Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCD Year 1 > Nucleic Acids and Gene Expression > Flashcards

Nucleic Acids and Gene Expression Flashcards

1
Q

What is a nucleotide made up of?

A

Nitrogenous base + Sugar (Deoxyribose) + Phosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What sugar is present in RNA?

A

Ribose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What bases are purines?

A

Adenine and Guanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What bases are pyrimidines?

A

Cytosine, Thymine and Uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What bases makeup RNA

A

A, C, U and G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is a nucleoside made up of?

A

Nirogenous base + Sugar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What does DNA helicase do?

A

Uses ATP to provide energy to break hydrogen bonds to unzip DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What does DNA polymerase do?

A

Synthesises a new strand of DNA. It cannot initiate replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Which direction is DNA synthesised in?

A

5’ to 3’ direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the leading strand?

A

DNA strand that is continuously synthesised

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the lagging strand?

A

Strand of DNA that is synthesised in Okazaki fragments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What does DNA ligase do?

A

Joins Okazaki fragments to the previous one

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What does DNA primase do?

A

Synthesises a short fragment to initiate DNA replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What enzyme proof-reads the DNA and removes any incorrect bases?

A

DNA polymerase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Where does DNA replication start in E.coli?

A

Ori.C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How long is M phase

A

1 hour

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How long is G1 phase?

A

10 hours

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How long is S phase and what occurs here?

A

9 hours, DNA synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How long is G2 phase?

A

4 hours

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is G1 phase prior to?

A

S phase (DNA synthesis)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is G2 phase between?

A

Synthesis and mitosis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What cells are in G0 phase

A

Cells that no longer divide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Are the chromosomes visible in interphase?

A

No

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What occurs in prophase?

A

Chromosomes condense and each contain two sister chromatids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What occurs in metaphase?

A

Condensed chromosomes align on central plane of spindle of microtubules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What occurs in anaphase?

A

Sister chromatids separate and are pulled to spindle poles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What occurs in telophase?

A

Sister chromatids move to opposite poles of spindle

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What occurs in cytokinesis?

A

Division of cytoplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What occurs in G1 interphase?

A

The condensation process is reversed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is the difference between DNA and RNA

A

RNA has ribose instead of deoxy ribose

RNA has uracil instead of thymine and is usually single standed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What is synthesised by RNA polymerase I?

A

rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is synthesised by RNA polymerase II?

A

mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is synthesised by RNA polymerase III?

A

tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is the sequence in DNA that brings about transcription?

A

Promoter regions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Is mRNA produced the same as the sense or antisense strand?

A

Sense

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Ribonucleotide bases are joined together with what bond?

A

Phosphodiester bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What transcription factor activates gene expression?

A

Transcription activators

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What is transcription repressors and what does it do?

A

Transcription factor that suppresses gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What is the first protein to bind in the basal transcription complex?

A

Transcription complex II D (TFIID)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Which transcription factor binds to TFIID and RNA polymerase II

A

TFIIB

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What does NFκB transcribe?

A

Cytokines for inflammation

42
Q

How does aspirin stop inflammation?

A

Inhibits the breakdown of IκB so NFκB remains in the cytoplasm and is unable to initiate transcription of cytokines

43
Q

How many types of RNA polymerase do bacteria have?

A

One

44
Q

What is heterogenous nuclear RNA?

A

pre-mRNA

45
Q

Are introns or exons used to transcribed the final RNA?

A

Exons

46
Q

What sequence do introns start and end with?

A

Start with GU

End with AG

47
Q

What is the splice donor sequence?

A

AGGU

48
Q

Explain the process of removal of introns?

A

1) U1 binds to the splice donor sequence (AGGU)
2) U2, U4 and U6 bind to the intron
3) U5 binds to the splice acceptor site Pyr15NCAG
This completes formation of the spliceosome and causes cleavage of the sequence at the end of the exon and beginning of the intron
4) Free end of intron folds back to specific A in the intron known as the branchpoint
5) The branch results from a phosphodiester bond between 5’ phosphate on G and the 2’ OH of A creating a loop
6) Phosphodiesterase bond between G at the end of the intron and next exon is cleaved and the intron is removed as “lariat” structure
7) The exposed, adjacent exon sequenced are finally ligated together

49
Q

What is the first post-transcriptional modification of RNA?

A

Addition of a 5’ cap

50
Q

Explain the process of addition of a 5’ cap?

A

1) Hydrolysis of the triphosphate on the 5’ end of the mRNA to form a diphosphate (by a phosphatase enzyme)
2) The diphosphate reacts with the α-phosphate of GTP, to form a 5’-5’ phosphate linkage (by guanylyltransferase)
3) The cap if further modified at N7 position in the purine ring to form 7-methyl guanylate cap (by methyl transferase)
Cap protects mRNA at 5’ end and greatly enhances translation

51
Q

What enzyme causes hydrolysis of the triphosphate on the 5’ end of the mRNA?

A

A phosphatase enzyme

52
Q

What enzyme forms a 5’-5’ phosphate linkage by reacting the diphosphate with the α-phosphate of GTP?

A

Guanylyltransferase

53
Q

What enzyme modifies the 5’ cap at the N7 position in the purine ring to form 7-methyl guanylate cap?

A

Methyl tranferase

54
Q

How does polio take over the nervous system and cause paralysis in hours?

A

Makes an enzyme that cleaves the 5’ cap and replaces it with its own so it is no longer a template for translation

55
Q

What enzyme ligates together adjacent exons?

A

Ligase

56
Q

What is the splice donor sequence?

A

AGGU

Ends the exon and starts the intron

57
Q

What is the splice acceptor sequence?

A

Pyr15NCAG

Ends the intron

58
Q

What is the process of adding the poly-A tail?

A

1) RNA polymerase reaches the end of the gene it is transcribing and recognises a sequence in the genome
2) RNA binding proteins that travel with RNA polymerase recognise this, in particular, Cleavage Stimulating Factor (CstF) and Cleavage and Polyadenylation Specificity Factor (CPSF).
3) Once the bind to a specific sequence, additional proteins assemble to create the 3’ end of the mRNA.
4) Poly-A polymerase (PAP) adds (one at a time) 200 A nucleotides to the end of the mRNA sequence

59
Q

What is CstF?

A

Cleavage Stimulating Factor

60
Q

What is CPSF?

A

Cleavage and Polyadenylation Specificity Factor

61
Q

What is PAP?

A

Poly-A Polymerase

62
Q

What causes β-thalassaemia?

A

A relative deficiency of β-chains.
Several types of β-thalassaemia feature splice site mutations in the β-globin gene
The intron cannot be spliced so mature mRNA is not formed and translation of a non-functional occurs

63
Q

What is Thalassaemia?

A

A genetic, haematological disease in which there is an imbalance in the relative amounts of α-chains and β-chains making up haemoglobin

64
Q

What does microRNA do?

A

Control the translation of most genes

65
Q

What does siRNA/RNAi do?

A

Viral defence, experimental tool

66
Q

What does piRNA do?

A

Clearly important for germ cell production

67
Q

What does long ncRNA do?

A

Xist- Important for X chromosome inactivation

68
Q

What is lyonisation?

A

The process where one of the female X chromosomes is inactivated. It is packaged so it has transcriptionally inactive heterochromatin. The choice of which X chromosome is inactivated is random.

69
Q

What is a codon?

A

A group of three nucleotides

70
Q

Protein synthesis always starts with what?

A

Met = AUG

71
Q

What are the stop codons?

A

UAA, UAG, UGA

72
Q

What is the typical structure of mRNA?

A

5’ cap - 5’ UTR - Coding Region - 3’ UTR - poly A

73
Q

What is the cap in mRNA?

A

7-methyl guanosine

74
Q

What is “wobble” with regard to translation?

A

The first two bases in a codon are really important with respect to binding energy of mRNA. The wobble is the third base which has a lower binding energy so may accept a different base, resulting in a different primary sequence

75
Q

What is stringency?

A

The conditions in a reaction (temperature, salt and pH) that dictate the annealing of single-stranded DNA.
High stringency only allows duplexes to form between strands with perfect complementarity
Lower stringency allows annealing between strands with some degree of mismatching

76
Q

What is a hybridisation probe?

A

A fragment of DNA or RNA of variable length (usually 100-1000) bases long) which is radioactively labelled. It can then be used in DNA or RNA samples to detect the presence of nucleotide sequences.
The probe hybridises to single-stranded nucleic acid (DNA or RNA) whose base sequence allows probe-target base pairing due to complementarity between probe and target

77
Q

Explain the process of hybridisation and blotting?

A

The labelled DNA or RNA probe is first denatured (by heating or alkaline conditions such as sodium hydroxide) into single stranded DNA (ssDNA) and then hybridised to the target ssDNA (Southern Blotting) of RNA (Northern Blotting) immobilised on a membrane or in situ

78
Q

The energy needed to denature the probe DNA is performed to disrupt the hydrogen bonds between the bases. What does this depend on?

A

Strand length
Base composition
Chemical environment

79
Q

Why does probe DNA strand length affect the energy require to denature it?

A

A longer strand has more hydrogen bonds to break

80
Q

Why does probe DNA base composition affect the energy required to denature it?

A

G-C pair has one more hydrogen bond than A-T so it is harder to break

81
Q

How many hydrogen bonds to A-T make?

A

2

82
Q

How many hydrogen bonds do G-C make?

A

3

83
Q

Why does the chemical environment affect denaturing of a chemical probe?

A

Monovalent cations (Na+) stabilise the DNA duplex by neutralising the charge on phosphate backbone. Denaturants (formaldehyde/urea) destabilise the DNA duplex, so less energy is required for separation

84
Q

What does the melting temperature of a nucleic acid show?

A

The midpoint temperature of transition from double stranded to single stranded forms of nucleic acid (half denaturation point)

85
Q

What is the melting temperature of mammalian genomic DNA?

A

∼87°C

86
Q

Exactly complementary sequences will hybridise at higher or lower temperatures or salt than sequences which are not exactly complimentary and have base mismatches?

A

Higher temperatures

Lower salt

87
Q

What polymerase enzyme is used in PCR?

A

Taq DNA polymerase

88
Q

What temperatures is PCR performed at?

A

Denature= 94°C
Anneal=50-60°C
Extend=72°C

89
Q

What length primer should you use for PCR?

A

About 20 nucleotides for a complex genomic DNA target

90
Q

What base composition should you use in a primer for PCR?

A

Avoid tandem repeats (can form hair pins)

%G-C and length should give an equal Tm for each primer (otherwise one may bind without the other)

91
Q

What consideration should you give to the 3’ end of a primer for PCR?

A

Avoid complementarity of the bases at the 3’ end. Primer dimers may result causing non-productive amplifications (the primers are then extended instead of the sequence)
Unimportant at the 5’ end because polymerisation proceeds 5’-3’

92
Q

What do type II restriction endonucleases do?

A

Cleave DNA at specific palindromic sequences, usually about 4-8bp long

93
Q

What ends do restriction enzymes produce after cleaving DNA

A

Blunt of sticky ends

94
Q

Explain the principle of electrophoresis

A

DNA phosphate backbone has a negative charge, so moves towards the anode (+) when an electrical force is applied.
When forced to move through a porous gel matrix (agarose/polyacrylamide gel) small fragments travel faster than larger ones
After resolution, DNA can be isolated from the gel or transferred to a membrane to form a replica for hybridiation

95
Q

What solid support would target DNA be immobilised on during nucleic acid blotting?

A

Nylon of nitrocellulose membrane which readily binds single-stranded nucleic acid

96
Q

What would be used to label the probe that will hybridise with the DNA to give exposure on a photographic film during nucleic acid blotting?

A

Radioactive or fluorescent labelling

97
Q

What is a Southern blot hybridisation?

A

DNA target and DNA probe

98
Q

What is a Northern blot hybridisation?

A

RNA target and DNA probe

99
Q

What is a Colony blot hybridisation?

A

Bacterial DNA target and DNA probe

100
Q

What is a tissue in situ hybridisation?

A

Chromosome target and DNA probe

101
Q

What is a reverse hybridisation?

A

Microarrays (Immobilised DNA or oligonucleotide probe, target DNA solution)

102
Q

What is a chromosome in situ hybridisation used for?

A

Used to locate specific genes on chromosomes using fluorescently labelled DNA probes

MCD Year 1 (10 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions