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BM 210: Introduction to Biochemistry > Block C Part 1: Human Genetic Variation and Use of Human Polymorphisms > Flashcards

Block C Part 1: Human Genetic Variation and Use of Human Polymorphisms Flashcards

1
Q

What does locus mean?

A

A place or location in our genome, as we have 2 copies of each gene, locus usually refers to both
(Lecture 1, Slide 4)

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2
Q

What is a DNA polymorphism?

A

An allelic (different) form of sequence difference that is present in at least 1 or 2% of a population
(Lecture 1, Slide 5)

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3
Q

How big can polymorphisms be?

A

They can range from being a single nucleotide (SNP) to thousands of bases depending on the chromosome and individual
(Lecture 1, Slide 5)

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4
Q

What are 2 differences between a polymorphism and a mutation?

A

Polymorphism may not have the phenotypic effects (such as cause traits / disease) and most are old and have been passed down through many generations whereas mutation indicates connection with a disease / phenotype
(Lecture 1, Slide 6)

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5
Q

What is a polymorphism appearing in less than 1-2% of a population called?

A

A “rare variant” or mutation
(Lecture 1, Slide 6)

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6
Q

What is 1 possible reason for a polymorphism being very rare?

A

Because it has just appeared de novo
(Lecture 1, Slide 6)

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7
Q

What does de novo mean?

A

a genetic variation / mutation that is not inherited from parents ( a brand new mutation)
(Lecture 1, Slide 6)

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8
Q

What are 4 types of polymorphic (mutant) DNA sequences?

A

SNPs (single-nucleotide polymorphisms)
Microsatellites
Minisatellites
CNV (copy new variant)
(Lecture 1, Slide 7)

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9
Q

What is an SNP?

A

A single nucleotide polymorphism - a sequence change e.g changing an A to a G
(Lecture 1, Slide 7)

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10
Q

What is a microsatellite polymorphism?

A

Short tandem repeats (STR) (AKA simple sequence repeats - SSR) - sequence repeats of 2-7 base pairs e.g [CAG]n
(Lecture 1, Slide 7)

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11
Q

What is a minisatellite polymorphism?

A

Variable number tandem repeats (VNTR) 8 to 50+ base pairs repeating e.g [CGT…..TAG]n
Essentially microsatellite but with a bigger sequence repeating
(Lecture 1, Slide 7)

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12
Q

What is a CNV polymorphism?

A

Copy number variant - 0,1,2,3 or more copies of a large stretch of DNA sequence
(Lecture 1, Slide 7)

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13
Q

What is an allele?

A

The term given to the specific DNA sequence present at any given polymorphic locus
(Lecture 1, Slide 8)

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14
Q

What is Repetitive DNA?

A

Strings of A,C,G and T nucleotides repeating themselves in patterns
(Lecture 1, Slide 11)

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15
Q

Repetitive DNA is often what?

A

Polymorphic
(Lecture 1, Slide 11)

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16
Q

What are 2 types of repetitive DNA?

A

Highly Repetitive DNA
Middle Repetitive DNA
(Lecture 1, Slide 11)

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17
Q

What is one form of highly repetitive DNA?

A

Satellite DNA
(Lecture 1, Slide 12)

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18
Q

Where is satellite DNA found?

A

In long tandem (end to end) strings of arrays, usually near telomeres (ends of chromosomes) or centromeres (middle of chromosome)
(Lecture 1, Slide 12)

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19
Q

What is α-satellite DNA?

A

It functions in the centromeres of chromosomes, with repeats potentially extending for millions of base pairs
(Lecture 1, Slide 13)

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20
Q

Why are there still some gaps in the human genome today?

A

As some DNA such as α-DNA are very difficult to study
(Lecture 1, Slide 13)

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21
Q

What can middle repetitive DNA be compared to?

A

A virus infecting your computer, or a parasite
(Lecture 1, Slide 14)

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22
Q

What are 2 types of middle repetitive DNA?

A

Transposons and retrotransposons
(Lecture 1, Slide 14)

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23
Q

Are transposons and retrotransposons DNA or RNA based?

A

Transposons are DNA based whereas retrotransposons use an RNA intermediate
(Lecture 1, Slide 14)

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24
Q

What do transposons and retrotransposons do?

A

They often encode the proteins needed to cut them out, copy them and insert them elsewhere in the gene
(Lecture 1, Slide 14)

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25
Q

How are most transposons and retrotransposons been inactivated?

A

Through mutation / truncation (part of it being removed) through human evolution
(Lecture 1, Slide 15)

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26
Q

How long do transposons and retrotransposons take to move locus?

A

~ 100 - 200 births
(Lecture 1, Slide 15)

27
Q

What is a consequence of transposons and retrotransposons?

A

Some inactivate genes - e.g vit c synthesis in humans is no longer possible
(Lecture 1, Slide 15)

28
Q

What do micro and minisatellites show polymorphic variation in?

A

Repeat number and hence variable length
(Lecture 1, Slide 19)

29
Q

Where do micro and minisatellites appear?

A

Throughout the genome - even in coding regions
(Lecture 1, Slide 19)

30
Q

What are 4 applications of polymorphisms?

A

Answers include:
Restriction fragment length polymorphisms (RFLPs)
Forensic sample identification
Biodiversity
Food quality
Ancestry / archaeology
Preparing to sequence the human genome
Mapping of disease genes
(Lecture 1, Slide 22)

31
Q

What are restriction enzymes?

A

Bacterial enzymes which act as a primitive immune system; they cut (restrict) a specific phage (viral) DNA sequence
(Lecture 1, Slide 23)

32
Q

What are restriction enzymes used by researchers as?

A

A molecular tool
(Lecture 1, Slide 23)

33
Q

What are restriction fragment length polymorphisms?

A

Restriction fragment sizes are altered by changes in or between enzyme recognition sites (e.g an SNP in the enzyme recognition site resulting in the enzyme not cutting there)
(Lecture 1, Slide 24)

34
Q

How can polymorphisms be used to permit DNA “fingerprinting”?

A

Techniques are used to distinguish the unique combination of polymorphisms present in one individual from another
(Lecture 1, Slide 25)

35
Q

What was the first use of DNA to find someone innocent / guilty of a crime?

A

By Prof. Sir Alec Jeffreys in the 1980s in England in a case where 2 girls were sexually attacked and murdered
(Lecture 1, Slide 26)

36
Q

Nowadays, what is used instead of restriction digests to obtain the DNA region of interests?

A

PCR based methods, and several single locus probes for minisatellites
(Lecture 1, Slide 27)

37
Q

What are SGM+ (second generation multiplex) markers?

A

Each individual produces a set of 20 numbers which can be placed on a database and compared to samples from the scene of a crime
(Lecture 1, Slide 28)

38
Q

What is interesting about the amelogenin gene?

A

PCR amplification shows us that the 2 alleles are different sizes, with AMELX on the X chromosome being 106 bp and AMELY on the Y chromosome being 112bp
(Lecture 1, Slide 29)

39
Q

What are 2 reasons that we needed a genetic map of how our genes are arranged on our chromosomes?

A

To enable the mapping and identification of disease genes
To tackle the human genome project
(Lecture 2, Slide 3)

40
Q

How are rough genetic maps of chromosomes possible for animals?

A

Some mutant traits do not independently segregate, with the presence of one affecting the presence of another which indicates their genes are in close physical proximity and not separated by recombination between chromosomes during meiosis
(Lecture 2, Slide 4)

41
Q

What is linkage in genes?

A

It’s a measure of how far apart genes are from each other, and in turn is how likely a meiotic recombination event is between two loci
(Lecture 2, Slide 5)

42
Q

Why is the linkage method of constructing a genetic map not possible in humans?

A

As we can’t set up crosses between humans and we don’t have enough visible traits / mutations to make it worthwhile
(Lecture 2, Slide 6)

43
Q

How did we make human genetic maps?

A

New molecular biology technologies were being developed which allowed polymorphisms without corresponding traits / phenotypes to be used as genetic markers
(Lecture 2, Slide 7)

44
Q

What polymorphisms are the genetic markers of choice today?

A

SNPs
(Lecture 2, Slide 7)

45
Q

How do you figure out what mutation causes certain genetic diseases?

A

You look for a genetic marker that co-segregates with the disease gene
(Lecture 2, Slide 10)

46
Q

What does co-segregate mean?

A

When two or more genetic markers are inherited together
(Lecture 2 Slide 10)

47
Q

What do you first need to do in order to figure out which genetic markers corresponds to specific genetic diseases?

A

Create a map of the chromosomal location of all the polymorphic markers and how they are positioned with respect to each other
(Lecture 2, Slide 10)

48
Q

How do you know what linkage exists between 2 microsatellite loci?

A

Genotype many mother, father & child “trios” or extended families

If alleles are always inherited together = complete linkage

If alleles are mostly inherited together = partial linkage

If 50/50 chance of inheritance = no linkage
(Lecture 2, Slide 13)

49
Q

What is meiotic recombination?

A

It’s a specific genetic process which occurs during the formation of the gametes (sperms / eggs) where genetic material is exchanged between homologous chromosomes
(Lecture 2, Slide 15)

50
Q

What is (meiotic) recominbation frequency?

A

It’s the measure of the likelihood that two genes on the same chromosome will undergo recombination (and will not be inherited together)
(Lecture 2, Slide 15)

51
Q

What does “phase” mean in the context of genetic markers?

A

That they are on the same chromosome
(Lecture 2, Slide 17)

52
Q

What does “haplotype” mean?

A

The order of in-phase alleles along a chromosome (also inherited together from a single parent apparently which isn’t mentioned in the PowerPoints)
(Lecture 2, Slide 17)

53
Q

What does 1 cM (centimorgan) represent?

A

The distance between 2 markers where on average 1% of offspring will exhibit a recombination event between the 2 markers
(Lecture 2, Slide 21)

54
Q

What is the problem with genetic mapping?

A

It’s a mathematical exercise which only provides a rough idea of where markers are and where a disease gene is located
(Lecture 2, Slide 23)

55
Q

What are 2 ways to collate, organise and distribute huge quantities of DNA to make a “physical map” and what specific purposes do they have?

A

Library - for storage / duplication / distribution
Database - for relationships
(Lecture 2, Slide 26)

56
Q

How are DNA sequences cut into a plasmid?

A

Restriction enzymes are used to cut the DNA at specific sequences in the DNA (such as GAATTC) the cut ends have overhangs which allow them to reform in the presence of the enzyme ligase
(Lecture 2, Slide 29)

56
Q

Why do we need to clone DNA into genomic DNA libraries?

A

As a whole genome is far too cumbersome and complex to work with so DNA strands are chopped up and stored to make a genomic DNA library
(Lecture 2, Slide 27)

56
Q

How can molecular biologists use plasmids to produce large quantities of DNA for analysis such as sequencing?

A

Bacteria sometimes carry genetic material present on plasmids / episomes. Molecular biologists can “engineer” the plasmids to carry bits of foreign DNA of interest, the bacteria then become photocopiers producing infinite quantities of identical (cloned) copies of that DNA
(Lecture 2, Slide 28)

57
Q

What is the first step of making a DNA clone library?

A

Break up the human genomic DNA into the bite-size chunks using random physical shearing or restriction digest
(Lecture 2, Slide 30)

58
Q

What is the second step of making a DNA clone library?

A

Place each fragment into a vector (cloning step) which is a DNA sequence that allows its selection and replication when introduced into a prokaryotic species
(Lecture 2, Slide 30)

59
Q

What do you do when making a genetic library after placing the fragments into a vector?

A

Store these in a bacteria (BACs) or yeast (YACs) as clone library
(Lecture 2, Slide 30)

60
Q

What do you do when making a genetic library the step after storing the DNA fragments into bacteria or yeast clone libraries?

A

A single bacterium with one BAC and it will grow into a clonal (identical) population / colony , this can then be further propagated, stored in a freezer or have the BAC + genomic DNA fragment isolated for analysis
(Lecture 2, Slide 30)

61
Q

How can you make a genetic library from mRNA found in a tissue?

A

Convert to cDNA and then clone to make a cDNA library representing all genes expressed
(Lecture 2, Slide 30)

62
Q

How do you turn genetic libraries into a true “physical map”?

A

Relationships between clones need to be worked out - USE BAC/YAC clones as probes for FISH - tells you where they are located and on which chromosomes
(Lecture 2, Slide 32)

BM 210: Introduction to Biochemistry (12 decks)

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