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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
How are RNA polymerases distinguished?
Their sensitivity to toxins like a-amantin (from fungi)
26
What RNA polymerase synthesises all mRNA?
Pol II
27
What does the binding of RNA polymerase do?
Detects the initiation sites (promoters) on DNA
28
What does the binding of RNA polymerase require?
Transcription factors
29
Why is DNA chain separation necessary?
To gain access to the nucleotide sequence
30
What is transcription initiation?
Selection of the first nucleotide of the growing RNA
31
What is elongation?
Addition of further nucleotides to the RNA chain
32
What is termination?
Release of finished RNA
33
Where is the TATA box?
25 nucleotides before the initiation site for transcription
34
What is the TATA box?
A type of promoter to signify to other molecules where transcription starts
35
What is the TBP?
TATA box Binding Protein
36
What does TBP do?
Recognises the TATA box and introduces a kink into DNA (determining transcriptional start and direction) - it is a part of TFIID
37
What is TFIID?
A general transcription factor that is required for all Pol II transcribed genes
38
What is TBP a landing platform for?
Further transcription factors and for RNA polymerase
39
What does initiation of transcription require?
General transcription factors
40
What do Pol II and TFIIF do in initiation?
Extend the transcript on their own
41
What does TFIID do in initiation?
Remains at promotor so a new initiation complex can assemble
42
What does initiation allow?
Transcription to occur at low, basal rates
43
What happens in transcription elongation?
A transcription bubble moves in one direction along the DNA strand, and DNA is unwound in front of polymerase and rewound behind it.
44
What direction is the RNA strand synthesised in?
5'-3' direction
45
What strand is the new RNA complementary to?
The template strand
46
What happens in transcription termination?
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
What do 'specific' transcription factors contain?
DNA binding proteins and two functional domains which can be physically separated; DNA binding domain and transcriptional activation domain
48
What do the 'specific' transcription factors bind to?
Specific DNA sequences in the vicinity of a promotor = enhancers
49
How can transcription be regulated?
Positively OR negatively
50
How are the ends of mRNA processed?
By addition of a poly A tail and addition of a 5' cap (made of modified GTP)
51
In the genetic code what does degenerate mean?
Many amino acids have more than one codon
52
In the genetic code what does unambiguous mean?
Each codon codes for only one amino acid or stop
53
What are the components of translation?
Amino acids, tRNAs, aminoacyl-tRNA synthetases, a specific set of protein factors for initiation/ elongation/ termination, ATP and GTP (energy), ribosomes and mRNA
54
What do aminoacyl-tRNA synthetases do?
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
How many rRNA molecules does each ribosome contain?
4 (as well as protein components)
56
What are the 3 binding sites of tRNA?
E(xit), P(eptidyl), A(minoacyl)
57
What does initiation require?
Initiation factors
58
Why is GTP hydrolysed in initiation?
To provide energy for initiation
59
Where do small ribosomal units bind in initiation?
5' end of mRNA, and move along the mRNA until finding start codon (AUG) - requires ATP
60
What is the role of initiator tRNA?
Has UAC (complementary) anticodon to pair with the start codon - carries methionine (located in P site)
61
What does an elongation factor do?
Brings the next aminoacyl-tRNA to the a site and anticodon pairs with codon
62
In elongation what happens when GTP is hydrolysed?
The elongation factor is released from tRNA and a second elongation factor regenerates the original EF to pick up the next aminoacyl-tRNA
63
What does peptidyl transferase catalyse?
Peptide bond formation between amino acids in the P and A sites (peptide in A site)
64
During peptide bond formation/ translocation what happens?
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
When does termination occur?
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
What happens during termination?
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
What is the polysome?
The collective process of initiation, elongation and termination
68
What types of chromosomal mutation are possible?
Deletions, duplications, inversions or translocations
69
What 3 things can happen to a protein?
Targeting (moving protein to its final destination dependent on the amino acids in the protein), modification or degradation (of unwanted or damaged proteins)
70
Where are proteins produced by free ribosomes in the cytosol destined for?
Cytosol, nucleus, mitochondria or translocated post-translationally
71
Where are proteins produced by bound ribosomes on the RER destined for?
Plasma membrane, ER, Golgi apparatus, secretion or translocated co-translationally
72
What are some examples of post-translational modifications?
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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