Genetics Flashcards

Question

What is prophase?

Answer 1

Chromosomes condense - now visible Each chromosome comprises 2 chromatids and a single centrosome Sister chromatids are help by a protein called cohesin Later in prophase - nuclear membrane breaks down and chromosomes start to move towards equator - prometaphase

Answer 2

Cytoskeletal structure made of microtubules - polymers of small tubulin protein subunits Job - separate sister chromatids This happens due to microtubules getting shorter

Answer 3

Centromeres: specialised chromosome regions which direct equal segregation of chromosomes - can be found at any point Defined by specific epigenetic markers Sister chromatids are joined by a centromere Centromeres are connected to microtubules by a large protein complex - kinetochore

Answer 4

Centromeres align at spindle equator - midway of poles Microtubules attaching to each pole - tension between these keeps chromosomes in centre

Answer 5

Sister chromatid cohesin breaks down Chromatids - now separate chromosomes Centromeres split and move to opposite poles Depending on position of centromere - chromosomes can form V shape as dragged

Answer 6

Chromosomes arrive at cell poles Chromosomes decondense - no longer recognisable threads Daughter nuclei reform

Answer 7

Division of cell Cleavage furrow (animals) or cell plate (plant) forms between poles Gives two daughter cells - can be symmetrical or two uneven shaped (e.g. in budding yeast)

Answer 8

They look very similar In diploid - homologous chromosomes act separately

Answer 9

Bridge chromosome: a chromosome that has erroneously has two centromeres is pulled towards both poles - ends up breaking Acentric chromosome - lacking a centromere - can't segregate properly

Answer 10

Two nuclear divisions - halves chromosome number Replication -> chromosome segregation -> chromatid segregation -> form tetrad (4 haploid products) Alternates between 2n and n Forms gametes

Answer 11

Haploid most of the life cycle Two mating types: a and alpha One a and one alpha = transient diploid stage Then meiosis occurs Gives 4 haploid products We can dissect these products (segregants) and culture them individually - gives us info on linkage relationships

Answer 12

Two nuclei both containing both chromatids of one chromosome from each pair of homologues - different than parent cell

Answer 13

Each replicated chromosome 2 sister chromatids with a single centromere

Answer 14

2 dyads joined together

Answer 15

1) Leptotene - replicated chromosome contract 2) Zygotene - chromosomes line up in homologous pairs = synapsis, held together by synaptonemal complex - bivalents 3) Pachytene - crossing over (genetic exchange) between non-sister chromatids, bivalents get shorter and thicker 4) Diplotene - chromosomes separate mostly - including centromere but sites of crossing over are still visible (chiasmata) 5) Diakinesis - chromosomes contract further

Answer 16

Sister chromatids line up - centromere splits and chromatids move to opposite poles Four nuclei - two contain one copy of first homologous chromosome, the other two contain one copy of the second

Answer 17

Sites of genetic exchange between homologous sequences on non-sister chromatids Double strand breaks are generated by an enzyme Homologous recombination occurs - relies on chromatids lining up correctly so identical sequences can be accessed. Sections of the chromosome are 'swapped' giving new allele combinations

Answer 18

Singular = chiasma Plural = chiasmata

Answer 19

Yes - but chromatids has separated slightly

Answer 20

Mitosis: sister chromatids line up Meiosis: I = homologous chromosomes, II = sister chromatids

Answer 21

The process that produces a gene or chromosome set differing to a wild type

Answer 22

The form that predominates in nature/in a standard lab stock

Answer 23

Pass down to all daughter cells - population is no longer clonal - could be 'genetic mosaic' - mutation only passed on if it's in the germline

Answer 24

Polyploidy = unusual number of chromosome sets e.g. triploidy = 3n, tetraploidy = 4n, monoploidy = 1n (when 2n is normal) Aneuploidy = one or a few individual chromosomes missing

Answer 25

Deletions: part of chromosome missing Inversions: part of chromosome has been flipped Translocations: part of chromosome has been moved

Answer 26

Mistakes during replication: point mutation (single nucleotide), small insertion/deletions (frameshift) Genes interrupted by transposons DNA breaks incorrectly repaired

Answer 27

Silent - no change to AA sequence Nonsense - introduction of stop codon in gene Missense - changes AA sequence Null allele - total loss of function

Answer 28

Mutants that are unable to synthesise essential compounds such as AA Cannot grow on minimal media - only on complete media or minimal media with the molecule they can't make

Answer 29

Minimal growth media - only nutrients that an organism cannot synthesise for itself Complete media - extra nutrients e.g. all AA. This allows all mutants to grow as it makes up for some defects in metabolic pathways.

Answer 30

+ = wild type Gene name in italics Genes are usually named after the phenotype of the null allele

Answer 31

Allelic = both mutations in the same gene/step of a pathway in two mutant organisms Non-allelic = both in different genes

Answer 32

The production of a wild-type phenotype when two haploid genomes bearing different recessive mutations are united in the same cell This can identify allelic vs non-allelic. Allelic = diploid still can't grow on minimal media - has two defective alleles, non-allelic = can grow on minimal media - has one wildtype allele on each gene.

Answer 33

Cross two homozygous recessive individuals - see the phenotype Allelic = non-complementation Non-allelic = complementation

Answer 34

Worked in his monastery garden in mid-1800's - concentrated on peas. He worked with 7 phenotypes. These were luckily: simple traits controlled by one gene, straightforward dominance relationships, on different chromosomes

Answer 35

All offspring from matings within those lines have that same character. E.g. following self-pollination, all offspring from a pure breeding plant giving green peas will also give green peas

Answer 36

Cross: pollen from another plant Self: pollen from self Each pea is one offspring

Answer 37

Law of equal segregation: during gamete formation - members of a gene pair separate equally. Each gamete carries one allele for each gene. Law of independent assortment: during gamete formation, chromosome pairs segregate independently from each other. Law of dominance: alleles can be dominant or recessive. An organism with at least one dominant allele will display the effect of that allele.

Answer 38

During gamete formation - members of a gene pair separate equally. Each gamete carries exactly one allele for each gene. You end up with the same allele ratio that you started.

Answer 39

Orientation of bivalents on meiosis I spindle is random Forms recombinants - combinations of alleles that are not found in parents

Answer 40

Alleles can be dominant or recessive - an organism with at least one dominant allele will display the effect of that gene. A slash shows alleles are a pair e.g. G/g

Answer 41

No! Some are several e.g. height

Answer 42

Parental P = first - round x wrinkled First filial F1 = second - all round Second filial F2 = third - (selfed) round and wrinkled

Answer 43

Punnet squares Probability trees These give you phenotypic ratios

Answer 44

Around 3:1

Answer 45

Cross pure-breeding parental lines with each of the phenotypes: predict all F1 offspring will have dominant phenotype Self-fertilise the F1 generation: predict 75% of F2 will have dominant phenotype Cross-fertilise the F1 generation with a homozygous recessive plant: 50% of F2 will have dominant phenotype

Answer 46

Cross an individual with a recessive offspring If homozygous dominant: all are Aa - dominant phenotype If heterozygous: 1/2 have dominant, 1/2 are recessive

Answer 47

Chi-squared

Answer 48

X^2 gives us the probability that we would get a deviation from the expected result as big as the one observed. 1) calculate observed and expected values 2) calculate chi-squared using the formula 3) use the table to get a p value 4) interpret this value

Answer 49

x2 = the sum of ((O - E)^2 / E)

Answer 50

The number of parameters that can vary independently = number of classes - 1 It is minus 1 because the last one has no choice e.g. wrinkled and round

Answer 51

0.05> - low probability = poor agreement between observed and expected >0.05 - high probability - doesn't contradict our hypothesis

Answer 52

Mendel's law of independent assortment only is true for genes that are not carried close together. e.g. B and C are close so are inherited together - these are linked

Answer 53

pr: mutant allele giving purple eyes pr+: wild-type (red eyes) vg: mutant allele giving small, vestigial wings vg+: wild type (long wings) Crossed pr/pr . vg/vg male (double recessive so only need to worry about genotypes from female) with pr+/pr . vg+/vg female - we would predict 2 parental and 2 recombinant all in equal proportions 1:1:1:1 However! - not matches this ratio - lots of parental (equal numbers), little recombinant (pr+/vg, pr/vg+)

Answer 54

Shows linkage but with a few recombinants - due to crossing over

Answer 55

Think of both genes e.g. RRMM x rrmm - F1 all heterozygous F2 - self pollinate RrMm - 9/16 have R and M, 3/16 have m and R, 3/16 have M and r, 1/16 are rrmm - 9:3:3:1

Answer 56

Cross with recessive - see if they hare recessive phenotype - is so it it heterozygous

Answer 57

RF = (recombinants/total meiotic products) x 100 = (NPD + 1/2 TT)/(PD + NPD + TT)

Answer 58

It is roughly proportionate to the distance between the two loci. During meiosis I - multiple recombination events ensure the homologues are held together - at random positions. The closer two genes are - less likely there will be a recombination event in-between them. So the strength of linkage depends on the distance between genes.

Answer 59

0 - 50% Two loci right next to each other - no crossing over - 0% RF Two loci on separate chromosomes - 50% recombinant, 50% parental, 50% RF If the distance is far enough, its impossible to know if the two genes are far away on the same chromosome or if they are on two separate chromosomes.

Answer 60

Permissive: all cells should be able to grow Selective: only wild-type

Answer 61

Auxotroph mutants: Selective - minimal media Permissive - complete media/MM + the relevant compound Temperature-sensitive mutants: Selective - slightly tough growing temp of 36 c - mutant proteins are unable to fold properly Permissive - ideal growing temp of 28

Answer 62

Parental ditype - all products of meiosis are the same as one of the parents

Answer 63

Group of four spores (haploid cells) that result from the meiosis of a diploid cell.

Answer 64

Independent assortment 50% of time = all non-parental - non-parental ditype 50% of the type = all parental - parental ditype

Answer 65

Two parental and two non-parental - 4 different products Happens due to crossover between two non-sister chromatids and two loosely linked genes Can happen for a single crossover between a gene and its centromere - also gives a tetratype for unlinked genes

Answer 66

RF = (NPD + 1/2 TT/ PD + NPD + TT) x 100

Answer 67

Length of stages - stages not in sync so you get cells in different stages

Answer 68

If PD = NPD - independent assortment - unlinked genes If PD>>NPD - inherited together - linked genes

Answer 69

Trisomy 18

Answer 70

Around 10^7 phage particles/ml

Answer 71

Genetic elements that cannot replicate independent of a living host They can exist as virus particles outside the host

Answer 72

Virus - 200 nm

Answer 73

Virus - 28 nm

Answer 74

0.5 - 1000 kb Some have fewer than 5 genes

Answer 75

Virion = extracellular form - nucleic acid surrounded by protein (and other molecules) Intracellular form - replicative state

Answer 76

ΦCD508 - tail fibres attach to S-layer - triggers a structural change so can inject its DNA We use cyro-electro microscopy to view it

Answer 77

- Very small and reliant on host replicative and metabolic machinery - DNA or RNA genome - single or double stranded - linear or circular

Answer 78

- One solution is to have a small number of protein species forming the capsid - The capsid proteins usually are self-assembly - e.g. TMV

Answer 79

Head Neck Tail (225 nm) Baseplate

Answer 80

Spherical animal viruses and phages have protein shells built of many copies of a few identical subunits

Answer 81

1) Attachment (absorption) - a structural change occurs 2) Penetration (injection) - protein coat remains outside 3) Synthesis of nucleic acid and protein 4) Assembly and packaging 5) Release (lysis) Some cases - viral proteins also enter

Answer 82

The timing is very important Early proteins = for replication of viral nucleic acid e.g. enzymes Late proteins = include coat proteins

Answer 83

T4 is a bacteriophage First = early mRNA/proteins = nucleases, DNA polymerase, new sigma factors Middle = middle mRNA/proteins = phage DNA Last = late mRNA/proteins = phage head proteins, tail, collar, base plate and tail fiber proteins Then self assembly Then T4 lysozyme production - lysis 25 minutes in total

Answer 84

RNA polymerase (core enzyme) and sigma factors Sigma recognises promotor and initiation site Transcription begins - sigma factor released Chain grows until termination site

Answer 85

T4 doesn't encode own RNA polymerase - uses host This is modified to specifically recognise promotors on phage DNA For early proteins - host sigma factors are used Also encodes an anti-sigma factor that binds to host sigma factor σ70 - preventing host transcription

Answer 86

Some early phage proteins modify host RNA polymerase α subunits Some bind to the host RNA polymerase These alter polymerase specificity to recognise middle promotors One early protein, MotA, recognises a sequence in the middle promotors and guides RNA polymerase to correct sites

Answer 87

Requires a new T4-encoded sigma factor Most late proteins are structural proteins

Answer 88

Lysogenic - incorporation of viral genome into host genome - infecting from within Lytic - reproduction of viruses using host cell to manufacture new viruses

Answer 89

The life cycle can result in a stable genetic relationship with the host called lysogeny Virus genome is integrated into host chromosome e.g. in λ phage, or in a plasmid form e.g. P1 phage - relies on a repressor

Answer 90

Most virus genes are not expressed The virus genome (prophage) is replicated in synchrony with host chromosome Lysogenic viruses may revert to lytic pathway and produce virions

Answer 91

Inactivation of repressor or prevention of repressor synthesis induced the prophase This results in lysis

Answer 92

Viral genome integrates at attachment site, attλ Requires the λ integrase enzyme 1) genome cyclases at cohesive ends 2) nuclease creates staggered ends of phage and host DNA 3) integration of λ (lambda) DNA and closing gaps by DNA ligase

Answer 93

The viral genome must be replicated ready for packaging and release from host Multiple copies of viral genome must be replicated

Answer 94

Rolling circle replication 1) 1 strand of the circular lambda genome is nicked - makes a long single-stranded concatamer using the unbroken strand as a template 2) second strand made using the single stranded concatamer as a template - the double stranded concatamer is cut into genome-sized lengths at the cos sites giving cohesive ends

Answer 95

1) binding 2) fusion 3) reverse transcription if the viral genome is RNA 4) integration 5) transcription 6) translation 7) assembly 8) budding 9) release

Answer 96

5' capped Splicing 3' polyadenylation

Answer 97

Typically very small (~30 nm) except coronaviruses e.g. poliovirus, rhinovirus (common cold), hepatitis A

Answer 98

Single linear ssRNA genome Genome acts as the mRNA but there is no capping - instead the RNA at 5' end folds into stem loops and has a protein, Vpg, bound - mimics cap

Answer 99

Genome RNA acts as mRNA Viral protein synthesised as one large polyprotein - common strategy in viruses Proteases then cleave the polyprotein to form structural coat proteins, RNA replicase ect.

Answer 100

Occurs in cytoplasm - does not involve DNA Host RNA and protein synthesis is inhibited as host cap-binding protein is destroyed RNA replicase - synthesises (-) from + then makes a - from the (+)

Answer 101

Includes rabies, influenza and ebola The - strand encodes the genome but cannot act as mRNA

Answer 102

A viral replicase is essential and carried by the virion 2 distinct classes of RNA are transcribed (-) strand parental (RNA pol makes mRNA from this) --> + strand RNA --> (-) strand genomic RNA

Answer 103

The (-) strand RNA is segmented Influenza A has 8 linear ssRNA molecules Structure: Inside (RNA genome - in 8 pieces, RNA endonuclease, viral RNA polymerase), Envelope, hemagglutinin, neuraminidase

Answer 104

The viral nucleic acid replicates in the host nucleus The overall pattern of viral genome RNA synthesis resembles rabies Transcription results in viral mRNA with 5' caps - primers are cut from 5' ends of newly synthesised host mRNAs by viral endonuclease - poly A tails are added - viral mRNA moves to cytoplasm for translation

Answer 105

The surface proteins are the main immunogenic regions of the virus Antigenic drift arises from mutations in the genes for the surface proteins Therefore, an annual vaccination mimicking the surface protein epitopes is needed

Answer 106

Portions of the RNA genome from 2 genetically different strains, both infecting a cell, are reassorted This leads to a different combination of surface proteins Antigenic shift is the origin of pandemics and epidemics

Answer 107

RETROVIRUS Genome has 2 strands of ssRNA Genome is replicated through a DNA intermediate - requires a reverse transcriptase Structure: - RNA and enzymes (reverse transcriptase, protease, integrase) - surrounded by core protein - Surrounded by a core shell protein - Lipid bilayer - Transmembrane envelope protein - Surface envelope protein

Answer 108

Retroviruses have 2 identical ss(+)RNA strands Have R terminal repeats (at end of strands) - essential for replication Has gag region - encode structural proteins Has pol region - encodes reverse transcriptase and an integrase Has env region - encodes envelope proteins that sit in the membrane

Answer 109

1) Entrance 2) Uncoating 3) Reverse transcriptase 4) Travel to nucleus and integrate in host DNA 5) Transcription 6) Encapsidation 7) Budding 8) Release

Answer 110

In provirus form - viral genome may be expressed or remain latent Activation of promotors in LTR region leads to mRNA transcripts that are capped and polyadenylated Viral mRNAs are either encapsidated or translated Similar to polio - polyproteins are synthesised and then processed

Answer 111

Simian virus 40 (SV40) One dsDNA circle (has early and late region) complexed with host cell histones No viral-encoded enzymes

Answer 112

A single RNA is made by the cellular RNA polymerase from the early region This is processed into 2 mRNAs - both capped The introns are excised out The expressed T antigen protein binds to origin of replication to initiate genome synthesis Genome too small to encode viral DNA polymerase - uses host DNA is replicated in a bidirectional fashion using host cell machinery

Answer 113

Begins at a promotor near origin of replication This late RNA is then spliced, capped and polyA'd to yield mRNA corresponding to the three coat proteins: VP1, VP2, VP3 The genes for these proteins overlap

Answer 114

See your photos!

Answer 115

Single (+) strand RNA virus Replication in cytoplasm (like polio) Causes resp infections in humans - cause 15% of common cold but occasionally fatal e.g. COVID

Answer 116

Enveloped virions Glycoprotein spiked give 'crown' like appearance Largest known RNA viruses ~ 30 kb

Answer 117

1) Entry - spike protein binds to receptor on host cell called ACE2 - host molecule TMPRSS2 cleaves spike protein exposing sites to fuse with 2) Inside - RNA is transcribed into non-structural proteins that quickly supress the translation of host messenger RNAs in favour of those belonging to virus 3) Remodelling - virus transforms the cell's ER into double-membrane vesicles - safe place for viral RNA to be transcribed 4) Exit - assemble into complete virus and leave through golgi/lysosomes 5) Furin cuts five amino acids on own spike protein - ready to infect another cell

Answer 118

Genome has 5' cap and poly(A) tail so can act as mRNA However only the replicase is translated This then generates a (-) strand of copied RNA From this - several monocistronic mRNAs are transcribed and translated into viral proteins - progeny genomes are also produced

Answer 119

Osmotic disruption of E.Coli - causes the DNA to spew out - 1500 times longer than the cell - use electron microscopy

Answer 120

A nucleoid - NOT NUCLEUS 30-100 domain loops in DNA after release from bacterial cell Supercoiled Some supercoils are relaxed in a nicked strand e.g. with endonuclease - loops out

Answer 121

Supercoiling of 300 bp circular DNA molecule Enzymes (topoisomerases) make a double strand break in the circle - passes another part of DNA through then reseal

Answer 122

15 minutes Semiconservative: at replication fork, DNA synthesis machine separates the two strands - forms a replication bubble, whilst extending the new strands From origin, oriC, to terminus, ter. 5'-3' Lagging has okazaki fragments

Answer 123

There are >8 arrest sites at the terminator regions Replication forks moving clockwise are trapped by terB, C, F, G, J Replication forks moving anticlockwise are trapped by terA, D, E, H, I

Answer 124

Circular - 4600kbp - 4288 genes No plasmids Order of transcription can be CW or ACW Replication proceeds in both directions from origin at 84.3 min There are restriction sites for Not1 and some Hfr origin ect.

Answer 125

Bacterial: tightly packed with coding genes with few mobile elements and little unused sequence Human: 95% non-coding, coding is separated with introns. Ancient gene duplications have decayed to pseudogenes (can't code for a protein)

Answer 126

Has big differences between itself and other strains of the same species The + and - strands are transcribed in opposite directions

Answer 127

One gene makes a monocistronic message (one protein) An operon of e.g. three genes makes a polycistronic message In a chromosome - genes and operons may form a regulon controlled by a common regulatory protein

Answer 128

A genetic structure in a cell that can replicate independently of the chromosomes - typically a small circular DNA strand in the cytoplasm Ranging from few hundred - many kbp

Answer 129

pBR322 Used in molecular cloning 1) origin of replication 2) two antibiotic resistance genes (amp and tet) 3) three unique 6bp restriction sites (HindIII, PstI and BamHI)

Answer 130

Antibiotic production Conjugation Metabolic functions Resistance Virulence

Answer 131

- Mercuric ion resistance - mer - Sulfonamide resistance - sul - Streptomycin resistance - str - Chloramphenicol (antibiotic) resistance - cat - Insertion sequences and transposon Tn10 - Transfer functions - can be transferred between enteric bacteria and are a threat to antibiotic therapy - tra - Replication functions - encode replication proteins

Answer 132

Heritable Rare Good/bad/neutral Usually small

Answer 133

IMPORTANT Gene name - 3/4 letters All except the 4th in lower case Always italicised e.g. cydA, cydD, hmp A wild-type gene is written with a + e.g. cydA+ A mutant is written cydA If there are several alleles we write cydA1, cydA2

Answer 134

Phenotype: Not in italics First letter is capitalised +/- used to show presence/absence of a property Encoded protein: No italics/superscript - first letter is a capital e.g. The CydA protein, CydD

Answer 135

Missense - faulty protein Nonsense - stop codon Silent - normal Genetic code is degenerate and different types of mutant proteins may result

Answer 136

GAG to GUG

Answer 137

Agents which increase mutation rates Radiation Intercalating dyes Chemicals reacting with DNA Base analogs

Answer 138

2-Bromouracil - substitutes T with itself and over time turns AT-GC or GC - AT 2-Aminopurine - over time turns AT-GC or GC-AT

Answer 139

Nitrous acid (HNO2) - deaminates A and C - turns AT-GC Hydroxylamine - reacts with C - GC - AT Alkylating agents: Monofunctional (e.g. ethyl methane sulfonate) - puts methyl on G - faulty pairing with T - GC -AT Bifunctional (e.g. nitrogen mustards, mitomycin) - crosslinks DNA strands - point mutations and deletions

Answer 140

UV - pyrimidine dimer formation Ionising e.g. x-rays - free radical attack Both may cause error or deletion when repaired

Answer 141

Auxotrophs - loss of enzyme in biosynthetic pathway - can't grow on media missing nutrient Temp-sens - heat sensitive Cold sensitive - can't grow at low temp as essential protein is inactivated at low temp Drug-resistant - detoxification of drug or alteration of drug target - can grow on media containing a normal amount of drug Rough colony - loss of liposaccharide layer - granular, irregular colonies Nonencapsulated - loss of surface capsule - small colonies Nonmotile - compact colonies

Answer 142

1) Transformation - uptake of naked DNA 2) Transduction - phage mediated 3) Conjugation - plasmid mediated

Answer 143

DNA may or may not be degraded 1) DNA binds via protein 2) one strand enters using DNA translocase - second is degraded 3) internalised single strand is bound by RecA protein 4) as RecA has more than one DNA binding site - it can hold the ssDNA and dsDNA together 5) the Rec-A-ssDNA complex stretches the dsDNA to increase complementary recognition (conformational proofreading) 6) branch migration and homologous recombination follows 7) Transforming DNA doesn't have to be a plasmid - often is

Answer 144

'normal' bacteriophage contains phage genes; transducing particles contain host genes too Lytic cycle or lysogenic cycle

Answer 145

Mating requires pili (sex pilus) responsible for cell pairing

Answer 146

NEEDED FOR CONJUGATION F = fertility - only in donor cells Tra region - genes needed for conjugative transfer including sex pilus oriT - origin of transfer during conjugation IS regions - insertion sequences may recombine with regions on chromosome

Answer 147

1) pilus retracts 2) cell pairs stabilized - F plasmid nicked in one strand 3) transfer of one strand from F+ (donor) to F- (recipient) - F plasmid is replicated in F+ cell 4) Complementary strand is synthesised in recipient cell by rolling circle mechanism 5) Completion of DNA transfer - cells separate

Answer 148

yes! due to integrated F plasmid Hfr strains were isolated (efficient genetic donors) - high frequency of recombination for chromosomal markers The plasmid can't control own replication now - tra function operates and cell forms pili Then Hfr encounters recipient strain - the F+ plasmid is integrates - the bacteria is Hfr

Answer 149

The Hfr strain transfers the F plasmid to a recipient as an F+ would The recipient does not become Hfr as part of the integrates Hfr is transferred Look at diagram

Answer 150

As strains transfer genes in different orders and from different regions - can identify the arrangement and orientation of almost all genes before the genome sequence of E.coli was known

Answer 151

Transformation - get plasmids/DNA in bacteria - some bacteria are natural competent to be transformed, some e.g. E.coli need chemical treatment or electroporation Transduction - second most important method - needed to move fragments of DNA/gene/plasmids from one cell to another Conjugation - has historical interest but used less

Answer 152

Each class must have more than 5 members

Answer 153

Maize or corn Kernels have two possible morphologies: starchy (smooth) and sweet (wrinkled) because starch is insoluble so contain less water so don't wrinkle when dried Also come in two colours: yellow or purple

Answer 154

Normal sex-chromosome complement of male locust is XO, not XY All chromosomes are telocentric - centromeres at one end

Answer 155

When the centromere is in the inverted segment Pericentric = around centromere Paracentric = besides centromere A diploid individual with one normal chromosome and one with pericentric inversion = inversion heterozygote

Answer 156

When pairing occurs when there is extensive inversion

Answer 157

Embryonic: predicted that 50% of embryos have chromosomal defects Newborn babies: 5% of babies suffer from congenital disorder - chromosomal, mitochondrial, single gene, complex (multi-factoral, genetic and environment) Later life: 2/3 diseases have genetic component in their aetiology

Answer 158

Prenatal: 8% of clinically recognised conceptions terminate due to chromosome abnormalities - predicted that 50% of terminations are due to it Live births: 0.1% of live births display chromosomal abnormalities: aneuploidy e.g. down syndrome, trisomy 21, chromosome abnormalities

Answer 159

Each cell has 100's of mitochondria - has own genome (2-10 copies of circular 16.6 kb genome) Normally all copies of the DNA are the same (homoplasmid) Mutation - mixture of genomes (heteroplasmid) Can lead to mitochondrial disease - don't follow mendelian patterns of inheritance

Answer 160

Single gene vs multiple genes (polygenic) Single follows mendelian inheritance pattern, complex has no simple pattern but runs in families Single conditions are rare but collectively common (1/17), complex are common Single are high penetrance, complex suggest a susceptibility not deterministic Single has predictive tests, complex has no reliable tests Complex are influenced by environment

Answer 161

3.2 Gb Only 1.1% is coding 20,500 protein coding genes Single: all mutations in coding sequence Complex: many disease variants lie outside coding

Answer 162

Human: 3.2 Gb, 20,500 genes Yeast: 12.1 Mb, 6000 genes Fly: 175 Gb, 14,000 genes

Answer 163

Regulatory elements, promotor Introns

Answer 164

ENCyclopedia Of Dna Elements Goal is to build a comprehensive parts list of functional elements in human genome Achieved through genomic, functional and bioinformatic approaches List includes elements that act at the protein and RNA levels and regulatory elements

Answer 165

In 2001 following 15 years ($3 billion) 2 competing consortiums: - International Human Genome Sequencing Consortium - Celera Genomics Sequencing the whole euchromatic region (92%) minus the heterochromatic and repetitive regions

Answer 166

- length of genome - generating enough clones to ensure complete coverage - accuracy-sequencing must be repeated - reassembling genome from individual sequences

Answer 167

Novel sequencing technologies reduce the time and cost Different approached but based upon sequencing a lot of small fragments of target DNA, in contrast to sanger sequencing Whole genome sequencing (WES): enormous amount of data, more expensive Whole exome sequencing (WES): targeted sequencing of only protein encoding region of genome (1%)

Answer 168

Average length of sequence read: 36 vs 800 for sanger Average number of reads: 35,000,000 vs 384 for sanger Total amount of sequencing: 1.3 Gb vs 300 kb (sanger) Cost/Mb: $4 vs $600 for sanger A whole genome can be sequenced in 24 hours for $600

Answer 169

6,466 phenotypes, 4,412 genes Autosomal: huntingtons - autosomal dominant, cystic fibrosis - autosomal recessive X-chromosome linked disease - Duschenes muscular dystrophy

Answer 170

1 copy of mutation is needed Wile-type allele is recessive, defective is dominant More likely that there is one defective allele than 2 Inherited in dominant pattern or new mutation arises in single copy Phenotype in every generation - parent can transmit to every progeny according to mendelian inheritance ratios

Answer 171

Late onset autosomal dominant disorder 1 in 10,000 Progressive neurogenerative brain disorder: - neuronal death - cerebral atrophy - CNS disorder - Uncontrolled movements - Decrease in cognitive function - Personality changes

Answer 172

1983 through positional cloning The HTT gene was identified and clones a decade later Dominant pattern - affects every generation

Answer 173

Polyglutamine repeat disease HTT encodes a protein with a poly glutamine tract (encoded by CAG codon) Normal copies have less than 36 repeats - more than 36 = Huntington's Greater number of CAG repeats - earlier onset CAG are unstable and are prone to expansion and can expand upon parental transmission

Answer 174

Shows incomplete penetrance Signs and symptoms appear at the earlier age as HD is passed from one gen to another - anticipation

Answer 175

Has poly Q expansion and has prosperity to misfold and aggregate These aggregates form inclusion bodies in neurones Impairs axon transport, mitochondrial dysfunction, dysregulation of transcription

Answer 176

2 recessive defective genes are needed Phenotype doesn't appear in every generation Both parents are carriers Transmission in accordance with mendelian inheritance

Answer 177

Most common severe autosomal recessive disorder 1 in 2000 are affected 1 in 22 are carriers Characterised by build up of thick mucus that can damage many body organs The CFTR gene and mutations were identified by positional cloning (like huntingtons)

Answer 178

Physiotherapy DNase to reduce mucus viscosity Antibiotics and anti-inflammatories Mannitol spray to increase osmolality of mucus

Answer 179

Encodes the cystic fibrosis transmembrane conductance protein CFTR transports Cl- across the plasma membrane of cells that line the lung Ensures the hydration of the airway surface layer

Answer 180

I - no protein II - no traffic III - no function IV - less function V - less protein VI - less stable I and V treatment: - production correctors (ataluren) - promote CFTR transcription e.g. nonsense mutations II and III - correctors (Lumacaftor) - improve intracellular processing of CFTR e.g. Phe508 IV and VI: - potentiators (Ivacaftor) - recovers function of CFTR

Answer 181

- potentiator alone is not affective - potentiator and a corrector (orkambi) received FDA approval and now available on NHS however orkambi is expensive (£100k per year)

Answer 182

Most are recessive Males can inherit from female carrier parent A female can inherit only when both the parents carry allele Females are generally unaffected but are carriers Affected males progeny never show disease phenotype

Answer 183

Most common X-linked recessive disorder Disease onset if before 6 years old Life expectancy = 20-30 Gene passed on by mother Multi-system disorder: causes muscle weakness, wasting and atrophy, skeletal muscle degeneration and cardiac myopathy

Answer 184

On X chromosome Largest known human gene (2.4 mb) - 79 exons and encodes dystrophin protein - 427 kDa

Answer 185

Located in skeletal and cardiac muscle In muscle: part of protein complex which strengthens muscle fibres by linking a muscle cell's cytoskeleton (actin) to ECM (connective fibres)

Answer 186

Approx 60% of DMD cases are due to deletions of at least one exon Hotspot deletion zone - between exons 40-54 Deletions can cause frameshifts

Answer 187

Anti-sense oligonucleotides - Eteplirsen - prevents recruitment of the splicing machinery

Answer 188

Identification of genetic determinants in: - novel conditions - characterised disorders - atypical presentation of a disease Analysis of genetic determinants of complex disorders

Answer 189

Haploid cells - MATa and MATalpha fuse to form a mating figure which buds off diploid cells. These diploids can reproduce by mitosis to produce a population of diploid cells - these can be studied directly to test dominance and complementation of genes contributed by the two haploid parents Alternatively, diploids can be sporulated to obtain haploid sexual progeny - study gene segregations, gene interactions and linkage - when diploids sporulate - each diploid nucleus divides meiotically to form four haploid products/segregants - the tetrad comprises four haploid ascospore enclosed in ascus

Answer 190

- parental ditype (PD) - tetrad only has parental genotypes - non-parental ditype (NPD) - tetrad only has non-parental (recombinant) genotypes - tetratype (TT) - tetras contains four different genotypes - 2 parental, 2 recombinant

Answer 191

For genes closely linked - we would see mostly parental (PD>>NPD) For two genes found on different chromosomes or far on the same - expect equal abouts (PD =NPD) Containing all four combinations - caused by single crossover between the two alleles or between one gene and the centromere - doesn't tell us about linkage

Answer 192

Changes thermal stability of protein - has normal phenotype at low temp (permissive/non-restricted) - mutated phenotype at high temp (restricted/non-permissive) The protein has a decreased stability meaning it denatures at a lower temp - if the protein is essential then the cells cannot grow cdc mutant - can grow at 25 - not 36

Answer 193

Common - 66% lifetime risk Multifactorial: polygenic, environmental Risk alleles suggest susceptibility - not deterministic Are familial

Answer 194

Obesity, rheumatoid arthritis, Type1/2 diabetes, MS, cardiovascular disease, epilepsy, peptic ulcer, hyperthyroidism, some cancers Alzheimer's, bipolar, depression, tourette's Congenital: cleft lip/palate, neural tube defects, pyloric stenosis

Answer 195

Early diagnosis and treatment Allow lifestyle changes to lower risk Help understand the molecular basis to develop therapeutics

Answer 196

11-15 million common variants - single nucleotide polymorphisms (SNPs) SNPs are found in both coding and non-coding regions Minor allele frequency (MAF) is the second most common allele in the population Common SNP/MAF > 5% Rare SNP/MAF < 5% Risk from SNP can be small - correlation between disease and genotype can be weak Identifying alleles which increase risk requires large number of individuals

Answer 197

Family based linkage analysis: - looks for linkage between mapping markers and occurence of disease in families Genome-wide association studies (GWAS): - search for alleles in a population that occur more frequently in disease cases than in matched controls - more powerful at identifying rare risk alleles and those that contribute a small increase of risk

Answer 198

The sum of genetic and environmental variation Vp = Vg + Ve Vp = phenotypic variance Vg = genetic variance Ve = environmental variance

Answer 199

The degree of variation within a population that is due to genetic variation = Vg/Vp Higher the heritability - greater the genetic contribution but environment can still influence likelihood

Answer 200

Twin studies allow the effects of genetics (heritability) and environment on phenotypic variance Monozygotic - identical twins - share 100% genes - shared environment Dizygotic - non-identical twins - share ~50% of alleles and share environment Assume equal environmental influence for identical and non-identical twins

Answer 201

ACE model A (genetic variance): - MZ = constant, DZ = variable C (common environment): - MZ = constant, DZ = constant E (specific environment): - MZ = variable, DZ = variable Environmental contribution is the same

Answer 202

Percentage of identical or non-identical twins which share phenotype/disease MZ: - correlation = A (100%) + C DZ: - correlation = A (50%) + C The difference in concordance between identical and non-identical is a measure of the effect of 50% of genes on variation in the population The greater the difference in concordance between MZ and DZ - greater the heritability of the trait

Answer 203

Most phenotypes show a continuous variation - some have complex - disease is controlled by multiple polygenes - each allele segregates by mendelian laws - many polygenes + environment = continuous phenotypic variation Threshold for developing disease: - most diseases are discontinuous - an individual either has or hasn't got the disease

Answer 204

Yes - many loci can contribute to variation -> broad range of phenotypic variation - environmental factors will also affect phenotype - same genotype will display different phenotypes - not all alleles will contribute the same risk - an increase in number of loci, greater the distribution of variation

Answer 205

Yes e.g. depression Identified 44 significant risk loci for major depression All humans carry greater or lesser Associated with clinical features and included drug targets

Answer 206

Most disease phenotypes are discontinuous Polygenes and environment produce a distribution of liability The disease occurs when liability exceeds threshold Relatives of affective individuals have an increased risk

Answer 207

Pyloric stenosis: - narrowing of opening between stomach and SI - projectile vomiting after feeding in infants - multiple genetic and environment factors have been identified as contributing to disease - five times more common in males - females have a higher liability threshold than males - affected females carry more risk alleles - relatives of affected females have greater risk than relatives of affected males

Answer 208

Different possible architectures: - small number of dominant alleles confer a large risk increase in risk - parkinsons - common disease, common variant model (CDCV) - many alleles confer a small increase in risk - type II diabetes - intermediate - one major allele exerts a large effect, numerous other lower risk alleles - breast cancer

Answer 209

Single nucleotide polymorphisms - between 11 and 15 million common SNPs (MAF (minor allele frequency) >5%) - uneven distribution of SNPs in genome - can occur at: coding regions - synonymous (no change in AA), non-synonymous (missense/nonsense), or non-coding regions - can affect expression/regulation of associated genes - complex diseases arise from combinations of multiple SNPs

Answer 210

There are exome and genomes from unrelated individuals sequenced as part of various disease-specific and population genetics studies - gnomAD aggregates over 730,000 exome and 76,000 genome databases - over 910 million variants mapped - records frequency of alleles in a population - documents rare mutations - highly pathogenic variants seen with a lower frequency in the general population

Answer 211

- examine a panel of SNPs in the genome for association with the disease phenotypes - search for alleles that occur more frequently in disease cases than in matched controls - requires many participants - GWAS studies have been performed for most common diseases - many risk loci have yet to be identified - missing loci contribute to the 'missing heritability problem' - GWAS compares the allelic frequency across the entire genome in case and control populations. - Significant differences in allelic frequency constitutes an association with disease.

Answer 212

Association studies can tell us if an allele is associated with disease The SNP itself can increase risk The SNP correlates with the risk allele due to linkage disequilibrium - they are inherited together

Answer 213

The non-random association of alleles at different genomic sites. Depends on: - distance between alleles - recombination rates The pattern of LD can be summarised as haplotype blocks

Answer 214

Region of high LD that are separated from other haplotype blocks by many historical recombination events In haplotype mapping - groups of alleles are clustered so a single SNP can identify cluster of alleles (Tag SNP)

Answer 215

GWAS studies identify SNPs associated with disease - not necessarily risk alleles Need integration with functional data on candidate regions to identify causality

Answer 216

Measured in an odds ratio OR is a statistic that quantifies the strength of the association between two events OR = 1 - events independent OR > 1 - events are correlated OR< 1 - events are negatively correlated Common disease common variant (CDCV) model of complex diseases - multiple alleles with OR< 1.2 showing weak association to disease phenotype

Answer 217

Statistical analysis and large cohorts Statistical significance is needed to differentiate true positives from false positives Genome wide significance is where p value < 5x10^-8 1/20 events are non-significant (0.05) For 1 million SNPS - expect 50,000 false positives Very large number of participants required Very large number of participants are required

Answer 218

Manhattan plot The threshold for significance is shown by red horizontal line (p = 5 x 10^-8) 44 risk loci defined with significant p-values (green stacks) GWAS susceptible to high number of false positives

Answer 219

Common chronic condition caused by inability to take up sugar Characterised by high BP, insulin resistance and a lack of insulin production Multifactorial (genetic and environmental): - familial - geographical and ethnicity - age, weight, diet, exercise

Answer 220

Red SNPs - previously identified common alleles Green SNPs - novel association loci determined due to increased statistical power The novel loci have low odds ratio (1.06-1.27) - each causes a small increase in risk TCF7L2 - allele providing greatest risk of type II diabetes, intronic variant, transcription factor required for pancreatic development FTO - intronic variant, involved in body weight regulation CDKN2A/B - non-coding regulatory variant

Answer 221

Lifetime risk in females - 8-12% Risk increases if first-degree relatives suffer Rare coding mutations and common non-coding increase risk - rare coding mutations e.g. BRCA1/2 - huge risk - common variants in polygenes contribute small increase 5% of cases - BRCA1/2 autosomal dominant alleles - mapped by linkage analysis

Answer 222

Identify high known risk factors that occur infrequently in the population Identify 66 common low-risk alleles - many in non coding regions of genome

Answer 223

Heritability = proportion of variance in a particular phenotype in a population that is due to genetic variation We can identify risk alleles for complex diseases but heritability is not fully explained by these alleles e.g. Crohn's - 32 loci - 20% heritability explained by these alleles Type II diabetes - 18 loci - 6% Early onset myocardial infarction - 9 loci - 2.8% Missing risk can arise from: - false negatives in GWAS studies - rare variant alleles with MAF 1-5% - structural alteration of the genome - epigenetics - 3D genome organisations - NONE ARE DETECTED IN GWAS

Answer 224

e.g. haemopoietic stem cell gives rise to different blood cells Cells within a defined ancestry = lineage Same DNA but differences in gene expression and proteome

Answer 225

The concept of position information proposes that cells acquire positional values as in a coordinate system - they interpret this by developing in particular ways to give rise to spatial patterns - e.g. organ placement Louis Wolpert made this concept

Answer 226

Yes - we see it in vast majority of organisms Molecular events define the polarities e.g. Apical basal symmetry - bilateral symmetry in fly Floral symmetry - flowers e.g. actinomorphic (radial), zygomorphic (bilateral) Dorsal-ventral - shark

Answer 227

Yes! epigenetics change differentiated -><- undifferentiated e.g. some diseases occur due to defects in development - can help us find treatments

Answer 228

Found in all multicellular organisms e.g. plants derive from stem cells generated in embryogenesis - shoot and root meristem

Answer 229

Undifferentiated cell of a multicellular organism which is capable of giving risk to indefinitely more cells of the same type - other types of cell can arise from differentiation Goes through self-renewal - when it divides, it generates a new stem cell and a second progenitor cell which can generate new lineages

Answer 230

Maintains stem cell population - forms a stem cell and progenitor cell Asymmetric division - mitotic division of progenator cell that gives rise to progeny with different rates

Answer 231

Totipotent - can form whole new organism. Mammals - can form embryo, extraembryonic membrane and placenta Pluripotent - can form many cell types but not all. Mammals - can form embryo Multipotent - can form fewer but still many cell types e.g. haemopoietic stem cell

Answer 232

Zygote - totipotent Blastocyst - pluripotent, self-renewal division type - embryonic stem cell Adult - multipotent, self-renewal division type - multipotent stem cell Organ - limited/no potential, limited self-renewal division = progenitor, division = committed progenitor, functional division = differentiated

Answer 233

From the mouse blastocyst (the outside = trophoectoderm (makes the extraembryonic membrane and placenta)) take the inner cell mass Place in tissue culture conditions - some will turn into embryonic stem cells (not totipotent - pluripotent)

Answer 234

Introduce genes - e.g. introduce human genes and study where protein is localised - fused to GFP or what its transcripts do Knockout genes - can study role of the gene Chromosomal rearrangements/deletions -generate disease models Make specific genome edits - can make mutation found in gene known to cause disease Need to see these changes in the mouse itself

Answer 235

Yes! But they are not totipotent Therefore, we need to take cultured ESCs and introduce them into a developing blastocyst (has an inner cell mass) This is then implanted into a pseudopregnant mouse Forms chimeric mouse - has cells of two genotypes from two different zygotes (not same as genetic mosaic as this is where it comes from one zygote)

Answer 236

Genetic markers - common to use mouse coat colour genes Fur colour is determined by banding pattern on bristles and the wildtype colour requires A and C to give agouti (greyish) colour whereas albino mouse has homozygous for a and c genes So if ESCs are derived from a AACC blastocyst and are transported into a albino mouse blastocyst - 1st gen will be a mixed genotype - patchy colour - NOT HETEROZYGOUS MOUSE - a cell will either be AACC or aacc Cells in reproductive system will hopefully be chimeric and give rise to gametes that are either AC (from transgenic ESC) or ac (from albino blastocyst)

Answer 237

The chimeric mouse would be crossed with an albino mouse again and you would look for WT (agouti) mice - will have genotype AaCc The A and C derive from cells which were originally the ESCs Can only happen if the reproductive organs in the 1st gen mouse had some cells from the ESCs

Answer 238

Significant research tool and same method in mice require human blastocysts. Therefore would have to sacrifice human blastocyst However, have been approved for limited experimentation including human-animal hybrids - must terminate early

Answer 239

Yes! e.g. shown in xenopus laevis - nuclei from embryonic tissue was placed into enucleated embryos to generate tadpoles - he took nuclei from somatic cells and placed it into enucleated eggs - resulted in tadpoles Demonstrated that a somatic nuclei did contain all the genetic make up to produce all cells of an organism - in egg environment it can be reprogrammed to become totipotent This paved the way for the first animal cloning - nuclei was transported into enucleated embryo - dolly the sheep

Answer 240

Yamanaka took adult fibroblast cells and using tissue culture and transcription factors - was able to reprogram a small percentage of cells to dedifferentiate and become like embryonic stem cells These can then be differentiated into different cell types

Answer 241

4 pairs of chromosomes : X, Y, 2, 3, 4 ~ 16,000 genes ~ 140 Mb

Answer 242

Fertilised egg (0 days) Embryonic development Hatching (1 day) Larva (three larval stages, separated by molts) Pupation (5 days) Pupa Metamorphosis Adult (9 days)

Answer 243

Can be mapped to larval segments e.g. head, prothorax, mesothorax, metathorax - easy to map so used as model organism - obvious polarity - formed basis for mutagenesis Body plan is determined by hierarchy of developmental genes - defects in segmentation pattern was easy to screen for and identified a hierarchy of genes

Answer 244

Maternal effect genes: phenotype of progeny is determined - by maternal genotype Zygotic genes: phenotype of individual is determined by the individual's genotype. 1) segmentation genes (determine features of the fly) 2) homeotic genes (determine structures - wings, legs ect.)

Answer 245

Maternal - Axis formation: Egg-polarity genes Zygotic - Segment identity: Gap genes Pair-rule genes Segment polarity genes

Answer 246

Germ cell-less mutant = gcl - results in sterile adult flies The parental genotype does not affect the fertility of the parents - all parents are fertile The genotype of the progeny has no impact on progeny It is the maternal genotype that determines the fertility, if the mother is gcl/gcl then ALL PROGENY are sterile, irrespective of own genotype

Answer 247

The oocyte The unfertilised oocyte is found in the egg chamber and is associated with Nurse cells and follicle cells. The nurse cells generate certain maternal transcripts that are then transported into unfertilised oocyte Has polarity before fertilised

Answer 248

30 genes e.g. BICOID and NANOS BICOID and NANOS mRNA's are polarised before fertilisation. BICOID mRNA is located at anterior, NANOS mRNA at posterior pole.

Answer 249

Result in large deletions of the body plan bicoid mutation - loss of head and thorax (anterior) nanos mutation - no abdomen sections

Answer 250

After fertilisation Create concentration gradients of mRNA and proteins

Answer 251

Regulate zygotic genes

Answer 252

Regulate the structures which develop on each segment of the adult fly Mutations can change positions e.g. segment 2 taking identity of segment 3 = two sets of wings (ultrabithorax) or antennae replacing legs (antennapedia)

Answer 253

Because in a mutation there is a transformation of organs in which the developmental fate of an organ is change of that of another - replacement not deletion

Answer 254

Into complexes - sequence correlates to order in which they are expressed on body axis 8 homeotic genes split into two groups on chromosome 3: - antennapedia complex - bithorax complex Collectively called Hom-C complex in drosophila Conserved but not universal

Answer 255

Yes Homeotic genes contain 180bp homeobox sequence Encodes 60aa homeodomain DNA (and RNA e.g. BICOID) biding domain Regulate genes that specify tissue/organ primordia Not all homeobox containing genes are homeotic genes Not all homeotic genes contain a homeobox

Answer 256

Mouse and human hox genes Homologous to drosophila Hom-C Share similar order Expression is anterior-posterior 4 hox clusters in mice and animals - A, B, C, D

Answer 257

Two-fused together digits Autosomal dominant of Hox D13

Answer 258

Yes! apetala1 - lacks sepals and petals pisillata - has only sepals and petals agamous - consists of sepals and petals

Genetics Flashcards

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