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BIO 1A03 > Theme 5 > Flashcards

Theme 5 Flashcards

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Biology 101 flashcards
1
Q

DNA polymorphisms

A

1 or 2 alternate forms (alleles) at a chromosomal region that differs in either a single nucleotide base or have variable numbers of tandem repeats (VNTRs) in a given population of individuals

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2
Q

DNA markers

A

on a genetic map, are DNA polymorphisms that occur in non-coding DNA
- detectable by microarray analysis, PCR, southern blot techniques or DNA sequencing

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3
Q

SNPs

A

Single Nucleotide Polymorphisms

  • variations brought on by single nucleotide base pair substitutions in DNA that occur in a significant portion of a population
  • one of the most common types of genetic variation, scattered throughout the genome
  • when found close to a gene, used as markers for finding a particular gene
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4
Q

detecting SNPs

A

genotyping microarray is used
- loading wells with:
C, G, A, T - they will match one strand of one allele of the SNP
and X, Y - deliberate mismatches adjacent to SNP
- 2 possible alleles are tested for and whichever wells they base pair in will fluoresce (the well will)
note: electrophoresis is not an option because a change in SNP won’t change bp length

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5
Q

tandem repeats

A

patterns of 1 or more nucleotides that are repeated directly adjacent to another, found in various lengths in individuals across a population
- results in the variations observed between species

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6
Q

detecting VNTRs

A

using PCR and gel electrophoresis

  • tandem repeats are targeted and amplified with primers specific to flanking regions
  • bands that migrate the least distance are larger and therefore contain a greater number of VNTR copies
  • used in DNA profiling (DNA fingerprinting) but is extremely unlikely that any unrelated individuals would have the same VNTRs
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7
Q

genotype

A

a representation of the pair of alleles carried by a person

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8
Q

phenotype

A

the cell or body’s interpretation of the genotype

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9
Q

sickle cell anemia phenotype

A
  • sickle shaped cells that don’t carry oxygen properly and lead to anemia
  • sickle cells can also block capillaries and cause acute pain
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10
Q

HbA / HbA genotype results for beta-globin

A

phenotype: regular RBC are produced
- no symptoms of sickle cell anemia
homozygous genotype for HbA alleles
- codes for AA glutamine

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11
Q

HbS / HbS genotype results for beta-globin

A

phenotype: symptoms of sickle cell anemia
- no functional beta-globin proteins
homozygous genotype for HbS alleles
- amino acid produced is valine instead of glutamine, causing altered tertiary 3D structure that has decreased oxygen binding ability and aggregation causes RBC to have sickle shape

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12
Q

HbA / HbS genotype results for beta-globin

A

heterozygous genotype, 2 alleles are different (1 from each parent)

phenotype: no symptoms of sickle cell anemia, though cells exhibit both protein variants (both glutamine and valine)
- enough of the normal beta-globin to give us normal enough Hb to carry oxygen properly

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13
Q

beta-globin variations in populations around the world

A
  • across nations with the highest prevalence of sickle cell anemia, it’s been found that there are 5 possible distinct B-globin haplotypes found across patients that correlate to each region with sickle cell anemia SNPs
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14
Q

individuals heterozygous for sickle cell allele

A

have a protective effect against malaria, a selective advantage

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15
Q

variation in gene copy number (CNV)

A
  • a region of a chromosome that may be duplicated or deleted compared to the normal amount of copies present
  • can occur in coding and non-coding regions
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16
Q

CNV detection

A

copy number variations detected based on fluorescence intensities during DNA microarray analysis where more fluorescence means there are more copy numbers

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17
Q

the effect of gene copy number on phenotype

A
  • variations are thought to be a direct result of selective pressures such as an advantage to digesting more starch if you have a greater copy number
    ex. AMY1 copy number is higher in individuals with a historically high starch diet
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18
Q

sequence polymorphism vs. length polymorphism

A

sequence: changes the message with one nucleotide
length: ex. tandem repeats - useful in paternity testing

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19
Q

linked SNPs

A

don’t necessarily cause a change but are close enough to a coding region that it gets copied with the genome

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20
Q

causative SNPs

A

affect the way a protein functions, correlating with a disease
ex. in an intron (indirectly) or an exon (directly) because exons code for genetic material

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21
Q

using PCR to detect VNTR differences in paternity testing

A
  • need to look at many VNTRs to be sure

- when neither fragment matches the father, the child is likely someone else’s

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22
Q

meiosis

A

replication of gametes which are haploid rather than diploid

  • has 2 rounds
  • allows production of offspring that are not genetically identical
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23
Q

prophase 1

A
  • homologous chromosomes condense and undergo synapsis

- final product is recombinant chromatids

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24
Q

recombination

A

a process that occurs in prophase 1

- involves the crossing over of homologous chromosomes and results in genetic variation

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25
Q

synapsis

A

pairing and physical connection of homologous chromosomes during prophase 1 via synaptromeal complex which holds the homologous chromosomes together during synapsis

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26
Q

sister chromatids vs. homologous chromosomes

A

sister chromatids: a pair of chromosomes that have been duplicated

homologous chromosomes: are individual chromosomes inherited from each parent and could be different

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27
Q

crossing over

A

exchange of corresponding segments of DNA b/w homologous chromosome pairs

  • occurs at x-shaped regions called chiasmata
  • increases genetic diversity
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28
Q

chiasmata

A

where 2 homologous chromosomes physically cross over to exchange DNA segments during prophase 1

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29
Q

reductional division

A

refers to meiosis 1
- called reductional division because of the reduction in chromosome number (each chromosome has 23 chromosomes by the end)

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30
Q

equational division

A

refers to meiosis 2

  • called equational because parent cells start off with the same number of chromosomes as the gametes produced at the end of meiosis 2
  • possible because duplicated sister chromatids gets separated
  • more similar to mitosis
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31
Q

dominant trait

A

the ones that appear in offspring of. cross b/w true breeding or homozygous parents

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32
Q

anaphase 1

A

homologous chromosomes separate but sister chromatids do not separate
- synaptonemal complex breaks down to allow this

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33
Q

telophase 1

A

daughter cells are ready to move into prophase 2 when each half has a complete haploid cell of duplicated chromosomes (with each chromosome consisting of a pair of recombinant chromatids)
- at the end of telophase 1, nuclear envelope reforms, chromosomes slightly uncoil and cytokinesis follows to produce 2 separate cells

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34
Q

prophase 2

A

nuclear envelope breaks down and chromosomes condense

- spindle apparatus reforms

35
Q

anaphase 2

A

sister chromatids separate (they are NOT genetically identical because of crossing over)
- proteins holding sister chromatids together break down to allow separation

36
Q

non-disjunction

A

results in some gametes having extra chromosomes and other gametes having less chromosomes

  • leads to detrimental effects in generated offspring
  • can also occur in mitosis and be observed in cancer cells
37
Q

homozygous organisms

A

carried 2 identical alleles for a specific trait

38
Q

Gregor Mendel

A

characterized traits as dominant or recessive

- developed 2 laws: law of segregation and the law of independent assortment

39
Q

why is the blended model of inheritance not valid

A

because F1 offspring would be a blend of the 2 colours but instead they were reflective of the ratio of dominant to recessive

40
Q

Mendel’s 1st law of segregation

A

states that 2 alleles of a gene separate from each other into different gametes during gamete formation in both parents

  • based on the assumption that alternate versions of genes account for variations in inherited traits
  • if 2 alleles at a locus differ, then the dominant allele determines the organism’s final trait
  • attributed to separation of chromosomes during anaphase 1
41
Q

Punnett square

A

illustrates prediction of offspring b/w individuals of known traits

  • must consider possible gametes produced
  • practice one
42
Q

Mendel’s 2nd law of independent assortment

A

only applies to non homologous chromosomes, and genes/allele pairs found on different chromosomes

  • states that the segregation of one set of alleles of a gene pair is independent of the segregation of another set of alleles in a different gene pair
  • depends on alignment of homologous chromosomes at metaphase plate during metaphase 1
43
Q

monohybrids

A

organisms that are heterozygous for the trait produced by the cross

44
Q

nondisjunction in meiosis vs. mitosis

A

in meiosis - it affects the embryo which will affect the whole organism
- when homologous chromosomes do not separate during meiosis 1
- when sister chromatids do not separate during meiosis 2
in mitosis - it affects only a certain cell types but can result in a tumour

45
Q

meiosis in males vs females

A

it is less energetically costly for males and so they can reproduce throughout their lifetime

46
Q

the result of nondisjunction in meiosis

A
  • one gamete gets an extra copy of a chromosome while the other receives no copy
  • other chromosomes are distributed properly
  • mostly happens because of spindle checkpoint malfunctions
47
Q

aneuploid cells

A

have an abnormal number of chromosomes

48
Q

chromosomal abnormalities result in

A

40-50% of spontaneous abortions

49
Q

monosomy

A

having one less chromosome in a gamete that combines with a normal gamete (the gamete therefore contains 1 copy of that particular gene)

50
Q

trisomy

A

has 3 copies of a chromosome

- therefore 2 of the same kind will be present in a gamete

51
Q

mitotic arrested males

A

can also produce sperm cells with abnormal chromosome numbers (aneupoloidy)

52
Q

down syndrome

A

3 copies of chromosomes 21

  • affects 1/700 children
  • usually parents are older, from oocytes that have undergone nondisjunction
  • dev’tal challenges
  • usually live to be 50-60, and die from immune disorders or heart disease
53
Q

bioinformatic analysis

A

allows scientists to analyze proteins present in amniotic fluid that are characteristic of down syndrome development

54
Q

Dr. Brian Golding

A

looks at biology and math - computational biology

- looks at trisomy of chromosome 21 and has seen abnormal interactions b/w proteins

55
Q

Klinefelter syndrome

A

males with an extra X chromosome (genotype XXY)

  • most common aneuploidy in humans (1/500-1000 men)
  • can come from males or females,
  • men have more feminized structure, breast dev’t
  • autosomes are find but males generally produce less viable gametes
56
Q

Turner syndrome

A

monosomy of the X chromosome (most result in spontaneous abortions)
genotype XO
- less development and sterile, webbed neck
- 1/5000 births

57
Q

Caster Semenya

A
  • a female track star who had a hypersensitivity to androgen (hyperandrogenism) which lead to an uproar about gender testing in south african track and field association which probably ruined her career
  • this sucks because other platforms (NBA) look for performance enhancing polymorphisms (ex. being very tall)
58
Q

causal relationship b/w aneuploidy and tumourigenesis

A
  • mitotic chromosome instability is a feature of most cancer cells and it can lead to aneuploidy
    ex. males w breast cancer - have multiple copies of many chromosomes with lots of mismatching compared to healthy cells – this variation makes it hard to treat cancer cells
59
Q

weakened mitotic checkpoint

A

results in chromosome instability

ex. delay in splitting of chromosomes or one gets pulled away super quickly affecting many genes and causes aneuploidy
- Taxol is the drug that targets this and can stabilize microtubules against depolymerization so the cell remains in metaphase-anaphase and leads to apoptosis of cancer cells

60
Q

symbols on pedigree charts: what do they mean

A
  • single horizontal line - mating b/w individuals
  • vertical line - offspring from these people arranged horizontally L to R in order of birth
  • double line = mating b/w relatives
  • circles: female
  • squares: male
  • open symbol: not affected
  • filled in symbol: affected
  • lines running at a 45 degree angle to 2 people: twins
61
Q

sex chromosomes

A
  • the tips of the arms on the X and Y chromosomes shares a small region of homology and that’s where recombination can occur
  • almost none of the genes in the X chromosome have the same counterparts on the Y chromosome
  • X is much larger than Y
62
Q

explain how default is female

A

fathers can pass on an X or Y chromosome

- in humans, the presence of the Y chromosome sets off a cascade of events leading the development of the male phenotype

63
Q

Ishihara colour test

A

R/G colour blind test

- composed of dots with an internal pattern forming a number in red and green

64
Q

red-green colour blindness

A

an X-linked trait

  • women who are heterozygous are carriers and can pass the trait to offspring
  • any male receiving the recessive colour blind allele will be colourblind because they have only 1 locus for this
  • only women heterozygous for the colour blind allele will be colour blind
65
Q

carrier

A

heterozygous individuals that do not show the phenotype but can pass the affected allele to their offspring

66
Q

haemophilia

A

an X-linked recessive blood clotting disorder

- queen victoria was the first member of the royal fam to have it

67
Q

linked genes on the X-chromosome

A

there are about 1100 genes on it
P arm: short arm
Q arm: long arm
- the genes for colour blindness and haemophilia are linked (both on the end of the Q arm)

68
Q

linked genes

A

genes positioned close enough together on a chromosome (autosomes or X chromosomes) and tend to be inherited together and do not segregate independently

69
Q

are linked genes always inherited together?

A

no. linkage can be broken in prophase 1 of meiosis 1 when crossing over occurs, as a result, offspring may inherit only one of the genes due to the recombination effects that occur b/w linked genes

70
Q

recombination of alleles

A
  • the position of the genes does not change but the relative association of the alleles would change: this is caused by crossing over
  • alternately, if linked genes were immediately adjacent to one another, there would be no crossing over b/w the 2 genes: thus recombination of genes depends on the distance b/w them
71
Q

recombination frequency

A

is less when genes are close together

- can help us determine the distance between genes if we know the recombination frequency

72
Q

linkage map

A

shows the relative distance b/w genes on a chromosome

ex. genes for haemophilia and colour blindness are 12 map units apart (12million bp) - this distance is large enough for crossing over to occur b/w the 2 genes
- these are somewhat impractical for human applications so we use SNPs and markers to create high density linkage maps

73
Q

high density linkage maps

A

identify genetic loci that are only a few bp apart and they can map human genes that determine various characteristics
- still looks at the frequency of recombination

74
Q

genome wide association studies (GWAS)

A

looks across SNP linkage maps for an association b/w a phenotype and a SNP
- human SNP linkage maps: quicker and allow us to look at hundreds of thousands of people

75
Q

HMGA2 gene

A

an example of a GWAS

- found to contribute to less than 1 cm variation in height in humans

76
Q

cellular proteomes

A

can interact with one another based on the presence of membrane bound surface proteins

77
Q

ABO gene

A

the alleles we carry determine our blood type

  • the ABO locus has 3 main alleles: A, B, and O
  • an example of a variation that does not alter function
78
Q

A, B and O alleles on the ABO gene

A
  • A and B alleles code for a specific glycotransferase enzyme that catalyzes formation of A or B agglutinogens that are expressed on the cell surface
  • O alleles code for an inactive glycosyltransferase enzyme
  • the AB blood type has several SNPs that lead to formation of slightly different transferases
79
Q

HIV

A

human immunodeficiency virus

  • invades T cells by interacting with 2 surface proteins: T cell surface CD4 receptor protein and CCR5 co-receptor protein
  • once attached, the virus is engulfed by the cell and the infection begins, leading to the death of the T-cell and a compromised immune system
80
Q

CCR5 allele alteration

A

a mutation that allows T-cells to be immune to HIV infection

  • after mutation, a stop codon results from a frameshift mutation that produces an inactive CCR5 protein
  • this mutation in 14th century Europe prevented people from getting bubonic plague and so this mutation has been selected for by natural selection
81
Q

where do SNPs occur most often?

A

more are in non-coding regins than in coding regions

82
Q

Dr. David Meyre

A

Austin Solek is working under him

  • Dr. Meyre has a population genomics program and was part of the team that published the 1st GWAS in complex diseases (2007)
  • studies the genetic basis of obesity and T2D - found that there was a region of linkage on chromosome 6q and identified 7 loci contributing to adult obesity
  • discovered SIM1 gene responsible for a form of childhood obesity
  • identified that OGTT is a good indicator of T2D
83
Q

Dr. Ghulam Mufti

A

hopes to provide more into upon diagnosis of cancer

  • uses microarray analysis to identify all the genes that a person has and when cancer cells are added to the chip, the squares that light up should reveal a type of gene expression happening
  • this might be the start to customized medicine in terms of predicting how a patient’s cancer will behave
84
Q

DNA sequences variations in humans many determine how humans:

A

develop diseases

respond to drugs, pathogens, chemicals and vaccines

BIO 1A03 (6 decks)

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