Cellular Processes
Cell Biology and Genetics
Dr Sarah Bajan
Cellular Processes, Dr Sarah Bajan
Learning Objectives
• To understand
• Laws of thermodynamics
• Gibbs free energy
• Equilibrium
• Le Chatelier’s Principle
• Reaction Coupling
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Cellular Processes, Dr Sarah Bajan
Life requires energy
• A cell is a chemical factory
• Many reactions occur simultaneously, some to create new molecules, some to digest others
• These reactions are precisely coordinated and controlled
– Highly complex, efficient and responsive
– Involves the regulated flow of energy
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Cellular Processes, Dr Sarah Bajan
Metabolism Transforms Matter and Energy
• All of an organism’s chemical reactions is
metabolism
• Functional cluster of metabolic reactions is a
metabolic pathway
• Sequential catalytic reactions to form product
• Enzyme activity is tightly regulated
– Balance metabolic pathways
• Metabolism manages the cell’s material and
energy resources
• Energy stored in in organic molecules
available to the cell – catabolism
• Energy is consumed to build large molecules
- anabolism
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Cellular Processes, Dr Sarah Bajan
Bioenergetics
• The study of how energy flows through living organisms
• Energy is the capacity to cause change
• Used to do work
• Transformed from one form to another
• Forms of energy
• Kinetic – relative motion of objects
– Thermal – random movement of atoms, transferred as heat/light
• Potential - due to location or structure e.g. arrangement of electrons in bonds
– Chemical – available for release in a chemical reaction
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Cellular Processes, Dr Sarah Bajan
Laws of Energy Transformation
• Organisms absorb energy (e.g. light or chemical) and release energy (e.g. heat and metabolic waste)
• These energy transformations follow the laws of thermodynamics
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Cellular Processes, Dr Sarah Bajan
The First Law of Thermodynamics
• Energy can be transferred of transformed, but cannot be created or destroyed
• Principle of conservation of energy
• Energy of the universe is constant
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Cellular Processes, Dr Sarah Bajan
The Second Law of Thermodynamics
• Every energy transfer/transformation increases disorder (entropy) of the universe
• Some energy becomes unavailable to do work
• Disorder – specific molecular definition relating to how dispersed energy is in a system
• Measured as entropy
• Molecular disorder or randomness
• If a process contributes to increased entropy, can proceed without input of energy
• Spontaneous process
• Energetically favourable
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Cellular Processes, Dr Sarah Bajan
Free Energy Change (∆G)
• Gibbs free energy of a system (G)
• Free energy is the portion of a system’s energy that can
perform work with temperature and pressure are uniform
throughout the system
• Energy available to do work
• Usable energy
• ∆G can be measured for any reaction
• Values depend on pH, temp, concentrations
• Can predict if process is energetically
favourable/spontaneous
– - ∆G
– Important in the study of metabolism
Change in enthalpy (heat)
Change in entropy
(randomness)
ΔG = ΔH – TΔS
Change in free energy
Temp (kelvin)
Cellular Processes, Dr Sarah Bajan
Free Energy Change (∆G)
• Free energy is also a measure of instability
• Tendency to change to a more stable state (less energy)
• State of maximum stability is equilibrium
• Free energy of mixture of reactants and products decreases
• Lowest G
– Can do no work
– A cell that has reached metabolic equilibrium is dead!
– Metabolism as a whole is NEVER at equilibrium
• Change from this state is a positive ∆G and requires energy
• A process is spontaneous and can perform work ONLY when is it moving TOWARDS equilibrium
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Cellular Processes, Dr Sarah Bajan
Le Chatelier’s Principle
• When a system at equilibrium is changed, the system adjusts to absorb that change
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Cellular Processes, Dr Sarah Bajan
Exergonic and Endergonic Reactions in Metabolism
• Exergonic – energy outward, net release of energy,
loses free energy, ∆G is negative
• spontaneous
• Greater the decrease in free energy, the more
work than can be done
• Endergonic – energy inward, absorbs energy from
surrounding, stores free energy, ∆G is positive
• Not spontaneous
• ∆G = quantity of energy required to drive reaction
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Cellular Processes, Dr Sarah Bajan
ATP Powers Cellular Work
• A cell does three main kinds of work:
• Chemical work – driving endergonic reactions
• Transport work – moving substances against
direction of spontaneous movement
• Mechanical work – beating of cilia, contraction of
muscles etc.
• Cells manage energy resources by energy coupling
• Use and exergonic process to drive and
endergonic one
• Mediated by Adenosine Triphosphate (ATP)
• Immediate energy source
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Cellular Processes, Dr Sarah Bajan
The Hydrolysis of ATP
• Chemical potential energy stored in ATP drives
most cellular work
• Hydrolysis can break the bonds between the
phosphate groups of ATP
• Exergonic reaction
• Releases ~13 kcal/ 1M of ATP in cell
conditions
• ATP is a ‘high energy’ molecule
• All phosphate groups are negatively charged
– Mutual repulsion contributes to instability
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Cellular Processes, Dr Sarah Bajan
Reaction Coupling
• The cell harness the release of energy to drive endergonic reactions
• OVERALL coupled reactions are exergonic
• Usually involved phosphorylation of reactant – phosphorylated intermediate
– More reactive
– Can change shape of reactant
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Cellular Processes, Dr Sarah Bajan
Reaction Coupling
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Cellular Processes, Dr Sarah Bajan
Reaction Coupling
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Cellular Processes, Dr Sarah Bajan
The ATP Cycle
• Use ATP continuously
• Renewable resource by recycling ADP
• Coupled reaction
• Working muscle cell turns over 10 million molecules
consumed and regenerated per second per cell
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Cellular Processes, Dr Sarah Bajan
Energy Flow and Chemical Recycling
• Energy flows through an ecosystem as sunlight and
heat
• Chemical elements are recycled
• Cellular respiration uses stored chemical energy in
organic molecules to generate ATP
• CO2 and H2O
• Photosynthesis uses CO2 and H2O to create organic
molecules and O2
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Cellular Processes, Dr Sarah Bajan
Cellular Respiration
Cellular Processes, Dr Sarah Bajan
Learning Objectives
• To understand
• Biological Oxidation and Reduction
• Respiration
– Product, equation and capture of energy
• ATP synthesis
• Relationship of NAD/NADH and ATP
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Cellular Processes, Dr Sarah Bajan
Catabolic Pathways Yield Energy
• Breaking down large molecules to release energy – catabolic pathways
• Energy results from electron arrangement in the bonds between atoms
• Involves electron transfer between molecules
• Enzymatic reactions degrade organic complex molecules (rich in potential energy) to simple waste
products (low in potential energy)
• Used to do work or lost as heat
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Cellular Processes, Dr Sarah Bajan
Cellular respiration
• Consumes O2 and organic ‘fuel’ – aerobic respiration
• Efficient catabolic pathway
• Fuel = carbohydrates, fats, proteins
• We will focus on glucose
• Exergonic Reaction
• Produces ATP
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Cellular Processes, Dr Sarah Bajan
Redox Reactions: Oxidation and Reduction
• Many reactions involve the transfer of one or more electrons from one reactant to another – redox
reaction
• Loss of electrons – oxidation (OIL)
• Addition of electrons – reduction (RIG)
• Electron donor – reducing agent
• Electron Acceptor – oxidising agent
• Electron transfer requires both a donor and acceptor, so oxidation and reduction are always paired
• O2 is one of the most powerful oxidising agents
• Requires lots of energy to remove and electron from O2
• If move electrons closer to O2 (reduced) - releases chemical energy
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Cellular Processes, Dr Sarah Bajan
Oxidation of Organic Molecules During Cellular Respiration
• Glucose is oxidised and oxygen is reduced
• Electrons lose potential energy in the transfer, releasing energy
• Generally molecules with lots of H are good fuels (electrons can easily pass to O2 – a lower energy
state)
– Liberates energy used for ATP synthesis
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Cellular Processes, Dr Sarah Bajan
Electron Carrier
+
NAD
• Glucose is broken down in a series of enzymatically catalysed steps
• Efficient energy harvesting
• At specific steps, electrons are removed from glucose
– Electrons in the form of a H atom (also comes with a proton)
• Electrons are transferred to an electron carrier – NAD+
– Nicotinamide dinucleotide
– Coenzyme
• NAD+ is a suitable molecule as it can cycle easily between oxidised form (NAD+) and its reduced
form (NADH)
– Functions as on oxidising agent during respiration
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Cellular Processes, Dr Sarah Bajan
Electron Carrier
+
NAD
Cellular Processes, Dr Sarah Bajan
Electron Transport Chains
• How do these electrons finally reach O2?
• An electron transport chain consists of many
molecules, mostly proteins, built into the inner
membrane of the mitochondria
• Electrons from glucose, shuttled by NADH, to the highenergy end of the chain
• At the lower energy end of chain, O2 captures the
electrons, with a H+ to form water
• Electron transfer from NADH to O2 is exergonic
• Energy release occurs in a cascade in an chain from
one carrier molecule to the next until reach O2 – the
terminal electron acceptor
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Cellular Processes, Dr Sarah Bajan
Stages of Cellular Respiration
• 3 metabolic stages
Cytosol
Mitochondria
Mitochondria
• Pathways to break down glucose
Cellular Processes, Dr Sarah Bajan
Overview of Cellular Respiration
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Cellular Processes, Dr Sarah Bajan
Substrate-Level Phosphorylation
• ATP is synthesized when enzyme transfers a
phosphate group from substrate molecule to ADP
• Substrate is an intermediate product during
catabolism of glucose
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Cellular Processes, Dr Sarah Bajan
Glycolysis – Sugar Splitting
• Glucose is split into 2 x 3-carbon sugars
• These sugars are then oxidised and rearranged to
form pyruvate
• During energy investment phase reaction consumes
energy (ATP)
• During energy payoff phase, ATP is produced
• Substrate-level phosphorylation
• NAD+ is reduced to NADH
• Electrons released from glucose
• Actually a 10 step process
• NOT dependent on O2
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Cellular Processes, Dr Sarah Bajan
Pyruvate Oxidation
• Glycolysis releases less than a quarter of chemical
energy in glucose
• Rest remains in pyruvate
• When O2 is present, pyruvate enters mitochondrion
(active transport)
• Pyruvate is converted to Acetyl Coenzyme A (acetyl
CoA) via pyruvate dehydrogenase (PDH) complex
• A carboxyl is oxidised to released as CO2
– Oxidative decarboxylation
• Remaining fragment is oxidised and transferred
to NAD+ to create NADH
• CoA is attached
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Cellular Processes, Dr Sarah Bajan
The Citric Acid Cycle
• Further oxidation of pyruvate
• 8 steps
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Cellular Processes, Dr Sarah Bajan
The Citric Acid Cycle
• Red C at the 2 atoms that
enter cycle via acetyl CoA
• Blue C indicate 2 carbons
that exit cycle as CO2
• Carbons that enter the cycle
DO NOT leave as CO2 in the
same turn of cycle
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Cellular Processes, Dr Sarah Bajan
The Citric Acid Cycle
• For each acetyl group
entering the cycle produces
• 3 x NADH
– Steps 3, 4 and 8
• 1 x FADH2
– Step 6
• 1 x GTP/ATP
– Step 5
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Cellular Processes, Dr Sarah Bajan
Free-Energy Change During Electron
Transport
• Collection of molecules in inner membrane of
mitochondria
• Folding of membrane increase surface area
• Series of sequential redox reactions
• Multi-protein complexes from I to IV
• Sequences of electron carriers and the drop in free
energy as electrons travel down the chain
• Carriers alternate between reduced and
oxidised states as they accept and donate
electrons
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Cellular Processes, Dr Sarah Bajan
Chemiosmosis: Energy-Coupling
Mechanism
• Also in the mitochondrial inner membrane –
ATP synthase
• Makes ATP from ADP and inorganic
phosphate
• Harnesses energy of existing ion gradient to
power ATP synthesis
– H+ concentrations on opposite sides of
inner mitochondrial membrane
– Chemiosmosis
• Protons bind to the protein, causing it to spin in
membrane – catalysing reaction
• H+ gradient – proton-motive force
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Cellular Processes, Dr Sarah Bajan
What generates the
+
H
gradient?
Cellular Processes, Dr Sarah Bajan
ATP Yield Per Glucose Molecule
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Cellular Processes, Dr Sarah Bajan
Photosynthesis
Cellular Processes, Dr Sarah Bajan
Learning Objectives
• To understand
• The stages of photosynthesis – the light reaction and the dark reaction
• The function of chloroplasts and chlorophyll
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Cellular Processes, Dr Sarah Bajan
Photosynthesis: Solar powered process that feeds the earth
• Plants contain cellular organelles called chloroplasts
• Contain specialised complexes that convert light energy to chemical energy
• Stored in organic molecules
• Conversion is called photosynthesis
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Cellular Processes, Dr Sarah Bajan
Chloroplasts: the site of photosynthesis
• Leaves are the major site of photosynthesis
• Chloroplast rich tissue of the plant, around 30-40 per cell
• Chlorophyll, green pigment, in chloroplast membrane
– Absorbs light energy
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Cellular Processes, Dr Sarah Bajan
Photosynthesis: Overview
• Chloroplasts, in the presence of light, produce organic compounds and O2 from CO2 and water
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Cellular Processes, Dr Sarah Bajan
Two Stages of Photosynthesis
• Light reactions
• Converts solar energy (visible light) to
chemical energy
– NADPH and ATP
• Water is split providing source of electrons
and protons
• O2 is formed as by-product
• Dark Reactions/Calvin Cycle
• Incorporates CO2 into organic molecules
• Organic molecule is reduced by NADPH and
converted to a carbohydrate by ATP
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Cellular Processes, Dr Sarah Bajan
The Light Reactions
• Pigments are substances that absorb visible
light
• Chlorophyll absorbs all visible light except
green light which is reflects back
• The absorbed light elevates an electrons
potential energy, moves to a higher orbital
• Molecule reaches an excited state
• Unstable
• Electron drop back down to ground state
releasing energy as heat/light
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Cellular Processes, Dr Sarah Bajan
The Light Reactions
• Chlorophyll and other molecules are arranged into
photosystems
• Organised association of proteins
• Reaction-centre complex surrounded by lightharvesting complexes
• Solar-powered transfer of electron from the reactioncentre chlorophyll to the primary electron acceptor
• NOT dissipated as heat/light
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Cellular Processes, Dr Sarah Bajan
The Light Reactions
• ATP and NADPH are
synthesized by
photosystems (I and II)
• Flow of electrons
through photosystems –
linear electron flow
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Cellular Processes, Dr Sarah Bajan
The Light Reactions
1. Light excites chlorophyll
electrons in PS II, energy is
transferred between pigment
molecules until reaches
chlorophyll molecules (P680)
in PSII reaction-centre
complex
2. Electron transferred from
excited P680 to primary
electron acceptor
3. Enzyme catalyses splitting of
H2O, released electrons are
passed to P680+
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Cellular Processes, Dr Sarah Bajan
The Light Reactions
4. Excited electron passes from
primary acceptor of PS II to PS
I via an electron transport
chain
5. Potential energy in proton
gradient is used to make ATP
via chemiosmosis
6. Energy has reached PS I
reaction-centre complex
exciting electrons of P700.
Transferred to primary electron
acceptor. P700+ is formed.
7. Second electron transport
chain
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Cellular Processes, Dr Sarah Bajan
The Light Reactions
8. Transfer of electrons to NADP+
to form NADPH (requires 2
electrons)
• These electrons are at a higher
energy level compared to water
• Big picture: light reactions
generate ATP and NADPH
which provide chemical energy
and reducing power
respectively
• Used in the dark reactions
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Cellular Processes, Dr Sarah Bajan
Chemiosmosis Take 2
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Cellular Processes, Dr Sarah Bajan
The Dark Reactions: The Calvin Cycle
1. Carbon Fixation
Each CO2 is attached to a 5C sugar RuBP.
Makes a 6C, energetically unstable molecule
which immediately splits in half to form two
3-phosphoglycerates
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Cellular Processes, Dr Sarah Bajan
The Dark Reactions: The Calvin Cycle
2. Reduction
Each 3-phosphoglycerate receives energy in
form of phosphate (from ATP) and is
reduced by NADPH
Forms G3P
Only net gain of one 3C sugar
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Cellular Processes, Dr Sarah Bajan
The Dark Reactions: The Calvin Cycle
3. Regeneration of RuBP
Carbon skeletons are rearranged into 3
RuBP. Requires three ATP molecules.
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Cellular Processes, Dr Sarah Bajan
The Dark Reactions: The Calvin Cycle
• For ONE G3P molecules. The cycle
consumes 9 ATPs and 2 NADPHs
• G3P is used as starting material to form
organic compounds such as glucose
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Cellular Processes, Dr Sarah Bajan
Questions and Kahoot