Module 1

Lecture 2: The Chemistry of Life

Appreciate the common origins and makeup of the molecules of life
- Genetic material encodes the molecules of life and is shared through generations
- All species share common genes and cellular functionalities
- Molecules of life:
- Nucleic acids (DNA/RNA)
- Proteins → functional molecules of our body/cells
- Fats/lipids → fats from membranes of cells
- Sugars/carbohydrates x

Describe the properties of living organisms

- Cell based, complex but organised
- Capture energy from the sun to use for growth and reproduction
- Respond to stimuli
- Can reproduce
- Tend towards Homeostasis → steady internal state, can cope with change because
regulatory processes brings the cell back to its original state
- Adapt to the environment
- Evolution (changes over time)

Classification of living organisms

Appreciate that life is made up of a small number of elements of which carbon is

particularly important
- Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulphur
- Life is carbon based
- Can bond with itself and other elements
- Stable but not too stable
- All major biopolymers have a substantially carbon backbone
Define the terms polar/hydrophilic and non-polar/hydrophobic
- Polar/hydrophilic molecules: partly/fully charged with a dipole (water liking)
- Non-polar/hydrophobic molecules: electrons/charge is even within the molecule (water
hating)
- Carbon is inherently neutral & non-polar
- Hydrogen is heavily influenced by what its near (C/H neutral, O/N polar)

Describe the building blocks of life: Water, carbohydrates (sugars), lipids, amino acids
and nucleic acids.
- Water → polar compound with extensive hydrogen bonding
- ~62% water
- Stabilises temperature
- Carbohydrates (sugars/saccharides)
- Monosaccharides → composed of C,H,O and form rings (e.g. glucose, ribose)

- Disaccharides: 2 monosaccharides joined together

- Sugar polymers: long chains of monosaccharides
- Starch → storage
- Chitin → protection
- Cellulose → structure
- Bacterial cell walls/surrounding coats (complex polymers)
- Lipids → fats, oils, waxes, steroids/sterols
- Poorly soluble in water but soluble in organic (hydrophobic/polar) solvents
- Functions
- Triglycerides → energy stores
- Steroids → signalling molecules
- Waxes → protection and waterproofing
- Waxes/phospholipids → structure/barriers
- Phospholipids form cell membranes: polar parts interact with aqueous
environment and hydrophobic parts cluster together
- Amino acids → building blocks of protein
- Nucleic acid (DNA/RNA) → made up of nucleotides
- Nucleotides: a phosphate group (- charge), a sugar (ribose/deoxyribose), a
nucleobase (A,G,C,T,U)
 - D - mononucleotide, dADP - dinucleotide, dATP - trinucleotide

Describe some chemical properties of amino acids (solubility hydrophobic/hydrophilic,

polarity, charge), given their chemical structures
- Electrically charged
- Basic → R group has -NH3+
- Acidic → R group has -COO-
- Electrically neutral (no charge overall)
- Non-polar → insoluble in water (hydrophobic)
- Polar → R group has -OH, -SH, -NH, dissolves in water (hydrophilic)

Lecture 3: Biopolymers
Identify the conventions of direction/ends of protein and nucleic acids.
- Synthesised in one direction only increasing the backbone
- Nucleic acids: from 5’ to 3’
- Proteins: from N-terminus (amino) to C-terminus (carboxy)

Describe the repeating units (backbones and side chains or bases) in proteins and
nucleic acids.
- Nucleic acids → nucleotide as building blocks
- Common sugar-phosphate backbone (phosphate, sugar, base/nucleobase)

- Proteins → amino acids as building blocks

- Common peptide backbone (sidechains (R) of different amino acids differ)

peptides (short), proteins (long)

Identify the main chemical components of nucleic acids and proteins/peptides.

- Nucleic acids
- Phosphate
- Sugar
- Base/nucleobase
- Proteins/peptides
- Amino acids

Describe how the physical and chemical properties of proteins and nucleic acids can be
exploited in experimental situations
 - Nucleic acids
- Hydrophilic due to sugars and phosphates
- Negative charge on phosphates
- Can be used for:
- Electrophoresis → nucleic acids migrate in an electric field because they
are charged, migrated distance depends on size
- Ethanol precipitation → nucleic acids become insoluble when mixed with
salt (neutralise charge) and ethanol
- Proteins
-

Appreciate and explain the evidence for DNA as the source of genetic information.
Describe the base pairing between nucleobases and appreciate that C/G base pairing is
stronger than A/T(U) base pairing in nucleic acids
- DNA is the source of genetic information
- Adenine, Thymine, Uracil, Cytosine, Guanine
- Two strands are held together by hydrogen bonds between complementary bases
(base pairing)
- C/G → 3 hydrogen bonds, while A/T(U) → 2 hydrogen bonds
- C/G has stronger bonding

Describe the double-helical structure of DNA.

- Two strands that run in opposite directions, wind around each other forming a right
handed double helix structure
- Flat bases stack on top of each other in the middle of the structure
- Negative phosphates repel each other
 - Major & minor grooves

Distinguish DNA from RNA, in terms of structure and stability

- DNA → deoxyribonucleic acid, RNA → ribonucleic acid
- RNA has a ribose sugar instead of deoxyribose sugar (DNA)
- RNA nucleotides have uracil base instead of thymine
- RNA does not form a B-type structure because there is an extra OH-group on the
sugar/ribose (RNA is single stranded)
- This makes it more susceptible to degradation
- Can base pair
- Both RNA and DNA have cytosine, which has the tendency to lose amine group
- Cytosine become uracil through spontaneous deamination
- Since uracil is normal in RNA, this is not repaired
- If uracil appears in DNA then it is recognised as a mistake and will be repaired

Lecture 4: The Central Dogma of Molecular Biology

Outline the central dogma of molecular biology and describe the information flow
between DNA, RNA and proteins.

Define the genome, transcriptome and proteome and how they differ from cell to cell.
- Genome → DNA (genetic information)
- Transcriptome → RNA (messenger for making proteins)
 - mRNA → message for making proteins, encodes proteins
- microRNA and snRNA → regulatory roles
- Ribosomal RNA and transfer RNA → important for protein synthesis
- Proteome → Protein
- Amino acid sequence determines the structure and function
- All cells have the same DNA. Each cell uses a subset of expressed genes to achieve its
structure & function
- Genome same in all
- Transcriptome & Proteome will differ in response to different stimuli

Describe the difference in size and construction between bacterial and eukaryotic
genomes.
- Bacterial genomes (most prokaryotes)
- ~150 kb (15 million bp)
- Small genomes
- Circular chromosomes
- Eukaryotic genomes
- 10 Mb - 150 Gb
- Big genomes
- Have linear chromosomes
- Condensed into chromatin
- Wrapped around histone proteins

Define the universal genetic code (triplet/non-overlapping/common)

- The combination of 3 bases which codes for an amino acid is called a codon
- 20 amino acids in proteins to codons in mRNA
- The genetic code is degenerate/redundant and universal (used by all life forms)
- How cells translate nucleotide sequence into protein sequence

Understand the concept of reading frames for translating a nucleic acid sequence into a
protein sequence
- Look for start codon: AUG
- Look for stop codon : UAA, UAG, UGA
Understand how to read a genetic code table and translate nucleic acid sequence into
protein sequence using such a table.

Describe the effect of mutations in DNA and effect on protein sequence

Lecture 5: Copying DNA and RNA

Outline the general mechanism for copying DNA to DNA before cell division - replication.
- Template is required for base pairing
- Replication travels in both directions, copying from 5’ to 3’
- Nucleotide triphosphate used as substrate but nucleotide monophosphate added to
3’OH end of the growing chain
- Deoxynucleotide triphosphate (dNTPs: dATP, dGTP, dTTP, dCTP) → substrate
- Form high energy phosphodiester bond and release pyrophosphate (PPi)
- Pyrophosphate is released and breaks down to 2 phosphates which provides
energy for reaction
- Uses DNA polymerase and need a primer (short piece of DNA/RNA) to start

- ORI (origin) site of replication are AT-rich → easier to pull strands apart because less
stable
- DNA binding proteins open up the site
- DNA helicase unwinds part of the DNA
- DNA topoisomerase/gyrase stops supercoiling
- Forms replication forks
- Single-stranded binding proteins coat single stranded DNA (ssDNA) to keep
strands apart & protect DNA
List the unique problems associated with replication and describe the strategies used by
the cell to overcome these, including unwinding DNA, and leading versus lagging strand
replication.
- Genomes are big and made up of long strands of dsDNA (circular in bacteria) and both
strands need to be copied
- Semi-conservative replication model: each newly generated dsDNA contains one
original and one new strand
- Helical DNA needs to be unwound but pulling long helical strands apart causes
supercoiling
- Use of topoisomerase enzymes cut strands apart, allowing it to unwind and stick
back together (only unwind small sections at a time)
- Use of helicase to unwind DNA
- Leading vs Lagging strand (DNA strands run in opposite directions, synthesise 5’ to 3’)
- 2 replication forks → 2 strands copied at each → 4 strands being copied

- Leading strand (top): continuous copying

- Primase makes RNA primer
- DNA polymerase III makes a DNA copy of the strand in 5’ to 3’ direction
- Lagging strand (bottom): made in small pieces that get joined together
- Primase makes multiple RNA primers along the template (because it
travels in the opposite direction)
- DNA polymerase III synthesises in 5’ to 3’ until it runs into the next primer
- Made in sections → Okazaki Fragments
- DNA polymerase I replaces RNA primer with DNA
- DNA ligase joins the pieces of DNA
Describe the general functions of proteins that are required for DNA-replication
- Helicase → unwinds the DNA strand
- Topoisomerase → cuts DNA strands allowing it to unwind
- Primase → makes RNA primer
- RNA primer → initiates replication
- DNA polymerase III → adds to new DNA
- DNA polymerase I → removes RNA primers and replace with DNA (lagging strand)
- DNA ligase → joins gaps (lagging strand)

Outline the general mechanism for copying DNA to RNA - transcription.

- Make RNA copy from a DNA template

- No primer needed to start transcription

- Uses ribonucleotide triphosphates (NTPs: ATP, GTP, CTP, UTP) as substrate
- RNA polymerase binds to the promoter and starts transcribing downstream from that
region, transcription stops at terminator
- Promoter: a region of DNA which sits just upstream (past to the 5’ end)
- Consensus sequence → -10 & -35 region
- -10 region often has sequence TATA which is easy to melt

- Promoter & terminator sequences as part of the DNA

- Only one strand of DNA is transcribed for each gene
- “transcription bubble” moves along as the RNA polymerase moves, after the RNA
polymerase has passed, 2 strands of DNA reanneal

- Transcription uses a signal encoded in the transcribed RNA to stop

 - G/C rich region form a ds hairpin structure and causes transcription to pause and
RNA polymerase to dissociate and the RNA to be released

- OR Rho protein binds, and uses helicase activity to travel up to and dissociate
the DNA/RNA hybrid complex from the DNA template (force apart the protein
nucleic acid complex)

List the unique problems associated with transcription (including unravelling DNA, and
making multiple copies of small sections of the genome at different frequencies) and
describe the strategies used by the cell to overcome these.
- No stop/start point
- Limited proofreading → make more mistakes
- Gene expression regulation
- Genes can be expressed at different frequencies
- Based on promotor strength → DNA sequence optimised for strong/weak sigma
factor/RNA pol binding
- Strong binding = more RNA copies made

- Only small sections of the genome need to be transcribed

- Sections have to be copied thousands of times
- Some sections are rarely copied in once cell but many times in another cell
- mRNA production rates vary (???)
- Repression → protein repressor binds and blocks the binding of sigma factor/RNA
polymerase complex → no gene expression
 - Metabolites can bind to the repressor and allow sigma factor/RNA pol to bind
- Accelerators → sigma factor/RNApol complex doesn’t bind strongly → low gene
expression
- Transcriptional Activator (protein) binds at specific DNA sequence and alters
structure of promoter so transcription factor can now bind more frequently

Describe the general functions of proteins that are required for RNA transcription
Compare and contrast the differences between making DNA and RNA
- Transcription factors → proteins capable of recognising specific base sequence
- Facilitates the binding of RNA polymerase to the single stranded DNA
- RNA polymerase → binds to promoter (region of DNA)
- RNA polymerase associated with the DNA-bound transcription factor(s)
- Rho protein → forces protein nucleic acid complex apart from DNA template
- Differences in making DNA & RNA
- DNA polymerases only need a primer to start, RNA polymerase don’t
- DNA polymerase use deoxynucleotide triphosphates (dNTPs), RNA uses
ribonucleotide triphosphates (NTPs)
- DNA → whole genome copied once only, RNA → short segments copied at
different frequencies

Lecture 6: Making Proteins

Explain the unique problems associated with converting the information from a nucleic
acid sequence to an amino acid sequence.
- Translation: converting nucleotide sequence to a protein sequence
- Amino acids need to be in the correct order (to be able to give structure and function)
- Peptide bond formation is very thermodynamically unfavourable (non-spontaneous)

Outline the unique problems associated with protein synthesis, with particular reference
to the unfavourable thermodynamics of peptide bond formation and the requirement for
order. Describe the strategies used by cells to overcome these problems.
- Peptide bond formation is thermodynamically unfavourable
- Two amino acids undergo condensation polymerisation to form a dipeptide
- There is a large amount of water around (since water is removed from the
reaction)
- Hydrolysis (opposite reaction) is favoured over condensation in an aqueous
environment
- Requirement for order

Describe the general functions of proteins and RNA molecules that are required for
Protein synthesis
- mRNA (messenger RNA) → contains template for protein synthesis
- Information about which amino acids to add in which order
- tRNA (transfer RNA) → matches the correct amino acids to the template
- Different tRNA for each amino acid/codon combination
 - Matching of anticodon (complementary) to codon
- rRNA (ribosomal RNA) → combines with protein to form the machinery for protein
synthesis & catalyses peptide bond formation
- Moves along mRNA to assemble amino acids into proteins
- Amino acyl(Aa)-tRNA-synthetases
- Attach the correct amino acid to its matched tRNA
- Catalyse the activation of amino acids
- Use ATP hydrolysis to get the energy to make a high energy bond

- Ribosome

- Small subunit of the ribosome binds mRNA and Met-tRNA

Think about different ways you could inhibit or block protein synthesis

Describe the differences between primary, secondary, tertiary and quaternary structure of
proteins
- Primary → amino acid sequence
 - Secondary → local structures (alpha helix & beta sheets)

- Amide groups can form H-bonds, sidechains can make interactions with other
parts of the protein
- α-helix → when H-bonds are intramolecular, sidechains point outwards
- Always RHS helix
- β-sheet → when H-bonds are intermolecular, sidechains point above & below
- Tertiary → overall 3D arrangement of a polypeptide chain
- Held together by: hydrogen bonds, ionic interactions, hydrophobic interactions
- H-bonds between: peptide groups, bases, side chains
- Ionic interaction between charges & lone pairs
- Hydrophobic effect → a driving force for protein folding
- Hydrophobic parts want to cluster together when in aqueous environment
- Quaternary → organisation of subunits (not all proteins have multiple subunits)
- Clump together
- Arrangement of folded protein subsunits

Appreciate that the protein sequence defines the protein fold and function, and that
protein molecules are held together by the combination of many bonds
- Protein folding: process of forming tertiary structure
- Information is encoded in the amino acid sequence
- Burial of hydrophobic surfaces/sidechains in aqueous solvent
- Collapse of protein chain/formation of secondary structure
- Firming up tertiary structure by interactions between different parts of the protein

Demonstrate how 3D protein structure is related to function using the example of

the alpha helix in DNA binding proteins
- α-helices are the perfect size to fit into the major groove of DNA

Lecture 7: Enzymes and Thermodynamics

Describe the difference between potential and kinetic energy
- Energy: capacity to do work
- Potential energy → energy stores in chemical bonds/interactions
- Kinetic energy → energy expressed as movement (e.g. heat/radiant energy)

Explain the concept of equilibrium and how it relates to energy

- Equilibrium: rates of forward & reverse reactions are the same
 - Total free energy difference = 0

Explain the difference between thermodynamic and kinetic properties of a reaction

- Thermodynamics (internal energy)
- Exothermic/exergonic → give out energy
- Reaction favourable = product more stable
- Endothermic/endergonic → need energy
- Reaction unfavourable = product less stable
- Starting & finishing states
- Thermodynamic control → higher activation energy, higher
(more negative) ΔG (forms more slowly but more
thermodynamically favourable)
- Kinetics (how reaction occur)
- For a reaction to occur, it needs to get over an energy barrier

- How quickly will the reaction happen

- Only S (substrate) molecules that have enough energy to get over the
barrier will be converted to P (product) molecules
- Kinetic control → lower activation energy, less negative (lower) ΔG

Explain how enzymes act as catalysts, including what effect they have on reaction rates
and final concentrations of substrates and products of a reaction.
- Catalyst: lower energy barrier, speeds up reaction rate but is not used up/doesn’t affect

equilibrium
- Enzymes are biological catalysts
 - Increase reaction rates by stabilising transition state

Appreciate how enzymes can be used experimentally

Understand that enzymes combine to form enzymatic pathways that are important for
living organisms.
- Enzymes have relatively big, highly functionalised binding pockets
- Highly specific for their substrates
- “Lock & key” analogy → substrate molecule fits directly into the active site

- Induced-fit model → substrate induces a shape change for optimal substrate binding and
activity

- Selection model → enzyme exists in multiple forms (↑↑) in equilibrium, only one of which
binds substrate, binding to it shifts equilibrium to enable more binding

Describe how a secondary reaction can drive equilibrium and provide energy for an
unfavourable interaction.
 - 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