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Flashcards in Bothwell Deck (86):
1

What is the principle of segregation?

Alleles divide into offspring randomly- only one parental allele is given at random to each gamete the parent produces

2

What is independent assortment?

Heredity factors assort independently, giving traits equal opportunities to be expressed together

3

Why did mendel use pure breeding lines?

To have parents that reliably produce offspring like them so it was easy to tell what information was being passed from parents to offspring

4

What are pure breeding lines?

Pure breeding plants have been inbred1 for several generations to produce strains that display very little variation in phenotype from one generation to the next.

5

How did mendel crossing pure breeding lines determine that inheritance is discrete?

When you crossed two pure breeding lines, all the offspring looked like one line, rather than like a mix of both.
- Each plant gets one piece of information from its mother and another from its father and the dominant one determines the phenotype.

6

What is a dihybrid cross and what are the ratios of F2 offspring expected from a dihybrid cross if the F1 generation was a TT YY crossed with tt yy.

When you cross pure breeding pea plants with two traits of interest.

F1 generation would produce 100% Tt Yy
F2 generation would produce a 9:3:3:1 ratio and units of 1/16

7

What experiment could you conduct to determine whether the individual was homozygous or heterozygous for a dominant trait?

Cross with a homozygous recessive individual and if the ratio of offspring is 3:1 then it is heterozygous but if all offspring are the same then it is homozygous dominant.

8

Describe the DNA content of the cell through the cell cycle.
G1
S
G2
Mitosis

G1- 2C (normal diploid)
S- 4C (diploid but replicated)
G2- still 4C (as not divided yet)
Mitosis- 4C at the start of mitosis but by the end returns to 2C as the 4C is split between two cells

9

What is the difference between n and C content and give an example to illustrate this.

n= genetic content
C= DNA content
A normal diploid cell in G1 is 2n and 2C, but a cell in G2 is 2n and 4C (there’s twice as much DNA in the G2 cell, as it’s replicated, but the same amount of genetic information - there’s still only two alleles per gene locus

10

Describe what happens in prophase, pro-metaphase, metaphase, anaphase and telophase.

Prophase
-Chromosomes condense
-Sister chromatids (as they have been replicated) held together by centromere

Pro-metaphase
-Nuclear envelope breaks down

Metaphase
Chromosomes align on equator of cell

Anaphase
-Chromatids pulled apart by a spindle that attaches to the centromere

Telophase
-Nuclear envelope reforms
-Daughter chromosomes relax and decondense

11

What was Theodor Boveri's theory? What experiment did he do to show this?

Cells would die if there was not correct assortment of chromosomes into cells.
Looking down microscope on polyspermic sea urchin embryos
Polyspermic ones meant zygotes would have the wrong number of chromosomes (e.g. some would get none) and die.

12

What are the p and q arms of a chromosome?

P= petite= small arm
Q= longer arm

13

What are the three main differences between mitosis and meiosis?

Mitosis
In somatic cells
Produces two daughter cells with one division
Meiosis
In germ cells
No association between chromosomes

Produces four daughter cells with two divisions
Homologous chromosomes pair up

14

Describe the six stages of meiosis I (prophase I and metaphase I)

Leptotene- chromosomes become visible
Zygotene- homologous chromosomes pair up
Pachytene- crossover occurs
Diplotene- homologous chromosomes move slightly apart
Diakinesis- homologous pairs move to equatorial plate

15

How do prophase, prometaphase, metaphase, anaphase and telophase differ in meiosis compared to mitosis?

Prophase- chromosomes condense BUT in homologous pairs in meiosis

Pro-metaphase- nuclear envelope breaks down (as in mitosis)

Metaphase- homologous pairs line up on equatorial plate

Anaphase- homologous chromosomes separate so each daughter nucleus is now haploid (in mitosis, daughters are diploid)

Telophase- nuclear envelope reforms like in mitosis

16

What is gene linkage?

When two alleles are inherited together because they are on the same chromosome

17

How was it shown that two genes in fruit flies were independent?

Parents crossed to produce an F1 generation which was heterozygous for both traits, then the F2 generation was produced in a 9:3:3:1 ratio whereas if the genes weren't independent, then a 3:1 ratio would be observed as they would be acting as a mono hybrid cross rather than a dihybrid cross

18

Why would a 10:2:2:2 ratio rather than 3:1 or 9:3:3:1 ratios be observed?

This is because the results sat half way between complete independence and complete linkage. Both W+ and M+ alleles were found on the same chromosome and one or both sometimes crossed over to the Ww/m chromosome to give either a W+/m or a Ww/+ chromosome which would allow the phenotype combinations of 10:2:2:2

19

How did the likelihood of crossover and how far apart the genes were on a chromosome give rise to genetic mapping?

The further apart genes on a chromosome, the more likely they were to be separated by random chromosomal breaks and crossovers. Therefore the frequency of linkage could be used as a rough estimate of how far apart the genes were on a chromosome

20

What are crossovers and when do they occur?

They are recombination between homologous chromosomes. They occur in prophase I (when chromosomes pair up during zygotene).

21

How can crossover products be formed?

A Holliday junction occurs when one strands invades and unwinds its homologous pair. Resolving the Holliday junction through vertically produces crossover products

22

How can cells initiate cell division?

By splitting sister chromatids or splitting homologous chromosomes

23

What are the three assumptions the strict Mendelian model of genetics proposes?

1) alleles are dominant or recessive
2) only one gene locus determines a trait
3) genes are on nuclear chromosomes

24

How can the three assumptions that Mendelian genetics make be flouted by nature?

1) alleles can be codominant, incompletely dominant and can show varying degrees of expressivity
2) more than one gene can be involved- gene interaction
3) sometimes a trait isn't determined by nuclear DNA sequence
-if it's determined by mitochondrial or chloroplast DNA
-determined by anything other than the DNA sequence e.g. Epigenetics

25

What is incomplete dominance?

Phenotype is determined by a blend of the products of different alleles e.g. A red and a white snapdragon crossed could produce a pink snapdragon

26

What is codominane?

Alleles produced are neither dominant nor recessive, both are expressed e.g. Blood type- types A and B can both be expressed together

27

What is one common complication to mendels ratios that would disturb this ratio? Give an example and explain.

Sometimes homozygous recessive traits can be lethal e.g. Agouti gene in mice- AyAy (y=yellow) is lethal and these mice die
y allele is dominant for coat colour but recessive for embryonic development

28

Agouti gene in mice- why is this an example of linking?

Ay allele contains a deletion in the agouti gene which causes yellow fur and this deletion knocks out the next door gene which is involved in embryonic development

29

How could more than one gene be involved in determining a phenotype?

If several genes take part in the metabolic pathway that determines the phenotype

30

What is epistasis? Give an example

Two genes working together. E.g. Blood groups which requires a H factor synthesis to allow the antigens to be synthesised properly

31

Why do you get an f2 ratio of 3:6:3:4 of A:AB:B:O rather than 1:2:1:0?

Because there are two genes (epistasis)
- the hh homozygote can't make any antigens so the O genotype is formed even though the blood group genotype of thee individuals is IAIA, IAIB or IBIB

32

What is complementation and what is it used for?

Complementations are used to tell whether mutants that are the same phenotype result from 1) mutants in the same gene or 2) mutants in different epistatic genes

Complementation is crossing pure breeds of each mutant. If a and b mutations are in different genes, the offspring inherits one working copy of either gene so the phenotype returns to normal. If a and b mutations are in the same gene, the offspring inherits two broken copies of both genes and so retains the mutant phenotype

33

What are the common epigenetic tags on DNA and histones?

DNA is often methylated
Histones are often acetylated

34

What does DNA methylation do to gene expression

Makes the DNA less likely to be expressed

35

Why would the agouti mouse ratio differ from the usual 1:2 brown:yellow ratio?

Agouti gene is recessive partly because it's got an epigenetic tag on it (DNA methylated). Sometimes this tag can be removed which would cause all mice to be yellow.

36

Describe two interesting things about epigenetic tags.

Tags can be passed from f2 generations but whether or not the tag is removed depends on whether the chromosome is being packed into sperm or eggs (leading to uni parental inheritance)

Many epigenetic tags are reset during meiosis in response to the cells environment- health of father and mother at the time of gamete production can impact the phenotype of their offspring

37

What is heritability?

To what extent a particular trait is determined by a gene. Proportion of phenotype variation that is due to genotype variation

38

What units in the ratios would crosses involving two, three, four and fife genes involve?

2=1/16
3=1/64
4=1/256
5=1/1024

39

How do you differentiate between a trait with (no genetic influence but lots of environmental influence) and one with (lots of genetic influence and little environmental influence)?

If observed phenotype depended more on environment, offspring of any two individuals would be in the same range as the original group- wouldn't depend on which two individuals you picked as parents

If observed phenotype depended more on the genetics, then range of phenotype would depend upon exactly which parents you picked

40

How would you use a graph to determine heritability?

Graph phenotype of offspring against mean phenotype of parents (e.g. My height against average height of my parents), the heritability (H^2) is the gradient

41

If heritability is the gradient of a graph, what does the severe mess of the gradient tell us about heritability?

The steeper the gradient, the higher the heritability

42

What is aneuploidy?

Where organisms lose or gain individual chromosomes or large chunks of them

43

What is polyploidy

More than one copy of a chromosome

44

When does aneuploidy usually arise?

Comes from chromosome non-dysjunction during meiosis

45

Why does polyploidy usually occur?

Usually arises from a failure of cell division during mitosis

46

How is aneuploidy subdivided?

Monosomy- loss of one individual chromosome or part of chromosome

Trisomy- gain of an individual chromosome

Tetrasomy, pentasomy etc... gain two or three etc

47

What is Robertsonian fusion?

??????

48

How does familial Down's syndrome occur?

Robertsonian fusion of chromosomes 14 and 21 causing a trisomic gamete with one copy of 14 but two copies of 21

49

What is the difference between AUTOpolyploidy and ALLOpolyploidy?

Auto- caused by endoreduplication

Allo- caused by hybridisation of two species

50

Why do few polyploid animals survive?

Because they struggle to get through meiosis correctly: improper chromosome segregation so the cell dies

51

Why does allopolyploidy occur?

Hybridisation of two gametes from different species means chromosomes are not similar enough to form homologous pairs so segregation of chromosomes into daughter cells is pretty much random and so there's a low chance of getting a full set in any one gamete

52

How do plants get around the sterility problem caused by allopolyploidy?

Somatic doubling- basically S phase without cell division after

Is produces a hybrid tetraploid meaning that each chromosome has a homologue and can undergo meiosis and produce gametes

53

What are the advantages of polyploidy?

Broadens the gene pool by allowing genes to be brought in through closely related species

More gene product produced per cell, making them more productive

Allows rapid speciation so plants can fill niches quickly

Having more copies of a gene allows some copies to change, providing raw material for evolution

54

What are the three possible determinants for sex?

1) environmental (eg crocodile gender relies on temperature)

2) genotypic - genes responsible for sex determination

3) sex chromosomes - recombination is suppressed in the Y chromosome. It codes for the difference between sexes

55

Why is the Y chromosome degenerate?

Because there is no recombination so it has accumulated mutations

56

What are the three options to solve the problem of the homozygous sex (xx) producing twice as much genetic product?

1) having one X chromosome shut down
2) having both X chromosomes expressed half as much
3) hyperactivate the X chromosome in males

57

Why are tortoiseshell cats all female?

Pattern arises from random inactivation of one of the X chromosomes in each cell, causing a mosaic like pattern

58

How does sequencing by synthesis (next generation sequencing) work?

DNA template exposed to one nucleotide per sequencing round. PPi is released when a nucleotide is added by DNA pol. PPi reacts with sulphate adenyltransferase to generate ATP. ATP is a substrate for luciferase to generate light. Apyrase then added to break down unreacred nucleotides and PPi, then washed and the whole cycle repeated

59

What is base calling?

Assessing the quality of the read (bioinformatics of a genome)

60

What happens when you use Giemsa stain on DNA?

Hetraochromatin in stained black and euchromatin is not stained

61

Why doesn't mitosis fit with Mendel's theory of segregation?

Because during mitosis, the daughter cells get both sets of alleles from both parents, rather than one randomly

62

What mechanism did Edouard Van Beneden propose to solve the theory of segregation problem?

He proposed that rather than one line of chromosomes lining up at metaphase, there were two lines on the equator rather than just one

63

What are contigs or supercontigs and what are they used for?

A contig is a set of overlapping DNA fragments that represent a consensus region of DNA.

A supercontig is an ordered and oriented set of contigs that still contains some gaps.

They are used in shotgun sequencing to order the DNA and make it into a sequence.

64

What are the stages of analysing genomes?

1) Quality of the read is assessed using PHRED
2) Draft assembled into contigs and supercontigs and assigned to linkage groups
3) (Automated annotation and curation) - a) coding regions identified by comparing to known coding regions and if the sequences are similar, it is likely that this region of DNA is also a coding sequence
b) proteins are assembled as modules so protein sequences can be fed into a protein prediction database to see if it contains any known structural motifs

65

What is PHRED?

Phil's Read EDitor- gives quality scores to gene sequences (how likely is it that it is the correct sequence), once the value drops below a certain value, the rest of the read is abandoned.

66

What are FASTA formatted sequences?

Text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes

E.g. CTATCGATGGTCCA for a nucleotide sequence
or MDSKGSSQKGSRLLLLLVV for an amino acid sequence

67

What are BLAST tools?

Basic Local Alignment Search Tool- an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences. E.g. for identifying similar sequences which may suggest the sequence is coding.

68

Why is expert annotation needed?

Because BLAST tools are very fast but not always accurate so experts need to draw proper
4 phylogenetic trees to distinguish orthologs (good) from homologs (bad) and paralogs (ugly ). This
takes ages and is a surprisingly skilled job, so needs to be done by experts.

69

Why do non model systems take longer to sequence?

Because there is no reference genome. If there is a reference genome, you can rely much more on short reads, without this, you need long and short reads and this therefore takes much longer

70

What are the 5 notable findings of the human genome project?

1) Gene distribution not homogenous (euchromatin and heterochromatin)

2) Fewer genes than expected (due to genes producing multiple products through splicing)

3) Lots of pseudogenes present

4) Lots of transposable elements

5) Variationin human genomes comes in many forms (transposons, indels (insertions or deletions), copy number repeats, and single nucleotide polymorphisms).

71

What is a pseudogene?

A section of a chromosome that is an imperfect copy of a functional gene.

72

What are the 4 main classes of transposable elements?

1) Short interspersed nuclear elements (most common is Alu element)

2) Long interspersed nuclear elements

3) Retroviral, or Long Terminal Repeat (LTRs), transposons

4) DNA transposons

73

What are retrotransposons and DNA transposons?

Retrotransposons (RNA intermediates) a transposon whose sequence shows homology with that of a retrovirus. Class I.

DNA transposons- a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genome size. Class II.

74

Why might retrotransposons be present in human genomes?

Our genome could have gotten used to them and might be being used as structural elements or spacers.

75

How much of the human genome is composed of repetitive DNA?

50%

76

Tandem repeats: what is the difference between minisats and microsats?

Minisats- nucleotide repeat sequences between 10-60 bp
Microstats- nucleotide sequence repeats of less than ^

77

What is satellite DNA?

Very repetitive DNA. Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin

78

What was the first evidence for transposable elements?

That mutant phenotypes could revert back to the original phenotypes in maize

79

Why is corn a very good experimental organism for studying phenotypes?

Because each kernel comes from a single embryo

80

What is the breakage fusion bridge mechanism?

When protective telomeres are lost off the ends of chromosomes so two chromosomes fuse, producing mutant with two centromeres. As the centromeres align, there is a twist between these two centromeres and when the centromeres attach to microtubules, the centromeres pull in opposite directions, creating a bridge, causing breakage. Sticky ends fuse again and after replication, the process repeats to form more bridges and breaks and fusion of broken pieces. This can increase the copies of some of the genes

81

How did McClintock use the breakage fusion bridge method to study corn?

McClintock was able to develop this into a way of nibbling away bits from the ends of target chromosomes. Basically, it meant that she had a way of removing chunks from the ends of chromosomes (and so had a way of removing alleles from chromosomes so that she could study their effects).

She began to investigate which other genes helped the C gene. By nibbling bits off the p arm of Chromosome 9, she showed that part of it was needed to make the yellow ‘mutant’ unstable, and she proposed that the p arm contained a gene that ‘activated’ the instability (= which, not unnaturally, she called the Ac, or Activator, gene)

82

What is the Ac gene in corn?

An activator gene which helps the C (colour) gene be expressed.

83

What does the blue freckling pattern in corn kernels tell us about transposition??

-Large freckles means transposition occurred early on (so more cells are affected because a large freckle would have come from one cell early on that had transposition which then grew into more cells)

-Lots of freckles shows a high frequency of transposition

84

What are the two classes of transposons?

1) Class I transposons-RNA transposons (or retrotransposons)- transposon is transcribed by RNA polymerase and then the RNA transcript is then reverse transcribed to give DNA that is inserted into the sequence elsewhere (uses an RNA intermediate)

2) Class II- DNA transposons- cuts out the DNA and transports it somewhere else (uses a DNA intermediate)- "copy and paste"

85

What are the subdivisions of class I transposons?

- Those that use long terminal repeats (LTR)
-Those that do not- non LTR transposons

-These are used to signal where the ends of the transposons are

86

What are LTR retrotransposons?

Long sequences that have signals for targeting and movement of transposons