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Year 2 > Molecular Cell Biology > Flashcards

Molecular Cell Biology Flashcards

1
Q

Which form of DNA does the majority occur in?

A

B form

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2
Q

What are the characteristics of the B form of DNA? (3)

A

The number of base pairs per turn of the helix can be altered
The helix in the cell is not straight, but rather coiled in 3D space
There are certain sequence features where bends occur

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3
Q

What is positive supercoiling?

A

When additional turns are introduced into the DNA helix (the twist is the same direction as the turn of the helix)

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4
Q

What is negative supercoiling?

A

When turns are removed from the DNA helix (the twist is the opposite direction as the turn of the helix)

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5
Q

What causes torsional stress of DNA?

A

DNA is coiled in 3 dimensions

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6
Q

How is the torsional stress of DNA accommodated? (2)

A

Formation of super helices

Altering number of base pairs per turn of helix

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7
Q

What is the linking number?

A

The total number of times that the two strands of the double helix of a closed molecule cross each other when constrained to lie in a plane

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8
Q

What do type one topoisomerases do?

A

They break one strand of the DNA, pass the other strand through the gap and seal the break

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9
Q

How much do type one topoisomerases change the linking number by?

A

Plus or minus one

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10
Q

What do type two topoisomerases do?

A

They break both strands of DNA, and pass another part of the helix through the gap

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11
Q

How much do type two topoisomerases change the linking number by?

A

Plus or minus two

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12
Q

What is a genomic island?

A

Horizontally acquired genomic regions that may have mutated to mask or destroy their modes of transmission and integration

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13
Q

Which is the main DNA replication enzyme?

A

DNA polymerase three

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14
Q

Which polymerase has a role in the removal of RNA primers from Okazaki fragments

A

DNA polymerase one

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15
Q

What is a replicon?

A

The basic unit of replication; a DNA molecule or sequence which has a functional origin of replication

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16
Q

What controls whether a round of replication is initiated?

A

When Dam methylase has methylated all 14 copies of GATC in oriC

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17
Q

How do terminators (ter sites) arrest the replication fork in only one direction?

A

ter sites bind a specific terminator protein, Tus. This interacts with and halts a replication in only one direction

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18
Q

Which are the two general classes of DNA damage?

A

Single base changes

Structural distortions

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19
Q

Name five DNA repair processes:

A 
Direct repair
Mismatch repair
Excision repair
Tolerance systems
Retrieval systems
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20
Q

Which repair process is photoreactivation an example of?

A

Direct repair

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21
Q

In photoreactivation, which enzyme binds to pyrimidine dimers in the dark?

A

(Deoxyribopyrimidine) photolyase

22
Q

Uracil DNA glycosidase is an enzyme involved in which DNA repair process?

A

Mismatch repair

23
Q

Which are the three modes of excision repair?

A 
Very short patch (between bases)
Short patch (20 nucleotides)
Long patch(1,500-10,000 bps)
24
Q

Which enzyme do short and long patch repair utilise?

A

Repair endonuclease

25
Q

What is the SOS response?

A

An expression of large number of diverse unliked genes involved in DNA repair, activated if E.coli is exposed to severe DNA damage

26
Q

What represses the genes and operons under SOS control?

A

Binding of LexA to the LexA boxes

27
Q

When RecA responds to DNA damage, which activities are induced?

A

Inhibition of 3’-5’ editing in DNA pol 3
Interacts with LexA, a repressor, which then autocleaves the dimerisation domain from the DNA binding domain and becomes inactive which activates the SOS response.
sulA expression inhibits cell division; cells become filamentous

28
Q

What are transposible genetic elements?

A

Specific DNA sequences which are capable of transferring copies of themselves to other parts of the same DNA molecule, to other DNA
molecules, or of altering their orientation within a DNA molecule

29
Q

What are insertion sequences?

A

Small components of bacterial chromosomes and plasmids:
Encode the protein(s) needed for transposition
Always bounded by inverted repeats
Cause direct repeats to occur at the site of insertion

30
Q

What do transposons (usually) encode?

A

Phenotypic characteristics such as drug resistance

31
Q

What are the four stages of transcription?

A

Template recognition
Initiation
Elongation
Termination

32
Q

What are the two general transcriptional mechanisms for the control of gene expression?

A

Induction

Repression

33
Q

What’s induction?

A

The switching on of genes when they are required

34
Q

What’s repression?

A

The switching off of genes when they are not required

35
Q

What is the name for genes that are always expressed?

A

Consititutively expressed

36
Q

What are repressors?

A

Regulatory proteins which prevent transcription when bound to the DNA

37
Q

What are activators?

A

Are regulatory proteins which must be bound for transcription to occur

38
Q

What are inducers?

A

They activate activators or inactivate repressors

39
Q

What are compressors?

A

They activate repressors or inactivate activators

40
Q

What is a regulon?

A

A collection of co-regulated genes all regulated by a single regulatory protein

41
Q

What does lacZ encode and what does the protein do?

A

β-galactosidase, which cleaves β-galactosides to their

constituent monosaccharides

42
Q

What does lacY encode and what does the protein do?

A

β-galactoside permease, a cytoplasmic membrane protein

which facilitates entry of β-galactosides into the cell

43
Q

What does lacA encode and what does the protein do?

A

β-galactoside transacetylase, which is thought to detoxify

toxic β-galactosides by acetylation

44
Q

What is quorum sensing?

A

The regulation of gene expression response to fluctuations in cell population density

45
Q

What are biofilms?

A

Structured clusters of cells, enclosed in a self-produced polymer matrix and attached to a surface

46
Q

Give three characteristics of biofilms:

A

Cells enclosed in polymer matrix of exopolysaccharides,
proteins and nucleic acid
Formation initiated by extracellular signals present in the
environment
Biofilm protects bacteria against the host immune response,
desiccation and biocides

47
Q

What are the five stages of biofilm development?

A
  1. Initial attachment
  2. Irreversible attachment
  3. Maturation 1
  4. Maturation 2
  5. Dispersion
48
Q

Are genes generally expressed in condensed or uncondensed chromatin?

A

Uncondensed

49
Q

Who won the rugby world cup in 1999?

A

Australia

50
Q

What does the addition of methyl groups do to chromatin structure?

A

Condenses it

51
Q

What does the addition of phosphate groups next to a methylated amino acid do to the chromatin structure?

A

Loosens it

Year 2 (5 decks)

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