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Molecular Biology 1 > Dr Hack's Lectures 2 > Flashcards

Dr Hack's Lectures 2 Flashcards

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1
Q

What controls cAMP concentration?

A

glucose

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2
Q

what does cAMP bind to?

A

catabolite activator protein (CAP)

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3
Q

why is the lac promoter weak?

A

sequences at -10 and -35 are non-standard

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4
Q

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

A

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

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5
Q

in what scenario is the lac operon transcribed?

A

CAP-cAMP binds to DNA

Lac repressor does not bind to DNA

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6
Q

What do catabolic operons contain genes for?

A

breakdown of metabolites

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7
Q

when are biosynthetic operons turned on?

A

when supply of end product is low

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8
Q

what does the trp operon contain genes for?

A

The biosynthesis of Tryptophan (an amino acid)

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9
Q

When does tryptophan repressor protein repress transcription of trp operon?

A

When tryptophan conc. in cell is HIGH

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10
Q

How does tryptophan stop transcription of trp operon?

A

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

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11
Q

Is the trp operon the same as the lac operon?

A

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

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12
Q

What bacteria does Euprymna scolopes have a symbiotic relationship with?

A

Vibrio fischeri

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13
Q

When does bioluminescence occur?

A

when the bacteria are at high density

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14
Q

How is density measured and under which operon?

A

Quorum sensing, the lux operon

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15
Q

What signals cell density?

A

Acyl homoserine lactones (AHL)

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16
Q

what protein catalyses synthesis of AHL?

A

LuxI

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17
Q

How do bacteria use AHL?

A

They take up AHL from the cytosol

They produce AHL

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18
Q

What does AHL bind to and when?

A

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

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19
Q

What does LuxR do?

A

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

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20
Q

Where is the lux box in DNA?

A

next to lux promoter P

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21
Q

What kind of feedback does quorum sensing produce?

A

positive feedback - the system increases its own activity

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22
Q

What are other examples of quorum sensing?

A

‘Milky seas’
Biofilm formation
Pathogenic bacteria

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23
Q

Define genomics

A

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

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24
Q

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

A

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

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25
Q

Where does the extra DNA come from within genes?

A

Introns

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26
Q

Where does the extra DNA come from between genes?

A

repetitive DNA

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27
Q

How are introns removed?

A

RNA Splicing

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28
Q

How is a lariat formed?

A

5’ cut, formation of loop with tail

3’ cut, joining of exons

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29
Q

What is intron excision catalysed by?

A

Spliceosomes

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30
Q

What do spliceosomes contain?

A

small, nuclear ribonucleoprotein complexes (snRNPs)

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31
Q

Where do snRNPs bind?

A

primary transcript

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32
Q

What is the lariat loop bond?

A

5’-2’ phosphodiester bond

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33
Q

what does alpha tropomyosin do?

A

helps regulate muscle contraction

stabilises actin filaments in cytoplasm

34
Q

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

A

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

35
Q

What is repetitive DNA?

A

DNA that occurs in many copies in the genome

36
Q

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

A

> 50%

37
Q

What are simple sequence repeats?

A

tandem arrays of very short sequences, eg. CACACACACACA

38
Q

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

A

~5%

39
Q

What is a transposon? Why is duplication so slow?

A

Mobile DNA elements, slow because it may cause mutations

40
Q

What are the two classes of transposons?

A

LINEs and SINEs

41
Q

What is the estimated current transposition rate in humans?

A

1 insertion for every 20-200 births

42
Q

What are Alu elements? How big are they?

A

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

43
Q

What does Alu transposition depend on?

A

They are non-autonomous and depend on LINE elements

44
Q

What is the current estimated transposition rate for Alu elements?

A

1 insertion for every 20 births

45
Q

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

A

5 genes and 1 non-functional pseudogene

46
Q

How has the gene cluster evolved?

A

gene duplication

47
Q

What is synteny?

A

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

48
Q

What are the ends of chromosomes called?

A

Telomeres

49
Q

What is the basic building block of chromatin?

A

nucleosomes

50
Q

What are the copies of the histones called?

A

H2A, H2B, H3 and H4

51
Q

What charge is a histone?

A

positive

52
Q

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

A

euchromatin

53
Q

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

A

heterochromatin

54
Q

The structure of expressed genes is more ______ than others

A

open

55
Q

How is the more open structure observed?

A

greater sensitivity to DNase

56
Q

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

A 
Histone modification (via acetylation)
Chromatin remodelling complexes
57
Q

What does RNA polymerase 1 transcribe?

A

ribosomal RNA genes

58
Q

What does RNA polymerase 2 transcribe?

A

genes coding for proteins

59
Q

What does RNA polymerase 3 transcribe?

A

genes coding for small RNAs

60
Q

Name two basal factors needed for transcription by RNA polymerase 2

A

TFIIA, TFIIB etc

61
Q

Where does transcription in eukaryotes start?

A

TATA box

62
Q

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

A

TATA box binding protein, binds DNA by 70 degrees

63
Q

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

A

TFIID - TAFs must also be bound

64
Q

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

A

TFIIF

65
Q

What does TFIIH do?

A

Phosphorylates Pol 2

66
Q

What does a cis-regulatory element do?

A

Increase/decrease basal level of transcription

Specify how gene expression responds to a particular signal

67
Q

What does the metallothionein gene do?

A

Bind toxic metal ions

Store Zn2+

68
Q

What induces transcription in humans?

A

Metal (Zn2+ ions)

Glucocorticoid hormone

69
Q

Which cis-regulatory elements increase expression?

A

GC box
BLE
TRE
E-box

70
Q

What are the response elements?

A

GRE

MRE

71
Q

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

A

cortisol - enters the cell and exerts its effects directly

72
Q

What does cortisol bind to?

A

glucocorticoid receptor (GR)

73
Q

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

A

Hsp90 - chaperone protein

74
Q

What are steroid hormone receptors?

A

Zinc finger proteins

75
Q

What does AP1 do?

A

Increases general chromatin accessibility

76
Q

When not bound, where is the activator protein?

A

Cytosol

77
Q

What do fibroblast cells differentiate into?

A

Muscle cells

78
Q

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

A

MyoD, myogenin, Myf5, Mrf4

79
Q

What are Somites?

A

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

80
Q

What TF can reprogram fibroblasts into iPS celsl

A

Oct4, Sox2, Klf4, Myc

81
Q

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

A

Pdx1, Ngn3, MafA

82
Q

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

A

it is eliminated

Molecular Biology 1 (3 decks)

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