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MBChB Year 1 Principles Biochemistry > Biochemistry of Nucleic Acids > Flashcards

Biochemistry of Nucleic Acids Flashcards

1
Q

What is a nucleoside?

A

Base and sugar (ribose in RNA, deoxyribose in DNA)

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2
Q

What is a nucleotide?

A

Nucleoside and phosphate group(s)

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3
Q

What are the 4 bases in DNA?

A

Adenine, thymine, guanine and cytosine

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4
Q

What are the 4 bases in RNA?

A

Adenine, URACIL, guanine and cytosine

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5
Q

What are the 5 bases’ associated nucleosides?

A 
Adenine - adenosine
cytosine - cytidine
guanine - guanosine
thymine - thymidine
uracil - uridine
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6
Q

What are the 4 DNA building blocks?

A

dATP, dCTP, dGTP, dTTP

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7
Q

What are the 4 RNA building blocks?

A

ATP, CTP, GTP, UTP

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8
Q

Where is a phosphodiester bond formed between?

A

3’ OH group and 5’ triphosphate - consumes 2 high energy bonds

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9
Q

What end of the DNA strand are new nucleotides added to?

A

Free 3’ end

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10
Q

Why does DNA have to be replicated before mitosis?

A

So that the daughter cells have a complete complement of the genome

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11
Q

Is replication conservative or semi-conservative?

A

Semi-conservative

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12
Q

What catalyses DNA replication?

A

DNA polymerase - also require an RNA primer to start the replication

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13
Q

How many origins of replication are there?

A

Several as replication starts simultaneously at several points in the genome to allow it to happen fast enough

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14
Q

What DNA strand has the free 3’ end?

A

Leading strand

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15
Q

What DNA strand is replicated discontinuously?

A

The lagging strand - segments are Okazaki fragments

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16
Q

What are the steps to DNA replication?

A

Helicase unwinds DNA (and stops it rewinding)
Primase synthesises an RNA primer
There is a replication fork with a leading (3’-5’) and a lagging (5’-3’) template strand
DNA polymerase synthesises a complementary DNA strand
The lagging strand is replicated as Okazaki fragments (more complex)
RNA primers are degraded
Gaps are filled by DNA polymerase

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17
Q

What activity does DNA polymerase have?

A

3’-5’ exonuclease activity - removes any incorrect nucleotides (repair system)

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18
Q

What are the main features of RNA?

A

Single stranded, local stretches of intramolecular base-pairing (stem-loops), ribose sugar and uracil not thymine

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19
Q

What are the 3 main classes of RNA?

A

Ribosomal RNA, messenger RNA, transfer RNA

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20
Q

What is the role of rRNA?

A

Combines with proteins to form ribosomes (for protein synthesis) - stable RNA

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21
Q

What is the role of tRNA?

A

Carries amino acids to be incorporated into the protein - stable RNA

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22
Q

What is the role of mRNA?

A

Carries the genetic information for protein synthesis

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23
Q

How many nucleotides does the anticodon of tRNA have?

A

3

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24
Q

How many types of RNA polymerase do eukaryotes have? What are they?

A

3 - Pol I, Pol II, Pol III

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25
Q

How are RNA polymerases distinguished?

A

Their sensitivity to toxins like a-amantin (from fungi)

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26
Q

What RNA polymerase synthesises all mRNA?

A

Pol II

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27
Q

What does the binding of RNA polymerase do?

A

Detects the initiation sites (promoters) on DNA

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28
Q

What does the binding of RNA polymerase require?

A

Transcription factors

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29
Q

Why is DNA chain separation necessary?

A

To gain access to the nucleotide sequence

30
Q

What is transcription initiation?

A

Selection of the first nucleotide of the growing RNA

31
Q

What is elongation?

A

Addition of further nucleotides to the RNA chain

32
Q

What is termination?

A

Release of finished RNA

33
Q

Where is the TATA box?

A

25 nucleotides before the initiation site for transcription

34
Q

What is the TATA box?

A

A type of promoter to signify to other molecules where transcription starts

35
Q

What is the TBP?

A

TATA box Binding Protein

36
Q

What does TBP do?

A

Recognises the TATA box and introduces a kink into DNA (determining transcriptional start and direction) - it is a part of TFIID

37
Q

What is TFIID?

A

A general transcription factor that is required for all Pol II transcribed genes

38
Q

What is TBP a landing platform for?

A

Further transcription factors and for RNA polymerase

39
Q

What does initiation of transcription require?

A

General transcription factors

40
Q

What do Pol II and TFIIF do in initiation?

A

Extend the transcript on their own

41
Q

What does TFIID do in initiation?

A

Remains at promotor so a new initiation complex can assemble

42
Q

What does initiation allow?

A

Transcription to occur at low, basal rates

43
Q

What happens in transcription elongation?

A

A transcription bubble moves in one direction along the DNA strand, and DNA is unwound in front of polymerase and rewound behind it.

44
Q

What direction is the RNA strand synthesised in?

A

5’-3’ direction

45
Q

What strand is the new RNA complementary to?

A

The template strand

46
Q

What happens in transcription termination?

A

Newly synthesised RNA makes a stem loop structure (followed by many uracils). A specific enzyme cleaves RNA and the RNA is released and polymerase dissociates

47
Q

What do ‘specific’ transcription factors contain?

A

DNA binding proteins and two functional domains which can be physically separated; DNA binding domain and transcriptional activation domain

48
Q

What do the ‘specific’ transcription factors bind to?

A

Specific DNA sequences in the vicinity of a promotor = enhancers

49
Q

How can transcription be regulated?

A

Positively OR negatively

50
Q

How are the ends of mRNA processed?

A

By addition of a poly A tail and addition of a 5’ cap (made of modified GTP)

51
Q

In the genetic code what does degenerate mean?

A

Many amino acids have more than one codon

52
Q

In the genetic code what does unambiguous mean?

A

Each codon codes for only one amino acid or stop

53
Q

What are the components of translation?

A

Amino acids, tRNAs, aminoacyl-tRNA synthetases, a specific set of protein factors for initiation/ elongation/ termination, ATP and GTP (energy), ribosomes and mRNA

54
Q

What do aminoacyl-tRNA synthetases do?

A

Bind amino acids to their corresponding tRNA molecules so are highly specific. There is at least one for each amino acid. ATP provides the energy for the covalent bond

55
Q

How many rRNA molecules does each ribosome contain?

A

4 (as well as protein components)

56
Q

What are the 3 binding sites of tRNA?

A

E(xit), P(eptidyl), A(minoacyl)

57
Q

What does initiation require?

A

Initiation factors

58
Q

Why is GTP hydrolysed in initiation?

A

To provide energy for initiation

59
Q

Where do small ribosomal units bind in initiation?

A

5’ end of mRNA, and move along the mRNA until finding start codon (AUG) - requires ATP

60
Q

What is the role of initiator tRNA?

A

Has UAC (complementary) anticodon to pair with the start codon - carries methionine (located in P site)

61
Q

What does an elongation factor do?

A

Brings the next aminoacyl-tRNA to the a site and anticodon pairs with codon

62
Q

In elongation what happens when GTP is hydrolysed?

A

The elongation factor is released from tRNA and a second elongation factor regenerates the original EF to pick up the next aminoacyl-tRNA

63
Q

What does peptidyl transferase catalyse?

A

Peptide bond formation between amino acids in the P and A sites (peptide in A site)

64
Q

During peptide bond formation/ translocation what happens?

A

After the peptide bond is formed between aminos in P and A, an elongation factor moves the ribosome one triplet along mRNA. the ‘empty’ tRNA moves to the E site to exit and become reloaded. tRNA with the growing peptide moves from A to P so the site is free for the next aminoacyl-tRNA

65
Q

When does termination occur?

A

When the A site of the ribosome encounters a stop codon (UAA, UAG or UGA) as no aminoacyl-tRNA base pairs with stop codons

66
Q

What happens during termination?

A

Release factor binds to stop codon - GTP hydrolysis. The finishes protein is cleaved off tRNA and the RNA components dissociate from one another. Process starts over

67
Q

What is the polysome?

A

The collective process of initiation, elongation and termination

68
Q

What types of chromosomal mutation are possible?

A

Deletions, duplications, inversions or translocations

69
Q

What 3 things can happen to a protein?

A

Targeting (moving protein to its final destination dependent on the amino acids in the protein), modification or degradation (of unwanted or damaged proteins)

70
Q

Where are proteins produced by free ribosomes in the cytosol destined for?

A

Cytosol, nucleus, mitochondria or translocated post-translationally

71
Q

Where are proteins produced by bound ribosomes on the RER destined for?

A

Plasma membrane, ER, Golgi apparatus, secretion or translocated co-translationally

72
Q

What are some examples of post-translational modifications?

A

Glycosylation (addition and processing of carbohydrates in the ER and the Golgi), formation of disulphide bonds in ER, multisubunit proteins in the ER etc

MBChB Year 1 Principles Biochemistry (4 decks)

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