DNA and RNA Flashcards
1
Q
What is Chargaff’s rule?
A
Nucleic acids contain equal amounts of G to C and A to T
DNA content varies from species to species
2
Q
In the simplest form, what happens in transcription and translation
A
Transcription = DNA to RNA Translation = RNA to protein
3
Q
What is the difference between drugs targeting DNA directly and indirectly?
A
Directly = interacts with DNA structure Indirectly = interacts with processing enzymes
4
Q
What is the overall structure of DNA
A
Double helix
5
Q
Give 2 examples of drugs that act indirectly on DNA
A
Acyclovir is an antimetabolite, it acts as a false metabolite and blocks essential enzymes for DNA synthesis
Etoposide blocks the action of topoisomerase
6
Q
What is the name of the 4 bases that make up DNA?
A
Adenine, Guanine, Cytosine, Thymine
7
Q
Which bases are purine and which are pyrimidine?
A
A+G = purine C+T = pyrimidine
8
Q
Which position on purine bases is the sugar attached?
A
N9
9
Q
Which position on pyridine bases is the sugar attached?
A
N1
10
Q
What is the sugar that is part of DNA?
A
Beta-D-2’-deoxyribose sugar
11
Q
What is the bond that connects the sugar and phosphate group on DNA? And at which positions on the sugar does this occur?
A
Phosphate diester bond at the 3’ and 5’ positons
12
Q
Which position is the base attached to the sugar on DNA?
A
1’ position
13
Q
What allows DNA to have a direction?
A
The 3’ and 5’ ends
14
Q
What is the sugar-phosphate backbone on DNA?
A
A sugar molecule bonded to a phosphate molecule by a phosphate diester bond and joins nucleotides in a DNA sequence
15
Q
What is a nucleotide?
A
Phosphate bonded to sugar bonded to a nucelobase
16
Q
What is a nucleoside?
A
Sugar bonded to nucleobase
17
Q
What is the name of the 2 purine nucleosides? (DNA)
A
2’-deoxyguanosine
2’-deoxyadenosine
18
Q
What is the name of the 2 purine nucleotides? (DNA)
A
Deoxyguanosine 5’-monophosphate (dGMP)
Deoxyadenosine 5’-monophosphate (dAMP)
19
Q
What is the name of the 2 purine nucleosides? (RNA)
A
Guanosine
Adenosine
20
Q
What is the name of the 2 purine nucleotides? (RNA)
A
Guanosine 5’-monophosphate (GMP)
Adenosine 5’-monophosphate (AMP)
21
Q
What is the name of the 2 pyrimidine nucleosides? (DNA0
A
2’-deoxythymidine
2’-deoxycytidine
22
Q
What is the name of the 2 pyrimidine nucleotides? (DNA)
A
Deoxythymidine 5’-monophosphte (dTMP)
Deoxycytidine 5’-monophosphate (dCMP)
23
Q
What is the name of the 2 pyrimidine nucleosides? (RNA)
A
Uridine
Cytidine
24
Q
What is the name of the 2 pyrimidine nucleotides? (RNA)
A
Uridine 5’-monophosphate (UMP)
Cytidine 5’-monophosphate (CMP)
25
What part of the nucleotide name changes when there is more than one phosphate group?
Monophosphate changes to diphosphate or triphosphate
26
Where does the sugar phosphate backbone and bases lie on the helical structure of DNA?
Sugar phosphate backbone is on the outside and the bases are on the inside
27
What bonds the complementary bases on the 2 DNA strands?
H bonding
28
How can you tell the structure of purine bases and how can you tell between the 2?
Purine bases have 2 rings, guanine has a carboxyl group, adenine doesn't
29
How can you tell the structure of the pyrimidine bases and how can you tell between the 2?
Pyrimidine bases have 1 ring, thymine has a carboxyl group, cytosine doesn't
30
How many H bonds connects C and G?
3
31
How many H bonds connects A and T?
2
32
What causes the helix shape in DNA??
Pyrimidines are smaller than purines so when they pair up, a helix shape is made
33
How is the base pairs being stacked in DNA important?
There are vdw (pi-pi) interactions between the pairs which results in the structure being stabilised. This interaction is strongest when the base pairs are offset.
34
What does it mean for a helix to be right handed? (DNA)
From left to right, the front of the helix goes in an upward direction.
35
The beta form of DNA is antiparallel, what does this mean?
The 2 strands run in opposite directions, (5'-3' and 3'-5')
36
DNA structure is polyanionic, what does this mean and why is it important?
There are negative charges at several sites at neutral pH. It has a hydrophobic effect in water, water surrounds the DNA which is clumped together. DNA carries counter-ions inside: Na+, K+, Mg2+, spermine and spermidine
37
What is the major and minor groove on DNA?
Looking at the double helix, there is a small inward groove and a large inward groove on the side
38
Which groove do proteins bind to on DNA and why?
Major groove since it is bigger. The groove motifs are also different making it easier for proteins to distinguish whereas in the minor groove, the motifs are the same
39
What does the major groove motif show
Whether the groups the proteins interact with are H donors or acceptors
40
Describe how to work out the major groove motif and how the protein interacts with this
Looking at the side atoms of the major groove, you can tell if it is a donor or acceptor. For example, H = donor, N and O = acceptor. The protein then provides the opposite to this so that it can interact
41
What is the word to describe how DNA is highly folded?
Supercoiled
42
Describe the parts to the tertiary structure of DNA
DNA double helix, forms a nucleosome by being wrapped around proteins which are then coiled to form chromatin which is densely coiled to form chromosome
43
Describe an nucleosome
DNA which is wrapped 1.65 times around a core of histone protein. "beads on a string"
44
Describe chromatin
A coiled string of nucleosomes
45
What is the role of topoisomerase II? (DNA)
DNA has to be unravelled during replication which leads to strain. The enzyme cuts and repairs the DNA to relieve this strain (reduce number of coils)
46
What are the 5 main differences between the structure of DNA and RNA
DNA sugar is deoxyribose where as in RNA is is ribose
Thymine is exchanged for Uracil
DNA is a double stranded whereas RNA is a single strand
DNA is much bigger than RNA
DNA is in the beta form whereas RNA is alpha form
47
What is the difference between Thymine and Uracil
Uracil doesn't have the methyl group
48
What is more stable, DNA or RNA and why?
DNA, RNA has an extra OH group
49
What is different between deoxyribose and ribose?
Ribose has an extra OH group
50
Describe the mechanism that occurs in RNA which makes it less stable than DNA
At pH 7.4 (alkaline), the H from the extra OH on the ribose molecule is removed resulting in O-. This attacks the negative phosphate group resulting in cleavage between the phosphate group and the next sugar
51
Why is RNA being broken down easily useful?
It means that proteins aren't always being made, it is a short term copy of DNA
52
Describe the A-form RNA double helices
They have a wide, shallow minor groove and a deep, narrow major groove
53
What is the most famous form of RNA and what shape is it?
tRNA which has a clover leaf shape
54
What is mRNA
Messenger RNA which relays the code for a protein from DNA to the protein production site
55
What is tRNA?
Transfer RNA which acts as an adaptor linking the triplet code on mRNA to specific amino acids
56
What is rRNA?
Ribosomal RNA which is found in ribosomes and is important structurally and catalytically
57
What is snRNA?
Small nuclear RNA which is involved in nuclear processes such as splicing
58
What is snoRNA?
Small nucleolar RNA which helps chemical modifications of RNAs
59
What is miRNA?
Micro RNA which regulates gene expression
60
What is siRNA?
Small interfering RNA which stops gene expression
61
What is lncRNA?
Long non-coding RNA which regulates gene expression
62
What are the 3 RNAs that are involved in protein synthesis and are the most common in order of most to least
rRNA (82%)
tRNA (16%)
mRNA (2%)
63
What are the 3 theories of DNA replication and what happens in each of them
Semi-conservative: Strands are split, the complimentary strand is then formed
Conservative: The entire DNA double helix is copied
Dispersive: A mixture of both (sections of the double helix)
64
How was it found to be that DNA replication was semi-conservative (vague)
Using nitrogen 14 and nitrogen 15 and E. coli cells
65
What must a cell do before it can divide?
Replicate its DNA
66
What is replication?
The process by which DNA molecules produce exact duplicates of themselves
67
What enzyme catalyses the addition of a nucleotide to the 3'-OH group of the polynucleotide chain and for what process is this for? I.e adding nucleotide onto the new DNA strand from the 3'-OH position
DNA polymerase
68
Which direction is DNA synthesised in?
5' to 3'
69
What 2 things are required in order to DNA to be synthesised?
Template strand and a starter
70
What does DNA polymerase also do as it moves long making the DNA?
Proof reads, removes incorrectly matching nucleotides
71
Describe the beginning of replication fork which is the same for the lagging and leading strand
Topoisomerase unravels the DNA and prevents supercoiling.
Single-strand binding proteins coat the DNA to prevent rewinding.
Helicase opens up the DNA strands (separates bases).
72
Describe the replication fork for the leading strand after helicase has opened up the DNA
DNA polymerase III builds new DNA onto the primers. Since this strand is in the correct direction (3' is ready to build from), the DNA is made as one continuous strand using DNA polymerase
73
Describe the replication fork for the lagging strand after helicase has opened up the DNA
DNA primase synthesises primers and works ahead DNA polymerase. It attaches primers to the DNA template strand. DNA polymerase II removes these primers and replaces it with DNA and builds the new DNA strand but in the backwards direction in fragments since it has to be form the 3' end and this is the lagging strand. DNA ligase then seals these fragments together to form one continuous strand
74
What is the Okazaki fragment?
The fragments of DNA formed for the lagging strand
75
Why is there a leading and lagging strand in DNA synthesis?
DNA can only be built form the 3' end however, since DNA is anti-parallel, one of the template strands (lagging) is in the opposite direction
76
What is transcription?
The copying of a segment of DNA which codes for a specific protein
77
What is the difference between DNA replication and trasncription?
Replication produces new DNA whereas transcription produces mRNA (one strand)
78
What organelle reads mRNA in the synthesis of the protein?
Ribosomes
79
Where does transcription occur in the cell?
In the nucleus
80
Describe transcription
RNA polymerase attaches to upstream (5') DNA strand at the promoter and initiates transcription. The DNA then unwinds, RNA polymerase II reads the template strand and adds nucleotides to the 3' end of the growing chain (strand elongation)
81
Describe what RNA pol I, II, and III do in transcription
RNA pol I transcribes the genes for rRNA
RNA pol II transcribes mRNA for protein synthesis
RNA pol III transcribes genes for one small rRNA and tRNAs
82
What stops transcription
A terminator sequence
83
What are the 2 strands of DNA called in transcription?
Template and coding/ sense strand
84
Which strand of the DNA is mRNA a replicate of?
Coding/sense strand
85
How do modifications to mRNA occur and why?
The middle section (intron) is removed, the end regions left (exons) are then spliced together. Introns are noncoding
86
After the mRNA has been made, what is done to it to add protection for when it leaves the nucleus?
A cap (5') and tail (3') are added
87
What is the cap and tail for mRNA?
```
cap = a single G nucleotide which allows both ends of mRNA being 3' to protect from exonucleases
tail = hundreds of A nucleotides
```
88
What is translation?
The process of protein synthesis after transcription of DNA to RNA (mRNA)
89
What is gene expression?
The overall process of information from a gene being used to synthesise a protein
90
What are the 3 phases of translation?
Initiation
Elongation
Termination
91
Describe a tRNA
tRNA is a sequence of nucleotides in a clover shape. It has 2 binding regions: one carries the amino acid, the other is an anticodon which is complementary to the codon on the mRNA. The anticodon is specific for the amino acid that the tRNA is carrying
92
Where does translation occur?
In the ribosome outside of the nucleus
93
What is a codon?
A sequence of 3 nucleotides on DNA or RNA that corresponds to a specific amino acid or stop signal
94
What is the full set of codons
The genetic code
95
How many codon combinations are there in the genetic code? And how many are stop signals?
64, 61 for coding amino acids, 3 for stop signals
96
What are the 3 stop codons?
UAA, UAG, UGA
97
What happens in initiation of translation?
The ribosome assembles around the target mRNA
| The first tRNA is attached to the start codon
98
What happens in elongation in translation?
The next tRNA transfers the amino acid it is carrying to the ribosomal subunit which binds it to the previous one (transpeptidation).
The ribosome then moves to the next mRNA codon (translocation) to continue making the amino acid chain
99
What happens in termination in translation?
A stop codon is reached and the ribosome releases the polypeptide chain
The ribosomal complex moves onto the next mRNA to be translated
