Dr Hack's Lectures 2

Question 1

What controls cAMP concentration?

Answer 1

glucose

Question 2

what does cAMP bind to?

Answer 2

catabolite activator protein (CAP)

Question 3

why is the lac promoter weak?

Answer 3

sequences at -10 and -35 are non-standard

Question 4

cAMP-CAP complex binds to DNA next to which region? how does it affect DNA?

Answer 4

binds next to -35 region, bends DNA by 90 degrees

Question 5

in what scenario is the lac operon transcribed?

Answer 5

CAP-cAMP binds to DNA

Lac repressor does not bind to DNA

Question 6

What do catabolic operons contain genes for?

Answer 6

breakdown of metabolites

Question 7

when are biosynthetic operons turned on?

Answer 7

when supply of end product is low

Question 8

what does the trp operon contain genes for?

Answer 8

The biosynthesis of Tryptophan (an amino acid)

Question 9

When does tryptophan repressor protein repress transcription of trp operon?

Answer 9

When tryptophan conc. in cell is HIGH

Question 10

How does tryptophan stop transcription of trp operon?

Answer 10

tryptophan binds to repressor, which in turn binds to trp operator, blocking transcription

Question 11

Is the trp operon the same as the lac operon?

Answer 11

No, tryptophan has an opposite effect on the operon than allolactose does on the lac repressor

Question 12

What bacteria does Euprymna scolopes have a symbiotic relationship with?

Answer 12

Vibrio fischeri

Question 13

When does bioluminescence occur?

Answer 13

when the bacteria are at high density

Question 14

How is density measured and under which operon?

Answer 14

Quorum sensing, the lux operon

Question 15

What signals cell density?

Answer 15

Acyl homoserine lactones (AHL)

Question 16

what protein catalyses synthesis of AHL?

Answer 16

LuxI

Question 17

How do bacteria use AHL?

Answer 17

They take up AHL from the cytosol

They produce AHL

Question 18

What does AHL bind to and when?

Answer 18

When there is enough protein in the cell, AHL binds to LuxR protein

Question 19

What does LuxR do?

Answer 19

With AHL bound to it, LuxR activates transcription of bioluminescence genes in the lux operon by binding to lux box in DNA

Question 20

Where is the lux box in DNA?

Answer 20

next to lux promoter P

Question 21

What kind of feedback does quorum sensing produce?

Answer 21

positive feedback - the system increases its own activity

Question 22

What are other examples of quorum sensing?

Answer 22

‘Milky seas’
Biofilm formation
Pathogenic bacteria

Question 23

Define genomics

Answer 23

the study of genome organisation and the identification of genes and their functions

Question 24

Of the examples given in the lecture, which organism has the smallest genome size and which has the largest? in order (small –> large)

Answer 24

Yeast > Plant > Nematode > Fruit fly > Pufferfish > Chicken > Human

Question 25

Where does the extra DNA come from within genes?

Answer 25

Introns

Question 26

Where does the extra DNA come from between genes?

Answer 26

repetitive DNA

Question 27

How are introns removed?

Answer 27

RNA Splicing

Question 28

How is a lariat formed?

Answer 28

5' cut, formation of loop with tail | 3' cut, joining of exons

Question 29

What is intron excision catalysed by?

Answer 29

Spliceosomes

Question 30

What do spliceosomes contain?

Answer 30

small, nuclear ribonucleoprotein complexes (snRNPs)

Question 31

Where do snRNPs bind?

Answer 31

primary transcript

Question 32

What is the lariat loop bond?

Answer 32

5'-2' phosphodiester bond

Question 33

what does alpha tropomyosin do?

Answer 33

helps regulate muscle contraction | stabilises actin filaments in cytoplasm

Question 34

Introns can contribute to variation in gene size, give an example of two species with the same gene but in different sizes

Answer 34

humans and pufferfish - both have huntingtin gene but in Fugu it is much smaller

Question 35

What is repetitive DNA?

Answer 35

DNA that occurs in many copies in the genome

Question 36

How much of the human genome is made up of repetitive DNA

Answer 36

>50%

Question 37

What are simple sequence repeats?

Answer 37

tandem arrays of very short sequences, eg. CACACACACACA

Question 38

How much of the human genome is made up of simple sequence repeats?

Answer 38

~5%

Question 39

What is a transposon? Why is duplication so slow?

Answer 39

Mobile DNA elements, slow because it may cause mutations

Question 40

What are the two classes of transposons?

Answer 40

LINEs and SINEs

Question 41

What is the estimated current transposition rate in humans?

Answer 41

1 insertion for every 20-200 births

Question 42

What are Alu elements? How big are they?

Answer 42

Members of the SINE class that make up 10% of human DNA, approx. 300bp long

Question 43

What does Alu transposition depend on?

Answer 43

They are non-autonomous and depend on LINE elements

Question 44

What is the current estimated transposition rate for Alu elements?

Answer 44

1 insertion for every 20 births

Question 45

What kinds of genes are in the human beta-globin cluster?

Answer 45

5 genes and 1 non-functional pseudogene

Question 46

How has the gene cluster evolved?

Answer 46

gene duplication

Question 47

What is synteny?

Answer 47

comparison of genomes of different organisms shows order of genes in chromosomes is is partly conserved through evolution

Question 48

What are the ends of chromosomes called?

Answer 48

Telomeres

Question 49

What is the basic building block of chromatin?

Answer 49

nucleosomes

Question 50

What are the copies of the histones called?

Answer 50

H2A, H2B, H3 and H4

Question 51

What charge is a histone?

Answer 51

positive

Question 52

The spread out parts of chromosomes in the nucleus are called...

Answer 52

euchromatin

Question 53

Some parts of the chromosomes condensed in interphase are called....

Answer 53

heterochromatin

Question 54

The structure of expressed genes is more ______ than others

Answer 54

open

Question 55

How is the more open structure observed?

Answer 55

greater sensitivity to DNase

Question 56

What are the two main processes involved with the opening of chromatin?

Answer 56

``` Histone modification (via acetylation) Chromatin remodelling complexes ```

Question 57

What does RNA polymerase 1 transcribe?

Answer 57

ribosomal RNA genes

Question 58

What does RNA polymerase 2 transcribe?

Answer 58

genes coding for proteins

Question 59

What does RNA polymerase 3 transcribe?

Answer 59

genes coding for small RNAs

Question 60

Name two basal factors needed for transcription by RNA polymerase 2

Answer 60

TFIIA, TFIIB etc

Question 61

Where does transcription in eukaryotes start?

Answer 61

TATA box

Question 62

What needs to bind to the TATA box for transcription to start? What does it do to DNA?

Answer 62

TATA box binding protein, binds DNA by 70 degrees

Question 63

What is the complex called that is formed by TBP? What else has to bind to TBP to form this complex?

Answer 63

TFIID - TAFs must also be bound

Question 64

Which TATA box binding protein does Pol 2 bind to, stabilising the complex?

Answer 64

TFIIF

Question 65

What does TFIIH do?

Answer 65

Phosphorylates Pol 2

Question 66

What does a cis-regulatory element do?

Answer 66

Increase/decrease basal level of transcription | Specify how gene expression responds to a particular signal

Question 67

What does the metallothionein gene do?

Answer 67

Bind toxic metal ions | Store Zn2+

Question 68

What induces transcription in humans?

Answer 68

Metal (Zn2+ ions) | Glucocorticoid hormone

Question 69

Which cis-regulatory elements increase expression?

Answer 69

GC box BLE TRE E-box

Question 70

What are the response elements?

Answer 70

GRE | MRE

Question 71

what is the principal glucocorticoid hormone? how does it work?

Answer 71

cortisol - enters the cell and exerts its effects directly

Question 72

What does cortisol bind to?

Answer 72

glucocorticoid receptor (GR)

Question 73

What protein keeps glucocorticoid receptor in cytosol? What kind of protein is it?

Answer 73

Hsp90 - chaperone protein

Question 74

What are steroid hormone receptors?

Answer 74

Zinc finger proteins

Question 75

What does AP1 do?

Answer 75

Increases general chromatin accessibility

Question 76

When not bound, where is the activator protein?

Answer 76

Cytosol

Question 77

What do fibroblast cells differentiate into?

Answer 77

Muscle cells

Question 78

What are the transcription factors that are expressed in fibroblasts for them to differentiate into muscle cells?

Answer 78

MyoD, myogenin, Myf5, Mrf4

Question 79

What are Somites?

Answer 79

Segmented blocks of cells that form along sides of the notochord in vertebrate embryos

Question 80

What TF can reprogram fibroblasts into iPS celsl

Answer 80

Oct4, Sox2, Klf4, Myc

Question 81

What TF can reprogram exocrine cells from the pancreas to islet beta cells?

Answer 81

Pdx1, Ngn3, MafA

Question 82

If a cis-regulatory element is deleted from a gene, what happens to its effect on transcription?

Answer 82

it is eliminated