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Molecular Biology BSc First Year > MBB11004 -Genetics 1 > Flashcards

MBB11004 -Genetics 1 Flashcards

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1
Q

What is genetics?

A

the study of genes and the way they are passed on (inherited)

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2
Q

What is heredity?

A

the inheritance of traits from parents to offspring, making offspring SIMILAR to parents

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3
Q

What are the three approaches to looking at genetics?

A

-molecular/developmental genetics (genes transmitted from DNA to affect cell function and phenotypes)
-transmission genetics (genes transmitted from parents to offspring)
-population/evolutionary genetics (genes transmitted over many generations within a large population)

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4
Q

How is genetic material organised differently in eukaryotes and prokaryotes?

A

eukaryotes:
-linear chromosomes in nucleus
-chromatin (DNA + histones)
prokaryotes:
-single, circular chromosomes condensed in nucleoid region
-no nucleus

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5
Q

What is chromatin?

A

DNA wrapped around histones (highly conserved proteins)

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6
Q

What is the structure of a linear chromosome?

A

-centromere (binding site for kinetochores)
-p arm (shorter arm of chromosome)
-q arm (longer arm of chromosome)
-telomeres (highly conserved, repeated DNA sequences at end of arms which protect ends from being degraded)

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7
Q

What is the p arm of a chromosome?

A

the shorter arm

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8
Q

What is the q arm of a chromosome?

A

the longer arm

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9
Q

What is a locus?
(pl loci)

A

set position on a chromosome which a gene can be found at

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10
Q

What is cytogenetics?

A

the study of chromosomes

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11
Q

What is a karyotype?

A

the chromosome complement of an individual
-cytogenetic techniques (eg. G-banding) are used to come up with a karyotype

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12
Q

What is a typical human karyotype like?

A

-22 pairs of autosomal chromosomes
-1 pair of sex chromosomes (XX = female, XY = male)

46 chromosomes total

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13
Q

What does diploid mean?

A

2 homologous chromosomes (same gene, diff alleles)
-2 copies of each chromosome
-2n

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14
Q

What does haploid mean?

A

1 copy of each chromosome
-n

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15
Q

What is a gene?

A

a unit of hereditary information that occupies a specific position (locus) on a chromosome
-determines phenotype
-passed from parent to offspring

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16
Q

What is an allele?

A

one form of a specific gene that exists at a single locus
-alleles can differ by one nucleotide or by hundreds of nucleotides

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17
Q

Why is most of the mitochondrial and chloroplast DNA from the egg?

A

-mitochondria and chloroplasts are located in the cytoplasm
-egg has larger volume of cytoplasm than sperm

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18
Q

What is euchromatin?

A

loosely packed chromatin which can readily be transcribed

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19
Q

What is heterochromatin?

A

condensed (tightly packed) chromatin which is not readily transcribed so not expressed

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20
Q

How is euchromatin/heterochromatin altered to the alternative?

A

via the addition of methyl and acetyl groups to histones

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21
Q

What is epigenetics?

A

the study of phenotypic changes caused by modifications to the chromatin structure to alter gene expression/activity without changing the DNA sequence itself
-addition of methyl and acetyl groups to histones
-euchromatin and heterochromatin

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22
Q

What is the asexual cell cycle?

A

cell divisions to give genetically identical daughter cells
-mitotic nuclear divisions

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23
Q

What is produced from unicellular organisms undergoing the asexual cell cycle?

A

clones
-causing a genetically identical population

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24
Q

What happens in binary fission?

A

-DNA duplicates
-cells increase in size
-replicated chromosomes move apart
-protein Fts2 marks middle of the cells, where a new cell wall forms
-2 daughter cells form

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25
Q

What are the stages of the cell cycle?

A

interphase
-growth 1 phase (increase in cell cycle, prod ribosomes and RNA)
-synthesis phase (chromosomes duplicate)
-growth 2 phase (DNA checed, prep for nuclear division)
mitotic phase
-mitosis (prophase, metaphase, anaphase, telophase)
-cytokinesis

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26
Q

What happens in terms of chromosomes during the cell cycle?

A

-chromosomes replicate in the S phase to produce sister chromatids
-sister chromatids separate in mitosis

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27
Q

What happens during prophase in mitosis?

A

-chromosomes condense, becoming visible thread-like structures
-nuclear membrane breaks down (end of prophase -known as prometaphase)

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28
Q

What is mitotic spindle?

A

structure of cytoskeleton made of lots of microtubules (polymers of small tubulin subunits) which separate sister chromatids into different daughter cells during mitosis

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29
Q

What is a centromere?

A

specialised chromosome regions at a fixed point along the chromosome (determined by specific epigenetic molecules) which direct the segregation of chromosomes in mitosis
-connected to microtubules by kinetochore (protein complex)
-sister chromatids are joined by centromere

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30
Q

What happens during metaphase in mitosis?

A

-centromeres align at equator of cell
-microtubules attach to centromeres and to ends of each pole, creating tension which keeps chromosomes at centre

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31
Q

What happens during anaphase in mitosis?

A

-cohesin (between sister chromatids) breaks down, causing the chromatids to become separate chromosomes
-microtubules contract, starting to move centromeres to opposite poles (chromosomes form V-shapes as chromosomes are dragged behind centromere)

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32
Q

What happens during telophase in mitosis?

A

-chromosomes arrive at poles
-chromosomes recondense
-daughter nuclei form

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33
Q

What happens during cytokinesis?

A

-cleavage furrow forms between 2 poles
-constriction
-2 daughter cells produced

-can be symmetric or asymmetric

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34
Q

How can mitosis go wrong?

A

-bridge chromosome (chromosome with 2 centromeres, pulled to both poles and breaks)
-acentric chromosome (chromosome missing a centromere, can’t separate properly)

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35
Q

What is a bridge chromosome?

A

error in mitosis where a chromosome has 2 centromeres, which both attach to centromeres, meaning the chromosome is pulled to 2 poles at once so breaks

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36
Q

What is an acentric chromosome?

A

error in mitosis where a chromosome lacks a centromere so can not separate properly

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37
Q

What is the sexual cell cycle?

A

meiosis
the halving of chromosome number through 2 successive nuclear divisions

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38
Q

What is a tetrad?

A

the four haploid products of meiosis

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39
Q

What is the nuclear cycle like in Saccharomyces cerevisiae?

A

-haploid most of life
-has 2 mating types: a and α
-one of each mating types combine to give transient diploid state
-meiosis to give 4 products

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40
Q

What happens in meiosis 1?

A

-homologous chromosomes are replicated to produce dyads (prophase 1)
-2 dyads join together to form a bivalent (metaphase 1)
-dyads move to opposite poles (with centromere kept intact) (anaphase 1)
-by end, have 2 nuclei, each with both sister chromatids of one of the parent’s homologous chromosomes

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41
Q

What is a dyad?

A

2 sister chromatids with a single centromere
(half a tetrad)

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42
Q

What happens in prophase 1 (in meiosis 1)?

A

-replicated chromosomes start to contract (leptotene)
-chromosomes line up in homologous pairs (synapsis) held together by synaptonemal complex (zygotene)
-crossing over occurs between non-sister chromatids (pachytene)
-chromosomes separate slightly (diplotene)
-chromosomes contract further (diakinesis)

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43
Q

What happens in meiosis 2?

A

-like mitosis
-sister chromatids line up
-chiasmata breaks down so that centromere splits and chromosomes move to opposite poles
-by end, have 4 nuclei, two of which contain 1 copy of one homologous chromosome and two of which contain 1 copy of the other homologous chromosome

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44
Q

How does meiosis generate variation?

A

-independent assortment of chromosomes (random how bivalents are orientated on meiotic spindle -all equally likely)
-crossing over (sections of chromosomes swapped via deliberate double-strand breaks by specialised enzymes to allow homologous recombination to give new allele combinations)

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45
Q

What are cross overs?

A

site of genetic exchange between homologous sequences on non-sister chromatids

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46
Q

What are chiasma?

A

site of crossover

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47
Q

When are cross overs visible in meiosis?

A

diplotene stage of meiosis 1
-can see chiasma

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48
Q

What is a mutation?

A

a gene/chromosome that differs to the wild type
(or the process that results in the different gene/chromosome)

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49
Q

What is the result of a spontaneous mutation in single-cellular organisms?

A

population is no longer clonal

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50
Q

What is the result of a spontaneous mutation in multi-cellular organisms?

A

mixture of genotypes
organism is “genetic mosaic”
mutation is only passed on if germline (in egg/sperm)

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51
Q

What is polyploidy?

A

an unusual number of chromosome sets
eg. monoploidy, triploidy, tetraploidy

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52
Q

What is aneuploidy?

A

when one/a few chromosome sets are missing/extra
eg. resulting in Downs syndrome, Edwards syndrome and Patau syndrome
sex chromosome aneuploidies like Turner syndrome and Klinefeller syndrome

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53
Q

What large scale chromosomal rearrangements are there?

A

-deletions (part of chromosome missing)
-inversions (part of chromosome flipped)
-translocations (part of chromosome moved)

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54
Q

What are the sources of mutation causing individual genes to differ from the wild type?

A

-mistakes in replication (point mutations, small insertions, small deletions)
-transposons interrupting genes
-incorrect repairs of DNA breaks

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55
Q

What are the types of point mutations?

A

-silent (no change in amino acid seq)
-non-sense (stop codon introduced in chain)
-mis-sense (changes in amino acid seq)

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56
Q

What are auxotrophic mutants?

A

mutants that can not synthesise essential compounds (eg. adenine, serine)
-study them by growing in minimal growth media and complete media

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57
Q

What is minimal growth media?

A

growth media which only contains nutrients organisms can not make for itself
-wild type can grow in it, auxotrophic mutants can’t

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58
Q

What is complete growth media?

A

growth media containing extra nutrients, making up for defects in metabolic pathways so that mutants can grow
-both wild type and auxotrophic mutants can grow in it

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59
Q

What are allelic mutations?

A

mutations where both mutations are on the same gene/step of pathway

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60
Q

What are non-allelic mutations?

A

mutations in different genes

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61
Q

How can complementation be used to determine whether mutations are allelic or non-allelic?

A

non-allelic mutations complement eachother (so that diploid contains one wild type allele so can grow on minimum media)
whereas allelic mutation don’t

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62
Q

Why were peas good for Mendel’s experiments?

A

-phenotypes are all simple traits controlled by a single gene
-no co-dominance
-genes controlling phenotypes are on different chromosomes
-peas are either cross-pollinated or self-pollinated

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63
Q

What are pure breeding lines?

A

when all the offspring from mating within the breeding lines have the same character

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64
Q

What are Mendel’s three laws?

A

-law of equal segregation
-law of independent assortment
-law of dominance

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65
Q

What is Mendel’s law of equal segregation?

A

during gamete formation, members of each gene pair separate equally
-each gamete carries 1 allele for each gene, meaning you end up with same allele ratio as at the start

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66
Q

What is Mendel’s law of independent assortment?

A

during gamete formation, chromosome pairs separate independently of eachother randomly
-large number of combinations possible -including recombinants

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67
Q

What is Mendel’s law of dominance?

A

alleles can be dominant or recessive

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68
Q

How can genetic hypotheses be designed and tested?

A

using Punnett squares or probability trees

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69
Q

How can you determine which allele is the dominant allele?

A

-cross pure-breeding parental lines with each genotype (100% of the offspring will have dominant phenotype)
-self-fertilise F1 generation (75% F2 gen will have dom phenotype)
-cross-fertilise F1 generation with homozygous recessive aka test cross (50% F2 gen will have dom phenotype)

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70
Q

What are dihybrid crosses used for?

A

considering 2 genes on different chromosomes to eachother

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71
Q

What are the two ways of coming up with a genetic hypothesis?

A

-predicting numbers of different types you expect before experiment is done
-look at experimental data and come up with ratios which closely fit

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72
Q

How can you go about testing a genetic hypothesis?

A

-start with biological hypothesis (predict numbers)
-expect numbers of observed and expected to not differ much if hypothesis is correct
-test using chi-squared

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73
Q

Chi-squared test
x^2 =

A

Σ (O-E)^2
_________
E

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74
Q

What are the degrees of freedom for the chi-squared test?

A

n-1

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75
Q

What is linkage?

A

genes positioned close to eachother on a chromosome to be more likely to segregate together at meiosis, and therefore be inherited together
-strength of linkage depends on the distance between the two genes

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76
Q

Where are linked genes in relation to eachother?

A

on loci next to eachother
-are carried and inherited together

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77
Q

recombination frequency (%) =

A

recombinants
_________________________ x100
total meiotic frequency

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78
Q

What is the recombination frequency?

A

the percent of meioses where two loci are exchanged by homologous recombination
-RF is roughly proportional to the distance between the two loci (closer the genes, the less likely recombination is)
-RF can be used to create maps showing the order of genes on a chromosome

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79
Q

What value is recombination frequency always between?

A

0 and 50%
0 = loci next to eachother, no recombinants
50 = loci on separate chromosomes, half recombinants

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80
Q

What does a recombination frequency of 0% mean?

A

loci are next to eachother
no recombinants

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81
Q

What does a recombination of 50% mean?

A

loci are on separate chromosomes
50% recombinant, 50% parental

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82
Q

What are the different types of tetrad?

A

-parental ditype (all segregants have parental genotypes)
-non-parental ditype (all segregants are recombinants)
-tetratype (2 parental and 2 recombinant genotypes in segregants)

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83
Q

What is a parental ditype?

A

a tetrad where all the segregants (products of meiosis) have parental genotypes
-all of them the same as one of their parents (2 of each parental genotype)

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84
Q

What is a non-parental ditype?

A

a tetrad where all the segregants (products of meiosis) have genotypes different to their parents
-all recombinants

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85
Q

What is a tetratype?

A

a tetrad where half of the segregants (products of meiosis) have parental genotypes and half have non-parental (recombinant) genotypes
-all 4 meiotic products are different

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86
Q

If there are more parental tetrads than non-parental tetrads, what does this suggest about the genes?

A

the genes are linked
-genes are inherited together

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87
Q

If there are roughly equal numbers of parents and non-parental tetrads, what does this suggest about the genes?

A

the genes are unlinked
-independent assortment can occur

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88
Q

recombination frequency for 2 loosely linked genes =

A

non-parental ditype + 1/2 tetratype
___________________________________________________ x100
parental ditype + non-parental ditype + tetratype

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89
Q

Why is it important to study viruses?

A

-discover new enzymes encoded by viruses (research, pharmaceuticals)
-phage therapy (treating disease)
-viruses can kill algal cells (agal blooms)

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90
Q

What is a virus?

A

genetic element that can only replicate inside of a living host cell
-can exist as viral particles outside host

-are small!

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91
Q

What is a virion?

A

an inert viral particle outside of a host made up of protein surrounding DNA or RNA
-has a limited number of hosts
-injects nucleic acid into host, protein coat generally stays outside
-intracellular form is replicative form

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92
Q

What are viral genomes like?

A

-very small (reliant on host machinery)
-DNA or RNA
-ss or ds
-linear or circular (can switch)

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93
Q

What does the tobacco mosaic virus (TMV) have in place to get round having a small size?

A

-only 1 kind of protein (capsomers) so only one gene needed for all its protein structure
-capsids can self-assemble so no machinery needed

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94
Q

What are early proteins for (in viral replication)?

A

replicating viral nucleic acids (transcription and translation)

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95
Q

What are late proteins for (in viral replication)?

A

packaging (coat proteins)

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96
Q

How does the T4 phage ensure viral transcription occurs?

A

-modifies host’s RNAP so that it binds to phage promotors (rather than host promotors)
-has sigma factors for early proteins
-T4 phage genome codes for anti-sigma factor, which binds to host sigma factor to prevent host transcription

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97
Q

How is the switch to middle proteins achieved in the T4 phage?

A

-some early phage proteins modify host RNAP α subunits
-other early proteins bind to RNAP, changing the complex
-these alter the RNAP specificity to recognise middle promotors
-early protein MotA recognises seq in middle promotors and guides RNAP to these sites

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98
Q

What are lysogenic viruses?

A

viruses which can integrate into the host genome, rather than escaping from the host

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99
Q

What happens in the lytic pathway of viruses?

A

(after attachment and injection)
-viral DNA replicates
-coat proteins are synthesised and viral particles assemble
-host cell lysis and viruses are released

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100
Q

What happens in the lysogenic pathway of viruses?

A

(after attachment and injection)
-viral DNA is integrated into host DNA (producing a prophage)
-lysogenized cell undergoes cell division

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101
Q

What is induction?

A

the switch between the lysogenic and lytic pathways

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102
Q

What is lysogeny?

A

the stable relationship between virus and host
-viral gene expression repressed
-prophage acts as part of host (viral genome is replicated in synchrony with host genome)

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103
Q

How does a viral genome exist during lysogeny?

A

integrated into host genome or as a plasmid

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104
Q

Why are repressors needed during lysogeny?

A

-repressors prevent lytic pathway and induction
-prevent viral gene expression

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105
Q

How does the lambda (λ) phage genome integrate into host DNA?

A

-viral genome integrated at attachment site attλ which requires λ integrase
-viral genome alters from being linear to circular inside host (due to cohesive ends)
-circularised DNA is nicked, creating staggered ends (same as host DNA) by site-specific nucleases
-λ DNA is integrated and gaps are closed by DNA ligase

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106
Q

How is a viral genome replicated in the lytic pathway?

A

by rolling circle replication

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107
Q

What happens in rolling circle replication?
(lytic)

A

-circular plasmid/genome (being replicated) rolls
-replication starts at origin, where RepA dimer makes nick
-polymerase moves along from nick, progressing in only one direction
-as it is replicated, a long single-stranded (continuous) concatemer is made
-this concatemer is used as a template to produce a double-stranded concatemer
-this is cut into genome-sized lengths at the cos sites (gives adhesive ends)

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108
Q

What happens in the lifecycle of eukaryotic viruses?

A

-binding
-fusion
-reverse transcription
(-integration)
-transcription
-translation
-assembly
-budding
-release

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109
Q

What are the issues for viruses living in eukaryotes?

A

-polycistronic mRNA can’t be translated in eukaryotes
-eukaryotic mRNA processing

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110
Q

How does Poliovirus undergo protein synthesis inside eukaryotes?

A

-genomic RNA acts as mRNA
-host translates it, synthesising one long polypeptide strand
-proteases cleave this polypeptide into diff proteins (structural coat proteins, proteases, RNA replicase, etc)

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111
Q

How does Poliovirus undergo replication inside eukaryotes?

A

-RNA replicase (made from translation) makes a -ve strand of viral RNA, which is used to make a +ve strand
-can occur in cytoplasm (no DNA invovled)
-host cap-binding protein is destroyed to inhibit host RNA and protein synthesis

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112
Q

What is the stucture of poliovirus genome?

A

-linear ssRNA (+) strand genome
-mimicks mRNA -has polyA tail at 3’ and Vpg (protein mimicking cap) at 5’
-RNA folds into stem-loops

113
Q

What is the Rabies genome like?

A

one linear (-) strand RNA genome
-virus has its own polymerase (animal host can’t transcribe - strand to + strand)

114
Q

What is the Influenza genome like?

A

(-) strand ssRNA genome segmented into 8 linear fragments

115
Q

What is the structure of Influenza like?

A

-genome is (-) strand RNA segmented into 8 fragments
-has accessory proteins (eg. RNA endonuclease, RNA viral polymerase)
-envelope
-membrane-bound proteins neuraminidase and hemagglutinin

116
Q

What does neuraminidase do?

A

cleaves neuraminic acids so virus can break through mucus

117
Q

What does hemagglutinin do?

A

bind to receptors on host envelope to allow the virus to be internalised

118
Q

How do Rabies and Influenza replicate their genomes inside host cells?

A

-use viruses own polymerase to transcribe (-) strand RNA to (+) strand RNA
-(+) strand RNA is used to produce copies of genomic (-) strand RNA and is used to translate viral proteins
-(-) strand RNA and structural proteins form progeny virus

119
Q

What are the consequences of Influenza genome changes?

A

-antigenic drift (mutations in genes encoding surface proteins)
-antigenic shift (re-association of portions of RNA genome from genetically distinct strains leads to different combinations of surface proteins)

120
Q

What is the HIV genome like?

A

2 identical (+) strand of ssRNA
(is a retrovirus)

-has R terminal repeats (essential for replication)
-has genes gap (structural proteins), pol (reverse transcriptase, integrase) and env (envelope proteins)

121
Q

How is HIV replicated?

A

-viral entry
-uncoating
-reverse transcription to produce dsDNA
-dsDNA moves into host nucleus and is integrate into host DNA, becoming a provirus
-is transcribed, producing viral genomic RNA and viral mRNA
-viral mRNA is used to translate viral proteins
-encapsidation
-budding and release

122
Q

How does HIV gene expression vary?

A

-when in provirus form (combined with host DNA), genome can be expressed or can remain latent
-activation of promotors in long terminal repeat regions (at ends of viral genome) causes capping and polyadenylation of mRNA transcript
-viral mRNAs can be encapsulated or translated
-polyproteins are synthesised and processed

123
Q

What is the simian virus 40 genome like?

A

one dsDNA circle
-has overlapping genes
-very small (doesn’t encode viral DNAP, uses host’s)

124
Q

How does the simian virus 40 replicate its genome?

A

using host cell machinery bidirectionally
-synthesis is initiated by T antigen protein binding to origin of replication

125
Q

What are coronavirus genomes like?

A

single (+) strand RNA viruses

126
Q

What is the structure of coronaviruses like?

A

-envelope
-glycoprotein spikes (giving “crown” appearance, hence “corona”)
-large (~30kb)

127
Q

What happens in the infection cycle of coronaviruses?

A

-genome has 5’ cap and poly(A) tail so can act directly as mRNA
-only translated gene encoding replicase
-RNA replicase makes copies of (-) strand of RNA
-(-) strand generated synthesises (+) strand copes of whole genome (progeny genomes) or monocistronic mRNAs (go onto translate proteins)

128
Q

Why is bacterial genomics important?

A

-mol bio dev -discovers in DNA rep, etc
-w/o genetic systems can’t clone genes, express proteins, etc
-synthetic bio and bact systematics

129
Q

What are the similarities/differences between eukaryotic and prokaryotic chromosomes?

A

-proks mainly have coding genes (v. lil space between) while euks have a lot of non-coding sections (introns) and genome-wide repeats
-both have pseudogenes

130
Q

What is a pseudogene?

A

sequence of DNA which resembles a functional gene but has been mutated into an inactive form over time so has no functional counterpart in wild-type populations

131
Q

How are genes organised in prokaryotes?

A

-in operons (can code for a monocistronic or polycistronic message)

132
Q

What is a monocistronic operon?

A

an operon consisting of only one gene so only codes for one protein
-rare

133
Q

What is a polycistronic operon?

A

an operon containing multiple genes so codes for multiple proteins
(eg. has 3 genes, codes for 3 proteins)

134
Q

How is a nucleoid structured?

A

-has 30-100 loops (domains) -generated by DNA-binding proteins
-helical within each loop
-supercoiled (supercoils can be same or opposite direction to helix) -generated by topoisomerases

135
Q

How are loops within a nucleoid generated?

A

by DNA-binding proteins
(relatively small anchoring proteins similar in function to histones)

136
Q

How are supercoils within a nucleoid generated?

A

-topoisomerases make double breaks
-another bit of DNA is passed through the break
-break is resealled

137
Q

What happens in DNA replication in bacteria?

A

-replication starts at origin
-replication bubble forms and DNA is replicated in opposite directions of fork (bidirectional)
-at each fork, 1 strand is synthesised continuously (from 5’ to 3’) and the other is synthesised discontinuously (from 3’ to 5’) in Okazaki fragments
-replication ends at terminus

138
Q

How is DNA replication terminated in bacteria?

A

-at termination regions (have specific seq)
-clockwise replication forks stopped by TerB, C, F, G and J
-anticlockwise replication forks stopped by TerA, D, E, H and I
(not all Ter sites necessary -more than needed so still functions is they are lost)

139
Q

How is the issue of a catenane of linked rings being produced in bacterial DNA replication solved?

A

either
-enzymes XerC and XerD recognise different sites on both molecules and catalyse them to be cut and re-joined
or
-by topoisomerase 5

140
Q

What is the chromosome of E.coli K-12 like?

A

-circular
-contains 4288 genes
-replicated bidirectionally from origin
-has restriction sites for Not1
-has some Hfr origins

141
Q

How can plasmids be visualised?

A

using metal shadowing
-EM technique where very thin elements can be visualised (also used for proteins and DNA)

142
Q

How are plasmids replicated?

A

by rolling circle replication

143
Q

What plasmid-conferred phenotypes are there?

A

-antibiotic production
-antibiotic resistance
-metabolic functions (v. specific)
-virulence

144
Q

How are resistance mutations in plasmids seen and selected?

A

-antibiotic resistant colonies grow around filter disc impregnated with compoound
-visible differences (eg. diff colour from diff pigment being produced)

145
Q

How is a bacterial genotype written (Nomenclature)?

A

-gene name 3-4 letters; all italics, all lowercase except 4th is capital (eg. cydA)
-subscript + for wild type, no subscript for mutant
-add number afterwards if multiple alleles (eg. cydA1)

146
Q

How is a bacterial phenotype written (Nomenclature)?

A

-only 1st letter capital
-presence or absence of property shown by + or -
-not in italics

147
Q

How is a bacterial encoded protein written (Nomenclature)?

A

-only 1st letter capital
-not in italics
-no subscript
eg. CydA protein

148
Q

How can mutants be screened?

A

-master plate (containing colonies) pressed onto velveteen
-velveteen (now with colonies imprinted onto it) is used to transfer colonies to fresh media (minimal and complete media -on diff plates duh)
-plates incubated

-all colonies will grow in complete media, mutants won’t grow in minimal media

149
Q

What is a mutagen?

A

an agent which increases mutation rates
-have diff modes of action eg. UV radiation, intercalating dyes

150
Q

How is genetic material transferred from donor to recipient in bacteria?

A

-transformation (uptake of naked DNA)
-transduction (phage-mediated)
-conjugation (plasmid mediated)

151
Q

What happens in the mechanisms of transformation?

A

-DNA binds via protein outside cell
-one strand enters using DNA translocase, whilst the other strand is degraded
-internalised single strand is bound by RecA protein (prevents it being degraded)
-RecA holds ssDNA and dsDNA together
-RecA-ssDNA complex stretched dsDNA to increase complementarity recognition (known as conformational proofreading)
-branch migration (bps on homologous DNA strands are exchanged)
-homologous recombination

152
Q

What is the role of RecA protein?

A

-prevents ssDNA being degraded (as cell will try to degrade ssDNA as it detects it as a sign of phage infection)
-holds ssDNA and dsDNA together to enable conformational proofreading to occur during transformation

153
Q

What is competency?

A

a cell’s ability to take up extracellular DNA from environment via transformation
-not all cells are naturally competent -can be induced by electroporation or chemical treatment

154
Q

What was the original experiment done to discover conjugation?

A

Lederberg and Tatum experiment
-2 auxotrophic E.coli strains each with diff mutations deficient for some factors
-alone, neither strain grew any colonies
-mixture of both strains, colonies grew (deficiencies overcome) -must be some transfer of DNA between cells
Davis U-tube experiment proved physical contact was needed between cells

155
Q

What experiment proved physical contact was needed between cells for conjugation to occur?

A

Bernard David
-used a U-tube with fine pore filter between 2 strains
-no genetic transfer
-therefore contact must be needed between cells

156
Q

What is an F plasmid?

A

Fertility plasmid

157
Q

What regions are found on a fertility (F) plasmid?

A

-tra region for conjugate transfer
-origin of transfer in conjugation (where it starts being taken up into recipient cell)
-insertion seqs (allow to recombine with chromosome)

158
Q

In what forms can fertility (F) plasmids exist?

A

either free as plasmid (F+ cell) or recombined as part of chromosome DNA (Hfr cell)

159
Q

What happens in the mechanism of conjugation?

A

-pili male contact between with cell
-pilus contracts by dis-assembling subunits, inducing contraction so that cells move closer to eachother and merge(?)
-strand moves from one cell to other (+ to -)
-DNA is synthesised by rolling circle mechanism to replace transferred strand

160
Q

What are Hfr cells?

A

cells with high frequency of recombination for chromosomal markers
-Hfr cells differ depending on the order genes are transferred and which regions they are inserted into

161
Q

How were Hfr strains used to map chromosomes?

A

-conjugation was disrupted at diff times to see how much had been transferred, which identifies their insertion sites
-map can be made (minute charts)

(not really done anymore)

162
Q

How is transformation used in labs today?

A

to move diff plasmids/DNA frags into diff bacterial cells (some are naturally competent, others need chemical treatment or electroporation)

163
Q

How is transduction used in labs today?

A

to move small DNA frags or genes from one cell to another

164
Q

How is conjugation used in labs today?

A

not used today (used to be used for chromosome mapping using minute charts)

165
Q

How does genetics affect health throughout lifespan?

A

embryonic: half of embryos have chromosomal defects
newborns: 5% have birth defects
later on in life: 2/3 diseases have genetic component

166
Q

What are mitochondrial disorders?

A

-when there is a mutation in one copy of mtDNA (out of the hundreds of copies present in cell)
-resulting in mixture of genotypes (heteroplasmic)
-causes mitochondrial disorder
-are maternally inherited (don’t follow Mendelian inheritance patterns)

167
Q

What are single gene disorders?

A

disease caused by mutation at a single gene
-follow Mendelian inheritance pattern
-high penetrance
-predictive tests

168
Q

What are complex disorders?

A

disease caused by mutations at multiple alleles (polygenic)
-susceptibility but not deterministic
-no reliable tests
-influenced by environment

169
Q

What is the human genome like?

A

-3.2Gb bps
-appox 1.1% genome is coding -20,500 protein-encoding genes (proportionally not very many)
-non-coding areas still functional, like regulatory elements (eg. enhancer), promotors, etc

170
Q

What is ENCODE?

A

Encyclopaedia of DNA Elements
-international research collaboration aiming to build list of functional elements (non-coding) in human genome including regulatory elements and elements acting at protein and RNA level
-achieved through genomic, functional and bioinformatic approaches

171
Q

Why was it technically challenging at the time to sequence the human genome(/large genomes)?

A

-length of genome
-enough clones needed to be generated to ensure complete coverage of genome
-sequencing needed to be repeated (to be accurate)
-genome had to be reassembled from individual seqs (especially difficult with repetitive regions)

172
Q

What is the difference between whole genome sequencing and whole exome sequencing?

A

-whole genome sequencing sequences entire genome, which generated masses of data and is more expensive
-whole exome sequencing is targeted to only the coding region of genome (1%)

173
Q

Where are mutations of single gene disorders identified in next generation sequencing?

A

all mutations in coding seq

174
Q

Where does next generation sequencing identify mutations of complex gene disorders?

A

some inside, some outside of coding seq

175
Q

What has next generation sequencing allowed?

A

-reduced cost
-reduced time

176
Q

What are the types of single gene disorders?

A

-autosomal dominant disorders (eg. Huntingtons disease)
-autosomal recessive disorders (eg. Cystic fibrosis)
-X-linked disorders (eg. Duchene Muscular Dystrophy)

177
Q

What are autosomal dominant disorders?

A

disorders where one copy of a mutation is sufficient for an individual to be affected
-wild-type allele is recessive, defective allele is dominant
-inherited in dominant pattern or new mutation arises in a copy of the gene
-phenotype appears in every gen
-affected parent can pass it onto any progeny, following Mendelian inheritance (typical ratios not always seen due to small progeny sample size)
Eg. Huntington’s disease

178
Q

What is Huntington’s disease?

A

a late-onset autosomal dominant disorder which is progressively degenerated brain neurones (causing neuronal dealth, CNS disorder, decreased cognitive function, etc)
-affects every generation
-follows Mendelian inheritance patterns
-caused by more than 36 CAG repeats in HTT prot

179
Q

Mutations in which gene cause Huntington’s disease?

A

HTT gene
-gene encoding huntingtin protein with poly glutamine tract (endoced by CAG codon)
-normally <36 CAG repeats, when >36 repeats Huntington’s disease is caused
-the more CAG repeats, the earlier the onset of disease

180
Q

What is the correlation between the number of CAG repeats and the onset of Huntington’s disease?

A

The more CAG repeats, the earlier the onset of disease
-CAG repeats are unstable and prone to expansion, including during parental transmission -meaning signs and symptoms appear at earlier age as disease is passed on from one generation to the next

181
Q

What has positional cloning been used to identify?

A

diseases including Huntington’s disease and cystic fibrosis

182
Q

What are autosomal recessive disorders?

A

disorders where two copies of a mutation are required for an individual to be affected
-wild-type allele is dominant, defective allele is recessive (inherited in recessive pattern)
-phenotype doesn’t appear in every generation
-both parents must be carriers for disease phenotype
-follows Mendelian inheritance patterns
Eg. cystic fibrosis

183
Q

What is cystic fibrosis?

A

an autosomal recessive disorder characterised by build-up of mucous, which can damage organs
-caused by CFTR gene and mutations

184
Q

What symptomatic therapies are there for cystic fibrosis?

A

-physiotherapy
-DNase (to reduce mucous viscosity)
-antibiotics and anti-inflammatories
-mannitol spray (to increase mucus osmolality)

185
Q

Mutations in which gene cause cystic fibrosis?

A

CFTR gene
-encodes transmembrane protein which transports Cl- ions across membranes of cells lining lungs, ensuring hydration of surface layers of airways
-can be mis-sense, nonsense or frame-shift mutations (most common mutation is deltaF508 mutation, other mutations referred to as private mutations)
-diff mutations result in diff molecular phenotypes (protein phenotypes)
-sufferers of cf can be homo or heterozygous to CFTR mutations

186
Q

What treatments are there for cystic fibrosis?

A

treatments depend on mutation/molecular phenotype
Diff drugs such as…
-production correctors
-correctors
-potentiators

-mutations may display multiple classes of phenotype ∴ require multiple drugs

-mutation specific targeted therapies -specific to individual genetic profile

187
Q

What are X-linked disorders?

A

disorders where genes on the X chromosome are affected
-mostly recessive
-males can inherit from carrier female parent, females can only inherit when both parents are carriers
-females generally unaffected but act as carriers
-progeny of affected males never show diseased phenotype (female progeny will be carriers though)
-male progeny of female carriers have 50% chance of getting diseased phenotype, female progeny of female carriers have 50% chance of being a carrier
Eg. Duchene Muscular Dystrophy

188
Q

What is Duchene Muscular Dystrophy?

A

a X-linked recessive disorder (gene responsible on X chromosome)
-onset is passed on by mother
-causes muscle weakness and degeneration

189
Q

Mutations in which gene cause Duchene Muscular Dystrophy?

A

gene on X-chromosome which is the largest human gene (2.4Mb) containing 79 exons and encodes dystrophin protein
-dystrophin is part of a protein complex in skeletal and cardiac muscle which strengthens the muscle by linking actin to connective tissue
-most mutations are deletions

190
Q

How can Duchene Muscular Dystrophy be treated?

A

using anti-sense oligonucleotides to block splicing machinery around the exons containing premature stop codons, so that a partially functional protein can be produced (rather than producing no protein)

191
Q

How does Beckers Muscular Dystrophy vary from Duchene Muscular Dystrophy?

A

-both caused by mutation in gene encoding dystrophin
-Beckers has in-frame mutation (no stop codon midway along) so produces a partially functional protein ∴ is less severe
-Duchene has stop codons part way along seq so doesn’t produce protein ∴ is more severe

192
Q

What has identification of gene and variants of single gene disorders allowed?

A

-diagnostics and carrier status
-prognostic info (likely outcome, recovery)
-scientific knowledge (eg. of mechanisms)
-tailored treatments to be developed

in future…
-identification and analysis of genetic determinants in novel conditions, characterised disorders, atypical presentation of disease and complex disorders

193
Q

What are complex diseases?

A

common diseases affected by polgenic and environmental factors
-familial
-not deterministic
eg. obesity, diabetes, psychiatric conditions (Alzheimers, depression, etc)

194
Q

Why do genetic components need to be identified for complex diseases?

A

-early diagnosis and treatment
-to identify lifestyle changes that can be made to lower risk
-develop molecular understanding for developing therapeutics

195
Q

What are the different possible forms of complex diseases?

A

-small number of dominant alleles causing a large increase in risk (eg. Parkinsons)
-many alleles causing a small increase in risk (common disease, common variant model) (eg. type 2 diabetes)
-one main allele causing a large affect and several other alleles causing a small increase in risk (eg. breast cancer)

196
Q

What is the common disease common variant (CDCV) model?

A

if a disease is common in a population, the genetic contributors will also be common in the population

197
Q

What are single nucleotide polymorphisms (SNPs)?

A

germline substitution of a nucleotide at a specific locus
-found in coding and non-coding regions
-common variants
-unevenly distributed in genome

198
Q

What is minor allele frequency (MAF)?

A

the frequency which the second most common allele exists in a population
-used as a measure as to how common/rare a single nucleotide polymorphism (nucleotide substitution at locus) is

199
Q

What is the minor allele frequency (MAF) of a common single nucleotide polymorphism (SNP)?

A

> 5%

200
Q

What is the minor allele frequency (MAF) of a rare single nucleotide polymorphism (SNP)?

A

<5%

201
Q

How can complex disease alleles be identified?

A

-using linkage analysis (linkage between mapping markers and occurrence of disease in families)
-using genome-wise association studies (GWAS) (searching for alleles in population that occur more in disease cases than in matched controls)

202
Q

What are genome-wide association studies (GWAS)?

A

studies looking for alleles in a population which occur more in disease cases than in matched controls

203
Q

Vp =

A

Vg + Ve

204
Q

What is phenotypic variation?

A

the sum of genetic and envrionmental variation

205
Q

What is heritability?

A

the degree of variance in a particular phenotype in a population due to genetic variation
-not fully explained by risk alleles

206
Q

heritability =

A

Vg/Vp

207
Q

Why are twin studies useful?

A

can study the effect of genetics (heritability) and environment on phenotypic variance

208
Q

What are monozygotic twins?

A

identical twins
-share ~100% of their genes
-shared environment

209
Q

What are dizygotic twins?

A

non-identical twins
-share ~50% of their alleles
-shared environment

210
Q

What is the ACE model of phenotypic variation?

A

model used in twin studies to show what proportion of variance is genetic and environmental
A = genetic variance
C = common environmental variance
E = specific environmental variance

211
Q

What is genetic variance (A in ACE model) like in monozygotic and dizygotic twins?

A

constant in MZ twins
variable in DZ twins

212
Q

What is common environmental variance (C in ACE model) like in monozygotic and dizygotic twins?

A

constant in both MZ and DZ twins

213
Q

What is specific environmental variance (E in ACE model) like in monozygotic and dizygotic twins?

A

variable in both MZ and DZ twins

214
Q

How can the ACE model show the extent a phenotype in one twin correlates in the other twin?

A

A + C
in MZ twins, A = 100%
in DZ twins, A = 50%

215
Q

What are the two models complex disease may exist, looking at phenotypic variation?

A

-disease with continuous phenotypic variation
-disease with threshold for development of disease

216
Q

How is a continuous phenotype seen in polygenic diseases?

A

large number of loci -the more loci, the more distribution, the more phenotypes

217
Q

What is the liability threshold model of disease susceptibility?

A

that when an individual reaches a specific liability (the threshold), they will have the disease
-liability increases with genetic and environmental factors
-discontinuous disease phenotypes (either have disease or don’t)

218
Q

How does the threshold model of disease susceptibility change with relatives?

A

increased risk
-threshold shifted

219
Q

What affect do SNPs have when they occur at coding regions?

A

synchronous (no change to aa encoded) or asynchronous (mis-sense or non-sense mutations)

220
Q

What affect do SNPs have when they occur at non-coding regions?

A

affect regulation/expression of associated genes

221
Q

What do having combinations of multiple SNPs lead to?

A

a complex disease

222
Q

What is Exome Aggregation Consortium (ExAC)?

A

a database containing exomes of unrelated individuals sequences as part of disease-specific and population genetic studies
-variants mapped, allele frequencies recorded, rare mutants documented

223
Q

How are genome-wide association studies (GWAS) used to identifiy risk alleles?

A

-fixed number of SNPs in genome examined for association with disease phenotype
-search for alleles that occur more frequently in diseased cases than matched controls
-need lots of participants (with and without disease, with and without allele)
-only subset of panels looked at rather than whole genome (to save money and time) -hence association

-identifies association with disease, not necessarily risk alleles -need to integrate with functional data to find causality

224
Q

What is linkage disequilibrium?

A

non-random association of alleles at different genomic sites
-deviation in haplotype frequencies from their expected frequencies in a population if loci defining the haplotypes are randomly associated
-SNPs correlate with risk alleles due to LD

225
Q

What are haplotypes?

A

a set of DNA segments on a chromosome defined by alleles on locus
-usually inherited together
-haplotype blocks summarise linkage disequilibrium -are regions with high LD separated from other regions from historical recombination events

226
Q

What is done in haplotype mapping?

A

groups of alleles clustered so that a SNP (tag SNP) can identify them

227
Q

What is an odds ratio?

A

statistic which quanitfies the strength of association between two events
-used to measure the likelihood that a single nucleotide polymorphism is associated with a disease
1 = events independent
<1 = events are negatively correlated
>1 = events are correlated

228
Q

What does an odds ratio of 1 mean?

A

events are independent of eachother

229
Q

What does an odds ratio greater than 1 mean?

A

events are correlated

230
Q

What does an odds ratio less than 1 mean?

A

events are negatively correlated

231
Q

What is a Manhattan plot used for?

A

-to show the frequencies of points on a chromsome
-can determine which alleles are risk alleles -threshold line drawn on plot -alleles above line are risk alleles (risk of lots of false -ves!)

232
Q

How have GWAS helped identify low risk alleles for type 2 diabetes?

A

-increased statistical power has enabled low risk loci to be identified -have odds ratios between 1.06-1.27
eg. FTO (intronic variant) and CDKN2A/B (non-coding region variant) discovered -both low risk alleles
TCF7L2 also visible (v large peak) -highest risk allele for type 2 diabetes

233
Q

How have GWAS helped identify low risk alleles for breast cancer?

A

-identified 66 common low risk alleles in non-coding region
-can also see BRCA1/2 which are autosomal dominant genes responsible for 5% cases of breast cancer (mapped by linkage analysis before GWAS)

234
Q

What is the principle of missing heritability?

A

the identification of risk alleles can not alone explain the heritability and phenotypes of diseases

235
Q

What can the missing risk (missing heritability not explained by risk alleles) arise from?

A

-false -ves in GWAS
(the following are not detected in GWAS…)
-rare variant alleles with a MAF of 1-5%
-genome structural changes
-epigenetics
-3D genome organisation

236
Q

What gives rise to different cell fates in development?

A

cell differentiation
-stem cells leading to diff lineages
-diff gene expression and proteome (but same DNA)

237
Q

What gives rise to different cell positions in development?

A

pattern formation
-cells acquire positional values, which develop to give spatial patterns
-established by polarity

238
Q

What gives rise to cells having different positional values in development?

A

polarity
-defined by molecular events

239
Q

What are stem cells?

A

undifferentiated cells (of a multicellular organism) capable of giving rise to indefinitely more cells of the same time and which can other cells can differentiate from

240
Q

How is the population of stem cells maintained?

A

via self-renewal

241
Q

How do progeny with different fates arise?

A

via asymmetric divisions of progenitor cells

242
Q

What are the different forms of stem cells?

A

-totipotent (can form whole new organism)
-pluripotent (can form most cell types but not all)
-multipotent (can form diff cell types but fewer that pluri)

243
Q

How are embryonic stem cells generated?

A

-inner cell mass (ICM) cells are extracted from a blastocyst
-extracted ICM cells are grown on specific tissue culture
-embryonic (but not totipotent) stem cells are produced

244
Q

What are the uses of embryonic stem cells?

A

-introduce new genes
-for gene knock-out
-chromosomal rearrangements/deletions can be done to see impact in model organism
-specific gene editing (CRISP)

245
Q

How are transgenic mice produced from embryonic stem cells?

A

-ESCs are introduced into a blastocyst
-implanted into pseudopregnant mother
-chimeric mouse produced (from 2 diff zygotes -ICM and ESC)

246
Q

How can somatic nuclei be reprogrammed to be totipotent?

A

extracting somatic cell nucleus and inserting it into an enucleated egg using UV irradiation

247
Q

How can pluripotent stem cells be induced?

A

incubating adult cells in tissue culture with transcription factors

248
Q

What are the genetics of Drosophila melanogaster like?

A

-4 pairs of chromosomes (X and Y, 2, 3, 4)
-16,000 genes (relatively small genome)
-~140Mb

249
Q

How is the Drosophila body plan determined?

A

by hierarchy of developmental genes

250
Q

What type of genes are involved in Drosophila development?

A

-maternal effect genes
-gap genes
-pair-rule genes
-segment polarity genes
-homeotic genes

251
Q

What is the role of maternal effect genes?

A

establish pattern
-maternal genotype determines progeny phenotype

252
Q

How is anterior-posterior polarity determined before fertilisation in Drosophila?

A

-by oocyte
-maternal effect gene transcripts present (just transcription, not translation)
-bicoid mRNA present at anterior and nanos mRNA present at posterior
-polarity informs system
-bicoid and nanos regulate gap genes

253
Q

What does a bicoid mutant affect?

A

anterior region

254
Q

What does a nanos mutant affect?

A

posterior region

255
Q

What can be seen in the Drosophila oocyte before fertilisation using in situ hybridisation?

A

mRNA localisation
-bicoid at anterior, nanos at posterior

256
Q

What can be seen in the Drosophila oocyte just after fertilisation using in situ hybridisation?

A

protein localisation
-conc gradient of bicoid protein with highest concs at anterior
-conc gradient of nanos protein with highest concs at posterior

sets up polarity

257
Q

What is the role of gap genes?

A

further compartmentalisation

258
Q

What is ultrabithorax?

A

homeotic mutant of Drosophila where there are 2 sets of wings (instead of 1)
-second segment is duplicated, replacing the third

259
Q

How are homeotic genes organised?

A

often into complexes/clusters
Drosophila: Hom-C complex containing antennapedia and bithorax complexes
Humans and mice: 4 hox complexes (instead of 1 in Dros)

260
Q

What is the relationship between the expression of genes and sequence of genes along the chromosome in hox complexes?

A

the same order

261
Q

Why are homeotic genes known as homeodomain transcription factors?

A

homeodomain = have 60aa homeodomain, which is involved in DNA binding
transcription factor = binds to DNA and regulates gene expression (homeotic genes give rise to particular organs)

262
Q

What is syndactyly?

A

mutant in human hox gene causing 2(+) digits to be fused
-caused by dominant mutation in Hox-D13

263
Q

How are homeotic transformations seen in floral development?

A

2 organs lost (out of petals, sepals, stamen and carpel)

264
Q

Why is it important to score random nuclei when counting cells in different mitotic stages?

A

so proportions reflect the asynchronous population of cells and the relative lengths of each of the stages

265
Q

How many cross-overs result in chromosomes appearing circular during meiosis?

A

2

266
Q

How many cross-overs result in chromosomes appearing cross-shaped during meiosis?

A

1

267
Q

What is a pericentric inversion?

A

a chromosomal mutation where a segment containing the centromere is inverted

268
Q

What is a paracentric inversion?

A

a chromosomal mutation where a segment not containing the centromere is inverted

269
Q

What chromosomal rearrangement leads to Edwards syndrome?

A

trisomy 18.
47, XX or XY, +18

270
Q

What chromosomal rearrangement leads to Patau syndrome?

A

trisomy 13
47, XX or XY + 13

271
Q

What chromosomal rearrangement leads to Downs syndrome?

A

47, XX or XY +21

272
Q

What chromosomal rearrangement leads to Klinefeller syndrome?

A

sex chromosome aneuploidy
47, XXY

273
Q

What chromosomal rearrangement leads to Turner syndrome?

A

sex chromosome aneuploidy
45, XO

274
Q

What is a null allele?

A

a mutant allele which has complete loss of function

275
Q

What happens in leptonene (during prophase 1)?

A

replicated chromosomes start to contract

276
Q

What happens in zygotene (during prophase 1)?

A

chromosomes line up in homologous pairs, held together by synaptonemal complex

277
Q

What happens in pachytene (during prophase 1)?

A

crossing over occurs between non-sister chromatids

278
Q

What happens in diplotene (during prophase 1)?

A

chromosomes separate slightly
-chiasma is visible

279
Q

What happens in diakinesis (during prophase 1)?

A

chromosomes contract further

Molecular Biology BSc First Year (10 decks)

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