genetic
determined by DNA
and passed on from parents to
offspring
heritable
a genetic trait which
can be passed on to offspring
trait
a characteristic that
distinguishes one individual
from
another, such as blood type
locus
(plural: loci) the specifi c
place where a gene is found on a
chromosome
base
the basic unit of the DNA
code, represented by A, T, C, or G
sequence
a series of bases in the
genetic code in a particular order
allele
version of a gene, differing
by one or more bases
mucus
a slimy, protective
secretion
mutation
an accidental change
in a genetic sequence
cystic fibrosis
a genetic disease
causing the overproduction of
mucus in
the body
HIV
human immunodefi ciency
virus, the virus that causes AIDS
AIDS
a viral infection caused by
HIV and resulting in weakening
of
the immune system
predator
an organism that hunts
and eats other organisms
base
substitution mutation an
accidental change in one base of
a
genetic sequence
anaemia
a low number of red
blood cells in the blood
parasite
plant/animal that lives
on/in another plant/animal
and
feeds from it
sequence
the order of bases in a
fragment of DNA
sequencer
machine that
determines the order of bases in a
fragment of DNA
codon
a group of three bases
that together code for a
single
amino acid
base pair
a matching pair of
nucleotides (A-T or C-G)
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
- For example, the gene for eye colour has alleles that encode different shades / pigments
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)
Cause of Sickle Cell Anaemia
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)
Consequence of Sickle Cell Anaemia
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
Below are examples of different genes that may be searched for:
- HBB – Haemoglobin beta gene
- COX1 – Cytochrome oxidase 1 gene
- F8 – Coagulation factor VIII gene
- IGF1R – Insulin growth factor 1 receptor gene
Comparing Gene Sequences
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’)
Below is a plain text file that can be uploaded to compare gene sequence fragments from different species:
- CHRNE – Cholinergic receptor epsilon (nicotinic) for various species
Point mutations are changes to one base in the DNA code and may involve either:
- The substitution of a base (e.g. ATG becomes ACG)
- The insertion of a base (e.g. ATG becomes ATCG)
- The deletion of a base (e.g. ATG becomes AG)
- The inversion of bases (e.g. ATG becomes AGT)
Effects of Point Mutations
Silent mutations occur when the DNA change does not alter the amino acid sequence of the polypeptide
- This is possible because the genetic code is degenerate and certain codons may code for the same amino acid
Missense mutations occur when the DNA change alters a single amino acid in the polypeptide chain
- Sickle cell anaemia is an example of a disease caused by a single base substitution mutation (GAG → GTG ; Glu → Val)
Nonsense mutations occur when the DNA change creates a premature STOP codon which truncates the polypeptide
- Cystic fibrosis is an example of a disease which can result from a nonsense mutation (this may not be the only cause though)
Frameshift mutations occur when the addition or removal of a base alters the reading frame of the gene
- This change will affect every codon beyond the point of mutation and thus may dramatically change amino acid sequence
Sickle cell anaemia is controlled by a single gene mutation (via a base substitution to the haemoglobin beta chain gene)
- The sixth codon is mutated (GAG → GUG) which changes the amino acid sequence (Glu → Val)
Individuals who only possess the sickle cell allele will have abnormally shaped red blood cells that are destroyed by the spleen
- This leads to a reduction in red blood cells and a variety of health complications associated with reduced blood cell circulation
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)
Incidence of Malaria
In areas where malaria is common, there is a higher incidence of
people who carry
both alleles (i.e. are heterozygous)
These
individuals produce enough normal blood cells to avoid the more severe
effects associated with sickle cell anaemia, but also
produce enough sickle cells to confer an increased resistance to the
malarial parasite
- This condition whereby the presence of both alleles is beneficial is known as heterozygous advantage
The human genome comprises of roughly 3.2 billion base pairs across 46 chromosomes
- However, only a small fraction of this sequence codes for functional genes (roughly 1.5% of the genome)
- The remainder is made up of repeating elements, pseudogenes, microsatellites and transposons
Pseudogene Formation
A transposon is a segment of DNA that inserts itself into another section within the genome (i.e. ‘jumping' genes)
- Transposition often results in the duplication of the transposable element
- If the duplicated sequence then undergoes random mutation, a pseudogene will result
A pseudogene is a non-functional sequence of DNA that is homologous to an active gene
- Pseudogenes may be processed (retrotransposed) or non-processed (duplicated)
Processed pseudogenes
- Arise when a portion of an mRNA transcript is reverse transcribed back into DNA and inserted into the chromosomal DNA
- Processed pseudogenes consequently lack introns and promoter sequences, but may include a poly-A tract
- These pseudogenes may be randomly integrated anywhere in the genome
Non-processed pseudogenes
- Arise as a result of gene duplication and subsequent inactivation by mutation
- Non-processed pseudogenes will often be flanked by transcriptional regulatory elements (e.g. promoters, etc.)
- These pseudogenes are usually located adjacent to the original gene