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MODULE ONE: INFORMATION TRANSFER

Explore the properes of living organisms.

Features of all living organisms
- Cell based
- Can reproduce
- Complex + organized
- Use energy for growth and reproducon
- Homeostasis (steady internal state/environment)
- Change over me
- Adapt to the environment
- Respond to smuli

Classicaon of living organisms (EAFPPA)

- Eubacteria (bacteria) Denions:

 Prokaryotes 1. Eukaryotes: organisms that contain
 Lack membrane bound organelles nucleus + DNA inside. Can be
 Unicellular mulcellular or unicellular
- Archaea
 Prokaryotes
2. Prokaryote: unicellular with no

nucleus, sll has DNA.
- Fungi
 Eukaryoc
 Decomposers
 E.g. yeast
- Prosts
- Plants
- Animals
 Mulcellular
 Heterotrophic

Appreciate the common origins and makeup of the molecules of life

Common molecules of life
- Carbon
- Hydrogen
- Nitrogen
- Oxygen
- Phosphorus
- Sulfur

Denions:
- Atom: smallest unit of an element
- Ion: a posively or negavely charged atom
- Polar or hydrophilic molecules: the uneven distribuon
of electrons/charge within a molecule
- Non-polar or hydrophobic molecules: the even distribuon
of electrons/charge within a compound
- Covalent bond: bond between two non-metals
- Ionic bond: bond between a metal and non-metal

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- Van der Waals (dipole-dipole): the aracon between two polar molecules
- Hydrogen bonds: bonds between H-O, H-F, H-N only
- Hydrophobic reacons:

Molecules of life
- Made of nucleic acids i.e. DNA/RNA, proteins, fats/lipids, sugars/carbohydrates/saccharides

About carbon
- Biopolymers dependent on carbon. Why? Because carbon creates stability (nature likes dis)
- Carbon compounds are inert/kinecally stable to undergo hydrolysis and oxidaon

Describe the general features of biopolymers

Biopolymers
- a polymeric substance occurring in living organisms such as DNA, protein, sugars etc. (all the molecules of
life)
- disnct beginning and end
- synthesized in one direcon only, increasing the backbone/length of it
- ** monomer lost in polymerizaon?? Amino acid ngs
-
Summarise the ow of genec informaon from DNA to RNA to protein in terms of the central dogma of molecular
biology.
Recap
- individual cells contain the same DNA which is expressed  gives the cell structure + funcon

Genomes: the genec composion of a cell or species

- bacterial  have circular genome + plasma DNA
- eukaryoc genomes  bigger, organised in linear chromosomes, wrapped around histone proteins
- human genomes (eukaryoc)
 linear
 22 pairs of chromosomes + sex chromosomes
 ~ 20,000 proteins
 one pair of copies of each genes

The central dogma of molecular biology (where informaon is used)

1. genome (DNA)
2. transcriptome (RNA)
- micro RNA
- ribosomal RNA
- messenger RNA
- transfer RNA
- small nuclear RNA

3. Proteome (protein)
- Ion channels
- Receptors
- Anitbodies
- Enzymes
- Transcripon factors
Note:

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DNA AND RNA

Identify the main chemical components of nucleic acids and their interactions involved in base pairing
between nucleic acid strands. Describe how these properties can be exploited in experimental situations.

DNA as genetic information

- DNA is a source of genetic information

Structure of DNA
- Chargaff  A/T and G/C are complementary base pairs
- Rosalind Franklin, Maurice Wilkins, James Watson and
Francis Crick  discovered the double helix structure of
DNA
- A nucleode consists of 3 parts: 5- carbon sugar, nitrogen
base, phosphate groups
- Nitrogenous base always connected via the 1-prime
sugar, phosphate group binds by the 3- prime oxygen
LHS and 5- prime RHS
hps://www.youtube.com/watch?v=o_-6JXLYS-k

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- Nucleosides are tied together via sharing phosphates, creating nucleotides

- One phosphate group = mononucleotide, e.g. AMP
- Two phosphate groups= dinucleotide, e.g. ADP
- Three phosphate groups = trinucleotide, e.g. ATP …etc.
- The double helix is held together by many hydrogen bonds between the bases… see below

Biopolymers
- Recall that all linear biopolymers have a defined beginning and end. They’re synthesized in one
direction only to increase the backbone.
- Sugar –phosphate background is hydrophilic (likes to be in water)
- Some of monomer is lost, leaving a residue that creates its own chain
- Hydrophilic molecules are polar molecules
- Hydrophobic molecules are non-polar molecules
**note: like attracts like, hydrophilic likes hydrophilic vs. hydrophobic likes hydrophobic

Distinguish DNA from RNA, and explain how these differences relate to their different roles

Nucleobases
- All bases are aromac rings, i.e. sp2 meaning they’re trigonal planar
- Dierent points of the aromac ring can be hydrogen bond donors or hydrogen bond acceptors.

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- hydrophilic = polar and hydrophobic = non-polar molecule

- The base pairs complement each other to make the strongest possible combinaon
- T/A = 2x H-bonds between (makes the major groove)
- G/C = 3x H-bonds between therefore ghter (makes the minor groove)

Absorbance

Melng DNA
- Can go from double stranded to single stranded
- Increasing G/C content =  melng point of DNA because of  h-bonds present

Double helix structure of DNA

- DNA is a right-handed double helix  i.e. walking up the stairs and the handrail
is on the RHS, turning with your le shoulder (Chris visual)
- Because the sugar is chiral (has a stereogenic centre and is non-superimposable)
- The two strands are anparallel, meaning when aened out, they
read opposite each other back to front i.e. 5’ 3’ vs. 3’  5’
- Bases are all at and stack on top of each other via π-bonds
between the aromac rings
- Negave phosphates repel each other
- Has major grooves (wide groove) and minor grooves (narrow
grooves)
hps://www.youtube.com/watch?v=o_-6JXLYS-k
- Helix structure is due to negave charge on phosphate  repel causes
pushing away
- Major groove and minor groove is due to the amount of h-bonds between the bases, i.e. G/C = 4
but A/T = 3

About RNA

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- DNA = deoxyribonucleic acid vs. RNA = ribonucleic acid

- RNA nucleodes have uracil base instead of thymine
- RNA has ribose sugar instead of deoxyribose sugar
stops it from forming ß – DNA helixes  how the
fuck
- i.e. note how the sugar is H – H for DNA vs H – OH for
RNA
- OH group on ribose stops the double helix structure
from forming because of the polarity (disrupts the neat arrangement)  is more suscepble to
degradaon

DNA vs RNA
- uracil vs. thymine
- cytosine in both RNA and DNA has tendency to lose amine group on base. The loss of amine group
is called deaminaon. This inuences the transcripon of DNA
- DNA is not prone to degradation; cells can repair cytosine’s loss of amine. RNA
doesn’t recover from degradation because the rate of RNA synthesis is rapid.

PROTEINS
Identify the major features of proteins – peptide bond, amino and carboxyl terminals,
side chains, alpha carbon
Introduction to proteins
- Proteins = chains of 50+ amino acids
- They determine the structure (shape), receptors, hormones, growth factors,
toxins, transporters and antibodies
- Amino acids = amine group + carboxylic
acid

Alpha amino acid (building block)

- The alpha amino acid is the ionic form (has a
charge) that predominates at physiological
pH (pH = 7)
- recall that amino acid = amine + carboxylic acid… + R (side chain).
- The alpha carbon is the one that “holds” everything
together

pH and ionization
- pH refers to the concentration of hydrogen ions
H+ ¿
H 3 O+¿
where ¿
pH =log ¿
- pure water has a pH = 7, where [H+]= 10-7M
- acids decrease pH by adding more H+ ions
- bases increase pH
- most organisms maintain a pH in a narrow range for optimal function through
buers (resist changes in pH)
- Recall that amino acids are able to be ionized (charged)

Peptide bond

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- Polypeptides form through condensation polymerization

- Not a spontaneous reaction
- This is formed when the amino group of one AA condenses with the carboxyl
group of another amino acid.
- Note: the amino acid has resonance structure

Polypeptide backbone
- At neutral pH  positive charge at N-terminus + the C-terminus has negative
charge

-
Predict some chemical properties of amino acid side chains (solubility
hydrophobic/hydrophilic, polarity charge), given their chemical strucutres
Types of side chains + charge
- Methyl = CH3
- Aromatic = non –polar therefore hydrophobic
- Polar = alcohol (-OH), thiol (-SH), amide (O=NH2)
- Acidic =
- Basic = amines

Describe the dierences between primary, secondary,

tertiary and quarternary structure of proteins.

Primary
- This is the sequence of AA that make up the chain
- N-terminus is wrien as the le-hand end of the sequence
and the C-terminus the right hand end.
o N-terminus = start of a protein or polypepde referring to the free amine group (-NH2).
o C-terminus = end of a protein or polypepde terminated by a free carboxyl group (-COOH).

Secondary
- Amide groups can form H-bonds. If these bonds are intramolecular, it forms
the α-helix but if they’re intermolecular (within itself) it forms the β- sheet

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- α-helix
 always RHS helix
 side chains point outwards
- β- sheet = made of mulple β - strands ed together
 side chains point inwards (towards itself)

- the direction of the side chain explains how tertiary structures are formed (via
hydrogen bonding)

Tertiary
- Tertiary amino acids are held together by; hydrogen bonds, ionic interactions,
hydrophobic interactions
- Hydrogen bonding occurs between; peptide groups, bases, side chains (a lot of
points of contact). How? Hydrophobic things don’t like solvents so they like to
clump together internally.
- Ionic attraction: between charges + lone pairs
- Note: hydrophobic interactions between carbon chains inuences the folding
eect of protein
- Disulde bonds: covalent bond between AA in pepdes and proteins  due to thiol found in side-
chain of cysteine.
o DS bonds covalently link 2 polypepde chains, or form a loop in a single chain
o 1x cysteine = free cysteines
o 2x cycsteine = disulde

Quanternary
- dierent proteins can
clump together
- e.g. haemoglobin = 4 polypeptide chains (proteins) each with a central heme
group, thus totalling 4 heme groups.

Demonstrate how 3D protein structure is related to

function using the example of the alpha helix in DNA
binding proteins
“Denaturing”
- most macromolecules e.g. proteins and nucleic
acids are unstable outside a narrow range of
temperature
- this is because proteins can be hydrolysed
(broken down to make a by-product of water) into

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their constituent amino acids. This occurs in very acidic or very basic conditions,
therefore they have both a narrow range of temperature + pH.
- Hence, proteins could unfold and lose their 3D structure. E.g. cooking an egg
permanently unfolds it.

Alpha helix in DNA

binding proteins

Explain the dierence

between the thermodynamic and kinetic properties of a reaction
Thermodynamics (internal energy)
- A reaction such as substrate (S)  product (P)
- If the reaction is favorable the product is more
stable  exothermic
- If the reactions is unfavorable, the product is less
stable  endothermic

Kinetics (how reactions occur)

- For a reaction to occur, they need to get over an
energy barrier
- Enzymes are biological catalysts that lower the energy barrier
- Note: enzymes DO NOT change the thermodynamics (energy required/exerted)
but DO change the rate of reaction

About standard state

-

ENZYMES
Explain how enzymes act as catalysts and including what eect they have on reaction
rates and nal concentrations of substrates and products of a reaction
About enzymes
- End is “-ase”, e.g. lipase
- Specic in function and are made of proteins
 Some RNA are enzymes
- they’re highly varied in function, size, need for co-factors, ability to be
regulated
- Enzymes form pathways for all of their functions, including metabolism,
synthesis of cellular materials, communication (signaling) etc. I.e. multiple
enzymes for a single process to produce a form a nal product
- Mutations of enzymes can reduce their activity causing them to make the
“incorrect” product. This is a primary cause of metabolic diseases.
- Location:

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 They can be found inside or outside the cell e.g. lysozyme or outside the cell
e.g. human lactate dehydrogenase.

- Summary, enzymes:
 Increase the rate of reaction but don’t get absorbed in the reaction (they’re
recyclable)
 Can be organized into pathways, localized in certain organelles
 Can be inside or outside the cell

Diagrams
- Induced t model shows how enzymes change shape and conformation as it
binds to substrates and stabilizes the transition state. Youtube video reference
to show how enzymes “ip”. Enzyme will change conformation a little to better
t the substrate. Once the reaction occurs, the product doesn’t t the enzyme
anymore and is released

Measuring the rate of reaction

- Note:
 If say we had one reaction running with 2x more enzymes (blue) vs. a
reaction with 1x enzymes (red) initially the blue would produce more but
over time, both reactions would produce the same amount of
product.
 Why? Because initially more enzymes decrease the activation energy, but the
amount of substrate available to both reactions is constant.

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DNA REPLICATION
DNA/RNA polymerases

- “ase” = enzymes +polymer = what is being made. Therefore DNA/RNA shows

they’re going to make either RNA or DNA

Process of DNA polyerisation

1. DNA template is available
2. Starting from the 5’ end, nucleotide triphosphates are used as substrates but
monophosphates are added to the 3’OH end of the newly synthesized end
3. Phosphatediester bonds are made between nucleotides
4. Pyrophosphates (P-P) are released.
5. Pyrophosphate bond breaks to release energy to promote the repetition of the
process
6. Repeat until it reaches the 5’ end of the template.

Appreciate how enzymes can be used experimentally (in combination with the labs),
and how they combine to form enzymatic pathways that are important for living
organisms

Describe the similarities and dierences between DNA and RNA polymerases.
Describe the main properties of polymerization of information containing biopolymers

DNA polymerase RNA polymerase

Need a primer (short piece of Don’t need primer to start

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nucleic acid complementary to the

template) to start Can’t proof read as well as DNA
and cant destroy them either
Proof read to make sure the right (exonuclease)
copy is made, has potential to
“chew” up incorrect parts of the Use ribonucleotide triphosphates
enzyme as substrate (NTPs: ATP, GTP, CTP,
UTP)
Use deoxynucleotide triphosphates
as substrate (dNTPS: dATP, dGTP,
dGTP, dTTP)

- Base pairing of nucleotides

About promcriptase
- DNA polymerases which make DNA from RNA

Outline the general mechanism for copying DNA to DNA before cell division –
replication. List the unique problems associated with the replication and describe the
strategies used by the cell to overcome these
Watson and Crick established the following:
1. The double stranded helix must be unwound to make a
template
- Pulling helical strands apart causes supercoiling
(twists in the strand)
- Topoisomerase enzymes cut strands apart, which allow it to
unwind and stick back together.

2. It must be semi-conservative.
- First generation (parent) contains two heavy strands
- Daughter from second generation thus has one heavy strand from parent + light
replications strand
- One daughter from the third generation will have one heavy + one light strand
and the other will have two light strands. See image w/ colour reference.

Biopolymer synthesis
Made up of three stages:
- Initiation (start) at ORI site (origin)
- Chain elongation (build)
- Termination (nish)

DNA replication (general). E.g. bacteria

1. Replication
- Starting from the ORI, replication travels in both
directions (5’ to 3’ w.r.t. new strand) based o
each parent strand. By the end of the circuit, the
two transcriptors “run into each other” and stop
replication
- The ORI site has to be A/T base pairing rich
because it has less hydrogen bonds, making it
easier to pull apart.
- Helicase, a multicellular subunit wraps itself
around the DNA to unwind it/unzips

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- Topoisomerase stops supercoiling

- Single stranded binding protein prevent the DNA from reforming again

2. Primase
- Makes RNA primer that initiates replication
- DNA polymerase III forms to make a new
strand of DNA
- DNA polymerase I removes the RNA primer and
replaces it with DNA
- DNA ligase joins the very last gap of the DNA
pieces together

Leading vs lagging strands

When helicase unwinds the DNA, it produces a leading strand (top) and lagging strand
(bottom)

Leading (top strand) Lagging (bottom strand)

Primase makes RNA primer at the Because it’s travelling in the
very beginning opposite direction, primase makes
 multiple RNA primers along the
DNA polymerase III makes a DNA template until it rungs into the
copy of the strand in the 5’  3’ next primer.
direction (continuous copying)
It’s made in sections called
Okozaki fragments

DNA polymerase I replaces the

RNA primer with the DNA

DNA ligase joins the pieces of DNA

Summary
- Helicase
- Topoisomerase
- RNA primer initiates replication
- DNA polymerase III adds to new DNA
- DNA polymerase I removes primer to replace w/
DNA
- DNA ligase joins gaps

Eukaryotic replication

mRNA SYNTHESIS
Outline the general mechanism for copying DNA to RNA – transcription. List the
problems associated with transcription and describe the strategies used by the cell to
overcome these
Transcription
- Making RNA copy of DNA to synthesise polypeptides
- Transcription factor(s) bind at the 35 base pair < promoter region < 10 base
pairs region
- Note, this region is has lots of A/T pairs (lesser amounts of hydrogen bonds)

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- RNA polymerase binds at the transcription factor(s). These are proteins that
recognize base sequencing
- Transcription factor “melts” DNA to lodge RNA polymerase between the strands
- Transcription bubble forms and moves along to open and copy the DNA
- Copying continues until the RNA polymerase forms a G/C sequence (v. stable)
followed by A/T rich sequence
- This causes RNA to dissociate from DNA template
- RNA polymerase then leaves DNA template  transcription bubble gone

- Alternatively, Rho protein binds to G/C rich signal in to wedge itself between
RNA and DNA

Challenges
1. No stop/start point
- RNA polymerase binds to the promoter on DNA, which is just past the 5’ end of
new strand (signies start point)
- Uses the 3’ strand to get a 5’ start
- See above on how it stops transcribing

2. Gene expression regulation

- Some sections are transcribed multiple times but others aren’t
- Alter promotor strength
- Repression molecules  binds to the promoter region where RNA binds.
Ultimately stops RNA from contacting DNA. Small molecule can bind to
repression molecules to undo it
- Accelerators  at a weak promotor site, transcriptional activator binds to
protein
-
3. Only small sections of the genome need to be transcribed
- These sections need to be transcribed multiple times
- Some sections are rarely copied in one cell but copied many times in another
cell

Compare and contrast replication and transcription in bacteria and eukaryotes

considering the delity of the molecules generated and complexity

PROTEIN SYNTHESIS
Explain the unique problems associated with converting the information as nucleic
acid sequence to an amino acid sequence. Describe how these issues are overcome,
with reference to the universality and redundancy of the genetic code.
Protein synthesis/translation (introduction)
- When RNA is used to make polypeptides
- Messenger RNA (mRNA): contains template for protein synthesis/information
about amino acids  needed to know what amino acids to add in what order
- Transfer RNA (tRNA): carries amino acid to mRNA via matching of anticodon to
codon
- Ribosomal RNA (rRNA): moves along mRNA to combine assemble amino acids
into proteins via c peptide bond formation

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- 4 RNA bases makes a code for 20 amino acids

https://www.youtube.com/watch?v=gG7uCskUOrA

Challenges for protein synthesis

1. Need to convert sequence of nucleotides to sequence of amino acids
2. Need to be in the correct order  gives this structure and function
3. Peptide bond formation is thermodynamically unfavorable (non-spontaneous)

Possible codes
- Singlet: four dierent bases (A,T, G, C)
- Doublet: 16 possible pairs (AT, GC, GA, etc…)
- Triplet: 64 possible pairs (AUG, GUC, CCG)
- Codes are read as a unit, each code makes one amino acid
- Combination of three bases that code for an amino acid = codon (or
triplet codon)
- On the mRNA codon sequence is read from the 5’ to 3’ end
- Condon will have same sequence of DNA strand that WASN’T copied, i.e. the
opposite of the template, except with U instead of T
- Some codons are STOP codons  signals protein synthesis to stop
- AUG = Metyamine is a start codon

Reading codons

- Type 1: split up codons by threes and nd which amino acid they make

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- Type 2: start from the second base and continue… it has a stop codon to begin
with? We can observe that in this frame, there’s and AUG code which is the
START codon. That means protein synthesis only begins here but discounts the
previous codons.
- Type 3: codes something completely dierent.

Therefore: the start codon makes the reading frame

About genetic codes
- Genetic codes are degenerate (break down) and universal. Which means that
genes from one organism can be expressed in another organism, i.e.
biotechnology, genetically modied food, medicine etc.

Mutations
- Silent mutation: incorrect base is part of the reading frame BUT coincidently, the
new codon codes for the same amino acid
- If AUG is changed  protein isn’t synthesised
- if one base is changed: framework is shifted  dierent protein is made
- Amino acid mutation  gives dierent amino acid

Translation
- Cells automatically start at AUG = Met because of tRNA
- One end of tRNA gets bound to an amino acid (needs to deliver)
- Other end of tRNA contains ANTICODON  opposite to what we need so that it
binds the the codon of the mRNA
- What attaches tRNA to an amino acid?
 Via enzyme called aminoacyl-tRNA synthases
 Unique for each tRNA amino acid combination
 Catalyse the activation/attachment of amino acids
onto tRNA via ATP hydrolysis to make a high-energy
bond between tRNA and the amino acid
 Is able to do this because it recognizes the anticodon
and other parts of the tRNA

Specically,
 Amino acid and ATP enter the active site on the enzyme
 AMP is joined to the amino acid  releases pyrophosphate
 AMP is displaced by tRNA  creates amino acetyl tRNA
 Amino acetyl tRNA is released from the enzyme

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Ribosomes
- enzymes made of RNA and protein
- “protein chain factory”
- Locks mRNA on the bottom
- tRNA comes to acceptor site on RHS where anticodon matches with codon
- the tRNA moves along to the polypeptide synthesis site on LHS is where amino
acids are added together
- Note: polypeptides are connected from the N to the C terminus (think chemistry
 hydrolysis reaction)
- SBS of protein chains:

 Initiation: start codon at AUG = Met.

o Small subunit (lower half) binds to mRNA and tRNA
o Large subunit of ribosome (upper half) binds
 Elongation
o Second tRNA is added via anticodon
o Amino acids are placed next to each other
o Peptidyl transferase catalyzes peptide bond formation from stored aa-
tRNA bond  throws over Met to
second amino acid
o First tRNA is released and the
ribosome moves along the mRNA to
continue the process
 Termination
o When the ribosome hits the STOP
codon, tRNA is not pulled in
o Protein factor binds and release factor
binds
o The peptidyl transferase adds water instead of an amino acid, which
releases the polypeptide chain from the ribosome (hydrolysis)

Dierence between prokaryotic and eukaryotic translation

Prokaryotic (bacteria) Eukaryotic (humans)

- Transcription/translation linked in - Transcription occurs in nucleus
bacteria, i.e. protein synthesis is - mRNA is processed and moves to
instant cytoplasm
- Ribosomes are dierent sizes - can control gene expression
- Dierent protein factors

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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.

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