- Driving unfavourable interaction by coupling reactions

- Unfavourable interactions need energy input

- Biopolymer formation is unfavourable (nucleic acids need to make high energy
phosphodiester bonds between successive nucleotides/amino acid activation
release PPi)
- Coupling reactions effectively combine the energy & affects the equilibria of both
reactions

- Removing products (PPi) shifts the equilibrium towards nucleic acid synthesis

- 2nd step is rapidly catalysed by pyrophosphatase enzymes

Module 2
Lecture 9: Photosynthesis I
Differentiate between anabolism and catabolism, and oxidation and reduction
- Metabolism → chemical reactions that occur inside the cells, including those that use
and release energy
- Anabolic → small molecules into large molecules, energy required
- Catabolic → breakdown of large molecules, energy released
- Oil Rig: oxidation = loss of electrons; reduction = gain of electrons
- NAD+ (oxidising agent) → NADH
- FAD → FADH2
 - NADP+ → NADPH

Explain how ATP can power cellular processes

- ATP = adenosine triphosphate ← like a rechargeable battery
- Energy is stored as ATP and released when cells need it (cells cannot store energy)
- Energy currency of cells

- Phosphate bonds → high energy bonds

- When bonds are broken, energy is released
- Organisms acquire energy through
- Heterotrophy → organisms eat other organisms/organic matter

- Autrotrophy → self-feeding organisms, e.g. plants

Describe the major evolutionary events to maximise light capture by plants

- 1st stage photosynthesis → light reactions
- Trap sunlight and convert to chemical energy for later use
- ATP and NADPH production
- Chlorophylls capture light energy
- Chlorophyll within thylakoid membrane of chloroplast
 - Form an antenna complex which works to transfer light energy to the
reaction centre

- 2nd stage photosynthesis → calvin cycle or light independent

- Capture C from air and covert into sugars using chemical energy produced in 1st
stage
- Photosynthesis
- 1st stage: ATP/NADPH
- 2nd stage: CO2 → sugars

Describe, in overview, the conversion of radiant energy into chemical energy

- 1st stage: light reactions

- H2O → O2 : oxidation
- NADP+ → NADPH : reduction

Explain the overall organisation of the light reactions in photosystems I and II

- Cyclic photophosphorylation
- Uses sunlight to make proton gradient
 - The proton gradient between stroma and lumen drives production of ATP

- No reducing power to convert CO2 to reduced form (glucose)

- Non-cyclic photophosphorylation
- Uses sunlight to make ATP and NADPH

Describe ATP synthesis during photosynthesis

- Proton pumping & oxidation of water lead to high proton concentration in lumen and low
proton concentration in stroma
- Proton diffuse from the lumen to the strome through a protein → ATP synthase
- ATP synthase catalyses phosphorylation leading to ATP production
- Phosphorylation: addition of phosphate to ADP

Lecture 10: Photosynthesis II

 - PSII and PSI produce ATP and NADPH
- ATP and NADPH used as energy and reducing power in Calvin cycle
- CO2 into sugars
- ATP → ADP AND NADPH → NADP+
- Go back to light reactions

Explain fixation of carbon dioxide in the Calvin Cycle

Calvin cycle

- Light independent → takes place in chloroplast during photosynthesis

- Takes place outside the thylakoids, in the stoma
- ATP + NADPH + CO2 → sugars + NADP (ATP used up)
- Cycle has to turn 6 times to make 1 glucose
Compare carboxylation and oxygenation by Rubisco
- Rubiso: Ribulose bis-phosphate carboxylase/oxygenase
- Carboxylase: fixes CO2
- Oxygenase: fixes O2
- Enzyme catalysing CO2
- Occurs in chloroplast stroma
- Rubisco can also fix oxygen

Describe the co-evolution of photosynthesis (C4) and the earth’s atmosphere over time
- C4 is a series of metabolic and structural adjustments exploiting phosphoenolpyruvate
carboxylase (PEP carboxylase/PEPC) to concentrate CO2 around Rubisco
- CO2 from the atmosphere is converted into malic acid then its pumped down and
released as CO2 around chloroplast

Describe the photosynthesis-transpiration compromise and how CAM photosynthesis

breaks the nexus between photosynthesis and transpiration
- CAM → Crassulacean acid metabolism
- Occurs solely in mesophyll cells
- Solves photorespiration and leads to higher water-use efficiency via a temporal
separation of biochemistry (closing the stomata at different times)
- Guard cells open to let CO2 in and also water leaves (same pathway)
 - When stomata is open, plant loses water because they have to let CO2 diffuse in

- Night → high humidity so lose less water if open

Lecture 11: Respiration in Plants

Describe, in overview, the TCA cycle and glycolysis
- Glycolysis → sugar splitting to extract energy from food
- Breakdown of glucose to extract energy for cellular metabolism
- Catabolic reactions in the cell cytoplasm
- Anaerobic process
 - Breakdown of glucose → pyruvic acid, ATP, NADH

- Krebs (TCA) cycle (citric acid cycle)

- Remove electrons from products of glycolysis
- Strip electrons from pyruvate to form NADH and FADH2
- Carry electrons to ETC

Describe the electron transport chain and oxidative phosphorylation in mitochondria

- Products from Kreb’s cycle and glycolysis used to generate a lot of ATP
- Occurs on the inner membrane of the mitochondria
- Pump protons from matrix into the intermembrane space
- Higher proton concentration in intermembrane space
- Protons flow back through ATP synthase → generate ATP
 - Oxidative phosphorylation → combination of ETC with ATP synthase

Compare photosynthetic electron transport and the electron transport chain in

mitochondria

Electron transport chain in chloroplast Electron transport chain in mitochondria

Source of energy → light Source of energy → high energy electrons

- Strip electrons from water - Carried by FADH2 & NADH

Raise electrons to higher orbital (excited) Flow through electron transport chain
- As it flows, used to pump protons

High energy electrons used to pump protons Protons pumped from mitochondria matrix
from 1 side of the membrane to another into intermembrane space

Proton gradient generated Protons move back through ATP synthase

- High proton concentration in thylakoid
lumen

Transported back through ATP synthase Movement through ATP synthase leads to
- Drives ATP synthesis ATP formation from ADP & phosphate
Describe variations on the basic model of cellular respiration
- Cellular respiration → in mitochondria

- 3 processes: glycolysis, Kreb’s cycle, ETC

- Aerobic respiration
- C6H12O6 + 6O2 → 6CO2 + 6H2O + energy

- 4 stages: glycolysis, link reaction, Krebs cycle, oxidative phosphorylation

 - Alternative oxidase (AOX)

- Non-energy conserving pathway → leads to energy being wasted

- Electrons flow down via AOX to oxygen as terminal electron acceptor instead of
passing through complex IV
- Protons are not getting pumped because electrons not going through
complex III or IV
- Proton gradient smaller → less ATP produced
- Uncoupling protein (UCP)
- Lets protons diffuse back through the phospholipid bilayer without going through
ATP synthase

Lecture 13: Metabolism

Distinguish between macronutrients and micronutrients
- Macronutrients → large nutrients
- Act as substrates
- Examples: carbohydrates, proteins, fats
- Micronutrients → small molecules
- Vitamins → act as confactors to enzymes
- Minerals → act as cofactors and also used as integral parts of the tissue
- Calcium for bones

Characterise the terms anabolism and catabolism

 - Anabolism → synthesis of complex molecules from simpler molecules by condensation
reactions
- Monomers → macromolecules
- Requires energy supplied by ATP
- Catabolism → breakdown of complex molecules into simpler molecules by hydrolysis
- Macromolecules → monomers
- Energy released which can be used to form ATP

Describe the composition of fats, carbohydrates and proteins

- Carbohydrates → glycogen

- Sugars joined together in long strings

- Glycosidic bond formation

(forward: anabolic)
- Glycogen is stored in many cells especially:
- Liver: breaks down sugars and release into blood stream
- Skeletal muscle: trap sugar within each muscle cell to be used for work
- Glucagon hormone → catabolism of glycogen
- Insulin hormone → anabolism of glycogen
- Proteins
- Passes from small intestine → epithelial cells on villi → blood stream
- Amino acids (what the blood absorbs)

- Fats

C chains saturated with H

 - Fats are stored in adipose tissue
- Most in omentum → tissue which covers the small intestine and can be
broken fown for metabolism
- Triglyceride (TG)

Explain how ATP can power cellular processes

- Phosphate → mineral micronutrient
- Hydrophilic

- ATP (adenosine triphosphate)

- Breakdown of 1 phosphate group creates energy, ATP → ADP + energy

Compare and contrast different nutritional sources of protein

- All essential amino acid components of protein are made by plants
- Humans and animals have lysine contingency → we don’t have the enzyme that can
manufacture lysine, it has to be obtained through food
- Non-essential amino acids → cells can manufacture itself
 - Essential amino acids → we need to get from food

Understand the basics of how fats, carbohydrates and proteins can be interconverted via
metabolism
- Fats, proteins and carbohydrates are interconvertible
- Glucose is split in half during glycolysis → form pyruvate
- Pyruvate goes into mitochondria and lose 1C as CO2
- Resulting molecule joined to Acetyle CoA, converted into citrate
- Citrate moves out of mitochondria, reattaches to Acetyl-CoA outside → forms fat
and fatty acid

Lecture 14: Cell Diversity

Describe the theories on cell evolution
- Over 3.5 billion years of cell evolution
 - Evolution of nucleus
- Evolution of mitochondria
Distinguish between prokaryotic and eukaryotic cells
Prokaryotic
- Single celled
- No membrane bound nucleus
- Singular loop of chromosome
- Bacteria, Archea
Eukaryotic
- All space between organelles is filled
with proteins
- Long fibrous protein within cytoplasm
along with globular protein
- Protist → single cell eukaryotes
- Fungi, Plants, Animals
 - Prokaryotic cells

- Flagellum: allows cells to move

- Plasmid: rings of DNA
- Capsule: made of sugars (carbohydrates)
- Pilus: sticky surface, allows cells to recognise and stick to one another and other
surfaces
- Eukaryotic cells

- Globular protein
- Fibrous proteins → allow transport of molecules within cells

Describe the composition of lipid bilayer cell membranes

- All cells have a plasma membrane
 - Phospholipids: phosphate group (head) and twol tails of fatty acids

- Head interacts with water and tail is hydrophobic so it pushes water away
- Heads face aqueous cytoplasm & aqueous tissue fluid
- Tails face towards inside of bilayer, formning hydrophobic core
- Animal plasma membranes are stabilised with cholesterol

→ cholesterol
- Cholesterol gives membrane different qualities of viscosities depending on how
much cholesterol is in there
- Allows cell to change shape
- Allow certain hydrophilic substances to pass through membrane
- Able to perform specialised function

- Functions of cell membrane:

- Cell signals (receive information)

- Border police (import and export of molecules)
- Shape, size and movement

Explain the roles of compartmentalisation in cellular function

Animal vs Plant cell

- Plasma membrane → selectively permeable membrane that separates cell’s contents

from surrounding environment, formed from phospholipid bilayer
- Cytoplasm → aqueous medium containing medium substances, site where all metabolic
reactions occur

- Nucleus

- Nuclear envelope → double membrane structure, separates nucleus contents

from cytoplasm
- Nuclear pores → allow substance exchange between nucleus and cytoplasm,
allow mRNA formed by transcription to leave nucleus
- Nucleolus → synthesise subunits of ribosomes
- Rough endoplasmic reticulum → occurs as series of interconnected flattened membrane
sacs (cisternae), endoplasmic reticulum with attached ribosomes, site that synthesise
proteins that are to be secreted
- Golgi apparatus → occurs as cisternae & vesicles, receives proteins from RER,
chemically modifies and package it into vesicles, forms lysosomes
- Ribosomes → composed of ribosomal RNA (rRNA) & proteins, bound to ER/free
cytoplasm, site where translation happens
- Mitochondria → rod-shaped/spherical structure, double membrane, produce ATP during
aerobic cell respiration

Animal Cell Plant Cell

 Lysosomes → contains hydrolytic enzymes Cell wall → made of cellulose, surrounds the
exterior of cell, maintains plant

Centrosome Chloroplast

Vacuole Vacuole

Centrioles → short, rod-like structures,

anchor point for microtubulues as they form
during cell division

Lecture 15: Compartmentalisation of Cells

1. Explain the major functions of the plasma membrane
2. Describe passive (diffusion and osmosis) and active processes which allow the flow of
substances across a semipermeable cell membrane
3. Define diffusion and osmosis and tonicity including hypo, iso and hypertonic solutions
4. Describe how proteins are exported and imported out and into the cell via vesicular
transport
5. Compare and contrast between the three components of the cytoskeleton

Lecture 16: Cell, tissues and communication

Explore the ways that cells aggregate with each other to form tissues
Compare and contrast the four types of animal tissue.

- Epithelium
- Connective
- Nervous
- Muscle
Explain how cells communicate and regulate cell growth in a healthy state (e.g.
differentiation of stem cells)
and what can go wrong to result in a pathophysiological state (e.g. cancer).