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Chemistry – Autumn Term
Atomic Structure
Atom – made of subatomic particles – proton, neutron and electron
AMU – weight of one proton, 6x1023 AMU = 1g
Valence – the number of bonds an atom can make
Cells
Cell – mostly water, contains inorganic ions – Na, K, Ca, most cell molecules C based, 4 families of
organic molecules in cell – sugars, fatty acids, AA’s (proteins) and nucleotides
Cell Doctrine (Theory) - all living things made of cells, cells are the basic structural/functional unit in
all living things, cells come from pre-existing cells (cannot come from nothing), all cells chemically
similar and all cells carry hereditary material (DNA)
Central Dogma of Biology – DNA TranscriptionRNATranslationProtein
Cell Origin – evolved from same ancestor (3
...
Function – aerobic, anaerobic,
photo/chemotrophic, Heterotrophic
Cells are specialised and differentiated into different cell types to divide up labour
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Phospholipid – fat derivative, 1 fatty acid replaced by phosphate group and a N containing molecule,
amphiphilic, chemical properties mean they form phospholipid bilayer, phosphate head –
hydrophilic, fatty acid tail – hydrophobic
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Microtubule –repeated heterodimers of alpha and beta tubulin  protofilaments (chains of tubulin)
 join to form microtubules
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DNA – made of nucleotides – basic repeating unit of DNA (Deoxyribose Nucleic Acid), nucleotides
made of phosphate group (x3 ATP (Triphosphate)very energetic)
Purines – Benzene and pentose (A,G), Pyramidines – Benzene only (C,T,U)
Deoxyribose – has one O less (a deoxyribose) H on one side not OH

Ribose – has no deoxyribose (OH on both sides)
Proteins – made of AA’s – AA + AA  Protein (joined by peptide bond) + H2O – AA = NH2-CRH-COOH
Mole – Used due to huge no of atoms in reaction, amount of pure substance that contains as many
particles as there are in 12g of C12
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02x1023 atoms, mass of 1 mole of substance = RAM
relative atomic mass
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Moles = mass/molar mass
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Down – groups
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Covalent compound – shares 1 or more e between the atoms forming a covalent bond
Ionic – atoms gain/lose e to form ions, oppositely charged ions are strongly attracted to each other,
groups 1 and 2 – want to lose 1 or 2 e
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Electronegitivity – determines bond type and indicates how strongly an atom attracts e – 2 non
metals (covalent) 1 non, 1 metal (ionic)
Carbon – valence of 4, 4 covalent bonds with 4 atoms = full outer shell, can form
double/triple/chains/rings
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Organic Compounds - simple frame gives structure + stability, functional groups give different
functions, simplest are hydrocarbons – C + H
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AA + protein – H,C,O,N
More proteins – H,C,O,N,S
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some proteins – Fe, Cu, Mg
Hydrocarbons – Aromatic or Aliphatic (everything else)
Molecular formula – indicates number of atoms present in one molecule of given compound
Structural formula – indicates how different atoms arranged in molecule
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E
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dichloromethane
Alkenes - unsaturated – double bonds (more H can be added)
Cis – groups on same side of C=C, Trans – groups on opposite side of C=C
Hydrogenation – used to increase saturation oilmarg
Halogenation – used to determine no of C=C in fat/oil – no of g of I reactied with 100g of fat = I no
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Ethene + ethene  polyethene
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OH is polar = short chain alcohols are
water soluble
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t
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Organic Acids – formed by oxidation of aldehyde – weak acids  dissociate carboxylate ion and H+
In liver alcohol oxidises to ethanol which oxidises to ethanoic acid
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Fatty acid + alkali  soap
Esters - formed by condensation reaction of carboxylic acid/alcohol, RCOOR, fruity smell – artificial
perfume, industrial solvent (making cellulose/paint/varnish), artificial flavourings in sweets
Organonitrogen compounds – amines (akyl group+amine = name) 2 akyl groups = 2nday amine,
synth of dyes, fibres, medicine, present in AA’s with carboxylic acid
Stereochemistry – 3D structure of a molecule, determines biological activity + function, minor
differences = vastly different properties
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Chiral/stereogenic centre – 4 diff groups attached to tetrahedral C atom, large
organic compounds may have 100s of chiral centres
D and L convention - config related to L-glyceraldehyde, L sterioisomers, D-glyceraldehyde are D
stereoisomers
R and S convention – Highest atomic mass – highest priority, if 2 atoms on chiral centre same –
priority based on atoms bonded to those atoms, if R – decreasing priority of groups clockwise, if S –
decreasing priority of groups anticlockwise
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Acid + metal  salt + water (if metal carbonate CO2 too)
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g
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Biological buffers (bicarbonate,
proteins, orthophosphate)
Ionisation of water – water molecules undergo reversible ionisation to make H+ and OH- - degree of
ionisation small at equilibrium
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8x10-16
So Ionic product of water always 1
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Water - =70% our mass, all biological reactions occur in (aq) medium, cell physiology is adapted to
physical and chemical properties of water, water is a polar solvent, it dissolves most charge
molecules, dissociates when acting as an acid – donates a proton
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Carbohydrates – C compounds, contain hydroxyl groups, CH2O – hydrated O
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Not enough O anaerobic little ATP + lactic acid (both start with glycolysis)
Glycolysis – initial stage of glucose oxidation, anaerobic process (no O needed), releases 2 ATP and
pyruvate – starting compound for further metabolic pathways, ubiquitous – take part in all living
cells, catalysed by enzymes in cell cytosol, emergency energy – needs no O
GlucosePyruvate (Glycolysis) – 10steps, 10 enzymes, 2 ATP used, 4 Produced, prepatory and pay
off phases
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Pay Off Phase – last 5 steps, forms 4 ATP + 2 NADH + Pyruvate
5 enzymes – Glyceraldehyde – 3 – phosphate dehydrogenase, phoshoglycerate kinase (2 ATP pro),
Phosphoglycerate mutase, enolase, pyruvate kinase (2 ATP out)

Pyruvate - central metabolic branch point, start material for many reactions, can be reduced to
ethanol or lactate, or oxidised further to acetyl CoA (depends on tissue and O availability)A (depends
on tissue and O availability)
Glycolysis summary – Glucose + 2NAD+ + 2ADP + 2Pi  2 pyruvate + 2NADH + 2 ATP + 2water + 2H+
Each 6 glucose – makes 2x 3C pyruvate, 2 ATP in step 1+3, 4 ATP out 2x Step 7+10, 2 NAD+ reduced
to 2NADH step 6
Pyruvate aerobic – loses CO2 linked to coenzyme Aacetyl coenzyme A
Pyruvate anaerobic – reduced to lactate, in organisms capable of fermentation loses CO2
aldehydereduced to ethanol, occurs when O limiting factor, produces little ATP quick, 
limited capacity – release 5% of ATP that could be released + lactic acid fatigue
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Occurs with O in mitochondria, products of CHO (fat and protein) hydrolysed to CO2 and water
Enzymes in matrix, process occurs in matrix, energy release, ATP formed
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e transferred to O, energy trapped by ATP, Krebs cycle – intermediates not consumed –
are regenerated
Amphibolic cycle, uses anaplerotic reactions to replenish intermediates
e transport chain – flow of e along IMM generates ATP, H+ transport also occurs across membrane
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O is reduced to water, energy from reactions pumps H+ across membrane into Inter membrane
space, H+ can then flow back into matrix via ATP synthase – leads to biosynth of ATP
Eat carbs Amylase breaks downmetabolised into glucoseinsulin in blood notices
glucoseglucose circulates + feeds body cells because blood+insulin takes glucose into cell
Edvard Buchner – 1897 – CO2 bubbles from sucrose and cell free yeast extract – confirmed Louis
Pasteurs observation that yeast ferments sugars to alcohol, thought no intact cells needed
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Regeneration of NAD+ - occurs during anaerobic conditons – Pyruvic AcidLactic acid (NADH + H+
 NAD+) catalysed by lactic dehydrogenase
Lipids – 1 of 4 macronutrients (carbs, prot, alcho, lipids) include oils, fats, waxes, other related
compounds – they are all soluble in organic solvents, usually unsoluble in water, behave similarly –
float on water
Structure – same structural elements as carbs – C,H,O – different proportions (more H/less O)
Classification – simple lipids – neutral fats(triglycerides/triacylglycerols (TG, TAGS)) and waxes
(beeswax)
Triglycerides – 90-95% of dietary fat requirement – most fat in body, major energy store + intake,
structure – 3 fatty acids linked to 3 carbon glycerol
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Fatty Acids – consists of long C backbone/chain of C with H or O attached, differ in chain
length/degree of saturation (no of C=C), position/geometry of C=C
Lipoproteins – spherical particles – lipid core, surrounded by hydrophilic layer of phospholipids,
proteins embedded in outer membranes
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g
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Acetyl CoA + oxaloacetate condensation to citrate
Intermediates covalently linked to acyl carrier protein
4 step repeating cycle – condensation, reduction, dehydration, reduction
7 enzyme complex – Acyl carrier protein (ACP)
1st step – Acetyl CoA carboxylated + CO2 (catalysed by Acetyl CoA carboxylase)  malonyl CoA
Malonyl CoA (attached to ACP) condenses with Acetyl CoA
Acetyl CoA formed still attached to ACP, Acetyl CoA reduced by NADPH to form Beta – 3hydroxybutyrl – ACP, reduced again to form Butyrl – ACP – 4C fatty acid, undergo 6 more elongation
cycles with 2C at a time till 16C long fatty acid Palmitoyl-CoA, can be further elongated/reduced to
introduce C=C
Fatty Acid Synthase – FAS – polypeptide chain with multiple domains – need distinct enzyme
activities for fatty acid biosynthesis
ACP – CoA is used as activator for beta oxidation, fatty acid synth activator is used as acyl carrier
protein (ACP) – part of FAS complex
Condensing Enzyme – also part of FAS – CE has cysteine SH that participats in thioester linkage with
carboxylate group of the fatty acid
During fatty acid synth growing fatty acid chain alternates between K-SH and ACP – SH
Fatty acid synthase – peptide with multiple enzyme domains
Triglyceride synth – glycerol backbone, glycerol activated by addition of phosphate or formed from
reduction of dihydroxacetone, Fatty acyl – CoA attached to glycerol backbone via Fatty Acyl
Transferase
Fat + energy - primary fatty acid sources – diet, mobilisation from cellular stores in adipocytes +
muscle cells
Triglycerides – major energy storage in cells
Enzymes cleave fatty acids of glycerol backbone –
lipolysis – fatty acids can then be oxidised
Adipose tissue – fatty acids are released from triglycerides – these are stored in adipose tissue (fat)
by HSL action (hormone sensitive lipase) HSL activated by adrenaline, nonadrenaline, cortisol,
glucagon, inactivated by insulin
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Converted to succinyl CoA (uses ATP), succinyl – CoA can enter Krebs for furher oxidation
Lipid Oxidation – oxidation of fatty acids yields more energy per C than carbohydrate oxidation – 1
mole of deic acid 146 moles of ATP

Beta Oxidation occurs through sequential removal of 2 C units by oxidation at beta carbon position
(COOH end) of fatty acyl molecule (+FFA) CoASH, fatty acyl CoA into matrix, oxidise fatty acyl –CoA
to Acetyl CoA
...
H bonds form between NH and C=O if
polypeptide backbone
Alpha Helix – can join with others to form Myoglobin
Beta Pleated Sheet – formed when H bond forms between 2 polypeptide chains – formed with a
parallel and anti-parallel strand
Tertiary Structure – folding of polypeptide into final 3D shape its subunit/domain, determined first
by primary structure then R groups on AA, determines protein function – electric charges are
distributed over molecule, shape + charge distribution determines how the protein interacts with
other molecules, shape = purpose
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g
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E
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hormone receptors – are transmembrane proteins, hormone binds to outside, enzymic portion
activated on inside
e
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keratin – forms long fibrous sheets composed of parallel protein strands, hydrophobic
Quaternary structure – domains of tertiary structure assemble e
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haemoglobin
8 Essential AA’s - cannot be synthed by organism from nothing – need to be obtained from diet
Non Essential AA’s – can be synthed by humans
Protein sources - meat, poultry, fish, shellfish, eggs, pulses, nuts, seeds
Protein digestion – in gastrointestinal tract, needed as proteins cannot be absorbed from GI tract
(neonates – babies, can absorb immunoglobin from milk)
Digested by GI tract enzymes into constituent AA’s – stomach – pepsin, pancreas – trypsin,
chymotrypsin, carboxypeptidases (cleaves protein at carboxy end)
AA’s - go into citric acid cycle, can be made into variety of biological molecules – protein synth and
oxidisation of AA carbons for energy post amino group removal
Non essential – all except tyrosine synthd from intermediates of the major metabolic pathways, C
skeleteons of NEAA correspond to alpha ketoacids
Ketoacid – organic compound with ketone + carboxylic acid
Glutamate synth – AA’s synthed from ketoacid, by reductive amination – reduction + oxidation 
amination
Alpha ketoglutarate + NH4+  glutamate (glutamate dehydrogenase catalyst)
Oxidation reaction – NADPH + H+  NADP+ - NADPH – coenzyme for this reaction (NADH can be
used)
Synth is in equilibrium - provides correct AA conc where needed
Coenzyme – organic compound, becomes essential component of the active site of certain enzymes,
act as group transfer reagents e
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H or large chemical groups
Required by apoenzymes (inactive enzymes) to convert to holoenzymes (active enzymes)
e
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NAD(P) involved in redox reactions – assist in e transfer from metabolites, oxidised to form
NAD+ and NADP+ - e deficient, reduced form NADH, NADPH – carry extra e pair, act as cosubstrate
for dehydrogenases, proton (H+) released from alpha ketoglutarate
Transamination – formation of an AA, enzyme involved – aminotransferase or transaminase, enzyme
transfer amino group from glutamate to keto acid glutamate is deaminated
Alpha keto acid + glutamate AA + alpha ketoglutarate
Transamination reaction – Amino group transferred from AA to alpha C of ketoacid, uses
aminotransferase or transaminase
Transaminases – catalyse reactions that are close to equilibrium
in biological system – direction of reaction depends on – substrate supply, product removal speed
Asparate aminotransferase – pyridoxal phosphate dependant enzyme, co enzyme comes from
vitamin B, important for group transfer to and from AA’s
Asparagine synthesis
Oxaloacetate (transaminase) glutamate changed to alpha ketoglutarate  aspartate
 Glutamine changed to glutamate, (asparagine synthetase)  asparagine
Enzymes – class of protein, act as catalyst for biochemical reactions (no permanent change), increase
Ror (every bodily reaction uses enzymes – too slow without), can work very fast (1 catalase breaks
down 5
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g
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g
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g
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g
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g
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8, Taq polymerase (PCR) at 72C
pH – each enzyme has characteristic optimum pH, dependant on active site AA’s, dependant on H
bonds required for 3D structure
Temp increase – causes increase in rate of reaction therefore rate of catalysis increases, too high –
denaturation of enzymes – shape change  loss of activity
Cofactors – catalytic activity of many enzymes depends on presence of cofactors, helper molecules –
assist in biochemical transformations, can be organic (small molecules), non organic (metals),
classified on how tightly they bind to an enzyme
Coenzymes – loosely bound, prosthetic groups – tightly bound
Coenzymes – small non protein molecules that catalyse reactions e
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e transfer, formation/breaking
of covalent bond, group transfer
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g
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g
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g
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g
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g
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, does not change
max rate of enzyme reaction (vmax) e
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allopurinol of xanthine oxidase
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g
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g
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1 x vol 1 = conc
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gradient, Chemical work – causes
reaction of glutamic acid + ammonia  glutamine
BUT – fat produces more energy than glucose
Glycolysis – break down of glucose into pyruvate
Gluconeogenesis – reformation of glucose for storage in liver/kidney
Glycolysis + gluconeogenesis need to keep energy balanced in the body
Glucose – metabolised into CO2, H2O and synthesises up to 32 ATP molecules, principle energy
source in animals, initial pathway of degeneration in cytoplasm, final steps in mitochondria (most of
ATP generated)
ATP – adenosine triphosphate – ATP + water (hydrolysis)  ADP + Pi + energy
Conversion produces 7
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gradient, membrane electric potential, mitochondria
use energy from sugar + fatty acid metabolism is used to pump protons across the mitochondrial
membrane
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g
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Triglycerides used – primary energy storage inn cells
Oxidative Degredation of AA’s – 2 fates – converted to glucose (Gluconeogenesis) or oxidised to CO2
via TCA
Gluconeogenesis – produces glucose from glucogenic AA’s (lactate + glycerol), keeps blood sugar up,
occurs during fasting (diabetics too), reverse of glycolysis
Atom – nucleus and e, nucleus – small but heavy centre, made of protons + neutrons, common
proportions 1:1 or 1
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Too many N  decay
Decay – several ways – alpha particle, beta particle, gamma ray (high energy photon), neutrons
Alpha – 2 prot + 2 neut, Beta – 1 neutron  1 proton + 1 e emitted,
Gamma – 1 proton converted into 1 Neu + 1 positron emited
Positron + electron annihalation  2 Gamma rays
Neutron – nuclei splits into lighter nuclei, emitting neutrons
Not all nuclear decay emissions occur at once
Radioactive – exhibits radioactivity or caused by radioactivity
Radioactive Decay – process by which unstable atomic nucleus loses energy by emitting ionising
particles + radiation
Isotope – 1 of several element forms – diff no of neutrons therefore diff atomic mass
Radioactive isotopes – common, all elements have at least 1, e
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heavy H – Tritium H3, Carbon 14 –
radioactive carbon dating
Radioactive elements – heavy – uranium, plutonium, radium, lighter radioactive elements found in
rocks
Half Life – amount of time taken for ½ of the atoms in a sample to decay, always the same for a
given isotope
Discovery of radioactivity – Henri Becquerel – 1896, exposed uranium salts to sunlight, during cloudy
weather – no illumination needed, radiation produced that passed through foil+darkens
photographic plate, spontaneous radiation
Term Radioactivity – Pierre and Marie Curie – discovered polonium + radium, work lead to modern
nuclear science, nobel prizes – 1903 phys, 1911 chem, discovered radioactivity is an atomic propery
Units – Curie – 3x1010 radioactive decays per second (Ci), Becquerel = 1 radioactive decay per second
(Bq) 2
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g
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Environmental contamination – external dose from radioactive materials deposited on the
ground, internal dose from inhalation of radioactive materials in the air, external radiation from
cloud, internal dose from eating/drinking radioactive material in food + water
Medicine – cancer radiotheraphy, radiography (Xray), in vivo imaging – computer tomography CT,
positron emission tomography (PET),
Science – radioactive decay – Willard Libby – 1940’s, ratio of C14 to C12, autoradiography – Tritim
T14, atom bomb
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Complementary base pairing – A + T – 2 H bonds, C + G – 3 H bonds (harder to pull apart need higher
temp PCR), explains chargaffs rules, nucleotide sequence of 1 strand dictates sequence in other
strand, specific pairing – mechanism for copying genetic material
Unzipping DNA – base pairing suggests DNA molecules can be copied, unzipping exposes template –
base sequence can be copied – another copy of DNA molecule made on opposite strand
DNA function – Provide template for copying itself during cell division to produce daughter cells,
unzipped DNA + A,C,T,G  new DNA
Provide template for production of proteins in a cell – unzipped DNA + A,C,U,G RNA
DNA replication – always semiconservative – chromosomes in daughter cells contain 1 DNA strand
from parent chromosome + one newly synthed
Always semidiscontinuous – DNA synth continuous on 1 template strand, discontinuous on other
Replication not faithful (done properly) Mutation
RNA – Ribonucleic Acid – ribose not deoxyribose, Uracil not Thymine (both pyrimidines) almost
always single stranded, genetic material of some viruses – HIV, important functions in euk cells
Several types –m messenger, t transfer, r ribosomal, reugulatory
Gene to Phenotype – Phenotype – observable characteristic of an organism e
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blood group, eye
colour, derived from DNA – DNA template for RNAtemplate for proteinprotein determines
phenotype (central dogma of molecular biology)
Organising DNA into chromosomes – 7
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80 nucleotides, Act as carriers of individual
specific AA’s to ribosome, each of 20 AA’s has at least on tRNA specific to that AA (some have
several)
Inititation – small subunit of ribosome binds to AUG start codon, specific intiator tRNA carrying
methionine binds to AUG start codon (always 1st code), large subunit of ribosome binds to complex
so tRNA occupies P site
Elongation – A tRNA with complementary anticodon binds to mRNA – occupies A site on ribosome,
peptide bond forms between 2 AA’s, ribosome moves one codon further along mRNA (translocation)
in 5’3’ direction (from AP), empty tRNA moves from P site to E site, A site empty for next tRNA,
1st now uncharged tRNA released from E site
Termination – ribosome reaches stop codon (UAG, UAA,UGA), polypeptide released from ribosome,
tRNA released from ribosome, ribosomal units dissociate from mRNA
Genetic code – how cells interpret long A,C,G,T residues into 20 AA’s
Triplet code – a 3 nucleotide codon codes for 1 AA, codons are successive and non overlapping,
genetic code is almost universal, is degenerate – some AA’s represented by more than 1 codon,
20AA’s – 64 diff codons
Genome – all DNA in a cell, all DNA on chromosomes, includes genes, intergenic sequences and
repeats, specific – all DNA in an organelle, Eukaryotes – 2-3 genomes (can have) – Nuclear +
mitochondrial (if not specified – nuclear genome)
Genomics – study of genomes, includes large chromosomal segements containing many genes, initial
phase – map + sequence initial set of entire genomes, functional – aims to deduce info about DNA
sequence function, want to know how close to all genes in a genome – and the sequence of proteins
they encode, no longer look at individual genes – examine whole genomes/systems of genes
Human Genome – 22 autosome pairs, 2 pairs of sex chromosomes – XX fem XY male, 3
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30k genes
Human Genome project – US gov project – dept of energy + national health institutes, sequencing
done in uni + research centres in USA, UK, france, Germany, Japan + china

Identified 30K genes in human DNA, determined sequences of 3 Bill bases that make Human DNA,
stored info in databases – develop tools for data analysis, address ethical, legal, social issues from
research
How – 10-20 primary samples from many donors across racial + ethnic groups
Components of genome – 3% - protein codes, 40-50% repetition, rest -?
Loads of DNA in large genomes is non coding, complex genomes 10-30x more DNA than needed to
code for proteins – non coding DNA – gene introns, gene regulatory elements, multiple gene copies
including pseudogenes, interspersed repeats
Areas benefited by project – medicine – improved disease diagnosis, microbial research – new
energy sources/biofuels, DNA forensics – identify crime suspects, Agriculture – more nutritious
produce, Evolution + human migration – studies based on female genetic inheritance, Risk
assessment – reduce likelihood of inheritable mutations
Bioinformatics – application of computer science techniques to the representation and processing of
biological data, needed because genetic material experiments can produce millions of data points,
computers + statistical tools can analyse and understand large volumes of data, links biologists to
computer scientists
History – 1957 – Frederick Sanger – sequenced first protein – Bovine insulin
Decade later – first nucleic acid sequence reported – yeast (tRNA 77 bases)
1965 – Margaret Dayhoff – created 1st bioinformatics database
1972 – Margaret Dayhoff – established first biological database – Protein identification resource,
organise proteins into families + superfamilies based on degree of sequence similarity, idea of
sequence alignment, special tables reflect frequency of changes observed in sequences of a group of
closely related proteins
1979 – First DNA database
1970’s – 1980’s – development of sequence retrival methods
1980’s – prediction of RNA secondary structure
1980’s - 1990’s – prediction of protein secondary + 3D structure, also the FASTA and BLASR methods
of DB search
1990’s – prediction of genes
1990’s-2000 – studies of complete genome sequences
Use of bioinformatics – biological comparisons (evolutionary analysis), how closely/distantly related
are 2 pops, Gene function prediction – how does a gene function/malfunction
Pharmaceutical design + silico testing
How to use bioinformatics – GeneBoy program – demonstrates DNA  RNA transformations,
analyses sequence composition, searches for specific patterns in sequences
Gen Bank – identify target disease – so treatment can be applied/new treatment synthed, must not
disrupt metabolism
Carbohydrates – 1 of 4 major classes of biological molecule, cellulose – most abundant carb (tree
structure), key intermediates in metabolism – sugar, key food source – sugar/flour,
Ribose C5H10O5, glucose C6H12O6, highly oxidised – have approx
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g
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When beta glucose molecules are joined – cellulose formed
Dissacharide Formation – Alpha D glucose + B D glucose Maltose (alpha 1-4 linkage) + water
Condensation reaction, joined by glycosidic bond
Reducing and Non reducing sugars - reducing – sugars that are oxidised by mild oxidising agents as
they reduce the oxidising agent
Non reducing sugars – sugar not oxidised by mild oxidisers
All common monosaccharide’s are reducing sugars, disaccharide sucrose – non reducing, oxidising
agents used to test for sugar – Benedict’s solution, Fehling’s solution, Tollens reagent



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