Semester 1 Flashcards

Question

What is false about polygenic risk scores?

Answer 1

They can be used for diagnostic purposes

Answer 2

Sanger sequencing Because it is a single gene, would NOT use next generation sequencing as that is done for whole genome! Justify and say why not Introduction about the disease

Answer 3

A multi subunit assembly that appears to be required for regulating expression of most RNA pol 2 transcripts

Answer 4

A protein or protein complex that activates genetic transcription usually by binding to a transcription factor

Answer 5

A molecule that is capable of combining with specific repressor molecule and activating it - thereby blocking gene transcription

Answer 6

A chemical compound composed of 2 similar subunits or monomers

Answer 7

A complex composed of NON identical components

Answer 8

A complex composed of identical components

Answer 9

Proteins that move into nucleus to bind to specific sequences (response elements) and recruit additional proteins to stimulate transcription

Answer 10

Sequence that comprises the most commonly encountered nucleotides found at specific locations in the DNA 2 main ones are pribnow box (10bp upstream of the TSS) and -35 sequence (35bp upstream of the TSS)

Answer 11

DNA or RNA that is NOT translated into protein

Answer 12

a single mRNA that generates multiple proteins mRNA is generated from multiple genes

Answer 13

DNA sequence where transcription apparatus binds to initiate transcription It indicates direction and which strand of DNA elongation occurs on, also contains TSS

Answer 14

The first DNA nucleotide that is transcribed into RNA

Answer 15

Proteins that move into nucleus to bind to specific sequences (response elements) and recruit additional proteins to stimulate transcription

Answer 16

They have discovered ALL of the estimated heritability for most traits

Answer 17

Diagnostic tests based on genetics Gene therapy Providing the correct dose of a drug based on a persons genetics Stratifying patients into more similar groups for more targeted treatment and follow up

Answer 18

It is used for sequencing multiple genes

Answer 19

Manhattan plot

Answer 20

Unamplified DNA

Answer 21

Is the correlation between genetic variants Is population specific Usually diminishes with physical distance Is used to select SNPs for genotyping arrays

Answer 22

3 billion - 3 000 000 000

Answer 23

Repetitive and transposable elements

Answer 24

100 000 000 - 100 million

Answer 25

Penta allelic

Answer 26

An insertion or deletion with less than 50bp

Answer 27

Translocations

Answer 28

Tri nucleotides

Answer 29

Nuclear lamina

Answer 30

Complementarity

Answer 31

Olfactory receptors

Answer 32

Signal transduction

Answer 33

Directly proportional

Answer 34

Non coding genes

Answer 35

Look at DNA binding proteins Look at RNA Use PCR to detect the RNA

Answer 36

How do we know what size we’re looking for? You’ve got to use your primer sequences!! Do a BLAST search and it searches for where those primers bind. There will be one at the beginning and one at the end - so find the distance between the two primers! Need to know how big the product is you’re looking for as BLAST will come up with more than one product

Answer 37

Sequences that are in the primers (if they’re inside the exons) will also exist in your genomic DNA. When you harvest cells, you are extracting RNA but some DNA may get through! May end up with some genomic copy which will be much larger because it has all the introns inside it as well as the exons Could try changing primers to overcome this

Answer 38

Have 2 plates of cells: some with endogenous p53 and some where you’ve added more p53. Compare and see when you do PCR where the specific primers for PUMA mRNA and see whether there is a more intense band where you’ve added p53 vs the non added one! NO - looking it on a gel is qualitative, to establish that you would need to use quantitative PCR

Answer 39

It monitors fluorescence Quantitative tells you how much brighter it might be as detector tells you how bright it is in comparison to others

Answer 40

When levels are low of certain amino acids you might end up getting use of the wrong amino acid = wrong code for protein. So want to avoid making those proteins that are missing the correct amino acids! Don’t want to waste energy when we don’t have all the right resources to make the proteins.

Answer 41

All viruses that infect cells may come in with their own RNA or DNA. They are totally dependant on the translation machinery of the cell that they’re infecting So it’s a good line of defence from the infected cell, stops virus infection! If it knows it’s infected, it can shut off protein synthesis = stops production of viral proteins

Answer 42

Protein will be non- functional! Can’t do job properly Waste of energy

Answer 43

When amino acids are low in the cell! So need to synthesise more eIF2 alpha is activated when amino acids are low, it is phosphorylated = a reduction in the amount of available ternary complex for translation initiation GCN4 helps synthesise amino acids to help get out of this cell stress situation!

Answer 44

Exons Introns Promoter Enhancer 5’ and 3’ untranslated region

Answer 45

Transcription is regulated by regions of DNA far away (100s of KB away from transcriptional start site)

Answer 46

Random diffusion and trapping and generalised degradation in combination with local protection by trapping - eg Drosophilia mRNAs enriched in pole plasma and posterior pole of the embryo Directed transport on cytoskeleton - eg neuronal RNPs along microtubuli and ASH1 mRNA along actin filaments to bud tip in yeast

Answer 47

She2, She3 and Myo4 (Myosin) proteins are required for ASH1 mRNA transport along acting ‘cables’ Khd1p is a translational repressor

Answer 48

RNA transport

Answer 49

Finally, the transport machinery is released and enables local translation of ASH1 at the bud tip. ASH1 protein in daughter cells prevents mating type switching

Answer 50

XIST associates with the X chromosome that it was expressed from (cis regulation) Initiates Histone modifications (methylation, deacetylation) which results in heterochromatin formation

Answer 51

Unbalanced X expression involved in diseases associated with infertility and mental retardation Eg Turner, Rett, Kliefelter’s Syndrome

Answer 52

Cis acting elements in mRNAs Trans acting factors Specificity given through: RBP / complexes that bind to sequence / structural elements in the RNA ncRNAs in association with RBPs anneal with sequences in the RNA target

Answer 53

Polyadenylation signals in pre mRNAs Splice sites in pre mRNAs Regulatory elements in mRNAs influencing translation / localisation

Answer 54

She2 protein (RBPs) as an adaptor for localisation of mRNA to the bud tip in yeast Iron response protein (IRP) binding to iron response element (IRE) in 5 UTR of ferritin mRNAs

Answer 55

Cleavage and polyadenylation (CPSF, CStF, CF and PAP) Spliceosome (U1, U2, U4, U5, U6 snRNPs) Exosome (RNA degradation in nucleus and cytoplasm)

Answer 56

Small nuclear RNAs (snRNAs) base pair with sequences in the pre mRNAs for splicing miRNAs partially hybridise with sequences in 3 UTR of mRNA target to repress gene expression Codon anticodon (tRNA) to read the genetic code Other examples: siRNAs, snoRNAs, IncRNAs

Answer 57

Being at least 200nts long

Answer 58

Average length of human exons is 150 bases On average 10 exons / gene

Answer 59

Average length of human introns 1,5 kB Largest intron is 1,1 Mb (intron 5 in KCNIP4) Since introns can be very long, additional strategies are required to improve splice site selection!

Answer 60

Exon skipping Intron inclusion Alternative splice site selection Alternative transcriptional start site selection Mutually exclusive exons

Answer 61

CPSF - cleavage and polyadenylation specificity factor CstF - cleavage stimulatory factor Two cleavage factors (CFI, CFII) Poly(A) polymerase (PAP)

Answer 62

Both repress translation by imperfect hybridisation with mRNA targets

Answer 63

Both are 20 to 22 nucleotides long RNA molecules Both anneal with complementary sequences preferentially located at 3 UTR of mRNAs (in complexes with several RBPs) siRNA may have originated as a defense mechanism miRNA and siRNA are NOT present in eukaryotes

Answer 64

Resuspend the cells in Lysis Buffer and vortex for 10s to mix thoroughly

Answer 65

RNA binds to the membrane allowing all the impurities to be washed away and removed

Answer 66

1. Press until STOP1 to expel air from outside the container 2. Go into container at 90 degrees and slowly release plunger to draw liquid in 3. Move the loaded pipette to the desired well and release the plunger to STOP2 4. Remove the tip from the well and only then release the plunger to resting position

Answer 67

You hold the pipette perpendicular to the reservoir and touch the liquid as little as you can to avoid carryover, while confirming visually that it is loading correctly

Answer 68

Put the labelled tubes in the centrifuge, so we can pellet cells at the bottom of the tube and then remove the media

Answer 69

Reverse transcriptase PCR

Answer 70

Positive control

Answer 71

Denaturation

Answer 72

Deliver amino acids to the ribosome

Answer 73

PABP - poly A binding protein

Answer 74

eIF4A - protein with helicase activity that physically unwinds RNA and uses ATP to do it Can’t do it without 4G and 4E

Answer 75

Stress (amino acid insufficiency, unfolded proteins, viral infections) eIF2a kinase activation eIF2a ph - reduced eIF2B available Reduced eIF2 GTP tRNA (ternary complex) availability Two outcomes: Global translation downregulation and Selective translation up regulation

Answer 76

Unfolded proteins in the ER

Answer 77

Viral infections

Answer 78

Low amino acids

Answer 79

Double stranded RNA - dsRNA

Answer 80

Don’t waste resources Redirect energy to stress recovery Don’t make faulty proteins when AAs are scarce Stop viral protein production Allow proper protein folding

Answer 81

Produce products to recover from stress eg GCN4 , ATF4 Turn translation back ON (GADD34)

Answer 82

NO Ternary complex is abundant under normal conditions

Answer 83

uORF translation impaired by eIF2a P and GCN4 translation is promoted

Answer 84

Normal - ternary complex abundant Stress - ternary complex limiting, only downstream AUG recognised

Answer 85

Easy scanning Tough scanning

Answer 86

Cap binding

Answer 87

c myc, VEGF, cyclin D1, FGF

Answer 88

Human tumour

Answer 89

The mTOR signalling pathway can regulate eIF4E activity - doing that through the phosphorylation of 4E BP

Answer 90

Exons Introns Promoter Enhancer 5’ and 3’ untranslated region

Answer 91

Transcription is regulated by regions of DNA far from (100s KB away from the transcriptional start site)

Answer 92

Operator regions - can recruit transcriptional repressors to promoter Cis regulatory elements - can recruit transcriptional activators to the promoter

Answer 93

True - in prokaryotes they can only activate transcription

Answer 94

NO Eg Tryptophan was required for binding to the operon Eg cAMP was required for activator binding to the cis regulatory elements to initiate transcription

Answer 95

Promotes regulator binding Recruit RNA polymerase 2 Releases RNA polymerase 2 either to begin transcription OR from a paused state

Answer 96

Require assembly of multiple independent protein complexes to form across Kbp of DNA

Answer 97

Controlled by the binding of fewer protein complexes located over a shorter span or non coding DNA

Answer 98

There can be more than one TSS There does NOT have to be a TATA box Chromatin structure can override all of this

Answer 99

Modification / changes of gene expression that aren’t caused by any changes in the base pair sequence within the genetic code Includes: condensation and relaxation of chromatin / activators and repressors / chromatin modifiers

Answer 100

Two molecules EACH of H2A, H2B, H3 and H4 histones. Makes an octamer 146nt of DNA winds 1.65 times around histone core to = nucleosome Hydrogen bonds form between DNA and histone octamer Each nucleosome separated from next by 80nt of linker DNA Histone H1 works as a clamp!

Answer 101

Heterochromatin = short and tightly bound Euchromatin = long and loose More tightly wound structure = less access to bases and transcription factors Folding protects DNA from being exposed for usage Unfolding will expose DNA to transcription factors = allows promoters to be bound by GTFs and other TF to allow genes to be expressed

Answer 102

Promoter 2

Answer 103

Histone modification enzymes ATP dependant chromatin remodelling complexes Histone chaperones

Answer 104

Nucleosome sliding Nucleosome eviction Histone variant exchange Histone tail modification and DNA methylation

Answer 105

Negatively Amino acids

Answer 106

Cis regulatory sequence facing inwards Changes to the shape of the binding site due to associated protein binding

Answer 107

Cis Transcription

Answer 108

DNA methylation - direct modification of DNA bases Interactions between DNA modification and protein modifications

Answer 109

DNA methylation Histone modification

Answer 110

Replication Transcription DNA repair

Answer 111

Inhibition of transcription Cell division

Answer 112

Histone chaperones - eg nucleosome assembly protein 1 (NAP1) ATP dependant chromatin remodellers - eg SWI2/ SNF2 All are ATP dependant complexes which interact with histones directly

Answer 113

Removal of entire nucleosome ATP dependant process May occur in conjunction with Histone exchange

Answer 114

Histone chaperones - eg Asf1 ATP dependant chromatin remodellers eg SWR complex

Answer 115

Changes in amino acid properties change the interaction interface with DNA HISTONE tails help to ‘grip’ the DNA so changes here can affect the attraction between them

Answer 116

DNA: protein interactions

Answer 117

Always retaining a + charge Different enzymes catalyse the addition of the 1st methyl group to the addition of subsequent methyl groups Added by Histone methyl transferases Removed by lysine demethylases

Answer 118

Occurs on lysine residues Neutralises the positive charge

Answer 119

Mostly at serine (but also threonine and tyrosine) residues Generates a negative charge

Answer 120

Occur at the same residue - eg lysine Acetylation and methylation Occur on consecutive amino acids, creating a steric hindrance Occur on consecutive amino acids and binding of 1 site stimulates binding of further proteins

Answer 121

Mediator complex Longevity

Answer 122

Insulator 2

Answer 123

Alternating high and low pressure regions travelling in the same direction Originate from a vibrating object Frequency of sound vibration = pitch Amplitude = how loud (decibel, dB)

Answer 124

Audible range = 20- 20 000 Hz Hears most acutely between 500-5000Hz

Answer 125

External ear - collects sound waves and channels them inward Middle ear - conveys sound vibrations to the oval window Internal ear - houses receptors for hearing and equilibrium

Answer 126

1. Auricle directs sound waves into the external auditory canal 2. Tympanic membrane vibrates back and forth 3. Vibrations transmit to malleus, incus and stapes 4. Stapes vibrates in the oval window 5. Fluid pressure waves in the peri lymph of the cochlea 6. Pressure waves transmit from scala vestibuli to scala tympani to the round window so it bulges into middle ear 7. Pressure waves deform walls of scalea vestibuli and scala tympani 8. Pressure waves cause basilar membrane to vibrate 9. Move hair cells out of spiral organ against tectorial membrane 10. Stereocilia bend and generate nerve impulses in 1st order neurons in cochlear nerve fibres

Answer 127

Stereocilia point straight up Cation channels are partially open Weak depolarising receptor potential Ca+ ions enter Low level NT release

Answer 128

Vibration of basilar membrane Stereocilia bend and open cation channels Larger numbers of K+ ions enter the cell Strong depolarising potential More Ca+ channels open Increased NT release

Answer 129

DNA methylation is carried out by DNA Metyl Transferases (DNMTs) De novo DNMTs add methyl groups to unmethylated DNA - eg DNMT3a and DNMT3b Other DNMTs add methyl groups to daughter stand during DNA replication - eg DNMT1

Answer 130

In around 1% of nucleotides of the genome Mostly occurs at CpG islands Causes different effects depending on the gene sequence

Answer 131

Regulating tissue specific gene expression Genomic imprinting X chromosome inactivation

Answer 132

Regulation of chromatin structure AND transcription factor binding by: Less nucleosomes Often close to TSS Usually encompass transcription factor binding sites Methylation of exon 1 helps recruit TF OPEN UP STRUCTURE AND RECRUITS ENZYMES

Answer 133

Regulation of chromatin structure AND transcription factor binding by: Recruitment of inhibitory TF Disrupting binding to TF binding sites Methylation of promoter causes gene silencing STABLE SILENCING

Answer 134

Chromatin structure can be changed with the association of a reader complex which is similar in theory to the mediator complex

Answer 135

The writers are the enzymes that change the modifications - eg Histone acetyl transferases, Histone methyl transferases and DNA methyl transferases

Answer 136

The erasers are enzymes that modify or remove these marks: Histone deacetylases and lysine demethylases

Answer 137

1. Regulatory proteins bind to specific cis sequence 2. These recruit Histone modifiers (writers) 3. A reader protein recognises the modification to the Histone / DNA 4. A writer recognises the reader and binds to it, providing a platform from which the writer can make another modification on the next nucleosome (goes back to step 3!)

Answer 138

Histone tails methylation (me3) Inhibition of DNMT

Answer 139

Methylation of DNA and Histone tail modification Recruit methyl binding proteins (MBD) Recruit Histone tail modifiers (eg HDAC and HMT)

Answer 140

Tethering a chromatin domain to a large fixed site, such as the nuclear pore complex Strong binding of a group of nucleosomes to a barrier protein Recruitment of a mediator complex containing chromatin modifying enzymes to erase modifications that will spread changes

Answer 141

A) competitive DNA binding B) masking the activation surface C) direct interaction with the general TF D) recruitment of chromatin remodelling complexes E) recruitment of Histone deacetylases F) recruitment of Histone methyl transferase

Answer 142

Progressive disease that affects motor neurons CAUSE = overall decrease in acetylated Histone levels within motor neurones by: Reduction in histone Acetyl transferase (HAT) activity Increased HDAC activity

Answer 143

Caused by silencing of FRM1 gene CGG tri nucleotide repeats in the 5 UTR FRM1 associated with disease onset Expansion of number of repeats (>200) - hyper methylation of promoter in an attempt to turn off expression C turned into 5mC by DNMTs = interaction with Histone marks / compacted chromatin structure / harder for TF to be recruited and enhance expression

Answer 144

Defined as the continuous uncontrolled growth of cells

Answer 145

Any abnormal proliferation of cells They are classified as to their cell type Can arise from any cell type in the body Benign - stay confined to original location Malignant - capable of invading surrounding tissue and spreading to entire body

Answer 146

Carcinomas Carcinomas cause 80% of cancer related death

Answer 147

Ionising radiation - x rays, UV light Chemicals - tar from cigarettes Virus infection - papilloma virus can be responsible for cervical cancer. Hepatitis B and C viruses = liver cancer Hereditary predisposition - some families are more susceptible to getting certain cancers

Answer 148

Mouth Upper throat Oesophagus Breast Liver Bowel

Answer 149

Damages cells Increases damage from tobacco Affects hormones linked to breast cancer Breaks down into cancer causing chemicals

Answer 150

Thousands have been identified Broad range of chemical structure Classified as direct acting and indirect acting

Answer 151

Can cause DNA damage, change sequence of DNA bases, change codon and affect protein function Most commonly occurring spontaneous change in DNA: Oxidative damage Spontaneous purine hydrolysis Deamination

Answer 152

Flame retardant Antibacterial additive Histidine Synthesise

Answer 153

High 60 Mutations Suppressor

Answer 154

DNA damage events in a single cell range from 10^4 to 10^6 Under physiological conditions, spontaneous purine hydrolysis takes place leaving a sugar without the attached base leading to generation of AP site

Answer 155

Mispairing of 8 oxoG with adenine during replication leads to C to A causing GC base pair to mutate to TA GC to TA mutation can also result from replication encountering an AP site

Answer 156

Cytosine and 5 methylcytosine are most common deamination reactions DNA bases can be deaminated and if unrepaired can cause mutations Deamination can change a GC base pair to AT

Answer 157

Deamination Cytosine

Answer 158

Predicts increase in cancer incidence with age Cancers arise by an evolutionary selection process following the theory of ‘survival of the fittest’

Answer 159

1st mutation - gives a slight growth advantage to mutant cells 2nd mutation - mutant cells grow more uncontrollably and form a small benign tumour 3rd mutation - mutant cells overcome constraints imposed by tumour surroundings. Outgrow others to form a mass of cells, each of which has all 3 genetic changes: 1st, 2nd and 3rd mutations 4th mutation - cells can escape (and survive) into the bloodstream and establish daughter colonies at other sites (hallmark of metastatic cancer)

Answer 160

Carcinogens

Answer 161

Multi step

Answer 162

5’ phosphate 3’ hydroxyl 5-3 directionality Phosphodiester bond Bases on the same side Negative charge outside Sequence of bases forms the primary structure 3 hydroxyl is the substrate for DNA polymerase

Answer 163

Activation Repair

Answer 164

Toxic Radiotherapy

Answer 165

Phosphodiester

Answer 166

DNA pol is the first line of defence against mutations DNA pol in E coli introduces 1 wrong base for every 10K bases incorporated, but the mutation rate is 1 wrong base per 1 billion Low mutation rate is due to the proof reading (3-5 exonuclease) function Proof reading is vital for all cells to avoid excessive mutations

Answer 167

PARP identifies DNA damage and signals the need for repair PARP1 detects DNA damage via its DNA binding domain Activated PARP1 adds ADP ribose units to PARP1 and leads to the formation of long and branched chains of poly (ADP ribose) (PAR) These PAR chains create a scaffold that recruits critical proteins for DNA repair

Answer 168

Inheritable loss of function mutation in msh2 or mlh1 genes cause predisposition to non polyposis colorectal cancer

Answer 169

A specialised DNA polymerase used in repair

Answer 170

UV induced

Answer 171

Xeroderma pigmentosum

Answer 172

DNA DSBs are highly toxic, a few sustained DSBs are enough to kill a cell Radiotherapy and many anti cancer drugs destroy tumour by causing DNA double stand breaks Incorrect joining of DSBs can create hybrid genes and can place a low expression gene under control of a strong promoter

Answer 173

1. Non homologous end joining (NHEJ) - error prone 2. Homologous recombination (HR)

Answer 174

Exploiting tumour defects to cure cancer It arises when a combination of deficiencies in the expression of two or more genes leads to cell death, whereas a deficiency in only one of these genes does not

Answer 175

Genomic integrity Diseases

Answer 176

Integrity Breast cancer

Answer 177

Breast Prostate

Answer 178

1. Sustaining proliferative signalling - oncogenes 2. Evading growth suppression - tumour suppressor genes 3. Reprogramming of energy metabolism 4. Inducing angiogenesis 5. Genome instability and mutations

Answer 179

Proto oncogenes Tumor suppressor genes Genome maintenance genes - mutation allows propagation of gene mutations as the DNA repair is inefficient

Answer 180

Rationale for their existence: required for normal growth and proliferation Proto oncogenes (ras) - gain of function mutations convert them into oncogenes

Answer 181

1. Point mutation (a change in single base pair) - altered protein product 2. Chromosomal translocation - fuses 2 genes together to produce a hybrid gene 3. Amplification - generation of numerous proto oncogene copies, leading to overproduction of the encoded protein

Answer 182

As a result of ‘gain of function point mutations’ in the receptor tyrosine kinases, the requirement of growth factor (ligand) to trigger receptor dimerisation may be abolished allowing cells to grow rapidly and uncontrollably

Answer 183

Growth factors

Answer 184

Normally the receptor and ligand are produced by different cells In some cancers, BOTH of these can be made by the same cell, losing regulated control of growth / division Eg EGF and EGFR being made by the same cells in cancer

Answer 185

1/3 Breast tumours express Her2, triggering sustained proliferation of cancer Trastuzumab (a monoclonal antibody) can target Her2 leading to repression of 1) Her2 mediated growth signalling 2) destruction by the immune system

Answer 186

Prostate cancer stimulated by androgen (testosterone), the male sexual hormone > activates androgen receptor AR Breast cancer stimulated by estorgens (female sex hormones) > activates estrogen receptor ER AR and ER are example of nuclear hormone receptors

Answer 187

Enzalmutamide = AR antagonist Tamoxifen = ER antagonist

Answer 188

Ensure cells with oncogenes are repaired / killed, hence anti cancer As long as they are intact, cancer cells should NOT survive Many cancers have inactivation of tumour suppressors and that’s how cells with oncogenes can make tumours Rationale for existence: controlling cell cycle checkpoints and development. They also regulate ‘apoptosis’

Answer 189

Loss of function mutation deletes an important brake on the cell cycle or checkpoint control

Answer 190

Lack of oxygen

Answer 191

Formation of new blood vessels

Answer 192

Cell death

Answer 193

Cellular ageing

Answer 194

Proto oncogenes + tumour suppressor genes = Regulated cell growth and proliferation

Answer 195

Gain of function mutation in proto oncogene + loss of function mutation in tumour suppressor genes = Abnormal growth and cancer

Answer 196

Specific characteristics found in cancer cells

Answer 197

Tumour growth Cancer

Answer 198

Prostate Breast

Answer 199

DNA replication

Answer 200

Inactivate

Answer 201

Cancer therapy

Answer 202

Genomic integrity

Answer 203

Distance between nucleosomes decreases Further packaging of DNA into solenoid then looped structures, which requires interaction with another level of proteins Cellular effects: decrease in transcription from some gene promoters

Answer 204

1. mRNA levels 2. Measure modification status of Histone complex - if acetylated lysine on histone H3 = transcription about to be turned on. If methylated = transcription turned off

Answer 205

1. Cross link DNA and proteins and isolate chromatin 2. Sonicate or digest chromatin 3. Immuno precipitate, reverse cross linking, purify DNA

Answer 206

Detect by microscopy (chip, chip) Or Detect by sequencing (chip seq) Or Western blotting procedure

Answer 207

1. Sonicate DNA 2. Bisulphite conversion 3. PCR amplification: Sanger sequencing or pyro sequencing (faster)

Answer 208

DNA replication

Answer 209

Oncogenes Cancer

Answer 210

Pyruvate Hypoxia

Answer 211

Warburg observed that tumours were taking up enormous amounts of glucose compared to surrounding tissue This glucose was fermented to produce lactate even in the presence of oxygen Because aerobic glycolysis is energetically INefficient - cancer cells increase glucose uptake

Answer 212

Fructose 6 phosphate

Answer 213

Mutant IDH (common in cancers) converts iso citrate into 2HG 2HG inhibits several enzymes that require alpha keto glutarate

Answer 214

DO NOT invade or metastasise eg Wart

Answer 215

Can invade nearby tissue, spread and seed additional secondary tumours in distant organs

Answer 216

Formation of new blood vessels to allow nutrition to reach tumour Stimulated by low oxygen conditions - hypoxia

Answer 217

1. Low oxygen conditions enhance erythropoietin (EPO) levels 2. EPO is a growth hormone produced by the kidney 3. Under normoxia (normal blood oxygen concentration) EPO is synthesised by inner cortex 4. Under hypoxia, cells of kidney can produce more than 100x EPO over normoxia 5. Tumour hypoxia is a COMMON phenomenon in solid tumours

Answer 218

Production

Answer 219

Angiogenesis, tissue invasion and metastasis

Answer 220

Angiogenesis Progression

Answer 221

Inefficient Competitive

Answer 222

Angiogenesis

Answer 223

Genomic DNA > transcription > mRNA > translation > protein

Answer 224

Free in the cell

Answer 225

In the cytoplasm, ER associated Can be localised to specific intracellular areas eg dendrites in neuron

Answer 226

Recruitment of initiation factors and ribosomal subunits Recognition of AUG start codon

Answer 227

Because it is the rate limiting step of mRNA translation

Answer 228

Recruitment of elongation factors and acyl tRNAs Building of polypeptide chain

Answer 229

Recruitment of release factors Recognition of stop codon and release of polypeptide chain

Answer 230

Most of it is cap dependant - starts at 5 prime cap (ribosome had to find the beginning) In prokaryotes, a Shine Dalgarno sequence helps to recruit ribosomes directly to RNA at any point of that mRNA

Answer 231

Protective for degradation and crucial for translation

Answer 232

Only part that contributes to the code of the protein being produced

Answer 233

Translational control

Answer 234

Cap binding 5-3 scanning to find AUG, requires: unfolding of 5 UTR and ATP hydrolysis AUG recognition - codon / anti codon pairing GTP hydrolysis / tRNA delivery eIF release + large subunit 80S joining GTP hydrolysis x2 and eIF release

Answer 235

To avoid frame shifts Particularly important for 1st codon to match up the right AA in the right place Nothing else will be coded for properly for the remainder of translation otherwise

Answer 236

Elongation

Answer 237

Regulation Dysregulation

Answer 238

eIF4E sequestration, phosphorylation eIF4G cleavage

Answer 239

eIF2 - GDP recycling eIF2 phosphorylation

Answer 240

Cap recognition Scanning AUG start codon recognition

Answer 241

Caspase 3/7 cleavage of eIF4G Disruption of cap binding complex Cap dependant translation Overall down regulation of translation in apoptosing cells

Answer 242

A structured RNA domain that recruits the ribosome

Answer 243

No need for the cap recognition and scanning Require only few eIFs Present on cellular mRNAs and viral RNAs

Answer 244

Open reading frame that encodes for reporter proteins

Answer 245

If 2 open reading frames are next to eachother in capped mRNA, the 1st cistron will be translated to = product But at the end of translation, the ribosome will terminate so no translation will happen downstream of 2nd cistron

Answer 246

Put the sequence between two cistrons!!

Answer 247

Gold standard to define IRES function

Answer 248

Easy scanning

Answer 249

Tough scanning - poorly translated in a cap dependant environment

Answer 250

eIF4E over expression increases efficiency of cap binding

Answer 251

c myc VEGF cyclin D1 FGF

Answer 252

Leads to increased translation of a subset of normally poorly translated mRNAs - eg VEGF, c myc Causes angiogenesis, proliferation, evasion of apoptosis, metastasis = CANCER

Answer 253

Phospho 4E BP

Answer 254

Cytokines Hormones Growth factors

Answer 255

eIF4A /B phosphorylation, eIF4E over expression, 4E BP phosphorylation and eIF43 phosphorylation all lead to.. Increased cap recognition which leads to … Increased translation of specific mRNAs

Answer 256

Regulated by phosphorylation of eIF2 alpha subunit of eIF2

Answer 257

Viral RNA recognition

Answer 258

eIF2 phosphorylation

Answer 259

Growth retardation and diabetes Imbalance between folded and unfolded protein

Answer 260

Impaired eIF2 recycling = less Protein synthesis and fail to recover protein synthesis after stress

Answer 261

Neurological deterioration Motor dysfunction

Answer 262

Regulation

Answer 263

eIF2 alpha phosphorylation

Answer 264

Translation initiation proceeds normally Multiple ribosomes (poly somes) translate nascent peptide chains

Answer 265

mRNA incorrect > NMD nonsense mediated decay > mRNA decay to avoid synthesis of non functional or potentially toxic truncated proteins

Answer 266

Stop codon further upstream than we would expect Could get introduced via transcription error or a mutation in DNA

Answer 267

mRNA export Monosome stalled onto PTC Stalled ribosome and EJC recruit the SURF complex triggering NMD Truncated polypeptides are ubiquitnated and degraded by proteasome

Answer 268

Nonsense mediated decay NMD - premature termination codons No go decay NGD - stalled in translation mRNAs Non stop decay NSD - mRNAs without natural stop codons

Answer 269

IRES 5 UTR structures Recruitment of RNA binding proteins - eg IRP Upstream ORF - uORF

Answer 270

Recruitment of RNA binding protein miRNA binding site

Answer 271

Ribosomes dissociate after translating the uORF Ribosomes stalled by the uORF encoded peptide

Answer 272

Ternary complex abundant GCN4 not produced

Answer 273

A transcription factor activating more than 50 genes involved in amino acid synthesis

Answer 274

Ternary complex limiting, only authentic AUG recognised uORF translation impaired by eIF2 alpha P GCN4 translation promoted

Answer 275

Caudal is an important patterning molecule during embryogenesis 4E HP blocks eIF4F binding and the translation of caudal mRNA

Answer 276

Bicoid (RBP) interacts with the 3UTR of caudal Bicoid recruits 4E HPn(4E homologous protein) to caudal cap

Answer 277

Is translated in males but not female during development

Answer 278

And UNR are RBPs that repress msl2 translation by binding the 3 UTR Prevents 43S binding by locking 5-3 interactions SXL only expressed in females

Answer 279

Where RNA bases can be chemically modified

Answer 280

Promotes RNA translation by multiple mechanisms Reader proteins or METTL3 can bind m6A and promote cap dependant translation Translation factor eIF3 can be recruited by mRNA directly

Answer 281

Regulatory

Answer 282

Regulation

Answer 283

Stress response Early development Sex determination

Answer 284

Decode the mRNA sequence during protein synthesis at the ribosome

Answer 285

80% of total RNA Transcribed by Pol 1 - expect for 5S by pol 3

Answer 286

40S - 18S rRNA 60S - 5S, 5.8S, 28S

Answer 287

Single transcript - the 45S precursor = rRNA processing in the nucleolus

Answer 288

Small nuclear RNAs U rich sequences involved in the splicing of pre mRNA (U1 2, 4, 5, 6) Highly expressed and evolutionary conserved

Answer 289

Help to process and chemically modify rRNAs Main function in nucleolus > RNA processing Encoded with introns of Pol 11 transcribed genes

Answer 290

C/D box - directs 2’ O ribose methylation by recruiting a methyl transferase enzyme H/ACA box - recruits an enzyme that converts uridine to pseudouridine

Answer 291

Specifically bind to complementary sequences located in 3 UTR regions of mRNAs

Answer 292

miRNAs - promote deadenylation, translation repression and decay siRNAs - cleavage of mRNA and exosome mediated degradation

Answer 293

Defence mechanism against invading double stranded RNA viruses and transposable elements Crucial in plants, worms and insects Less in mammals

Answer 294

Eliminates generation of miRNAs in mammals and is embryonic lethal

Answer 295

Leads to defects in tissue morphogenesis / development

Answer 296

Control genes with crucial functions in cell proliferation, development, inflammation and ageing Have been linked to cancer oncogenes and tumour suppressors Target for bio markers and drug development

Answer 297

Transcribed by pol 11 Contain 5’ cap and poly A tail at 3’ end Not translated into proteins Tissue / cell type specific expression Involved in cell differentiation, development and anti viral responses Many functions are unknown!

Answer 298

Proteins, RNA and DNA Regulatory

Answer 299

A large 17kb cis acting regulatory LncRNA Associates with X chromosome Initiates histone modifications which results in heterochromatin formation

Answer 300

microRNA decay RBP decay Protein turnover Organelle function Signalling mRNA translation and degradation

Answer 301

The lncRNA TINCER interacts with complementary sequences and recruits RNA binding protein STAU1 THIS promotes stability of mRNA

Answer 302

Under stress conditions, lncRNA antisense moves from nucleus to cytoplasm and binds to end of Uchl1 mRNA to promote translation

Answer 303

Decoy Mitosis

Answer 304

Normal PUMILIO activity Normal mitosis

Answer 305

Hyperactive PULMILIO Aberrant mitosis

Answer 306

Generated via back splicing mechanism Highly abundant and stable

Answer 307

tRNAs and rRNAs

Answer 308

Gene expression post transcription ally by annealing to sequences in 3’ UTRs of mRNA targets

Answer 309

Drosha, Dicer to form the RISC complex

Answer 310

Nuclear and cytoplasmic functions in gene expression and control

Answer 311

Pre mRNAs are capped, polyadenylated and spliced in the nucleus

Answer 312

They are recruited co - transcriptionally By carboxy terminal domain CTD of pol 11

Answer 313

Added at the 5’ end of eukaryotic pre mRNAs Protects the mRNA from degradation by nulceases

Answer 314

Catalyses 2 transesterification reactions that joins 2 exons and REMOVES the intron as a Lariat structure

Answer 315

Splice site selection

Answer 316

Bind to specific sequences near the splice site Regulate alternative splicing (SR proteins > activators > hnRNPs > repressors)

Answer 317

Diverse RBPs and complexes Alternative polyadenylation can have important physiological implications (eg antibodies)

Answer 318

Directional export of mRNAs from nucleus to the cytoplasm through the NPC The mRNP exporters are phosphorylated in the cytoplasm and release the mRNA cargo

Answer 319

Co transcriptionally

Answer 320

Regulates nuclear export of mRNAs Protects mRNAs from RNA digesting enzymes (5’ exoribonucleases) Promotes translation through interaction with a translation initiation factor (eIF4E - the cap binding protein)

Answer 321

The removal of introns from the pre mRNA

Answer 322

Define the splice sites in eukaryotic pre mRNAs

Answer 323

5 small nuclear RNAs - snRNAs U1, U2, U4, U5 and U6 between 107-210nts long 170 proteins

Answer 324

10 Splice site

Answer 325

Generating mRNA variants from the SAME gene

Answer 326

The Drosophilia DSCAM gene

Answer 327

Exon skipping - most prominent in eukaryotes Intron retention Alternative 5’ and 3’ splice site Mutually exclusive exons

Answer 328

B-thalassemia - autosomal recessive blood disorder. Mutation of splice site in B globin gene Myotonic dystrophy - neuromuscular disease. Depletion of MBNL splicing factor Cystic fibrosis Parkinson’s disease Premature ageing Cancer

Answer 329

By the processing of pre mRNA

Answer 330

The poly A tail

Answer 331

CPSF CstF TWO cleavage factors Poly A polymerase - PAP

Answer 332

Required for export of mRNA from the nucleus to the cytoplasm = binding of PABPII Promotes translation initiation and translation Stabilises the mRNA > shortening of polyA tail may lead to reduced translation and eventual decay of the mRNA!

Answer 333

Small molecules and proteins (<60 kDa) can diffuse through membrane Macromolecular complexes (eg RNPs) need active transport

Answer 334

Post transcriptional control at the global level

Answer 335

RNA binding proteins - that bind to particular elements within the mRNAs (often reside within the 3’ UTRs)

Answer 336

Initiation factors More specifically by RNA binding proteins and non coding RNAs Eg IRP - control of intracellular iron concentrations

Answer 337

Processing bodies (P bodies) Followed by activity of decapping enzymes and exonucleolytic degradation

Answer 338

Gene activity / mRNA levels do NOT necessarily correlate with protein abundance

Answer 339

Translation (ribosome) Localisation (organelle) Storage (granule) Decay (exo / endo nuclease in P bodies)

Answer 340

Target protein to appropriate region in cell Prevents expression elsewhere Response to local requirement (NT production in neurons) Independent control in different cellar Regions Localised synthesis necessary for assembly of protein complexes More efficient transport (one mRNA molecule vs many proteins)

Answer 341

Universal Prokaryotes and archea

Answer 342

Directed transport on cytoskeleton - eg neuronal RNPS along microtubuli, ASH1 mRNA bud yeast tip Random diffusion and trapping - eg drosophilia mRNAs enriched in pole plasma Generalised degradation in combination with local protection by trapping - same as above

Answer 343

It is a transcriptional repressor of HO = No HO transcription and No switching HO expression is required for mating type switching

Answer 344

She2, she3 and myosin4 proteins form a complex with ASH1 mRNA for transport to the bud tip of the daughter cell

Answer 345

A translational repressor that prevents translation of ASH1 mRNAs during transport to the bud tip

Answer 346

U1A GFP fusion protein is tethered to the mRNA via U1A binding sites > this enables visualisation of mRNA via GFP

Answer 347

Global regulation - modification of translation initiation factors or their regulators MRNA specific regulation - RNA structure / specific RBPs / microRNAs

Answer 348

Bind to iron response element IRE and prevents recruitment of the 43S pre initiation complex via Steric Hindrance

Answer 349

NO ferritin made - ferritin > storage (translation blocked) Transferrin receptor made - transferrin > iron uptake! (mRNA stable and translated)

Answer 350

Ferritin made - mRNA translated No transferrin receptor made - mRNA degraded

Answer 351

Shortening of poly A tail to <20 bases = stops translation Degradation by exonucleases

Answer 352

Condensed aggregates of mRNAs and proteins in the cytoplasm In stressed cells - leading to rapid shut down of translation

Answer 353

Enhancer Promoter Transcription start site

Answer 354

Enhancer Promoter TSS 5’ UTR start codon Exons Introns Donor, acceptor and splice sites STOP codon 3’ UTR Polyadenylation site

Answer 355

Rate of transcription Rate of mRNA degradation Rate of protein synthesis Rate of protein degradation

Answer 356

Slow rate of transcription or a high degradation rate Small amount of protein will be translated

Answer 357

Non coding part of the gene that controls where transcription starts and which direction and what strand it occurs on!

Answer 358

-10 and -35 consensus sequences, TSS that recruit proteins able to assist in the control of initiation of transcription

Answer 359

DNA recognition sequence Protein structure - can it bind as a monomer / dimer etc Mediator contents DNA packaging

Answer 360

Protein conformation and DNA structure

Answer 361

Enables electrostatic interactions Fine tunes recognition of a specific sequence Changes to shape of DNA or protein can affect the strength of binding - stronger the interaction, the more it will stimulate transcription! Needs to be a nice stable interaction

Answer 362

Homeodomain containing proteins - eg HOX Beta sheet recognition protein -eg p53 Zinc finger domain proteins - eg nuclear receptors Leucine zipper proteins -eg Fos Helix loop helix -eg Myc

Answer 363

RNA polymerase and sigma factors (starts transcription) for progression from the promoter

Answer 364

Stops RNA polymerase processing DNA = termination

Answer 365

Polycistronic (multiple) mRNAs generated from a single gene Usually proteins / enzymes involved in regulation of a process Cis regulatory regions and operator regions control initiation of transcription 1 promoter generates multiple genes

Answer 366

Cis regulatory sequences in promoter and enhancer bind the protein Trans regulatory factors - ie transcription factors Control recruitment of accessory factors to RNA polymerase, to control initiation of transcription

Answer 367

It binds to repressor > ACTIVE! This causes a shape change > can bind to operator site > RNA polymerase can’t bind > all genes under expression of promoter are turned OFF Operon OFF Absence of trytophan > operon is ON > RNA polymerase can bind! = transcription

Answer 368

Binding of activator to the cis regulatory region recruits RNA polymerase to ‘turn on’ transcription Operon is ON Eg: - glucose, + lactose

Answer 369

Polycistronic mRNAs

Answer 370

Less non coding DNA and less elaborate control of gene transcription

Answer 371

Consensus sequences Transcription factors (trans activators) Ability to inhibit transcription with binding of repressors

Answer 372

Non coding DNA in the form of promoters and enhancers controls initiation of transcription Promoters contain consensus sequences to recruit GTF The components of the mediator complex control initiation through 3D positioning

Answer 373

Quite long and attaches to multiple parts of promoter

Answer 374

Activators Mediators Chromatin modifying proteins

Answer 375

Non coding DNA Cis regulatory and trans activating factors regulate this area 3D EFFECT that brings a complex of proteins together to the form a mediator complex

Answer 376

The recognition of bases and the recognition of DNA shape

Answer 377

Sequence dependant DNA structures that are optimised to promote assembly

Answer 378

Movement to the nucleus may require a change in shape or dissociation from another protein The change reveals the NLS - key to bind to Importins Then allows the protein to bind to Importins to allow it to move through the NPC and into the nucleus Once in the nucleus it can dimerise with other proteins and DNA And therefore can affect gene expression by controlling initiation of transcription

Answer 379

Protein synthesis Ligand binding Covalent modification - post translational modification Addition of a 2nd subunit - eg dimerisation Unmasking - eg of a chaperone protein that may be covering up NLS Release from membrane - eg protein kinase C that moves into nucleus

Answer 380

HOX proteins control body patterning during (foetal) development - eg HOX9 is involved in limb development They contain homeodomains - contain 3 alpha helices > packed closely together by hydrophobic interactions

Answer 381

Typical tumour suppressor gene - stops us having continuous proliferation Contains a DNA binding protein made of 2 b sheets - almost every mutation that causes cancer happens in the DNA binding domain! Forms multimers through its OD domain - can modify its DNA sequence specificity

Answer 382

Finger like domains that interact with DNA Regulate processes like bile acid detoxification - eg FXR Must bind as a dimer (2 of the same protein) Contents of the dimer are key to sequence specifity and effect

Answer 383

Stops the cell cycle but promotes DNA repair

Answer 384

Always binds to DNA as dimers Dimer formation enabled by hydrophobic interactions between alpha helices Have a globular domain with basic leucine zipper (bZIP) - determines if it has open or closed structure Activated by phosphorylation - by MAP kinase

Answer 385

Signalling cascade of kinases > Fos phosphorylation Heterodimerisation with Jun enables binding to the AP1 response element Proliferation of fibroblasts and differentiation

Answer 386

Components of the heterodimer control the outcome of the signalling pathways Myc associated with: cell cycle progression / apoptosis / proliferation / metabolism Myc can associate with Max. When they bind to M21, they repress genes and promoters!

Answer 387

If dimer formed 1st: increase number of sites bound on DNA = quickly increases protein concentration If dimer takes longer to form: protein concentration increases slowly

Answer 388

Co repressors Co activators

Answer 389

An emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment and lifestyle for each person Ones size fits all approach

Answer 390

Personalised: older term with risk of misleading interpretation Individual, unique treatment Precision: treatments for groups of people based on genetic, environmental and lifestyle factors

Answer 391

Multiple sources of data Electronic health records Collaborative data sharing Extensive research Education and awareness in multiple levels

Answer 392

Aberrant gene expression or splicing effects in RNA!

Answer 393

Sequencing a single gene - eg cystic fibrosis Sequencing a panel of genes - eg Kabuki syndrome The clinical exome WES and WGS

Answer 394

Not diagnostic! To identify high risk sub groups who undergo diagnostic test Statistically quantifying the performance of a test At different times of life (prenatal, newborn, adulthood) Must be evaluated: benefits vs costs

Answer 395

Complex = multi factorial (polygenic, lifestyle, environment) Find people at high genetic risk to offer targeted advice Polygenic risk scores

Answer 396

Sum the risk alleles of multiple variants, usually weighted by their effects as observed in large scale studies Population specific!

Answer 397

Individual effects are modest Only 10% of genetic predisposition found Currently over 500 variants across the genome associated with T2D

Answer 398

How people respond to drugs based on their genetics Adverse side effects - eg Warfarin Targeted cancer drugs for specific mutations Future: the most efficient dose

Answer 399

Decreases availability of vitamin K which is an essential cofactor in blood clotting Excessive bleeding in people who have low activity enzymes involved in drug metabolism

Answer 400

To treat or cure a disease by modifying a persons genes - replace with a healthy copy, introduce a new gene Mechanisms - plasmid DNA, viral and bacterial vectors, gene editing technologies If targeting RNA transcripts > RNA therapeutics Somatic vs germline Tightly regulated

Answer 401

A blood clotting disorder causing easy bruising and bleeding Mutation in the gene causing deficiency of clotting factor IX

Answer 402

Prenatal screening Incidental findings - screen only selected genes and not the whole genome Baby editing Germline gene therapies The safety of gene therapies Costly treatments Who gets treatment

Answer 403

A single nucleotide substitution characterised by its alleles and position in the chromosome Most SNPs (99%) are bi allelic (two alleles) and uncommon (MAF <5%)

Answer 404

Second most common Two alleles

Answer 405

Insertions, deletions and duplications

Answer 406

Mega base pair SVs

Answer 407

Most frequent

Answer 408

55 million tandem repeats.

Answer 409

Micro satellites Abundant

Answer 410

STR mutations Large expansions

Answer 411

Mitochondria Y chromosome DNA

Answer 412

Molecular clocks of DNA

Answer 413

Adaptations to new environments

Answer 414

The genome is the set of all genetic information of an organism

Answer 415

DNA is the only fundamental molecule that stores genetic info! Good evidence that the chromosome and DNA are good candidates for being molecules that start genetic information Also evidence that mitochondria has DNA, but NOT fundamental to define your species!

Answer 416

Mother mouse was induced with stress> didn’t properly groom offspring So 1st generation didn’t properly groom their offspring 2nd and 3rd generation still didn’t groom offspring So besides DNA, mice will also inherit behaviour from their mother!

Answer 417

Will have the phenotype of NOT grooming children properly > problem transferred to next generations! DNA is still the same > but what changed is the way the DNA spreads! So genome is still the DNA, but the way we read the genome can change depending on circumstances

Answer 418

Mother Father

Answer 419

Useful as allow recombination to occur

Answer 420

Mobile DNA elements that can insert themselves into another position of DNA sequence

Answer 421

Are responsible for most antibiotic resistance in bacteria Can jump from chromosomal DNA to plasmids and vice versa This facilitates the horizontal transfer of genetic material between species - including antimicrobial resistance genes

Answer 422

Transposons include enzymes required for their movement in the coding sequence They jump to any DNA molecule Transposed plasmids and viruses may conjugate / infect another organism New transposons can integrate into the human genome

Answer 423

Because it keeps copying and replicating our genomes!

Answer 424

The human genome is relatively stable because most of the transposons are silent!

Answer 425

Transposons are also called ‘junk DNA’ because they replicate without an apparent benefit to the host!

Answer 426

The adaptive immune system The placenta

Answer 427

Transposition may re arrange DNA Transposons facilitate horizontal gene transfer between species Deactivated transposons accumulate mutations over generations

Answer 428

DNA replication and repair errors Horizontal gene transfer Transposition

Answer 429

Natural selection Genetic drift

Answer 430

An insertion or deletion of up to 50 nucleotides in a specific location of the DNA sequence

Answer 431

The 3 nucleotides CTT are deleted in people that develop Cystic Fibrosis Therefore Phenylalanine is NOT in the amino acid sequence > conformation change in protein > exchange of ions in surface of bronchi is affected > people develop disease later on in adulthood!

Answer 432

Are large >50bp rearrangements of DNA segments

Answer 433

The length, indels are <50 bp

Answer 434

Because recombination doesn’t occur there! (Heterochromatin) A lot of mutations occur in Y chromosome that don’t occur in other chromosomes > mostly junk!

Answer 435

Both parents

Answer 436

1 parent only

Answer 437

A group of alleles that are inherited together from the same parental chromosome Reveals relatedness between individuals

Answer 438

Environmental stresses: lower atmospheric pressure, lower oxygen, lower temps and changes in diet Evolutionary responses: positive selection of variants conferring adaptation to environment

Answer 439

Coding and non coding SNPs may have phenotypic effects - ie may cause Mendelian diseases Eg - Phenylketonuria PKU is an autosomal recessive disease caused by substitution in the sequence of the phenylalanine hydroxylase gene

Answer 440

Included DNA from multiple volunteers Published in 2001 Human genome project

Answer 441

NON - Mendelian patterns of inheritance

Answer 442

Using Punnet tables

Answer 443

With quantitative genetics methods, like heritability

Answer 444

Phenotypic heritability, without genotyping individuals Using Falconers Formula

Answer 445

Traits explained by mutations in a single gene Do NOT have intermediate phenotypes - are either dominant or recessive! Phenotype is NOT influenced by environment or epigenetics

Answer 446

Occurs when a phenotype is controlled by a gene with multiple alleles 2 or more alleles are expressed simultaneously

Answer 447

Causes by multiple genes Phenotype can show a range of continuous variation The extremes tend to be less frequent - induces almost a normal distribution

Answer 448

Genetic phenomenon when the effect of a mutation in a gene is dependant on mutations on other genes!

Answer 449

A phenomenon where mutations on a gene affect 2 or more apparently unrelated phenotypes! Eg a single mutation on the B globin gene may cause sickle cell disease - which is protective against malaria. Therefore, the SAME gene is a risk factor for sickle cell anaemia and a protective factor for malaria!

Answer 450

Genetics and a multiplicity of unknown environmental effects Cannot be described by a Punnet square

Answer 451

The proportion of variance in a phenotype explained by genetic factors Does not quantify whether a trait is genetic or not

Answer 452

RNA and amino acid sequence

Answer 453

Insert stop codons and disrupt the protein!

Answer 454

SVs Mechanisms

Answer 455

Velo cardio facial syndromes Williams Beuren syndrome Prader Willi and Angelman syndrome

Answer 456

Single amino acid substitution

Answer 457

Results in a shorter unfinished protein product typically by substitution of an amino acid with a STOP codon

Answer 458

Results in alteration of all amino acids after an insertion or deletion

Answer 459

Phenylketonuria - PKU - monogenic disease Caused by substitutions in the sequence of PAH gene that codes for phenylalanine hydroxylase enzyme Coding SNPs in exons and non coding SNPs in the introns, 5’ and 3’ UTR of phenylalanine hydroxylase gene causes PKU

Answer 460

Similar to linkage studies but in unrelated individuals Better than linkage studies at detecting weak genetic effects To identify personal genetic disease risk To identify pharmacogenetic variants (drug response) Identity variants contributing to gene environmental interactions

Answer 461

Advances in genotyping technologies and lowered costs Advances in software Biobanks Large scale projects - HGP, international HapMap project

Answer 462

Single nucleotide polymorphisms SNPs

Answer 463

SNP Minor allele frequency MAF Hardy Weinberg equilibrium Linkage disequilibrium Haplotypes

Answer 464

A DNA sequence variation occurring when a single nucleotide (A, T, C or G) in the genome differs between members of a species OR between paired chromosomes in an individual at a particular locus

Answer 465

The frequency of the SNPs less frequent allele in a given population Population specific

Answer 466

Both allele and genotype frequencies remain constant in a population unless specific disturbing influences are introduced (mutation, migration, non random mating)

Answer 467

The non random association of alleles at 2 or more loci so they are inherited together more frequently than expected by chance Genetic correlation between the markers Observed in various regions of the genome Decreases with physical distance Segments of high LD = haplotype blocks LD structure is population specific

Answer 468

Using tagSNP selection

Answer 469

The most important and time consuming part of GWAS! To reduce systematic bias

Answer 470

Used as a diagnostic tool by plotting observed p values against expected If p values are close to the grey line (null hypothesis) this implies there a few systematic sources of spurious association Deviation of small p values from null line indicates possible associations Log scale helps to emphasise the smallest p values

Answer 471

1. There is a causal relationship between the SNP and trait 2. The marker is in linkage disequilibrium with a causal locus 3. False positive

Answer 472

Genotyping quality control is particularly important

Answer 473

Increase sample size - biobanks Gene x environment interaction studies Analysis of rare variants Analysis strategies increasing power - eg multi phenotype analysis

Answer 474

Identify the causal variant to understand molecular mechanisms and pathways behind them Most identified SNPs are in NON coding regions, could still have consequences for nearby genes - enhancer elements, DNase hypersensitive regions

Answer 475

Working out the order of the 4 bases (A, T, C, G) in fragments of DNA Usually by amplified PCR or DNA cloning Increasingly sophisticated and affordable

Answer 476

RNA is sequenced indirectly through the sequencing of DNA

Answer 477

Time consuming and requires relatively high amounts of protein Increasingly replaced by modern methods

Answer 478

SR: Maxam Gilbert method - based on chemical degradation. Now obsolete. Sanger method - based on primer extension chain termination. Still used but dominating method is NGS MPS: Next generation sequencing NGS - based on primer extension, fully automated, a revolution in progress

Answer 479

DNA sequencing with chain terminating inhibitors = dideoxy sequencing Used for sequencing SINGLE genes and fragments of DNA - mutation screening in specific genes, validations of findings from NGS Highly accurate

Answer 480

1. Need to produce multiple copies of DNA - clone DNA fragment into plasmid and grow in E.coli OR amplify DNA fragment by PCR 2. Denature the sequence by heating (or adding NaOH) to produce single stranded DNA 3. Prepare DNA polymerase, primer, dNTPs and ddNPTs

Answer 481

DNA polymerase will start synthesising a complementary stand Starting from the primer (adding bases) Forms a complementary copy to the template strand - extending the primer therefore

Answer 482

Terminator nucleotides Modified version of the normal DNA building blocks (dNTPs) Use the SAME bases (ATCG) but the sugar is modified! Wherever a ddNTP has been incorporated, DNA synthesis CANNOT proceed any further

Answer 483

Lack of the 3’ OH group in the deoxynucleotide prevents the formation of the phosphodiester bond

Answer 484

There are multiple strands due to DNA amplification There is an excess of normal dNTPs against the amount of ddNTPs (100:1) These compete against eachother in the DNA synthesis Termination happens at different places at different strands The result is a set of DNA sequences varying in length - each ending with a ddNTP

Answer 485

Primer, DNA polymerase and a mix of normal (unlabelled) dNTPs and labelled ddNTPs Label used to be radioactive BUT today fluorescent dyes are used The correct order is reached through gel electrophoresis and fluorescence detection In genotyping where only a SINGLE SNP is genotypes, process is similar but NO normal unlabelled dNTPs are added!

Answer 486

Nucleic acids carry numerous negatively charged phosphate groups They will migrate towards the positive electrode when placed in electric field Porous gel acts as a sieve - small molecules pass through easily than larger fragments

Answer 487

Nucleic acids carry numerous negatively charged phosphate groups They will migrate towards the positive electrode when placed in electric field Porous gel acts as a sieve - small molecules pass through easily than larger fragments

Answer 488

Radioactive labelling requiring 4 separate reaction tubes for each ddNTP Separated individually on large slab electrophoresis X ray film and dark room manipulation Manual reading and feeding into computer 1.5 days from setup to results

Answer 489

Radioactive labelling requiring 4 separate reaction tubes for each ddNTP Separated individually on large slab electrophoresis X ray film and dark room manipulation Manual reading and feeding into computer 1.5 days from setup to results

Answer 490

Fluorescent dye for labelling, use of a mixed reaction tube containing ALL 4 ddNTPs Automated optical detection system using a laser Direct automated entry of DNA base sequence into computer Still time consuming due to handling of gel plates

Answer 491

Slab gel is manual - slow and prone to human error Capillary is largely automated Gel is not run for a finite time, fluorescent labelled DNA samples migrate through gel Allows longer reads up to 1000 bases - each fragment is allowed to run to bottom of gel where resolution is highest Faster and cheaper

Answer 492

Highly accurate sequences - about 99.95% Several hundred bases long 800-1000bp Gel electrophoresis is NOT suitable for handling large numbers of samples at a time because it is not fully automated Therefore not suitable to genome sequencing

Answer 493

Also known as massively parallel sequencing - meaning it sequences millions of DNA fragments at same time From 2005 onwards - a technological revolution Vast increase in amount of sequence per data run (the sequence throughput) = dramatic loss in cost Moving from sequencing single genes and exons to: whole genome and exome sequencing, methyl seq, CHIP seq and ribo seq

Answer 494

The amount of sequence data processed in one run

Answer 495

Length of DNA fragments measured in nucleotides Short read lengths = high throughput

Answer 496

The sequence coverage - how many times each sequence is represented Important for small read lengths for genome assembly

Answer 497

The sequence coverage - how many times each sequence is represented Important for small read lengths for genome assembly

Answer 498

The sequence coverage - how many times each sequence is represented Important for small read lengths for genome assembly

Answer 499

Aligning and merging the sequenced pieces to make sense of the sequenced genome

Answer 500

From short (35 nucleotides) to medium length sequences (up to 800 nucleotides) High to very high sequence throughput Quite a high rate of sequencing errors in individual reads

Answer 501

Roche / 454 pyrosequencing The ABI SOLID technique Illumina / Solexa sequencing Ion torrent systems

Answer 502

Uses bead surfaces, water and oil Allows simultaneous amplification of each sequence without risk of contamination Each beads acts as a microreactor for PCR, each containing one strand of DNA The terminators are reversible - after chemical de protection synthesis can continue!

Answer 503

Long sequences (thousands of nucleotides) - important for assembly of genomes from newly sequenced species, and for distinguishing large scale variations Release of protons which is recorded as an electric current Avoids problems related to DNA amplification - eg under or over representation of DNA Simple and cheap technology - small portable machines eg Oxford Nanopore High error rates

Answer 504

Works on cell populations > resulting data are aggregate values For understanding cell to cell variation and identifying new cell types A catalog of human cells - stable cell properties / cell positions / lineage relationships Widely employed in cancer research

Answer 505

Output files contain millions of short (100bp) reads (2nd generation) or longer reads (3rd generation) Reads are mapped to reference genome if species is known Variants are identified Requires several software tools and computational skills

Answer 506

Sanger: Cheap, fast, simple Highly accurate Gives an answer about a single, specific question NGS: Getting cheaper with more technologies More error prone Highly versatile - WGS, WES, RNA seq, methyl seq etc Computationally laborious

Answer 507

3’ to 5’ exonuclease activity

Answer 508

Exposure to UV light

Answer 509

Loss of function mutations can inactivate them Loss of function mutations can contribute to cancer

Answer 510

Cancer cells show growers repression by growth suppressive signals

Answer 511

Viral borne cancers can be transmissible

Answer 512

2 hydroxy glutarate

Answer 513

Repetitive and transposable elements

Answer 514

Zygotes Gametes Brain

Answer 515

100 million

Answer 516

A short DNA sequence repeated in tandem that vary in number

Answer 517

Multiple variants / multiple mutations

Answer 518

Yes! Eg cystic fibrosis in Europeans - recessive allele carried by 0.8% of population

Answer 519

No! Genetic info has not changed

Answer 520

The proportion of phenotype variance explained by genetic factors

Answer 521

eIF2 is a guanine exchange factor for eIF2B

Answer 522

The mTOR signalling pathway can regulate eIF4E activity

Answer 523

m6A and m1A modifications are mutually exclusive on an mRNA

Answer 524

Contain the same number of rRNAs than those of prokaryotic ribosomes

Answer 525

Non stop decay

Answer 526

UAG is always a premature termination codon

Answer 527

Is a result of diminished ability to recycle eIF2-GDP to eIF2-GTP

Answer 528

Translation repression by SXL

Answer 529

HRI is an ER resident eIF2 kinase that responds to unfolded proteins

Answer 530

Sequencing process: ddNTPs Gel electrophoresis Highly accurate

Answer 531

Second vs third generation Genome assembly WGS vs WES vs RNAseq Analysis of NGS data

Answer 532

A hypothesis free approach that has revolutionised complex traits genetics Testing millions of imputed SNPs for association between the genome and the trait of interest Results are combined from multiple studies (meta analysis) to provide evidence Quality control PRIOR to analysis is very important to avoid systematic errors coming from data! The difficult starts after GWAS to understand the underlying biology Although successful, a lot of ‘missing heritability’ remains

Answer 533

Genetic testing for Mendelian disorders Genetic testing for screening Polygenic risk scores PRS for complex traits to help prediction Genetics to help understand response to drugs (pharmacogenetics) Gene therapy Challenges and future perspectives

Answer 534

Normal distribution Population specific Important to go genetic studies in different ancestries as genetics may differ in different ancestries

Answer 535

Normal distribution Population specific Important to go genetic studies in different ancestries as genetics may differ in different ancestries

Answer 536

Normal distribution Population specific Important to go genetic studies in different ancestries as genetics may differ in different ancestries

Answer 537

For prediction purposes Try to maximise area under the curve > the higher it is, the better the test! Optimal combination of sensitivity and specificity

Answer 538

Melting temp Tm - temp that dictates the annealing step GC content - Lower the number of Gs and Cs in the primer, the lower the melting temp! Salt content - sodium acetate Other buffer components - like denaturant > may change structure of DNA, may not allow base pairing!

Answer 539

Tells you how much mRNA was there to start with and can compare it to other mRNAs in sample

Answer 540

Tells you how much mRNA was there to start with and can compare it to other mRNAs in sample

Answer 541

Detects proteins binding to specific sequences (response elements) Always a band at the bottom because that’s where the probe is and the probe hasn’t bound ! You will never get every piece of DNA bound by protein > some left over

Answer 542

Nucleosome eviction Nucleosome sliding

Answer 543

Nucleosome sliding

Answer 544

To allow transcription factors to bind to a promoter and therefore induce gene expression To bring arts of DNA closer together in a complex that might enable gene expression to occur To change interaction of Histones with DNA therefore changing chromatin structure To work in concert with DNA methylation to manipulate the access of DNA to transcription factors and transcription machinery

Answer 545

Hi-C and ChiA-PET

Answer 546

Western Blot

Answer 547

DNA methyl transferase 3 (DNMT3a and b)

Answer 548

Ubiquitinylation Di methylation Acetylation Tri methylation

Answer 549

Nucleosome eviction

Answer 550

Cytosine to uracil

Answer 551

They prefer to carry out aerobic glycolysis even in the presence of oxygen!

Answer 552

Proto oncogenes are derived from tumour suppressor genes

Answer 553

How cells sense and adapt to oxygen availability How kidneys stimulate erythrocyte production by erythropoietin up regulation How hypoxia inducible factor is stimulated upon low oxygen How cancer cells form new blood vessels to disseminate themselves

Answer 554

An exclusive characteristic feature of a cancer cell

Answer 555

Tumour suppressor Negative E2F

Answer 556

A valine to glutamine mutation in this gene causes constitutive activation

Answer 557

2 keto glutarate

Answer 558

Causing thymine thymine dimers

Answer 559

Base excision repair

Answer 560

It undergoes P-450 mediated activation in lungs causing G to T conversion

Answer 561

Viruses can mutate cellular proto oncogenes into oncogenes

Answer 562

Kinase Activate Phosphorylation

Answer 563

Cancer cells show growth repression by growth repressive signals

Answer 564

It also has a 3’ to 5’ exonuclease activity to remove any incorrect base pairing

Answer 565

Lack of nucleotides

Answer 566

Loss of function mutations can inactivate them!

Answer 567

Aerobic glycolysis produces HIGH ATP output

Answer 568

It’s a nuclear receptor that drives prostate cancer Found inactive in cytoplasm and activated by androgen binding Regulates gene expression in prostate epithelial cells A target of anti androgen is drugs in the clinic

Answer 569

It’s a tumour suppressor gene that opposes uncontrolled cell growth caused by oncogenes

Answer 570

Stabilised Low Prolyl hydroxylase Covalent modification

Answer 571

Limited proliferation

Answer 572

It is a metabolite specific to cancer cells! Oncometabolite

Answer 573

Tumour formation Inability of a tumour suppressor to inhibit proliferation of a cell with DNA damage Uncontrolled growth of cells that harbour oncogenes Loss of balance between cell proliferation and cell death

Semester 1 Flashcards

(656 cards)