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Biology - Year 1 > Molecular Biology and Genetics > Flashcards

Molecular Biology and Genetics Flashcards

0
Q

What does DNA ligase do?

What are Okazaki fragments?

A

Joins Okazaki fragments

Short sequences of DNA sequenced on the anti
parallel DNA stand.

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1
Q

What does DNA polymerase do?

A

Adds deoxynucleotide triphosphate groups to create a new DNA strand.

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2
Q

What does helicase do?

What do topoisomerases do?

What does the (PCNA) sliding clamp do?

What does primase do?

A

Separates DNA

Relieves twists in DNA

Holds polymerase to DNA

Synthesises RNA primers

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3
Q

What are the types of regulatory RNAs? What do they do?

A

microRNA (miRNA) - acts through RNA interference. Regulates gene expression. Single strand and very small.
small interfering RNAs. Act through RNA interference. Regulate gene expression. Double stranded and very small.

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4
Q

What are the secondary structures formed by RNA?

Give an example of a tertiary structure formed by RNA.

A

Loops and hairpins

Pseudoknot

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5
Q

How big is a ribosome in eukaryote? How big are all it’s component parts?

How big is a ribosome in a prokaryote? How big are all it’s component parts?

A 
80s
Large subunit (60s) made of 5s, 5.8s and 28s
Small subunit (40s) made of 18s
70s
Large subunit (50s) made of 5s and 23s
Small subunit (30s) made of 16s
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6
Q

What’s a TATA box?

A

A regulatory region that initiates the synthesis of a new polypeptide/ protein

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7
Q

What are the stages of transcription?

A

Initiation

Elongation

Termination

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8
Q

What is a mutation?

What is a transition mutation?

What is a transversion mutation?

A

Heritable change in the nucleotide sequence of DNA molecule

When a purine is replaced by a purine and vise versa.

When a purine changes to a pyrimadine and vise versa.

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9
Q

When considering mutations what is a reversion?

What is a suppression? What are the two types?

A

Genotype restored, e.g. mutation that produces synonymous codon

Restoration of phenotype by a second unrelated mutation.
Extragenic suppression - another gene is mutated to compensate for, or suppress the original mutation
Intragenic suppression - a second mutation occurs in the same gene to suppress the effect of the first mutation

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10
Q

When lactose is present how many transcription factors are bound to the lac operon?

A

1

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11
Q

When both lactose and glucose are present how many transcription factors are bound to the lac operon promoter region?

A

0

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12
Q

When e.coli is grown on a mixture of lactose and glucose which is used first?

A

Glucose

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13
Q

In the presence of L-arabinose and absence of glucose which transcription factors are bound to the upstream promoter region of an E.coli arabinose operon.

A

AraC and CRP

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14
Q

What are snRNA’s?

What are snoRNA’s?

What are scaRNA’s?

A

Small nuclear RNA’s - function in splicing of pre-mRNA

Small nucleolar RNA’s - process and chemically modify rRNA.

Small cajal RNA’s - modify snoRNA and snRNA

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15
Q

Does DNA or RNA polymerase need a primer?

Which has a higher error rate RNA or DNA polymerase? Why can it afford more error?

What is the combined error rate for DNA replication?

A

DNA polymerase does, RNA polymerase doesn’t

RNA polymerase but RNA doesn’t affect a cells viability so can afford error, faulty proteins can be removed faulty DNA can lead to cell death.

1 in 10^9

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16
Q

What are three types of RNA processing?

A

5’ capping - a 7methylguanosine cap is added which protects degradation and aids export

Polyadenylation of 3’ tail - protects degradation and aids export

Introns are also spliced out

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17
Q

How does splicing aid evolution?

A

Splicing can yield multiple proteins from the same gene increasing the coding potential of the genome

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18
Q

What is DNA base excision repair?

What is nucleotide excision repair?

A

Where a base is removed and replaced

Where a stretch of DNA around the damage is removed and replaced

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19
Q

If glucose is transported in a bacteria what happens to adenylate cyclase?

What happens when a cell runs out of glucose?

What is the CRP, what does it do?

A

It’s inhibited and cyclic AMP cannot be generated

Adenylate cyclase is activated and cyclic AMP is produced

Cyclic AMP receptor protein, acts positively as a transcriptional activator

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20
Q

What is AraC? What does it do?

A

AraC is a dimer and a specific regulator, in the presence of arabinose it adopts a rigid structure and binds to L1 and L2 and contacts RNA polymerase starting transcription

If arabinose is absent, the dimer AraC protein represses the structural gene by binding to stuff and forming a loop. The loop prevents RNA polymerase from binding to the promoter of the ara operon, thereby blocking transcription.

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21
Q

What happens if trp is present?

What happens if no trp is present?

A

Trp binds to the repressor allow it to bind to he operator and stop transcription

The repressor is not activated

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22
Q

Why does DNA have thymine instead of uracil?

What is cytosine deamination?

A

Because if uracil was in DNA the cells repair system would not be able to distinguish deaminated cytosine form uracil.

A type of chemical modification where cytosine is converted to uracil

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23
Q

What are levels of control of gene regulation in bacteria?

What effect do these levels of control have on levels of protein?

A 
Transcription initiation
Transcription termination
Translation initiation
Translation elongation rate
Translation 'frameshifting'
Rate of RNA 'turnover'
Rate of protein 'turnover'
Modification of protein activity

Levels of control helps determine the concentration of active protein in a cell

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24
Q

Describe a typical bacteria promoter?

A

Comprised of two conserved hexanucleotide ‘boxes’, this consensus promoter sequence is recognised by a sigma factor

25
Q

What is a bacterial operon?

A

Two or more genes transcribed as single mRNA molecule (a polycistronic mRNA)

26
Q

There are two modes of regulation of the trp operon.
How is transcription initiation controlled?

How is transcription termination controlled?

A

By the Trp repressor protein

Attenuation of transcription of trp operon (regulation of transcription termination) relies on the coupling of transcription and translation

27
Q

In the recombination of bacteria, what is a holiday junction?

A

The position that is formed when a recombination intermediate is rotated

28
Q

When looking at DNA recombination what is transposition?

A

Also called non-homologous or illegitimate recombination. Doesn’t require sequence similarity between the two DNA molecules

29
Q

What is a cosmid?

A

A type of plasmid used to clone large gene fragments

30
Q

What is heterochromatin?

What is euchromatin?

A

Tightly packaged DNA, genes inactive

DNA not as compact, genes active, DNA and RNA polymerase can bind

31
Q

What is chromatin?

What is heterochromatin?

What is euchromatin?

A

DNA + histone proteins

Highly packaged inactive genes

Not as compact, active genes

32
Q

What dimers make up a nucleosome?

What does H1 do?

A

Two lots of H2A, H2B, H3 and H4

Link nucleosomes

33
Q

What are the levels of DNA packaging?

A

10nm fibre ‘beads on a string’

30nm fibre

300nm fibre (loops)

700nm chromatid

1400nm chromosomes

34
Q

What type of modification activates genes?

What types of modification (usually) inactivates genes?

A

Histone acetylation

Histone methylation and histone phosphorylation

35
Q

What percentage of the genome codes for genes and related sequences?

What percentage of the genome codes for protein?

A

25%

2%

36
Q

What percentage of the genome codes for pseudogenes?

What percentage of the genome codes for repetitive sequences?

A

23%

55%

37
Q

What are homologues?

What are orthologues?

What are paralogous genes?

A

Genes with similar sequences

Derived from a common ancestor gene but in different species

Derived from a common ancestral gene but in the same species

38
Q

What is the name of factors that bind close to the promoter?

What is the name of factors that behind further away from the promoter

A

Proximal factors

Distal factors

39
Q

What does constitutive expression mean?

A

The gene is always being expressed (is on all the time)

40
Q

Describe a lysogenic bacteria.

A

When a bacteriophage injects its DNA into a bacteria instead of replicating the DNA intergrates into the bacterial chromosome and forms a lysogen cell, this can remain dormant for years

41
Q

When considering horizontal gene transfer in bacteria, what do the the following mean?

Conjugation

Transduction

Transformation

A

Plasmid mediated transfer (cell-to-cell)

Phage mediated transfer

Uptake of ‘naked’ DNA

42
Q

Are TATA boxes present in all protein coding genes?

A

No some gene have housekeeping genes or initiator factors instead

43
Q

What domain of RNA polymerase 2 must be phosphorylated for transcription to begin?

A

C terminal domains

44
Q

What do reporter gene assays test for?

What do EMSAs test for?

A

Transcription activity

Directly show binding of nuclear proteins to a specific part of the promoter

45
Q

What DNA binding domain is found in nuclear receptors?

A

Zinc finger

46
Q

What are the four main types of DNA binding domain?

A

Helix-turn-helix

Zinc-finger

Leucine zipper

Basic helix-loop-helix

47
Q

What are the two genes involved in X inactivation?

What is the mechanism for X inactivation in females?

A

Xist and Tsix

  1. During early development XIC centers pair
  2. Xist is transcribed on one chromosome and Tsix on another
  3. Xist produces a long non-coding RNA which coats the X chromosome and causes it to condense (and so not be expressed)
48
Q

What is the pseudoautosomal region on the X and Y chromosome?

A

A short region that is homologous on both the X and Y chromosome and allows for recombination

49
Q

What is a mutation, what is a polymorphism and how are they different?

A

A mutation is rarer and is a change in the base sequence that has a deleterious (harmful/ damaging) effect on function

A SNP (single nucleotide polymorphism) has a small/ no effect on genetic function and so is more common

50
Q

What does the abbreviation dATP stand for?

What does it do?

A

2’-deoxyandenosine-5’-triphosphate

Used in DNA synthesis as a substrate of DNA polymerase

51
Q

What is the difference between a nucleotide and nucleoside?

A

A nucleotide consists of a nitrogenous base a sugar and a phosphate group. A nucleoside consists of a nitrogenous base attached to a sugar but without a phosphate group

52
Q

How many copies of rRNA genes are there in the human genome?

A

200

53
Q

What type of bond links phosphate groups?

How many rings do purines have?

How many rings do pyimidines have?

A

Phosphoester bond

2

1

54
Q

What’s the error rate of RNA polymerase?

A

1 in 10^4

55
Q

What is the name of the enzyme that adds amino acids to tRNA?

What type of bond is created between the tRNA and amino acid?

A

Aminoacyl-tRNA synthetase

High energy ester bond

56
Q

What stabilises a proteins 3D structure?

What type of interactions help form the tertiary structure of proteins?

A

Interactions (mostly noncovalent) between amino acids

Hydrophobic interactions by non-polar side groups and H-bonds by polar groups

57
Q

What sort of damage to DNA can UV light cause?

What is the difference between a missense and a nonsense mutation?

A

The formation of pyrimidine dimers

Misssense is where one a change in the base sequence produces another amino acid
A nonsense mutation is where a change in the base sequence produces a stop codon

58
Q

What happens to RNA polymerase if there is a high tryptophan concentration?

What happens to RNA polymerase if there is a low Trp content?

A

The ribosome covers region 2 of the Trp operon, a 3-4 stem loop forms and transcription terminates

RNA polymerase is stalled at region 1, a 2-3 step loop forms and RNA polymerase continues transcription

59
Q

At what stage of cell replication does DNA condense into visible chromosomes?

A

Prophase

60
Q

How big are micro satellites?

How big are mini satellites?

How big are satellites?

A

2-4 bp

15-35 bp

36+ bp

61
Q

What do linkage analyses study?

What do association studies look at?

A

Affected siblings

Unrelated cases/ controls

Biology - Year 1 (6 decks)

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