3.1 GENES
DNA is the genetic blueprint which codes for, and determines, the characteristics of
an organism, This includes the physical, behavioural and physiological features of
the organism.
DNA is packaged and organised into discrete structures called chromosomes. A
gene is a sequence of DNA that encodes for a specific trait (traits may also be
influenced by multiple genes). The position of a gene on a particular chromosome is
called the locus (plural = loci)
Alleles are alternative forms of a gene that code for the different variations of a
specific trait. As alleles are alternative forms of the one gene, they possess very
similar gene sequences. Alleles only differ from each other by one or a few bases.
A gene mutation is a change in the nucleotide sequence of a section of DNA coding
for a specific trait. New alleles are formed by mutation.
Gene mutations can be beneficial, detrimental or neutral
★ Beneficial mutations change the gene sequence (missense mutations) to
create new variations of a trait
★ Detrimental mutations truncate the gene sequence (nonsense mutations) to
abrogate the normal function of a trait
★ Neutral mutations have no effect on the functioning of the specific feature
(silent mutations)
Sickle cell anaemia is an example of a disorder caused by a gene mutation. The
disease allele arose from a base substitution mutation – where a single base was
changed in the gene sequence. Sickle cell anaemia results from a change to the 6th
codon for the beta chain of haemoglobin.
★ 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)
The amino acid change (Glu → Val) alters the structure of haemoglobin, causing it to
form insoluble fibrous strands. The insoluble haemoglobin cannot carry oxygen as
effectively, causing the individual to feel constantly tired.
The formation of fibrous haemoglobin strands changes the shape of the red blood
cell to a sickle shape. The sickle cells may form clots within the capillaries, blocking
blood supply to vital organs and causing myriad health issues. The sickle cells are
,also destroyed more rapidly than normal cells, leading to a low red blood cell count
(anaemia).
The genome is the totality of genetic information of a cell, organism or organelle.
This includes all genes as well as non-coding DNA sequences (e.g. introns,
promoters, short tandem repeats, etc.)
The human genome consists of:
★ 46 chromosomes (barring aneuploidy)
★ ~3 billion base pairs
★ ~21,000 genes
The Human Genome Project (HGP) was an international cooperative venture
established to sequence the human genome. The HGP showed that humans share
the majority of their sequence, with short nucleotide polymorphisms contributing
diversity
The completion of the Human Genome Project in 2003 lead to many outcomes:
★ Mapping – The number, location, size and sequence of human genes is now
established
★ Screening – This has allowed for the production of specific gene probes to
detect sufferers and carriers of genetic diseases
★ Medicine – The discovery of new proteins have lead to improved treatments
(pharmacogenetics and rational drug design)
★ Ancestry – Comparisons with other genomes have provided insight into the
origins, evolution and migratory patterns of man
The number of genes present in an organism will differ between species and is not a
valid indicator of biological complexity. The number of genes in a genome is usually
predicted by identifying sequences common to genes. These identifying regions may
include expressed sequence tags (ESTs) or sequences that are homologous to
known genes. The presence of pseudogenes and transposons make accurate
counts of unique gene numbers very difficult.
As scientists may use different approaches to predicting gene numbers, final
estimations can vary significantly . For instance, the number of genes in rice (Oryza
sativa) is estimated as being between 32,000 – 50,000. The number of genes in
humans is estimated as being between 19,000 – 25,000.
Gene sequences from different species can be identified and then compared using
two online resources:
★ GenBank – a genetic database that serves as an annotated collection of DNA
sequences
, ★ Clustal Omega – an alignment program that compares multiple sequences of
DNA
GenBank can be used to identify the DNA sequence for a gene in a number of
different species
To identify a specific gene sequence:
★ Change the search parameter from nucleotide to gene and type in the name
of the gene of interest
★ Choose the species of interest and click on the link (under ‘Name / Gene ID’)
★ Scroll to the ‘Genomic regions, transcripts and products’ section and click on
the ‘FASTA’ link
Clustal Omega aligns multiple gene sequences to allow for the determination of
differences in the base sequence
To construct a multiple alignment:
★ Change the input sequence type to DNA and paste the relevant FASTA
sequences into the provided space
★ Before each sequence designate a species name preceded by a forward
arrow (e.g. '>Human’ or ‘>Chimpanzee’)
★ Alternatively, sequences can be saved as a document in plain text format
(.txt) and then uploaded
★ When all sequences have been included, click ‘Submit’ (under step 3)
Clustal Omega possesses several useful features that are absent in alternative tools
like BLASTN:
★ Multiple (more than two) sequences can be compared at once
★ Sequence consensus is colour coded in a Jalview applet found under ‘Result
Summary’ (requires Java)
★ Branched phylograms can be generated to show evolutionary relationships
(under ‘Phylogenetic Tree’)
3.2 CHROMOSOMES
Prokaryotes do not possess a nucleus – instead genetic material is found free in the
cytoplasm in a region called the nucleoid. The genetic material of a prokaryote
consists of a single chromosome consisting of a circular DNA molecule (genophore).
The DNA of prokaryotic cells is naked – meaning it is not associated with proteins for
additional packaging. In addition to the genophore, prokaryotic cells may possess
additional circular DNA molecules called plasmids.
DNA is the genetic blueprint which codes for, and determines, the characteristics of
an organism, This includes the physical, behavioural and physiological features of
the organism.
DNA is packaged and organised into discrete structures called chromosomes. A
gene is a sequence of DNA that encodes for a specific trait (traits may also be
influenced by multiple genes). The position of a gene on a particular chromosome is
called the locus (plural = loci)
Alleles are alternative forms of a gene that code for the different variations of a
specific trait. As alleles are alternative forms of the one gene, they possess very
similar gene sequences. Alleles only differ from each other by one or a few bases.
A gene mutation is a change in the nucleotide sequence of a section of DNA coding
for a specific trait. New alleles are formed by mutation.
Gene mutations can be beneficial, detrimental or neutral
★ Beneficial mutations change the gene sequence (missense mutations) to
create new variations of a trait
★ Detrimental mutations truncate the gene sequence (nonsense mutations) to
abrogate the normal function of a trait
★ Neutral mutations have no effect on the functioning of the specific feature
(silent mutations)
Sickle cell anaemia is an example of a disorder caused by a gene mutation. The
disease allele arose from a base substitution mutation – where a single base was
changed in the gene sequence. Sickle cell anaemia results from a change to the 6th
codon for the beta chain of haemoglobin.
★ 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)
The amino acid change (Glu → Val) alters the structure of haemoglobin, causing it to
form insoluble fibrous strands. The insoluble haemoglobin cannot carry oxygen as
effectively, causing the individual to feel constantly tired.
The formation of fibrous haemoglobin strands changes the shape of the red blood
cell to a sickle shape. The sickle cells may form clots within the capillaries, blocking
blood supply to vital organs and causing myriad health issues. The sickle cells are
,also destroyed more rapidly than normal cells, leading to a low red blood cell count
(anaemia).
The genome is the totality of genetic information of a cell, organism or organelle.
This includes all genes as well as non-coding DNA sequences (e.g. introns,
promoters, short tandem repeats, etc.)
The human genome consists of:
★ 46 chromosomes (barring aneuploidy)
★ ~3 billion base pairs
★ ~21,000 genes
The Human Genome Project (HGP) was an international cooperative venture
established to sequence the human genome. The HGP showed that humans share
the majority of their sequence, with short nucleotide polymorphisms contributing
diversity
The completion of the Human Genome Project in 2003 lead to many outcomes:
★ Mapping – The number, location, size and sequence of human genes is now
established
★ Screening – This has allowed for the production of specific gene probes to
detect sufferers and carriers of genetic diseases
★ Medicine – The discovery of new proteins have lead to improved treatments
(pharmacogenetics and rational drug design)
★ Ancestry – Comparisons with other genomes have provided insight into the
origins, evolution and migratory patterns of man
The number of genes present in an organism will differ between species and is not a
valid indicator of biological complexity. The number of genes in a genome is usually
predicted by identifying sequences common to genes. These identifying regions may
include expressed sequence tags (ESTs) or sequences that are homologous to
known genes. The presence of pseudogenes and transposons make accurate
counts of unique gene numbers very difficult.
As scientists may use different approaches to predicting gene numbers, final
estimations can vary significantly . For instance, the number of genes in rice (Oryza
sativa) is estimated as being between 32,000 – 50,000. The number of genes in
humans is estimated as being between 19,000 – 25,000.
Gene sequences from different species can be identified and then compared using
two online resources:
★ GenBank – a genetic database that serves as an annotated collection of DNA
sequences
, ★ Clustal Omega – an alignment program that compares multiple sequences of
DNA
GenBank can be used to identify the DNA sequence for a gene in a number of
different species
To identify a specific gene sequence:
★ Change the search parameter from nucleotide to gene and type in the name
of the gene of interest
★ Choose the species of interest and click on the link (under ‘Name / Gene ID’)
★ Scroll to the ‘Genomic regions, transcripts and products’ section and click on
the ‘FASTA’ link
Clustal Omega aligns multiple gene sequences to allow for the determination of
differences in the base sequence
To construct a multiple alignment:
★ Change the input sequence type to DNA and paste the relevant FASTA
sequences into the provided space
★ Before each sequence designate a species name preceded by a forward
arrow (e.g. '>Human’ or ‘>Chimpanzee’)
★ Alternatively, sequences can be saved as a document in plain text format
(.txt) and then uploaded
★ When all sequences have been included, click ‘Submit’ (under step 3)
Clustal Omega possesses several useful features that are absent in alternative tools
like BLASTN:
★ Multiple (more than two) sequences can be compared at once
★ Sequence consensus is colour coded in a Jalview applet found under ‘Result
Summary’ (requires Java)
★ Branched phylograms can be generated to show evolutionary relationships
(under ‘Phylogenetic Tree’)
3.2 CHROMOSOMES
Prokaryotes do not possess a nucleus – instead genetic material is found free in the
cytoplasm in a region called the nucleoid. The genetic material of a prokaryote
consists of a single chromosome consisting of a circular DNA molecule (genophore).
The DNA of prokaryotic cells is naked – meaning it is not associated with proteins for
additional packaging. In addition to the genophore, prokaryotic cells may possess
additional circular DNA molecules called plasmids.
