Transcript Topic 3.1 powerpoint

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.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.U5 New alleles are formed by mutation.
Learn.Genetics: What Is
Mutation?
http://learn.genetics.utah.edu/content/vari
ation/mutation/
3.1.U5 New alleles are formed by mutation.
3.1.U5 New alleles are formed by mutation.
3.1.U5 New alleles are formed by mutation.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
3.1.A1 The causes of sickle cell anemia, including a base substitution mutation, a change to the base
sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.
https://youtu.be/1fN7rOwDyMQ
3.1.S1 Use of a database to determine differences in the base sequence of a gene in two species.
Once 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