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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.

3.1 Genes

Essential idea: Every living organism inherits a blueprint for life from its parents.

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Statement

Guidance

3.1.U1

A gene is a heritable factor that consists of a length of DNA and influences a specific characteristic.

 

3.1.U2

A gene occupies a specific position on a chromosome.

 

3.1.U3

The various specific forms of a gene are alleles.

 

3.1.U4

Alleles differ from each other by one or only a few bases.

 

3.1.U5

New alleles are formed by mutation.

Deletions, insertions and frame shift mutations do not need to be included.

3.1.U6

The genome is the whole of the genetic information of an organism.

 

3.1.U7

The entire base sequence of human genes was sequenced in the Human Genome Project.

 

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.

Students should be able to recall one specific base substitution that causes glutamic acid to be substituted by valine as the sixth amino acid in the hemoglobin polypeptide.

3.1.A2

Comparison of the number of genes in humans with other species.

The number of genes in a species should not be referred to as genome size as this term is used 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.

3.1.S1

Use of a database to determine differences in the base sequence of a gene in two species.

The Genbank® database can be used to search for DNA base sequences. The cytochrome C 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 Genes

Essential idea: Every living organism inherits a blueprint for life from its parents.

Syllabus Reference

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Chromosome made of DNA and protein

Genes – heritable factors which control specific characteristics

Alleles – different forms of a specific gene

Gene locus – specific position of a gene on a chromosome

All individuals of a species carry the same genes at the same loci on the same chromosomes

3.1 Genes

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)

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.

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3.1 Genes

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)

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.

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Differing from other alleles by 1 to 2 bases only and occupying the same gene locus as other alleles of the same gene.

  • (homozygous) two of the same alleles
  • (heterozygous) two different alleles

3.1 Genes

Allele: One specific form of a gene

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.

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3.1 Genes

The genome is the complete set of genetic information

3.1.U6 The genome is the whole of the genetic information of an organism.

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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.

When analysing an organisms’ complexity, what other than the count of an organisms’ genes needs to be considered?

Virus

Bacterium

Insect

Bird

Plant

Mammal

3.1 Genes

Humans see themselves as being more complex and evolved than other species.

3.1.A2 Comparison of the number of genes in humans with other species.

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3.1 Genes

Humans see themselves as being more complex and evolved than other species.

3.1.A2 Comparison of the number of genes in humans with other species.

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3.1 Genes

Allele: One specific form of a gene

3.1.U5 New alleles are formed by mutation.

Genes consist of a certain sequence of DNA bases which can be 100’s to 1000’s bases in length. Usually different alleles of the gene vary by only 1 to 2 of different bases.

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3.1 Genes

The allele for Sickle Cell Anemia is created by a mutation of a single nucleotide.

3.1.U5 New alleles are formed by mutation.

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  • DNA:  The DNA sequence changes from GAG to GTG on the non-transcribed strand (CTC to CAC on the template strand)
  • mRNA:  The mRNA sequence changes from GAG to GUG at the 6th codon position
  • Polypeptide:  The sixth amino acid for the beta chain of haemoglobin is changed from glutamic acid to valine (Glu to Val)

This variation when one nucleotide is switched for another is called a single nucleotide polymorphism (SNPs for short)

3.1 Genes

The allele for Sickle Cell Anemia is created by a mutation of a single nucleotide.

3.1.U5 New alleles are formed by mutation.

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3.1 Genes

The allele for Sickle Cell Anemia is created by a mutation of a single nucleotide.

3.1.U5 New alleles are formed by mutation.

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3.1 Genes

The allele for Sickle Cell Anemia is created by a mutation of a single nucleotide.

3.1.U5 New alleles are formed by mutation.

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  • What they found: Most of the genome does not code for proteins (originally labeled “junk DNA”). Some of these regions consist of areas that can affect gene expression or are highly repetitive sequences called satellite DNA. Scientists can now also predict which sequences do code for protein (approximately 21000-23000 sequences)
  • A complete description of the Human genome project can be found at http://www.genome.gov/10001772

3.1 Genes

The allele for Sickle Cell Anemia is created by a mutation of a single nucleotide.

3.1.U5 New alleles are formed by mutation.

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2 sickle cell alleles

This leads to the production of abnormal red blood cells

Decreased Haemoglobin

Tired and Fatigued

Carrier (1 normal and 1 mutant allele)

This leads to the production of mostly normal red blood cells

Although decreased normal haemoglobin levels decrease the likelihood of malaria surviving

3.1 Genes

The allele for Sickle Cell Anemia is created by a mutation of a single nucleotide.

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.

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Those who only possess the normal blood cell allele do not suffer from sickle cell anaemia but are more susceptible to malaria

Malaria is caused by an endoparasite (Plasmodium falciparum) which reproduces inside red blood cells (but not sickle cells)

3.1 Genes

The allele for Sickle Cell Anemia is created by a mutation of a single nucleotide.

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.

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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.

*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.

3.1 Genes

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.

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3.1 Genes

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“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 Genes

Nature of Science: Developments in scientific research follow improvements in technology - gene sequencers are used for the sequencing of genes. (1.8)

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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).

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

3.1 Genes

3.1.S1 Use of a database to determine differences in the base sequence of a gene in two species.

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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).

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)

3.1 Genes

3.1.S1 Use of a database to determine differences in the base sequence of a gene in two species.