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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
Q

What % of human genome is simple sequence repeats ?

A

3%

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26
Q

What % of human genome is DNA transposon fossils?

A

3%

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27
Q

What % of human genome is retrovirus-like elements?

A

8%

28
Q

What % of human genome are SINEs ?

A

13%

29
Q

What % of human genome are LINEs?

A

21%

30
Q

How many separate human genome sequences are there?

A

Over 1,000,000

31
Q

Why are genomic databases needed?
(3)

A

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
Q

What are the three classifications of genetic diseases?

A

Autosomal dominant

Autosomal recessive

X-linked

33
Q

Give two examples of autosomal dominant disorders

A

Huntington’s Disease

Myotonic dystrophy

34
Q

Give three examples of autosomal recessive disorders

A

Cystic fibrosis
Mental retardation
Spinal muscular atrophy
Wilson’s disease

35
Q

Give some examples of X-linked disorders

A

Red-green colour blindness

Fragile X Mental retardation

Duchenne muscular dystrophy

haemophilia A

36
Q

List the six different types of mutations

A

Point mutations

Large deletions

Small deletions

Insertions

Truncating mutations

Trinucleotide repeat diseases

37
Q

Give an example of a disease caused by a point mutation

A

Most conditions e.g. cystic fibrosis or Wilsons

38
Q

Give an example of a condition caused by a large deletion

A

Duchenne muscular dystrophy

39
Q

Give an example of a disease caused by small deletions

A

Familial adenomatous polyposis (FAP)

Hereditary nonpolyposis colorectal cancer (HNPCC)

40
Q

What diseases are caused by truncating mutations

A

FAP
HNPCC
Breast/ovarian cancers

41
Q

What is a truncating mutation?

A

A mutation that results in a shorter protein being formed

42
Q

Give some examples of trinucleotide repeat diseases

A

Fragile X (CGG repeat)
Huntington’s disease (CAG repeat)
Myotonic dystrophy (CTG)

43
Q

What approach have we taken to cloning genes?

A

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
Q

What is the positional gene cloning approach used for?

A

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
Q

How does the positional cloning approach of genes allow us to identify candidate genes in location?

A

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
Q

What is the basis of linkage analysis?

A

The ability to follow individual chromosomes through a family and identify chromosomes and chromosome regions that segregate (follow) the disease

47
Q

When is linkage analysis used?

A

If no cytogenetic information is available

48
Q

Explain in your own words what linkage analysis is?

A

We follow mutated chromosomes through a family by looking at the phenotypes (we look for polymorphisms)

Need to know diagrams for linkage analysis

49
Q

What is the frequency of cystic fibrosis in ireland?

A

1 in 19 people

50
Q

What is the chance that both your parents are carriers of CF?

A

1/400

51
Q

If both your parents are carriers of CF what is the chance of you having CF?

A

1 in 4

52
Q

What is the birth incidence of CF in Ireland

A

1/19 x 1/19 = 1/361
1/361 x 1/4 = 1,444 approximately

53
Q

What is the most common mutation for CF?

A

delta F 508

54
Q

What % of Irish cystic fibrosis patients have the deltaF 508 mutation?

A

80%

55
Q

What causes CF?

A

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
Q

What chromosome is the CF gene located on?

A

Chromosome 7

57
Q

The mutation for CF is found on what gene?

A

Cystic fibrosis transmembrane conductance regulator gene

58
Q

Where is the mutation for CF located on CFTR gene?

A

Exon 10

59
Q

Write about X-linked muscular dystrophy
(6)

A

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
Q

Why do X-linked conditions predominantly affect males?

A

Because females have two copies of the X chromosome and can use the other chromosome if need be

61
Q

What is the gene for muscular dystrophy called?

A

Duchenne muscular dystrophy gene
The DMD gene or dystrophin gene

62
Q

What does the DMD gene make?

A

Dystrophin protein

63
Q

What is so special about the DMD gene?

A

It is the largest known gene

64
Q

What is the most common mutation in DMD?

A

About 60% of males have a deletion of at least one exon

65
Q

How many exons does the DMD gene have?

A

79 exons

66
Q

Where are the two hotspots for deletions in the DMD gene?

A

5’ end of gene (from the promoter to exon 19)

3’ end of gene (from exon 40 to exon 19)

67
Q

How would you go about detecting DMD?

A

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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