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2.1 Bioinformatics > Fergus - Lecture 1 - part 1 > Flashcards

Fergus - Lecture 1 - part 1 Flashcards

1
Q

What is bioinformatics?

A

The application of information technology and computer science to the field of biology

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2
Q

What is computational biology?
(4)

A

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

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3
Q

Who is responsible for discovering the DNA structure?

A

Watson and Crick

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4
Q

What is CML?

A

Chronic myeloid leukemia

Presence of the philadelphia chromosome -> reciprocal translocation involving chromosomes 9 and 22

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5
Q

What 8 parts make up a eukaryotic gene?

A

Exons
Introns
Promoter
Enhancer
TATAA region
GAAT region
GC region
OCT region

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6
Q

What does an enhancer do?

A

It modulates the rate of transcription

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7
Q

What does the TATA box do?
(2)

A

This is the binding site of the TATA-binding protein

Transcription is initiated at the TATA box

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8
Q

What does the CAAT box do?

A

Signals the binding site for the RNA transcription factor

NF1 = box binding protein

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9
Q

What does the GC region

A

Similar function to enhancers an example of GC box-binding protein = SP1

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10
Q

What is the Oct region

A

Transcription factor

Octamer binding protein

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11
Q

What does UTR stand for?

A

Untranslated region

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12
Q

How many chromosomes do we have?

A

46

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13
Q

How many genes do we have?

A

20,000

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14
Q

How many single nucleotide polymorphisms do we have?

A

50,000

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15
Q

How many polymorphic markers do humans have?

A

5,800

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16
Q

What is a polymorphic marker?

A

Markers that show some degree of variability in a population
e.g. height

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17
Q

What were the aims of the human genome project?

A

Sequence the entire human genome by September 30th 2005

Generate a 100kb resolution physical map

Identify, map and sequence all genes

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18
Q

How many eukaryotic genomes have been completed?

A

303

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19
Q

How many microbial genomes have been completed?

A

3137 -> easier to identify bacteria via gene sequence then preliminary identification

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20
Q

List the different types of sequences that make up the human genome
(9)

A

LINES
SINES
Retrovirus like elements
DNA transposon fossils
Simple sequence repeats
Segmental duplications
Introns
Exons
Heterochromatin

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21
Q

What % of human genome is heterochromatin?

A

8%

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22
Q

What % of human genome is exons?

A

1.5%

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23
Q

What % of human genome is introns ?

A

About 25%

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24
Q

What % of human genome is segmental duplications?

A

5%

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25
What % of human genome is simple sequence repeats ?
3%
26
What % of human genome is DNA transposon fossils?
3%
27
What % of human genome is retrovirus-like elements?
8%
28
What % of human genome are SINEs ?
13%
29
What % of human genome are LINEs?
21%
30
How many separate human genome sequences are there?
Over 1,000,000
31
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
32
What are the three classifications of genetic diseases?
Autosomal dominant Autosomal recessive X-linked
33
Give two examples of autosomal dominant disorders
Huntington's Disease Myotonic dystrophy
34
Give three examples of autosomal recessive disorders
Cystic fibrosis Mental retardation Spinal muscular atrophy Wilson's disease
35
Give some examples of X-linked disorders
Red-green colour blindness Fragile X Mental retardation Duchenne muscular dystrophy haemophilia A
36
List the six different types of mutations
Point mutations Large deletions Small deletions Insertions Truncating mutations Trinucleotide repeat diseases
37
Give an example of a disease caused by a point mutation
Most conditions e.g. cystic fibrosis or Wilsons
38
Give an example of a condition caused by a large deletion
Duchenne muscular dystrophy
39
Give an example of a disease caused by small deletions
Familial adenomatous polyposis (FAP) Hereditary nonpolyposis colorectal cancer (HNPCC)
40
What diseases are caused by truncating mutations
FAP HNPCC Breast/ovarian cancers
41
What is a truncating mutation?
A mutation that results in a shorter protein being formed
42
Give some examples of trinucleotide repeat diseases
Fragile X (CGG repeat) Huntington's disease (CAG repeat) Myotonic dystrophy (CTG)
43
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
44
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
45
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
46
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
47
When is linkage analysis used?
If no cytogenetic information is available
48
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
49
What is the frequency of cystic fibrosis in ireland?
1 in 19 people
50
What is the chance that both your parents are carriers of CF?
1/400
51
If both your parents are carriers of CF what is the chance of you having CF?
1 in 4
52
What is the birth incidence of CF in Ireland
1/19 x 1/19 = 1/361 1/361 x 1/4 = 1,444 approximately
53
What is the most common mutation for CF?
delta F 508
54
What % of Irish cystic fibrosis patients have the deltaF 508 mutation?
80%
55
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
56
What chromosome is the CF gene located on?
Chromosome 7
57
The mutation for CF is found on what gene?
Cystic fibrosis transmembrane conductance regulator gene
58
Where is the mutation for CF located on CFTR gene?
Exon 10
59
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
60
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
61
What is the gene for muscular dystrophy called?
Duchenne muscular dystrophy gene The DMD gene or dystrophin gene
62
What does the DMD gene make?
Dystrophin protein
63
What is so special about the DMD gene?
It is the largest known gene
64
What is the most common mutation in DMD?
About 60% of males have a deletion of at least one exon
65
How many exons does the DMD gene have?
79 exons
66
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)
67
How would you go about detecting DMD?
2 multiplex PCR reactions can detect 98% of deletions A 5' multiplex and a 3' multiplex

2.1 Bioinformatics (7 decks)

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