KHS
CfE Higher Biology Notes
DNA and the Genome
CfE Higher Biology Record of Achievement
Initial target grade:
UNIT 1: DNA and the Genome
Task 2.1
Key Area
1st Attempt
2nd attempt
KU
KU
/24
/
1. The structure of DNA
/5
2. Replication of DNA
/4
3. Control of gene expression
/5
4. Cellular differentiation
/1
5. The structure of the genome
/2
6. Mutations
/2
7. Evolution
/3
8. Genome sequencing
/2
/24
TOTAL
Date unit passed:
UNIT 1 PRELIM (A/B Test)
Signature of Parent/ guardian:
Date:
Comment:
%
WORKING
GRADE
NEW
TARGET
You should have a clear understanding of the following areas of content from NAT 5 Biology:
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Cell division and chromosomes
Base sequence and base pairing of DNA
Function of proteins
Evolution by natural selection
Species
Classification of life
Cell ultrastructure and function
Higher Biology Unit 1: DNA and the Genome
Learning intentions and success criteria
Key Area: 1 The Structure of DNA
Learning Intention:
We are learning to understand the structure of DNA and how it is organised in different types
of cell
Success criteria:
I can…
(a) The structure of DNA
Name the molecules in a DNA nucleotide and identify them in a diagram
Name the type of bond on the backbone of the DNA molecule
Give the names of the 4 DNA bases
Describe the base pairing rule for DNA bases
Describe the role of hydrogen bonds in the DNA structure
State the name of the coiled structure adopted by DNA
Identify the positions of 3’ and 5’ carbons on a DNA nucleotide
Identify the positions of 3’ and 5’ ends on a DNA strand
Describe how 2 strands of DNA align themselves to each other
(b) Organisation of DNA
Identify prokaryotes and eukaryote cells from diagrams
Describe the key similarities and differences between prokaryote and eukaryote
cells
Describe structure of a plasmid and can name the types of cells where they are
found
Describe structure of circular chromosomes and identify the location and types of
cells where they are found
Compare the DNA found in mitochondria and nucleus of eukaryote cells
Describe the DNA in linear chromosomes found in nucleus of eukaryote cells
The Structure of DNA
DNA (deoxyribonucleic acid) is
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found in all living cells
contains the genetic information that controls the cell function
determines the types of proteins that the cell can produce
determines the cell’s genotype and phenotype
DNA is made up of repeating units called nucleotides. Nucleotides are composed of:
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a deoxyribose sugar
a phosphate and
a base
There are 4 types of base:
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adenine (A)
thymine (T)
guanine (G)
cytosine (C)
The diagram above shows how the carbon atoms in the sugar molecule are numbered. These
numbers are used to show which way the nucleotide is facing. (In the diagram below 3’ is read
as “three prime” and 5’ as “five prime”.)
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A always pairs with T
G always pairs with C
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Base pairs are held together by hydrogen bonds
between the complementary bases
The nucleotides are joined from the sugar to the
phosphate on the next nucleotide to form a
sugar-phosphate backbone
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All Trains
Go Choo choo
When they are joined together to form a double helix, one strand runs in the 5’ to 3’ direction
and the other stand runs antiparallel i.e. in the opposite direction.
Discovery of DNA Structure (You do not need to learn the information in this box)
Several scientists contributed to the discovery of the structure of DNA, but Watson and Crick
collated the research and built the first model of DNA.
Timeline:
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Griffiths 1923 – discovered a chemical was passed between bacteria that changed
(transformed) them
Avery et.al. 1944 – discovered that DNA fragments, not protein, passed between
bacteria
Chargaff 1950 – worked out the ratio of A-T and C-G in DNA
Hershey and Chase 1952 – confirmed that DNA is the genetic material
Wilkins & Franklin 1951-2– used x-ray crystallography to discover DNA was a double
helix
Watson & Crick 1953 – discovered the structure of DNA
Meselson and Stahl 1958 – confirmed that DNA replication is semi-conservative
Organisation of DNA in Prokaryotes and Eukaryotes
Prokaryotes
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A bacterium is a prokaryotic cell
It has no distinct nucleus
Its DNA is usually found as a circular
chromosome, with small additional
structures (containing a few genes)
called plasmids
Eukaryotic cells
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Plant and animal cells are
eukaryotic cells
Have a true membrane-bound
nucleus
linear chromosomes found in
the nucleus
The chromosomes are tightly
coiled around associated
proteins like thread around a
cotton reel to prevent the DNA
from becoming tangled
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Eukaryotic cells also possess
mitochondria and they contain small
circular chromosomes
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Chloroplasts also contain circular chromosomes
In yeast (a eukaryotic cell) the
chromosomes in the nucleus are
linear, but they may also possess
circular plasmid
https://www.youtube.com/watch?v=q6PP-C4udkA DNA structure Boseman Science
http://www.cellsalive.com/ Choose ‘Interactive Cell Models’ you have a choice of plant/animal or bacterial.
http://courses.scholar.hw.ac.uk/vle/scholar/
Key Area: 2 Replication of DNA
Learning Intention:
We are learning to understand the process of DNA replication and the use of polymerase
chain reaction (PCR) in the amplification of DNA.
Success criteria:
I can…
(a) Replication of DNA
State 4 things that must be present for DNA replication
Describe the stages in DNA replication
Describe what a primer is and explain its role in DNA replication
Name 2 enzymes in involved in DNA replication
Explain the role of each enzyme in DNA replication
Describe the direction of replication on each DNA strand
Explain why the direction of DNA replication is always in this direction
(b) Polymerase chain reaction (PCR)
Describe the purpose of PCR
Explain how primers are chosen for a particular PCR
Explain what is involved in the ‘thermal cycling’ of PCR
Describe the role of heat tolerant DNA polymerase (e.g. Taq polymerase) in PCR
Describe 3 practical applications of PCR
Replication of DNA
Before cells divide during mitosis, the DNA must be copied (replicated) in order for the new cell
to contain a copy of the genes/ chromosomes. This process is controlled by enzymes.
Requirements for DNA replication
The following must be present in the nucleus for DNA replication to occur:
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DNA to act as a template
primers
free DNA nucleotides (with A,T, C
and G bases)
DNA polymerase enzyme
ligase enzyme
Stages of DNA replication
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DNA unwinds
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Weak hydrogen bonds between the complementary base pairs break
allowing the 2 strands to separate (unzip) to form 2 template strands.
The point where the 2 strands separate is known as a replication fork.
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Replication forks occurs at several locations on a DNA molecule as it allows the
chromosome to be replicated quickly and precisely.
Original DNA strand to act as a
template
Multiple replication forks on a
chromosome
New DNA strand forms alongside
the template
DNA is replicated quickly and
precisely
2 new duplicated DNA molecules
are formed
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Formation of the leading strand:
 A primer (short chain of nucleotides) attaches to 3’ end of the DNA template
If there is no primer, DNA
replication cannot occur.
 Individual complementary nucleotides align with the bases on the template
strand (in order and one at a time) from the 3’ to 5’ end of the template
strand, so the leading strand is formed by continuous replication from its 5’ to
the 3’ end
 DNA polymerase enzyme joins the individual nucleotides together to form the
sugar-phosphate backbone of the new strand
 DNA polymerase can only add nucleotides in one direction, so DNA replication
is continuous on the leading strand, but on the lagging strand it is replicated in
fragments which are then joined by ligase enzyme
http://www.bing.com/videos/search?q=dna+replication+simple+animation&qpvt=DNA+Replication+Simple+animation&FORM=VDRE
#view=detail&mid=EF43A48523D578A32D75EF43A48523D578A32D75
https://www.youtube.com/watch?v=8kK2zwjRV0M
http://courses.scholar.hw.ac.uk/vle/scholar/
https://www.youtube.com/watch?v=FBmO_rmXxIw
Polymerase Chain Reaction (PCR)
PCR is a laboratory technique used to amplify DNA (make many copies) in vitro, which
involves many cycles of heating and cooling the DNA.
[In vitro means ‘in glass’, so it takes place ‘outside the body’ i.e. in laboratory conditions]
Primers are short sequences of DNA that are complementary to the target sequences at
either end of a DNA sequence and so are used to locate the specific sequence of DNA that is
to be amplified (“finding a needle in a haystack”). The stages in the PCR cycle are:
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DNA is heated (to about 90oC) to break the hydrogen bonds between the bases and
separate the strands
DNA is cooled (to about 60oC) to allow the primers to bind to the 3’ end of the target
sequence
Heat-tolerant DNA polymerase adds nucleotides to the 3’ end of the original DNA
strand
Temperature is raised (to over 70oC) to allow replication of the new strands
The cycle of heating and cooling is repeated many times to make many copies of the
desired DNA sequence 1>2>4>6>16 copies, etc.
This process can be carried out using a thermal cycler or water baths
Applications of PCR
PCR can be used in forensics to amplify DNA collected from crime scenes as the samples
(e.g. blood and semen) that are found may only have tiny quantities of DNA in them. It can
then allow individuals to be identified as suspects.
PCR can also be used to amplify DNA for evolutionary studies as it can be used to work out
how closely related species are.
http://learn.genetics.utah.edu/content/labs/pcr/ - virtual PCR lab
https://www.youtube.com/watch?v=7uafUVNkuzg - a very annoying song about PCR
https://www.youtube.com/watch?v=HMC7c2T8fVk PCR animation
http://courses.scholar.hw.ac.uk/vle/scholar/
Key Area: 3 Control of Gene Expression
Learning Intention:
We are learning to understand how genes on DNA are expressed and used to synthesise
proteins
Success criteria:
I can…
(a) Determination of phenotype
Define ‘phenotype’
Explain what determines the phenotype of an organism
Give examples of 2 factors that influence gene expression
Explain why only a fraction of genes in a cell are expressed
State which processes are regulated to control gene expression
(b) Structure and functions of RNA
Name the molecules in a RNA nucleotide and identify them in a diagram
Name the type of bond on the backbone of the RNA molecule
Give the names of the 4 RNA bases
Describe the base pairing rule for RNA bases
Describe 3 differences between RNA and DNA molecules
State what mRNA is and describe its role
Describe the structure of a ribosome
State what tRNA is and describe its role
(c) Transcription of DNA
State the location of transcription
State 4 things that must be present for transcription to occur
Describe the process of transcription
Describe the role of RNA polymerase
Identify introns and exons on a diagram
Explain what introns are
Explain what exons are
Explain the difference between primary and mature RNA transcripts
Describe RNA splicing
(d) Translation of mRNA
State the location of translation
State 4 things that must be present for transcription to occur
Define ‘amino acid’, ‘polypeptide’ and ‘protein’
Describe the process of translation
Describe the structure of tRNA
Describe the function of tRNA
Define ‘codon’
Define ‘anticodon’
Explain how the sequence of bases on mRNA acts as a code for protein synthesis
Describe the complementary pairing of bases between mRNA and tRNA
Explain how codons on mRNA recognise incoming tRNA
Explain the function of ‘start’ and ‘stop’ codons and identify them in a diagram
Name the bond formed between amino acids of a polypeptide
Describe the fate of tRNA as the polypeptide is formed
(e) Expressing different proteins from one gene
Explain the mechanism by which different proteins can be expressed from one gene
Define ‘alternative RNA splicing’
Define ‘post translational modification’
Explain why many different mRNA molecules are produced from the same primary
transcript
Describe 3 post translational protein structure modifications
(f) Protein shape and structure
Describe the overall shape of protein molecules
Describe what can happen to polypeptide chains as they are transformed into
protein
Identify the position and function of peptide bonds and hydrogen bonds in protein
Explain how interactions of amino acids can determine the final shape of a protein
Phenotype
An organism’s phenotype (outward
appearance) is determined by the proteins it
produces. The proteins that can be
produced are determined by the genetic
code (genotype) of the organism.
Only a fraction of the genes an organism
possesses are actually expressed as not all
cells require all proteins e.g. the cells on
the palms of your hands do not produce
keratin (hair); the cells found in heart tissue
do not produce any digestive enzymes like
pepsin or amylase, as they are not required.
Production of Proteins
The genetic code used to make (synthesise) proteins is found in all forms of life. This could
indicate that all organisms have evolved from a common ancestor. (See ‘Evolution’ later on in
notes)
Proteins are produced when genes are expressed in a cell, but this expression of genes can
be influenced by intra- and extra-cellular environmental factors, such as the presence of a
specific hormone, enzyme or other chemical.
Structure of Proteins **See N5 notes on proteins**
Proteins contain carbon (C), hydrogen (H),
oxygen (O) and nitrogen (N) and a small
quantity of sulphur (S).
Proteins are composed of 100s of amino acid
subunits joined together by peptide bonds to
make a polypeptide chain. There are about
20 different types of amino acid, each coded
for by a triplet of bases called a codon (e.g.
AGU). These amino acids are joined in a
specific order which is determined by the
sequence of bases on the original DNA strand.
Hydrogen bonds form between amino acids on different sections of the chain, causing it to
fold in a characteristic way, which determines the final structure and function of the protein
Interactions between individual amino acids may occur on different sections of one folded
polypeptide chain or between multiple polypeptide chains. These interactions may involve
hydrogen bonds or including sulphur bridges and these determine the final 3D shape of the
protein molecule.
Functions of Proteins
Proteins have a large variety of structures and shapes,
resulting in a wide range of functions such as:
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Enzymes (speed up respiration,
photosynthesis,etc.)
Structural proteins (found in the phospholipid
bilayer of plasma membrane)
Hormones (chemical messengers e.g. ADH to control
water balance/ adrenaline/ insulin, etc.)
Antibodies (to immobilise invading bacteria or viruses)
Glycoproteins (made of proteins and carbohydrate
e.g. mucus)
Haemoglobin (made of protein and non-protein
structure containing iron)
Structure of RNA (ribonucleic acid)
There is another type of nucleic acid known as RNA (ribonucleic
acid).
RNA is composed of nucleotides containing ribose sugar:
RNA is single stranded and also contains the bases guanine (G), cytosine (C) and adenine
(A), however in RNA thymine is replaced by uracil (U).
Function of RNA
There are 3 types of RNA:
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mRNA (messenger RNA) carries a copy of the DNA code from the nucleus to the
ribosome
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tRNA or transfer RNA has an attachment
site for a specific amino acid which it then
carries from the cytoplasm to the mRNA at
the ribosome
the tRNA folds due to base pairing
it has a triplet anticodon site for binding to
the codon on the mRNA
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rRNA or ribosomal RNA, together with proteins forms the ribosome
Transcription of DNA into mRNA
In order to synthesise (build) a protein, a copy of the information carried on the DNA (in the
nucleus) must be made and transferred to a ribosome (in the cytoplasm). This is done by a
process known as transcription, using an enzyme called RNA polymerase.
Stages of Transcription
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RNA polymerase attaches to the promoter region of the DNA strand and moves along
the strand unwinding and unzipping the double helix to expose the bases.
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An mRNA strand forms alongside the exposed DNA bases, assembling free RNA
nucleotides into a chain by using complementary base pairing to ensure they are in
the correct order.
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RNA polymerase adds the RNA nucleotides to the 3’ end of the new mRNA strand,
until it reaches the terminator region of the DNA strand. The newly formed mRNA
strand, now known as the primary RNA transcript, detaches from the DNA template.
RNA nucleotides
Modification of Primary Transcript
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The primary mRNA transcript then undergoes RNA splicing to remove introns (the
non-coding regions) and splice (join) together the remaining exons (the coding
regions that will be expressed).
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The modified mRNA strand is now known as the mature RNA transcript
The mature RNA transcript now leaves the nucleus and travels to the cytoplasm where
it attaches to a ribosome
Translation
The mature transcript is now used to place the amino acids in the correct order to form the
protein.
Triplet codons on the mRNA and their complementary anticodons on the tRNA molecules
translate the genetic code (CGAU) into a sequence of amino acids (lys-his-leu).
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The translation of a mature transcript into a polypeptide chain occurs at the ribosome
There are 3 sites in the ribosome as shown in the diagram below:
The middle site (P) holds the tRNA
molecule that carries a specific amino
acid.
The right hand site (A) holds the tRNA
that carries the next amino acid that will
be added to the chain. The growing
chain can be seen leaving the top of the
ribosome.
The left hand site (E) releases the tRNA
from the ribosome once the amino acid
has been added to the strand.
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Before translation can start, a ribosome binds to start codon (AUG) on the 5’ end of the
mRNA and amino acids will be added until it reaches the stop codon (e.g. UAA)
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As the tRNA recognises its complementary sequence on the mRNA, the anticodon on
the tRNA binds to its complementary codon on the mRNA inside the ribosome.
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The amino acids carried by the tRNA molecules are positioned adjacent to one another
and this allows strong peptide bonds to form between these amino acids to make the
polypeptide.
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Amino acids continue to be added until the stop codon is reached.
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The growing polypeptide chain emerges from the ribosome and the now redundant
tRNA molecule is released into the cytoplasm.
Many proteins from one gene
If the primary mRNA transcript undergoes alternative RNA splicing, then several
different proteins can be made using the same gene, depending on which exons are
included in the mature mRNA transcript:
Post-translational Modification
Some proteins are changed or modified after translation by:
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cutting (cleavage) of polypeptide chains e.g. in the production of insulin hormone
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combining polypeptide chains e.g. in haemoglobin
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molecular addition
by adding phosphate to activate or inactivate the protein
OR
by adding carbohydrate to make glycoprotein e.g. mucus
https://www.youtube.com/watch?v=h3b9ArupXZg Bozeman Science Transcription and Translation
https://www.youtube.com/watch?v=itsb2SqR-R0 Crash Course Biology Transcription and Translation
Scholar on-line: Gene Expression
Key Area: 4 Cellular Differentiation
Learning Intention:
We are learning to understand the key ideas regarding cellular differentiation from meristems
and stem cells and the use of stem cells in research and medicine
Success criteria:
I can…
(a) Cellular differentiation
Explain what ‘cellular differentiation’ means
Define ‘meristem’
Define ‘stem cell’
Give 3 examples of specialised plant cells and describe the types of genes that are
expressed in each
Describe the process of differentiation into specialised cells from meristems in plants
Describe the process of differentiation into specialised cells from embryonic and
tissue (adult) in animals
(b) Embryonic and tissue (adult) stem cells
Describe 3 examples of present or future therapeutic uses of stem cells
Describe 3 other areas in which stem cell research can be useful
Describe the main ethical issues relating to the different types of stem cell use
Explain how the use of stems cells is regulated
Topic: 5 The Structure of the Genome
Learning Intention:
We are learning to understand the nature of the genome
Success criteria:
I can…
(a) The structure of the genome
Define ‘genome’
Define ‘gene’
Describe the structure of the genome
Explain the difference between coding and non-coding sequences of DNA
Describe the functions of non-coding sequences
Topic: 6 Mutations
Learning Intention:
We are learning to understand the nature, impact and importance of mutations
Success criteria:
I can…
(a) Mutations
Define ‘mutation’ and describe the effect of one
(b) Single gene mutation
Define ‘single gene mutation’
Name 3 single gene mutations
Describe 3 single gene mutations
Name 3 single-nucleotide substitutions
Explain the difference between missense, nonsense and splice-site mutations
Describe the effects of missense, nonsense and splice-site mutations
Describe 2 possible effects of nucleotide insertions or deletions
(c) Chromosome structure mutations
Define ‘chromosome structure mutation’
Name 4 chromosome structure mutations
Describe 4 chromosome structure mutations
Describe the effects of each of the 4 chromosome structure mutations
(d) The importance of mutation and gene duplication to evolution
Explain the importance of mutation and gene duplication to evolution
(e) Polyploidy
Define ‘polyploidy’
Define ‘whole genome duplication’
Explain the importance of polyploidy in evolution
Explain the importance of polyploidy for human food crops
Topic: 7 Evolution
Learning Intention:
We are learning to understand the key concepts and mechanisms involved in evolution
Success criteria:
I can…
(a) Evolution
Explain what ‘genomic variations’ are
Define ‘evolution’
(b) Gene transfer
Describe how ‘vertical gene transfer’ can take place
Explain why vertical gene transfer can be referred to as inheritance
Describe how ‘horizontal gene transfer’ can take place
Explain the implication for evolution of prokaryotes carrying out horizontal gene
transfer
Describe how viruses and prokaryotes can transfer DNA sequences horizontally into
the genomes of eukaryotes
Explain the significance of viruses and prokaryotes transferring DNA sequences
horizontally into the genomes of eukaryotes
(c) Selection
Define ‘natural selection’
Give 2 examples of natural selection
Define ‘sexual selection’
Give 2 examples of sexual selection
Explain what happens as a result of ‘stabilising selection’
Explain what happens as a result of ‘directional selection’
Explain what happens as a result of ‘disruptive selection’
(d) Genetic drift
Explain what ‘neutral mutations’ are
Explain what the ‘founder effect’ involves
Define ‘genetic drift’
Explain why genetic drift has a greater impact on small populations
(e) Speciation
Define ‘species’
Define ‘speciation’
Explain the role of isolation in speciation
Name 3 types of isolation barriers
Describe the difference between allopatric and sympatric speciation
Give an example of allopatric evolution of a species
Give an example of sympatric evolution of a species
Explain the role of mutation in speciation
Explain the role of selection in speciation
Define ‘hybrid zone’
Explain the significance of hybrid zones
Topic: 8 Genomic sequencing
Learning Intention:
We are learning to understand the importance of genomic sequencing in relation to evidence
for evolution and personal genomics in medicine
Success criteria:
I can…
(a) Genomic sequencing
Define ‘genomic sequencing’
Name 2 methods of genomic sequencing
(b) Evidence of evolution
Explain what ‘phylogenetics’ is and how it can be used as evidence for evolution
Explain what ‘molecular clocks’ are and how they can be used as evidence for
evolution
Explain the term ‘last universal ancestor’
Explain how the evolution of prokaryotes and eukaryotes provides evidence for the
sequence of events in evolution
Describe 2 sources of evidence that can be used to support the sequencing of
events in evolution
Name the 3 domains of cellular life
Describe the evidence for the existence of the 3 domains of cellular life
(c) Comparisons of genomes from different species
Describe the outcome of comparing the genome from different species
Explain what ‘many genes are conserved across different organisms’ means
(d) Personal genomics and health
Describe 2 benefits of using analysis of an individual’s genome in medicine
Describe 2 difficulties with personalised medicine