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CELS191 > Module 3: Human Molecular Genetics > Flashcards

Module 3: Human Molecular Genetics Flashcards

1
Q

Why was the human genome sequenced?

A

Identify all human genes and their roles, analyse genetic variation between humans, sequence genomes of several model organisms, develop new sequencing techniques and computational analyses, share genome information with scientists and the general public as fast as possible

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2
Q

What does the human genome consist of

A

22 autosomes, 2 sex chromosomes (6 billion base pairs, <20000 genes), single circular mitochondrial DNA (16,569 base pairs, 37 genes)

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3
Q

What were the key findings of the human genome?

A

There are fewer genes than expected (<20000), less than 2% of our genome codes for proteins, the genome is dynamic, we still don’t know what many protein coding genes do, most human genes are related to those of other animals, humans are 99.9% similar at a sequence level

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4
Q

How many genes does the human genome have

A

<20000

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5
Q

What percentage of the genome is exons

A

<2%

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6
Q

What percentage of the genome is introns

A

20%

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7
Q

What percentage of the genome has an unknown function

A

~20%

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8
Q

SNPs

A

Single nucleotide polymorphisms: sites in the DNA that commonly vary within populations

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9
Q

How common are SNPs

A

Around 1 in 300 nucleotides

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10
Q

Where do SNPs come from

A

Mostly from your parents

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11
Q

Why sequence a genome?

A

Find out who you’re related to, where some of your ancestors come from, disease risk/association, hair loss risk, muscle type, drug response, crime solving

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12
Q

Causative vs linked SNPs

A

In vs not in gene

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13
Q

Non-coding vs coding SNP

A

Non coding changes amount of protein produced, coding may change amino acid sequence

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14
Q

What makes it a SNP not a mutation

A

If present in more than 1% of the population

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15
Q

STRs

A

Short tandem repeats: repeats of 2-5 nucleotides found in specific regions of the genome. Inherit a gene from each parents, may be different lengths. E.g could be 3,8 at STR1

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16
Q

InDels
(e.g cystic fibrosis)

A

Small insertions or deletions, can cause frameshift if not a multiple of 3

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17
Q

What is the second most common variant type in the human genome

A

InDels

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18
Q

CNVs
(e.g Huntington’s, trisomy 21)

A

Copy number variations: chunks of DNA >500bp that are present at different amounts or copy numbers relative to a reference genome

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19
Q

How many CNVs do humans have

A

10000

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20
Q

Many genes found in CNV are associated with ________

A

Sensory perception and immunity

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21
Q

What are human genomics likely to be used for in the future

A

Further research into evolution and descent, complex polygenic and rare diseases, drugs and personalised medication

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22
Q

What ethnicity genomes vary the most

A

African as they have had the most time to evolve

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23
Q

What is comparative genomics

A

Comparing genomes to examine what is conserved and what is different

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24
Q

Why is it hard to sequence ancient DNA

A

DNA degrades and is masked by more modern DNA. DNA bases are also modified as they degrade, sometimes changing the sequence

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25
Q

What were the most outstanding findings from sequencing neanderthal genomes

A

Some of us (Asian and Europeans) carry neanderthal DNA (~2-4%). Africans show no sign of these alleles

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26
Q

Where is Denisovan variation seen in modern humans

A

4-6% of the genomes of present day Melanesians

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27
Q

How are sequenced genomes compared

A

Alignment

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28
Q

Mutation definition

A

Permanent change to the base sequence of a gene

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29
Q

The outcome of a mutation can depend on

A

Environmental effects (e.g diet, exposure to toxins), other genes (genetic background)

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30
Q

How are mutations classified

A

Dominant vs recessive and loss vs gain of function

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31
Q

What is a dominant mutation

A

Causes a phenotype when heterozygous

32
Q

What is a recessive mutation

A

Causes a phenotype only when homozygous

33
Q

A loss of function mutation is often

A

Recessive, as a normal copy exists on the other chromosome which can replace the lost function

34
Q

A gain of function mutation is often

A

Dominant because having an allele that works too well or does something novel will not be replaced by the normal copy of the gene.

35
Q

Give an example of an autosomal recessive disease

A

Cystic fibrosis

36
Q

Give an example of an autosomal dominant disease

A

Huntington’s

37
Q

Give an example of an X-linked recessive disease

A

Haemophilia A and B

38
Q

Inheritance patterns step 1

A

Are only males affected and are all sons of fathers affected (Y linked)

39
Q

Inheritance patterns step 2

A

Are there any cases where an affected child does not have at least one affected parent (recessive)

40
Q

If recessive, inheritance patterns step 3

A

Are all sons of an affected mother affected and are more males than females affected (x-linked vs autosomal)

41
Q

If dominant, Inheritance patterns step 3

A

Are all daughters of an affected father affected (x-linked vs autosomal)

42
Q

How to find a disease causing gene using sequencing

A

Map to human reference, identify novel variants and whether they’re likely to be harmful, then validate and test

43
Q

Examples of polygenic disorders

A

Obesity, diabetes, rheumatoid arthritis, gout, bipolar disorder

44
Q

How to find genes contributing to polygenic diseases

A

Identify variations from human reference, identify variations shared in cases not controls, validate and test

45
Q

Most genetic disorders are probabilistic not deterministic, meaning

A

Having a disease related genetic variation doesn’t mean you’ll get the disease

46
Q

How do we get information about the function of a gene from its phenotype

A

By studying organisms that are naturally mutant for a particular gene we can work out what that gene might do (where no natural mutants exist we make our own)

47
Q

Variation is common but phenotype causing mutations are

A

Rare

48
Q

What is functional molecular genetics

A

Increase rate of mutation, select for phenotype of interest, take gene you’re interested in, copy and insert into another organism, deliberately break particular gene you’re interested in to see what happens

49
Q

What are model organisms (e.g mouse, zebra fish, drosophila)

A

Ones that can be easily raised in a controlled environment and are easy to manipulate genetically

50
Q

What is transgenesis

A

Engineering a multicellular organism by adding in foreign DNA (e.g regulatory sequence to turn on production of a protein in an organism)

51
Q

What is CRISPR/Cas9 used for

A

Damage or modify gene interested in, examine organism or offspring and work out what gene normally does, i.e targeted mutation

52
Q

What is needed for CRISPR/Cas9

A

Short guide RNA to bind to gene of interest, Cas9 protein to cut DNA (double stranded cut at site)

53
Q

How does CRISPR/Cas9 result in mutation

A

In the absence of a template DNA repair enzymes try to repair cut, often resulting in errors

54
Q

What type of mutations usually occur at CRISPR/Cas9 cut site

A

Small indels

55
Q

How can CRISPR/Cas9 be used in gene editing

A

By providing a repair template for the DNA to be fixed based off

56
Q

Can we fix genetic disease

A

Yes but only if we know what causes it and have a way to correct the defect

57
Q

How does gene therapy work with cystic fibrosis (CFTR gene)

A

Plasmid containing normal gene in liposome fuses into cell, enters nucleus, incorporated into DNA, functional protein for chloride ion channel made

58
Q

How can germline mutations be fixed if mutation is in mitochondrial DNA (called 3 parent babies)

A

Remove nucleus of fertilised egg, transplant into donor egg with healthy mitochondrial DNA (and destroyed nucleus)

59
Q

What is pre-implantation genetic diagnosis

A

Parents with identified risk create IVF babies, embryos screened for genetic diseases before implantation

60
Q

What are the 5 stages of embryonic development

A

8 cell stage, cell polarisation, compaction, inner apolar cells cut off, blastocyst

61
Q

What is the outer layer of the blastocyst called (formerly polar)

A

Trophectoderm

62
Q

What type of cells does an embryo begin as

A

Totipotent

63
Q

What type of cells are embryonic stem cells

A

Pluripotent (give rise to anything except trophectoderm)

64
Q

Once specific genes have been turned on and off, the cell type is:

A

Determined

65
Q

Once the cell has become a certain type it is said to be:

A

Terminally differentiated

66
Q

Approximately how many types of cells are there in our body

A

200

67
Q

What are iPS cells

A

Induced pluripotent stem cells, made by reprogramming adult skin cells

68
Q

Adult tissue stem cells are

A

Multipotent (give rise to a few types of cells including stem cells: regeneration)

69
Q

Umbilical cord stem cells are

A

Multipotent as they are immature blood stem cells

70
Q

Stem cells are important for what types of tissue

A

Blood and skin which need constant renewing

71
Q

Blood stem cells are also called

A

Hematopoietic stem cells

72
Q

What is gene therapy

A

A way to correct single gene disorders

73
Q

How can viruses be used in gene therapy

A

Insert RNA version of normal allele into retrovirus or other viral vector, let virus infect bone marrow cells tht have been cultured, viral DNA carrying normal allele inserts into chromosome, cells reinjected

74
Q

What is regenerative medicine

A

The idea that pluripotent stem cells can be used to repair or replace damaged organs or tissues by being encouraged to differentiate into needed cell type, then transplanted into patients.

75
Q

Example of IPSC transplants

A

Corneal transplants

76
Q

What kind of variation is captured by commercial genetic sequencing companies?

A

SNPs

CELS191 (7 decks)

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