Fergus - Lecture 1 - part 1 Flashcards
What is bioinformatics?
The application of information technology and computer science to the field of biology
What is computational biology?
(4)
Finds the genes in the DNA sequences of various organisms
Develops methods to predict the structure and or function of newly discovered proteins
Aligning similar proteins and generating phylogenetic trees
Clustering protein sequences into families of related sequences
Who is responsible for discovering the DNA structure?
Watson and Crick
What is CML?
Chronic myeloid leukemia
Presence of the philadelphia chromosome -> reciprocal translocation involving chromosomes 9 and 22
What 8 parts make up a eukaryotic gene?
Exons
Introns
Promoter
Enhancer
TATAA region
GAAT region
GC region
OCT region
What does an enhancer do?
It modulates the rate of transcription
What does the TATA box do?
(2)
This is the binding site of the TATA-binding protein
Transcription is initiated at the TATA box
What does the CAAT box do?
Signals the binding site for the RNA transcription factor
NF1 = box binding protein
What does the GC region
Similar function to enhancers an example of GC box-binding protein = SP1
What is the Oct region
Transcription factor
Octamer binding protein
What does UTR stand for?
Untranslated region
How many chromosomes do we have?
46
How many genes do we have?
20,000
How many single nucleotide polymorphisms do we have?
50,000
How many polymorphic markers do humans have?
5,800
What is a polymorphic marker?
Markers that show some degree of variability in a population
e.g. height
What were the aims of the human genome project?
Sequence the entire human genome by September 30th 2005
Generate a 100kb resolution physical map
Identify, map and sequence all genes
How many eukaryotic genomes have been completed?
303
How many microbial genomes have been completed?
3137 -> easier to identify bacteria via gene sequence then preliminary identification
List the different types of sequences that make up the human genome
(9)
LINES
SINES
Retrovirus like elements
DNA transposon fossils
Simple sequence repeats
Segmental duplications
Introns
Exons
Heterochromatin
What % of human genome is heterochromatin?
8%
What % of human genome is exons?
1.5%
What % of human genome is introns ?
About 25%
What % of human genome is segmental duplications?
5%
What % of human genome is simple sequence repeats ?
3%
What % of human genome is DNA transposon fossils?
3%
What % of human genome is retrovirus-like elements?
8%
What % of human genome are SINEs ?
13%
What % of human genome are LINEs?
21%
How many separate human genome sequences are there?
Over 1,000,000
Why are genomic databases needed?
(3)
So they are available for medical genetics
To identify genes of medical importance i.e. in diseases such as cystic fibrosis or duchenne muscular dystrophy
Designing diagnostic tests for genetic disorders
What are the three classifications of genetic diseases?
Autosomal dominant
Autosomal recessive
X-linked
Give two examples of autosomal dominant disorders
Huntington’s Disease
Myotonic dystrophy
Give three examples of autosomal recessive disorders
Cystic fibrosis
Mental retardation
Spinal muscular atrophy
Wilson’s disease
Give some examples of X-linked disorders
Red-green colour blindness
Fragile X Mental retardation
Duchenne muscular dystrophy
haemophilia A
List the six different types of mutations
Point mutations
Large deletions
Small deletions
Insertions
Truncating mutations
Trinucleotide repeat diseases
Give an example of a disease caused by a point mutation
Most conditions e.g. cystic fibrosis or Wilsons
Give an example of a condition caused by a large deletion
Duchenne muscular dystrophy
Give an example of a disease caused by small deletions
Familial adenomatous polyposis (FAP)
Hereditary nonpolyposis colorectal cancer (HNPCC)
What diseases are caused by truncating mutations
FAP
HNPCC
Breast/ovarian cancers
What is a truncating mutation?
A mutation that results in a shorter protein being formed
Give some examples of trinucleotide repeat diseases
Fragile X (CGG repeat)
Huntington’s disease (CAG repeat)
Myotonic dystrophy (CTG)
What approach have we taken to cloning genes?
Positional cloning approach -> finding the gene by searching in the most likely position i.e. if only males in the family are affected you should look at the X chromosome
What is the positional gene cloning approach used for?
To get information on chromosomal location of abnormal gene
Identify candidate genes in location
Screen candidate genes for mutations in affected individuals
Design diagnostic test for mutations
How does the positional cloning approach of genes allow us to identify candidate genes in location?
The human genome has already been sequenced
We just have to compare the diseased sequence to the healthy sequence and see what genotype is causing the diseased phenotype
What is the basis of linkage analysis?
The ability to follow individual chromosomes through a family and identify chromosomes and chromosome regions that segregate (follow) the disease
When is linkage analysis used?
If no cytogenetic information is available
Explain in your own words what linkage analysis is?
We follow mutated chromosomes through a family by looking at the phenotypes (we look for polymorphisms)
Need to know diagrams for linkage analysis
What is the frequency of cystic fibrosis in ireland?
1 in 19 people
What is the chance that both your parents are carriers of CF?
1/400
If both your parents are carriers of CF what is the chance of you having CF?
1 in 4
What is the birth incidence of CF in Ireland
1/19 x 1/19 = 1/361
1/361 x 1/4 = 1,444 approximately
What is the most common mutation for CF?
delta F 508
What % of Irish cystic fibrosis patients have the deltaF 508 mutation?
80%
What causes CF?
the deletion of phenylalanine at position 508 of the CFTR protein
Small deletion of the last G of 507 isoleucine and the first and second T of phenylalanine
ATT amino acid results instead = stop codon
What chromosome is the CF gene located on?
Chromosome 7
The mutation for CF is found on what gene?
Cystic fibrosis transmembrane conductance regulator gene
Where is the mutation for CF located on CFTR gene?
Exon 10
Write about X-linked muscular dystrophy
(6)
Two types:
- Duchenne
- Becker (progresses slower - people can live to their 40s)
Affects 1 in 3500 male births
Causes severe muscle wasting resulting in wheelchair by 12-13
Dead by 20 years old
Why do X-linked conditions predominantly affect males?
Because females have two copies of the X chromosome and can use the other chromosome if need be
What is the gene for muscular dystrophy called?
Duchenne muscular dystrophy gene
The DMD gene or dystrophin gene
What does the DMD gene make?
Dystrophin protein
What is so special about the DMD gene?
It is the largest known gene
What is the most common mutation in DMD?
About 60% of males have a deletion of at least one exon
How many exons does the DMD gene have?
79 exons
Where are the two hotspots for deletions in the DMD gene?
5’ end of gene (from the promoter to exon 19)
3’ end of gene (from exon 40 to exon 19)
How would you go about detecting DMD?
2 multiplex PCR reactions can detect 98% of deletions
A 5’ multiplex and a 3’ multiplex
