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BM210 > Block 3 > Flashcards

Block 3 Flashcards

1
Q

what are two traits of polymorphisms?

A
  • may or may not have phenotypic effects
  • generally very old and are passed down through numerous generations
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2
Q

what is a general distinction between variants and mutations?

A
  • mutations are usually linked to a disease or phenotype whereas variation may not be.
    (- both are present in <_ 1% of the population)
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3
Q

what is an SNP?

A

Single Nucleotide Polymorphism - DNA sequence variation occurring commonly within a population in which a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes.
For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles.

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4
Q

what are microsatellites?

A

Short, tandem repeats of 2-7 nucleotides (=STR, SSR)

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5
Q

What are minisatellites?

A

variable number tandem repeats (=VNTR, 8 to <50 base pairs)

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6
Q

what are copy number variants?

A

0, 1, 3 or more copies of a large stretch of DNA sequence (1000bp (1kb) > Mb)

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7
Q

where is highly repetitive satellite DNA generally found?

A

near telomeres and around centromeres

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8
Q

alpha-satellite DNA (alphoid) is mostly present at …… and repeats extend for …… of base pair. Each repeat unit contains …….. between 3 and 32 base pairs

A
  1. centromeres
  2. millions
  3. smaller repeat units
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9
Q

what are transposons and retrotransposons?

A

transposons - DNA based
retrotransposons - RNA intermediate

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10
Q

in what way can mobile DNA elements be harmful?

A

they move and may copy proteins that cut them out and insert them elsewhere in the genome

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11
Q

what are the two types of tandem repeats?

A
  • microsatellites
  • minisatellites
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12
Q

what are seven applications of polymorphisms?

A
  • restriction fragment length polymorphisms (RFLP)
  • forensic sample identification
  • biodiversity
  • food quality
  • ancestry and archaeology
  • preparing to sequence the human genome
  • mapping of disease genes
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13
Q

what are restriction enzymes?

A

enzymes that act as primitive immune system for bacteria
they cut viral DNA sequences and can be used as a research tool

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14
Q

in forensic scenarios, ……. were originally needed to detect ……. from DNA. Now, ……. is used for this

A
  1. restriction digests
  2. microsatellites/VNTRs
  3. PCR
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15
Q

which alleles can be used as a sex marker and how is this done?

A
  • AMELX and AMELY
  • AMELX is 106bp long, AMELY is 112bp long
  • by amplifying a segment of DNA and analysing the sizes of the fragments, the sex of the sample donor can be determined
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16
Q

how can polymorphisms be used in ancestry?

A

the polymorphisms present in DNA give an indication of the donor’s ancestry and origin

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17
Q

how can polymorphisms be used in food quality testing?

A

PCR can detect polymorphisms in meat for certain animals (eg. cow vs horse)

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18
Q

what is the difference between a physical and a genetic map?

A

genetic - based on the recombination frequency between molecular markers
physical - alignment of DNA sequences with distances between markers measured in bps

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19
Q

why are genes considered “linked” and how can this be helpful in creating rough genetic maps?

A

they are positioned close together on the chromosome, not separated by recombination between chromosomes during meiosis therefore rough genetic maps are possible

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20
Q

why was this process not feasible for human genetic mapping and what was the solution?

A

unethical to breed humans, not enough visible traits to observe eg. no antennae.
polymorphisms without corresponding phenotypes/traits to be used as genetic markers

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21
Q

what were four lab techniques that helped with the above process?

A
  • RFLPs
  • DNA sequencing
  • gel electrophoresis/Southern Blotting
  • PCR
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22
Q

what does it mean if two microsatellite loci are completely, partially or unlinked?

A

completely - inherited together all of the time
partial - inherited together most of the time
unlinked - inherited 50% of the time

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23
Q

what are linkage maps based on?

A

determining the relative position of genetic markers by frequency of marker separation during meiosis through the generations

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24
Q

what is a centimorgan (cM)? (include conversion)

A

human genome linkage measurement
recombination fraction of 1/100 meioses
physically equivalent to between 0.7 and 1 Mb of DNA (depending on recombination frequency)

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25
Q

why are genetic maps not the be all and end all of mapping?

A

they only provide a rough idea of where markers are and where a disease gene is located

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26
Q

what are the functions of DNA libraries and databases?

A

libraries - offer infinite clones of any bit of the genome
databases - can map relationships/links (same chromosome, linked? etc)

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27
Q

why is DNA cloned into genomic DNA libraries?

A

a whole genome is too large and complex

28
Q

what is a BAC/YAC and how are they useful?

A

bacterial/yeast artificial chromosome - DNA fragments of interest can be inserted into them , which can then be added to the plasmids of bacteria/yeast cells. The fragments will then be replicated endlessly by the cell

29
Q

what does FISH stand for and what is it used for in BACs/YACs?

A

fluorescent in situ hybridisation - indicates where in the chromosome the DNA in a B/YAC is located based on their genetic markers and how they overlap with other B/YACs

30
Q

what is chromosome walking?

A

the process of “stitching” together a section of the genome by layering overlapping contigs to create the whole section

31
Q

what were the four goals of the human genome project (HGP)?

A
  • determine the sequence of the 3 billion chemical base pairs in human DNA
  • identify all genes in human DNA to their position on chromosomes
  • attempt to predict the function of all genes
  • utilise this info to understand disease, develop medicines, understand human variability, compare humans to other species etc.
32
Q

what were the two groups working of the HGP, who were their leaders and what was a key difference between the two?

A
  • International Human Genome Sequencing Project IHGSP, Dr Francis Collins, publicly funded
  • Celera Corporation, Dr J. Craig Venter, privately funded
33
Q

what were the three phases of the HGP?

A
  • Phase 1 - produce high resolution chromosomal maps, position genetic markers, create libraries of BAC clones for sequencing
  • Phase 2 - sequence each BAC DNA
  • Phase 3 - assemble all sequences to produce final draft and annotate to identify genes
34
Q

how were BACs ordered?

A

by combining genetic and physical maps via overlapping contigs

35
Q

what are shotgun clones?

A

the tiny fragments produced when BACs are broken up

36
Q

why were the genomes of non-human species sequenced before humans?

A

they acted as “dummy runs” while researchers waited for sequencing technologies to improve

37
Q

what is an example of a DNA sequencing technique?

A

Old Sanger Sequencing

38
Q

what is the method behind new sanger sequencing?

A

it is similar to PCR but used fluorescent terminators. A ddNTPs with fluorescent markers are introduced to a PCR reaction. This results in many DNA fragments of various lengths. When these are ran on a gel, the products are separated by size and a laser can scan the bonds to tell their terminating ddNTP. This shows you the order of bases by ordering the fragments by size and checking the terminating ddNTP.

39
Q

what were the pros and cons of the clone-by-clone method used by IHGSC?

A

pros - able to retrieve clones and can skip over highly repetitive sequences
cons - slow and expensive

40
Q

what is shotgun sequencing, why did Celera use it and what were its shortcomings?

A

It involved blasting the genome into fragments, sequencing them using computers to put them in order; it was quick; this process piggybacked off the work of the IHGSC, as it utilised public databases of sequencing mapping to assemble their generated sequence. Additionally, highly repetitive DNA caused difficulties as it couldn’t be determined where they came from

41
Q

why was simultaneous publishing beneficial for both the IHGSC and Celera?

A

Celera did not have enough genome sequenced and the IHGSC’s sequence was poor quality

42
Q

roughly how many genes do humans have and how much of the genome is this?

A

20-25,000 and ~1.5-5%

43
Q

what are pseudogenes?

A

genes that do not currently function but may have in the past and may do in the future

44
Q

what is population genetics?

A

the study of genetic differences in and between populations

45
Q

what is dbSNP?

A

a public and online database of SNP polymorphisms

46
Q

What was the aim of the International HapMap project, and which four populations did it study?

A

to determine the most common SNP variants in the world’s population; Nigeria, Japan, China, Utah

47
Q

humans have similar genome sizes to other less complex species. How do humans still end up more complex?

A

alternative splicing , lots of different final protein products can be produced from one primary RNA transcript

48
Q

what is a principal component?

A

a collection of polymorphisms that can be analysed in studies (eg. heritance studies)

49
Q

what can be determined from comparing two species’ genome?

A

how related they are & how genes and proteins change during evolution

50
Q

why were genomes helpful for early mammalian genome researchers?

A

It was the same number of genes as humans, but - only 3mil bases Because of this, it acted as a super concentrated genome for researchers

51
Q

what do modular domains allow for?

A

the development for novel genes/proteins over evolution

52
Q

what is it likely to mean if genes/ pathways are highly conserved across species?

A

they are likely to be very important to life

53
Q

What are three examples of protein families/ domains that higher organisms selectively expand?

A

any of the following:
- immune function
- intercellular signalling
- metabolic function
- olfaction
-haemostasis
- apoptosis
- neural function
- mRNA splicing
- translation

54
Q

how can a species most pressing selection pressures be determined by their genome?

A

by identifying the genes that change the quickest/the most recently

55
Q

what genes in humans show fast/recent changes?

A
  • pathogen response
  • cell cycle and DNA metabolism
  • protein metabolism
  • reproduction
  • neuronal activity
  • skin pigmentation
56
Q

CCR5 delta32 is a variant of a chemokine receptor 5 that prevents HIV viral particles from entering cells. However, it predates HIV significantly. Why could this be?

A

it may have protected populations from other viruses like smallpox

57
Q

what is the gene FOXP2 potentially involved in, and which 2 species (apart from humans) present in?

A

human-specific development of language, Neanderthals and Denisovans

58
Q

what can strategic sequence loss in species indicate?

A

an evolved way of life, eg. loss of olfactory genes like smell is not as important to the species as other senses like sight/hearing

59
Q

what are linkage disequilibrium (LD) blocks?

A

“units of inheritance”
haplotypes that remain intact over many generations

60
Q

what are the “peaks and troughs” on a recombination frequency graph?

A

peaks - recombination hotspots, where chiasma form
troughs - common haplotypes/LD blocks

61
Q

African populations are more diverse then others. True or False, and why?

A

True, populations migrating out of Africa were subject to bottleneck effects. These drastically lowered the population numbers and diversity so populations deriving from these are less diverse

62
Q

how did migrating populations gain genetic variation?

A

by mating with “cousin” species, like Neanderthals and Denisovans

63
Q

what is pharmacogenomics/genetics?

A

the study of the role of the genome in drug response

64
Q

what are five examples of factors under genetic control that pharmacogenomics can analyse?

A
  • inactivation/activation by oxidative pathways
  • conjugation for excretion through the kidneys
  • target sensitivity
  • toxicity
  • disease mutation type
65
Q

what are six research applications of the HGP?

A
  • all genes known forever
  • vast and integrated information set based on genome publicly available on the internet
  • bioinformatics is king and AI may help us solve many of the complex problems
  • equipment, reagents and materials now commercially available to exploit this information in the research setting
  • any genetic study can be (and should be) ‘Genome-wide’
  • population genetics has told us what it means to be human
66
Q

what are four medical applications of the HGP?

A
  • pharmacogenomics: the right drugs for the right people
  • genome-wide genetic studies offer best hope of cracking complex genetic disorders such as cancer, mental illness, type II diabetes etc
  • transcriptomics and proteomics: now possible to identify disease/state biomarkers, consequences of illness, consequences of drug action
  • diagnostic tests for simple and complex disorders: We may be able to predict future disease risk for everyone

BM210 (3 decks)

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