the

enzyme a-ketogluterate
dehydrogenase
 Citric acid cycle
Step 5: CoA of succinyl CoA
replaced with a phosphate group
Phosphate then transferred to ADP
🡪 ATP
◦ In some cells guanosine
diphosphate (GDP) is used instead
of ADP 🡪 GTP
Left with 4 carbon molecule called
succinate
 Citric acid cycle
Step 6: Succinate is oxidized 🡪 4
carbon molecule called fumerate
In this step 2 Hydrogen atoms are
transferred to FA D 🡪 FADH2
Step 7: water is added to
fumerate 🡪 malate
Step 8: malate is oxidized 🡪
oxaloacetate
NAD+🡪 NADH
PRODUCTS OF THE CITRIC ACID CYCLE
For each turn of the cycle (for one molecule of acetyl
CoA):
◦ 3 molecules of NADH and 1 molecule of FADH2 created
◦ 2 molecules of CO2 released
◦ 1 molecule of ATP or GTP produced
Although direct ATP yield is low, indirect ATP yield is
higher through high energy NADH and FADH2
OXIDATIVE PHOSPHORYLATION
AEROBIC RESPIRATION – respiration in the presence of oxygen
Why is oxygen important?
◦ Essential for oxidative phosphorylation – the final stage of cellular respiration

Oxidative phosphorylation made up of two components

◦ Electron transport chain – transfer of electrons between molecules = release
of energy that creates an electrochemical gradient
◦ Chemiosmosis – energy stored in the gradient is used to make ATP

Oxygen is invloved at the end of the electron transport chain,

accepting electrons
◦ No oxygen = no ETC = no ATP production
Electron transport chain (ETC)
Series of proteins and organic molecules
found in the inner membrane of
mitochondria
Electrons are passed from one
component of ETC to another through
REDOX reactions
Energy released in these reactions
captured as a proton gradient 🡪 used to
make ATP
ETC consists of 4 main steps
ETC STEPS
Step 1: Delivery of
electrons NADH AND
FADH2-
NADH and FADH2
transfer their electrons
to molecules near the
beginning of the ETC 🡪
NAD+ and FAD
ETC STEPS
Step 2: Electron transfer and
proton pumping
Electrons are passed down
the chain, moving from
higher to lower energy levels
= release energy
Some energy used to pump
h+ ions into intermembrane
space = electrochemical
gradient
ETC STEPS
Step 3: splitting oxygen
to form water
End of ETC electrons
are transferred to a
molecule of oxygen- O2
splits and takes up H+ =
H2O
ETC STEPS
Step 4: gradient driven
synthesis of ATP
H+ passivly flos back into
matrix down its gradient
Passes through and
enzyme called ATP
synthase = harnesses
flow to produce ATP
OVERALL FUNCTION OF ETC
1. Regenerates NAD+ and FAD needed for glycolysis and
citric acid cycle
2. Produces a proton gradient
◦ Active pumping of H+ into intermembrane space of mitochondrial
membrane = higher conc of H+ in intermembrane space
◦ Represents a stored form of energy that can be converted to ATP
CHEMIOSMOSIS
Complex I, III and IV are proton pumps
◦ Electrons moving downhill – allows complexes to capture
released energy and use this energy to pump H+ from matrix
🡪 intermembrane space
◦ This forms and electrochemical gradient = form of stored
energy

H+ ions can use protein channels to passively move

from intermembrane space to mitochondrial matrix
◦ Protein channel they use called ATP SYNTHASE

ATP synthase functions using the flow of H+ to

catalyze the addition of phosphate to ADP 🡪 ATP
ATP yield
ANAEROBIC RESPIRATION (in aerobic cells) –
lactic acid fermentation
When there is a lack of oxygen the ETC
cannot be completed
NAD is still required for glycolysis, so
some eukaryotic cells have adapted a
mechanism for temporary anaerobic
respiration = lactic acid fermentation