3.1 Genes
Essential idea: Every living
organism inherits a blueprint
for life from its parents.
Genes and hence genetic information is inherited from parents, but the
combination of genes inherited from parents by each offspring will be
different. In sexual reproduction each parent can only pass on 50% of there
genes as the other 50% comes from the second parent.
By Chris Paine
http://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/5
6538/shaw_family_FULL.jpg
http://publications.nigms.nih.gov/insidethecell/images/ch4_meiosissex.jpg
https://bioknowledgy.weebly.com/
Understandings, Applications and Skills
Statement
3.1.U1
3.1.U2
3.1.U3
3.1.U4
3.1.U5
3.1.U6
3.1.U7
3.1.A1
3.1.A2
3.1.S1
Guidance
A gene is a heritable factor that consists of a length of
DNA and influences a specific characteristic.
A gene occupies a specific position on a chromosome.
The various specific forms of a gene are alleles.
Alleles differ from each other by one or only a few
bases.
Deletions, insertions and frame shift mutations do
New alleles are formed by mutation.
not need to be included.
The genome is the whole of the genetic information of
an organism.
The entire base sequence of human genes was
sequenced in the Human Genome Project.
Students should be able to recall one specific
The causes of sickle cell anemia, including a base
substitution mutation, a change to the base sequence base substitution that causes glutamic acid to be
substituted by valine as the sixth amino acid in the
of mRNA transcribed from it and a change to the
hemoglobin polypeptide.
sequence of a polypeptide in hemoglobin.
The number of genes in a species should not be
Comparison of the number of genes in humans with
referred to as genome size as this term is used
other species.
for the total amount of DNA. At least one plant
and one bacterium should be included in the
comparison and at least one species with more
genes and one with fewer genes than a human.
Use of a database to determine differences in the base The Genbank® database can be used to search
for DNA base sequences. The cytochrome C
sequence of a gene in two species.
gene sequence is available for many different
organisms and is of particular interest because of
its use in reclassifying organisms into three
domains.
3.1.U1 A gene is a heritable factor that consists of a length of DNA and influences a specific characteristic.
AND 3.1.U2 A gene occupies a specific position on a chromosome. AND 3.1.U3 The various specific forms
of a gene are alleles. AND 3.1.U4 Alleles differ from each other by one or only a few bases.
A gene is a heritable factor that controls or influences a specific characteristic,
consisting of a length of DNA occupying a particular position on a chromosome (locus)
http://learn.genetics.utah.edu/content/m
olecules/gene/
3.1.U1 A gene is a heritable factor that consists of a length of DNA and influences a specific characteristic.
AND 3.1.U2 A gene occupies a specific position on a chromosome. AND 3.1.U3 The various specific forms
of a gene are alleles. AND 3.1.U4 Alleles differ from each other by one or only a few bases.
A gene is a heritable factor that controls or influences a specific characteristic,
consisting of a length of DNA occupying a particular position on a chromosome (locus)
http://learn.genetics.utah.edu/content/m
olecules/gene/
3.1.A2 Comparison of the number of genes in humans with other species.
Humans see themselves as being more complex and evolved
than other species. Therefore you might well expect to see a
larger number of genes in humans than in other organisms.
It is not just plants such as the
grapevine that have large
numbers of genes; water fleas
are an animal example of an
organism with more genes
than humans.
Q - When analysing an organisms’ complexity, what other than the count of an organisms’
genes needs to be considered?
https://www.sciencenews.org/sites/default/files/storyone_backstory_2.gif
http://learn.genetics.utah.edu/content/chromosomes/in
tro/
DNA Supercoiling: https://youtu.be/AF2wwMReTf8
3.1.U6 The genome is the whole of the genetic information of an organism. AND 3.1.U7 The entire
base sequence of human genes was sequenced in the Human Genome Project.
http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml
The Human Genome* Project (HGP) was an international
13-year effort, 1990 to 2003. Primary goals were to discover
the complete set of human genes and make them accessible
for further biological study, and determine the complete
sequence of DNA bases in the human genome.
http://www.ncbi.nlm.nih.gov/geno
me/guide/human/
https://www.dnalc.org/view/15477-The-publicHuman-Genome-Project-mapping-the-genomesequencing-and-reassembly-3D-animation-.html
*The genome is the entire genetic material of an
organism. It consists of DNA (or RNA in RNA viruses)
and includes both the genes and the non-coding
sequences.
Nature of Science: Developments in scientific research follow improvements in technology - gene
sequencers are used for the sequencing of genes. (1.8)
http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml
“The first methods for sequencing DNA were developed in the mid-1970s. At that time, scientists
could sequence only a few base pairs per year, not nearly enough to sequence a single gene,
much less the entire human genome. By the time the HGP began in 1990, only a few laboratories
had managed to sequence a mere 100,000 bases, and the cost of sequencing remained very high.
Since then, technological improvements and automation have increased speed and lowered cost
to the point where individual genes can be sequenced routinely, and some labs can sequence well
over 100 million bases per year.” (https://www.genome.gov/10001177)
Key advances in technology:
• Biotechnology techniques such as PCR are used to prepare samples: the DNA needs to
be copied to prepare a sufficiently large pure samples to sequence
• Computers automate the sequencing process
• Fluorescent labeling techniques enable all four nucleotides to be analysed together
• Lasers are used to fluoresce the dye markers
• Digital camera technology reads the dye markers
• Computers are used to assemble the base sequence
3.1.S1 Use of a database to determine differences in the base sequence of a gene in two species.
One use of aligning base sequences is to determine
the differences between species: this can be used to
help determine evolutionary relationships.
Your task is to analyse the differences between three or more species
(the skill asks for two species, but the online Clustal tool works better
with a minimum of three).
GenBank
http://www.ncbi.nlm
.nih.gov/genbank
For each chosen species retrieve the base sequence:
• Go to GenBank website http://www.ncbi.nlm.nih.gov/genbank
• Select ‘Gene’ from the search bar
• Enter the name of a gene (e.g. AMY1A for salivary amylase 1A or COX1 for
cytochrome oxidase 1) AND the organism (use the binomial) and press ‘Search’
n.b. if you are comparing species the gene chosen needs to be the same for each
species
• Select the ‘Name/Gene ID’ to get a detailed view
• Scroll down to the ‘Genomic regions, transcripts, and products’ section and click on
‘FASTA’
• Copy the entire sequence from ‘>’ onwards
• Save the sequence – you will need to align with the other species next
http://bitesizebio.s3.amazonaws.com/wp-content/uploads/2012/10/header-image-copy18.jpg
3.1.S1 Use of a database to determine differences in the base sequence of a gene in two species.
To align the sequences:
• Go to the Clustal Omega website
http://www.ebi.ac.uk/Tools/msa/clustalo/
• In STEP 1 Select ‘DNA’ under ‘a set of’
• Paste the chosen sequences into the box
(each sequence must start on a new line)
• Press ‘Submit’ (and wait – depending on
the size of the sequences you may have to
wait for a couple of minutes)
http://www.ebi.ac.uk/Tools/msa/clustalo/
Analysis:
• ‘Alignments’ allows you to visually check the results – this is easier
if the chosen gene has a short base sequence
• Under ‘Results Summary’ use the ‘Percent Identity Matrix’ to
quantify the overall similarity (0 = no similarity, 100 = identical)
• Under ‘Phylogenic Tree’ chose the ‘Real’ option for the Phylogram
to get a visual representation of how similar the species are (based
on the chosen gene).
http://bitesizebio.s3.amazonaws.com/wp-content/uploads/2012/10/header-image-copy18.jpg
Bibliography / Acknowledgments
Bob Smullen
3.2 Chromosomes
Essential idea: Chromosomes carry genes
in a linear sequence that is shared by
members of a species.
The asian rice (Oryza sativa) genome can be seen illustrated above. Rice
possesses up 63,000 genes divided up between 12 chromosomes.
Below is a map of part of the first chromosome showing the gene loci present on it. Although different
varieties (estimated 40,000 worldwide) will possess different alleles for genes, all individuals will share the
same twelve chromosomes and the alleles of each variety will occur at the same position on same
chromosome, i.e. at the same gene loci.
By Chris Paine
http://www.cambia.org/daisy/RiceGenome/2959/version/default/part/Ima
geData/data/Rice%20chromosomes.png
http://rgp.dna.affrc.go.jp/E/publicdata/naturegenetics/chr01.gif
https://bioknowledgy.weebly.com/
Understandings
Statement
3.2.U1
Guidance
Prokaryotes have one chromosome consisting of a
circular DNA molecule.
3.2.U2 Some prokaryotes also have plasmids but eukaryotes
do not.
3.2.U3 Eukaryote chromosomes are linear DNA molecules
associated with histone proteins.
3.2.U4 In a eukaryote species there are different
chromosomes that carry different genes.
3.2.U5 Homologous chromosomes carry the same sequence
of genes but not necessarily the same alleles of those
genes.
3.2.U6 Diploid nuclei have pairs of homologous chromosomes.
The two DNA molecules formed by DNA
3.2.U7 Haploid nuclei have one chromosome of each pair.
replication prior to cell division are considered to
be sister chromatids until the splitting of the
centromere at the start of anaphase. After this,
they are individual chromosomes.
3.2.U8 The number of chromosomes is a characteristic feature
of members of a species.
3.2.U9 A karyogram shows the chromosomes of an organism The terms karyotype and karyogram have
in homologous pairs of decreasing length.
different meanings. Karyotype is a property of a
cell - the number and type of chromosomes
present in the nucleus, not a photograph or
diagram of them.
3.2.U10 Sex is determined by sex chromosomes and
autosomes are chromosomes that do not determine
sex.
Applications and Skills
Statement
3.2.A1
3.2.A2
3.2.A3
3.2.A4
3.2.S1
Guidance
Cairns’ technique for measuring the length of DNA
molecules by autoradiography.
Comparison of genome size in T2 phage,Escherichia Genome size is the total length of DNA in an
coli, Drosophila melanogaster, Homo sapiens and Paris organism. The examples of genome and
japonica.
chromosome number have been selected to allow
points of interest to be raised.
Comparison of diploid chromosome numbers of Homo
sapiens, Pan troglodytes, Canis familiaris, Oryza
sativa, Parascaris equorum.
Use of karyograms to deduce sex and diagnose Down
syndrome in humans.
Use of databases to identify the locus of a human gene
and its polypeptide product.
Review: 1.2.U1 Prokaryotes have a simple cell structure without compartmentalization.
Ultrastructure of E. coli as an example
of a prokaryote
http://www.tokresource.org/tok_classes/biobiobio/biomenu/metathink/required_drawings/index.htm
•
E. Coli is a model organism
used in research and
teaching. Some strains are
toxic to humans and can
cause food poisoning.
•
We refer to the cell
parts/ultrastructure of
prokaryotes rather than use
the term organelle as very
few structures in
prokaryotes are regarded as
organelles.
3.2.U1 Prokaryotes have one chromosome consisting of a circular DNA molecule.
3.2.U2 Some prokaryotes also have plasmids but eukaryotes do not.
Prokaryotes have two types of DNA:
• single chromosome
• plasmids
The single prokaryotic chromosome is coiled up
and concentrated in the nucleoid region.
Because there is only a single chromosome there
is only one copy of each gene.
A copy of the chromosome is made just
before cell division (by binary fission).
https://commons.wikimedia.org/wiki/File:Plasmid_%28english%29.svg
https://commons.wikimedia.org/wiki/File:Average_prokaryote_cell-_en.svg
3.2.U2 Some prokaryotes also have plasmids but eukaryotes do not.
Prokaryote bacteria may have plasmids, but these structures are not found in
eukaryotes.*
Features of Plasmids:
• Naked DNA - not associated with histone
proteins
• Small circular rings of DNA
• Not responsible for normal life processes –
these are controlled by the nucleoid chromosome
• Commonly contain survival characteristics, e.g. antibiotic resistance
• Can be passed between prokaryotes
• Can be incorporated into the nucleoid chromosome
n.b. Plasmid characteristics mean that Scientists have
found them useful in genetic engineering. Plasmids can
be used to transfer genes into bacteria.
*Scientists have found plasmids in archea and eukaryota, but very rarely.
https://commons.wikimedia.org/wiki/File:Plasmid_%28english%29.svg
https://en.wikipedia.org/wiki/File:PBR322_plasmid_showing_restriction_sites_and_resistance_genes.jpg
Review: 3.1.U1 A gene is a heritable factor that consists of a length of DNA and influences a specific
characteristic. AND 3.1.U2 A gene occupies a specific position on a chromosome. AND 3.1.U3 The various
specific forms of a gene are alleles. AND 3.1.U4 Alleles differ from each other by one or only a few bases.
A gene is a heritable factor that controls or influences a specific characteristic,
consisting of a length of DNA occupying a particular position on a chromosome (locus)
http://learn.genetics.utah.edu/content/m
olecules/gene/
3.2.A1 Cairns’ technique for measuring the length of DNA molecules by autoradiography. AND Nature of
Science: Developments in research follow improvements in techniques - autoradiography was used to
establish the length of DNA molecules in chromosomes. (1.8)
John Cairns produced images of DNA molecules from Escherichia coli (E.coli)
• E. Coli was grown with thymidine containing a
radioactive isotope of hydrogen (the DNA was labelled).
• The E. Coli cells were broken open by enzymes to
release the cell contents
• The cell contents were applied to a photographic
emulsion and placed in the dark (for two months)
• The radioative isotopes reacted with the emulsion
(similarly to light does)
• Dark areas on the photographic emulsion indicated the
presence of DNA
• The images showed that E. coli possesses a single
circular chromosome which is 1,100 μm long (E. coli
cells have a length of only 2 μm)
• Cairns images also provided evidence to support the
theory of semi-conservative replication
n.b. The insights and improvements in theory would not have been possible without the
development and use of autoradiography (exposure of photographic emulsion by
radioactive isotopes).
http://schaechter.asmblog.org/.a/6a00d8341c5e1453ef017c37accbac970b-300wi
3.2.U3 Eukaryote chromosomes are linear DNA molecules associated with histone proteins.
Linear strands of DNA held in a helix
Eukaryotic chromosomes may be up to
85mm in length. To fit such a length of DNA
into a nucleus with a diameter of 10 μm it
has to be coiled in a predictable fashion
that still allows for processes, such as
replication and protein synthesis, to occur.
Nucleosomes are formed by wrapping DNA
around histone proteins
n.b. Prokaryotic DNA is, like eukaryotic DNA, supercoiled, but
differently: Prokaryotic DNA maybe associated with proteins,
but it is not organised by histones and is therefore
sometimes referred as being ‘naked’.
http://en.wikipedia.org/wiki/File:DNA_to_Chromatin_Formation.jpg
3.2.U4 In a eukaryote species there are different chromosomes that carry different genes.
Eukaryotes possess multiple chromosomes. All
individuals of a species possess the same
chromosomes, with the same gene loci. For
example all humans have twenty three pairs.
Chromosomes can vary by:
• Length – the number of base pairs in the DNA molecule
• Position of the centromere
• Genes occur at a specific locus (location), i.e. it is always
found at the same position on the same chromosome
(the locus and genes possessed vary between species)
https://public.ornl.gov/site/gallery/originals/
3.2.S1 Use of databases to identify the locus of a human gene and its polypeptide product.
Use the online database (http://www.genecards.org/) to search for the
genes and the loci responsible for synthesising the following polypeptides:
•
•
•
•
Rhodopsin
3 different types of Collagen
Insulin
One other protein of your choice
n.b. the list of polypeptides reflects the examples you were required to learn for 2.4.A1
3.2.U8 The number of chromosomes is a characteristic feature of members of a species.
The chromosome number is an important characteristic of the species.
Organisms with different numbers of
chromosomes are unlikely to be able to
interbreed successfully
Chromosomes can fuse or spit during
evolution – these are rare events and
chromosome numbers tend to stay the
same for millions of years.
The number of chromosomes possessed by a
species is known as the N number, for example
humans have 23 different chromosomes.
A chromosome number does
reflect the complexity of an
organism
https://commons.wikimedia.org/wiki/File:NHGRI_human_male_karyotype.png
3.2.U6 Diploid nuclei have pairs of homologous chromosomes. AND 3.2.U7 Haploid nuclei have one
chromosome of each pair.
A diploid nucleus has two of each chromosome (2N). Therefore diploid nuclei have
two copies of every gene, apart from the genes on the sex chromosomes. For example
the Diploid nuclei in humans contain 46 chromosomes.
The fertilised egg cell (Zygote)
therefore is a diploid (2N) cell
containing two of each
chromosome.
Gametes are the sex cells that
fuse together during sexual
reproduction. Gametes have
haploid nuclei, so in humans both
egg and sperm cells contain 23
chromosomes.
n.b. Diploid nuclei are less susceptible to genetic diseases: have
two copies of a gene means organisms are more likely to
possess at least one healthy copy.
A haploid nucleus has
one of each chromosome
(N). Haploid nuclei in
humans have 23 different
chromosomes.
http://www.biologycorner.com/resources/diploid_life_cycle.gif
3.2.A3 Comparison of diploid chromosome numbers of Homo sapiens, Pan troglodytes, Canis
familiaris, Oryza sativa, Parascaris equorum.
Humans (Homo sapiens) 46
46 is the number of diploid
chromosomes in each human cell.
https://upload.wikimedia.org/wikipedia/commons/f/f6/Usain_Bolt_100_m_Daegu_2011.jpg
3.2.A3 Comparison of diploid chromosome numbers of Homo sapiens, Pan troglodytes, Canis
familiaris, Oryza sativa, Parascaris equorum.
Asian rice (Oryza sativa)
Equine roundworm (Parascaris equorum
http://pic20.picturetrail.com/VOL176/4853602/20795519/357799225.j
How many diploid
chromosomes does each
https://commons.wikimedia.org/wiki/File:Hinohikari.jpg
species possess?
Domestic Dog (Canis familiaris)
Chimpanzee (Pan troglodytes)
https://commons.wikimedia.org/wiki/File:Dog_%28Canis_lupus_fa
miliaris%29_%281%29.jpg
https://commons.wikimedia.org/wiki/File:Pan_troglodytes_Sweetwaters_Ch
panzee_Sanctuary,_Kenya.jpg
3.2.A3 Comparison of diploid chromosome numbers of Homo sapiens, Pan troglodytes, Canis
familiaris, Oryza sativa, Parascaris equorum.
Asian rice (Oryza sativa) 24
2
Equine roundworm (Parascaris equorum
http://pic20.picturetrail.com/VOL176/4853602/20795519/357799225.j
How many diploid
chromosomes does each
https://commons.wikimedia.org/wiki/File:Hinohikari.jpg
species possess?
Domestic Dog (Canis familiaris) 78
48
https://commons.wikimedia.org/wiki/File:Dog_%28Canis_lupus_fa
miliaris%29_%281%29.jpg
Chimpanzee (Pan troglodytes)
https://commons.wikimedia.org/wiki/File:Pan_troglodytes_Sweetwaters_Ch
panzee_Sanctuary,_Kenya.jpg
3.2.U5 Homologous chromosomes carry the same sequence of genes but not necessarily the same
alleles of those genes.
3.2.U5 Homologous chromosomes carry the same sequence of genes but not necessarily the same
alleles of those genes.
3.2.U10 Sex is determined by sex chromosomes and autosomes are chromosomes that do not determine
sex.
Sex Determination: It’s all about X and Y…
Humans have 23 pairs of chromosomes in
diploid somatic cells (n=2).
22 pairs of these are autosomes, which are
homologous pairs.
One pair is the sex chromosomes.
XX gives the female gender, XY gives male.
Karyotype of a human male, showing X and Y chromosomes:
http://en.wikipedia.org/wiki/Karyotype
SRY
The X chromosome is much larger than the Y.
X carries many genes in the non-homologous
region which are not present on Y.
The presence and expression of the SRY
gene on Y leads to male development.
Chromosome images from Wikipedia:
http://en.wikipedia.org/wiki/Y_chromosome
3.2.U10 Sex is determined by sex chromosomes and autosomes are chromosomes that do not determine
sex.
Sex Determination: It’s all about X and Y…
Chromosome pairs segregate in meiosis.
Females (XX) produce only eggs containing
the X chromosome.
Males (XY) produce sperm which can contain
either X or Y chromosomes.
Segregation of the sex chromosomes in meiosis.
SRY gene determines maleness.
gametes
X
Y
X
XX
XY
X
XX
XY
Therefore there is an even chance*
of the offspring being male or female.
Find out more about its role and
just why do men have nipples?
http://www.hhmi.org/biointeractive/gender/lectures.html
Chromosome images from Wikipedia:
http://en.wikipedia.org/wiki/Y_chromosome
3.2.A2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo
sapiens and Paris japonica.
Humans (Homo sapiens)
3.2 billion base pairs
Genome size is the total number of
DNA base pairs in one copy of a
haploid genome.
https://upload.wikimedia.org/wikipedia/commons/f/f6/Usain_Bolt_100_m_Daegu_2011.jpg
3.2.A2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo
sapiens and Paris japonica.
Canopy plant (Paris japonica)
T2 phage
Escherichia coli
https://s-media-cacheak0.pinimg.com/736x/2d/0e/3e/2d0e3ea8ddf652f25a5f2c3b1050
af79.jpg
n.b. T2 phage (orange) is a virus that attacks E. Coli
bacterium (green and white).
What is the genome size of
each species?
Fruit fly (Drosophila melanogaster)
https://commons.wikimedia.org/wiki/File:Dr
osophila_melanogaster__side_%28aka%29.jpg
https://commons.wikimedia.org/wiki/File:Paris_japonica_Kinugasasou_in_Hakusan_2003_7_27.jpg
3.2.A2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo
sapiens and Paris japonica.
Canopy plant (Paris japonica)
150 billion base pairs
T2 phage
164 thousand base pairs
Escherichia coli
4.6 million base pairs
https://s-media-cacheak0.pinimg.com/736x/2d/0e/3e/2d0e3ea8ddf652f25a5f2c3b1050
af79.jpg
n.b. T2 phage (orange) is a virus that attacks E. Coli
bacterium (green and white).
What is the genome size of
each species?
Fruit fly (Drosophila melanogaster)
130 million base pairs
https://commons.wikimedia.org/wiki/File:Dr
osophila_melanogaster__side_%28aka%29.jpg
https://commons.wikimedia.org/wiki/File:Paris_japonica_Kinugasasou_in_Hakusan_2003_7_27.jpg
3.2.U9 A karyogram shows the chromosomes of an organism in homologous pairs of decreasing length.
Karyogram is a diagram or photograph of the chromosomes present in a nucleus (of
a eukaryote cell) arranged in homologous pairs of decreasing length.
The chromosomes are visible in cells that are undergoing
mitosis – most clearly in metaphase.
Stains used to make the chromosomes visible also give each
chromosome a distinctive banding pattern.
A micrograph are taken and the chromosomes are arranged according to their
size, shape and banding pattern. They are arranged by size, starting with the
longest pair and ending with the smallest.
https://commons.wikimedia.org/wiki/File:NHGRI_human_male_karyotype.png
3.2.U9 A karyogram shows the chromosomes of an organism in homologous pairs of decreasing length.
Karyogram is a diagram or photograph of the chromosomes present in a nucleus (of a
eukaryote cell) arranged in homologous pairs of decreasing length.
Karyotype is a property of the cell described by the number and type of chromosomes
present in the nucleus (of a eukaryote cell).
a Karyogram is a diagram
that shows, or can be used to
determine, the karyotype.
http://learn.genetics.utah.edu/content/chromosomes/karyotype/
Bibliography / Acknowledgments
Bob Smullen