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MCD > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

Compare deoxyribose to ribose

A

Deoxyribose lacks an oxygen atom that ribose has

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2
Q

What is the base and phosphate attached to on the sugar

A

base - 1’ C

phosphate - 5’ C

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3
Q

Give the purines and pyrimidines

A

purine (big) - A and G

pyrimidine (small) - C and T

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4
Q

What are the functional groups present on the bases

A 
A - NH2
G - =O, NH2
C - NH2
T - =O, CH3
U - O
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5
Q

What are nucleosides

A

Sugar and base with no phosphate

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6
Q

Give the corresponding nucleosides for each base

A 
A - adenosine
G - guanosine
C - cytidine
T - thymidine
U - uridine
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7
Q

How are nucleotides linked to one another

A

3’ OH of one is linked to the 5’ OH phosphate of another

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8
Q

Describe the structure of DNA

A 
Asymmetry due to 5' and 3'
right handed double helix
anti-parallel chains
bases point inwards and perpendicular (-ve inside)
10 bp per helical turn
minor and major grooves
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9
Q

How many H-bonds are there between bases

A 
A-T = 2
C-G = 3
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10
Q

How is DNA analysed

A

Separation by heating or low salt and then re annealing/hybridised by cooling or high salt
karyotype can be found

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11
Q

How is DNA arranged in the nucleus

A

Tightly packaged with histones (+ve) to form chromatin. 8 core proteins.

  1. DNA
  2. nucleosome
  3. 30nm fibre
  4. chromatin
  5. chromosome
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12
Q

Explain what semi-conservative replication is

A

Each daughter DNA inherits one old and one new strand

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13
Q

What is the function of DNA helicase

A

unwinding of the DNA helix using ATP

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14
Q

In which direction is DNA replicated

A

5’-3’ as nucleotides are added to the 3’ end by DNA polymerase

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15
Q

What does DNA polymerase require

A

Template strand
Oligonucleotide primer
Deoxynucleotide triphosphates (dNTPs)

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16
Q

Describe the replication fork

A

Begins at the origin of replication

Asymmetric replication as both strands are synthesised 5’-3’

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17
Q

Explain the process in the replication fork

A

Leading strand is synthesised continuously while the lagging strand is synthesised as Okazaki fragments

  1. DNA primase synthesises a short RNA primer fragment
  2. Ribonuclease removes the previous primer 5-3- exonuclease activity
  3. repair DNA polymerase replaces the primer with DNA
  4. DNA ligase joins the two fragments using ATP
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18
Q

Explain the purpose of the following: single strand DNA binding protein, sliding clamp, exonuclease

A

SSDBP - prevents the single strands from folding
Sliding clamp - prevents DNA polymerase from shifting or falling
3’-5’ exonuclease - checks and fixes mutations

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19
Q

Describe the replication of E. Coli

A

Begins at OriC
2 replication forks in opposite directions
B-directional

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20
Q

Describe the replication of eukaryotes

A

multiple replication origins distributed at intervals

each give bi-directional forks

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21
Q

Describe the cell cycle

A 
G1 - 10 hrs of gap phase
(G0 - cells stop dividing)
S - 9 hrs of DNA synthesis
G2 - 4 hrs of gap phase
M - 1 hr mitosis
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22
Q

Describe the stages of mitosis

A

G2 - chromosomes not visible
Early prophase - chromosomes pair + crossing over
Late prophase - chromosomes condense and become visible, spindle fibres move
Metaphase - chromosomes aligned on the central plane
Anaphase - sister chromatids pulled apart
Telophase - sister chromatids move to opposite poles
Cytokinesis

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23
Q

Name 4 nucleoside analogues and explain how they work

A 
AZT - N3 group for HIV
Acyclovir - no ring sugar for herpes
ddC - H group for HIV
Cytosine Arabinose - tetrose sugar for chemotherapy
Absence of a 3' OH group
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24
Q

Explain the basic differences between DNA and RNA

A

DNA - deoxyribose, RNA - ribose
AGCT, AGCU
long and double stranded, short and single stranded
RNA: rRNA, tRNA, mRNA

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25
Q

Explain what transcription means

A

Production of mRNA from DNA

Growth from 5’-3’ (Sense)

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26
Q

List the major functional classes of RNA and the classes of RNA polymerases involved in synthesising each of these.

A

I - rRNA
II - mRNA
III - tRNA and 5S RNA genes
Grooves in the helix allows for adherence to the strands

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27
Q

Explain what a gene promoter is

A

DNA sequences at which the initiation complex assembles at. Gives the initiation point. e.g. TATA

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28
Q

Explain what is meant by a transcription factor

A

Proteins that regulate genes acting collectively to bring about expression. They activate or repress transcription or may model chromatin. May be signalled by hormones, growth factors, stress etc.

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29
Q

What is the process involved in transcribing a eukaryotic gene

A
  1. TF II D unwinds the DNA to widen the minor groove
  2. TF II A and TF II B bind.
  3. RNA polymerase binds to TF II B
  4. Other TFs bind to promote further unwinding. TF II H further unwinds the DNA helix (E,F,H,J)
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30
Q

Explain how acetylation can affect transcription

A

Hyperacetylation - expression

Hypoacetylation - repression

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31
Q

What does TF II D contain and how does it assist transcription

A

TBP (TATA binding protein)
TAF (TBP accessory factor)
unwinds the DNA asymmetrically so that transcription is unidirectional

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32
Q

How does aspirin work

A

inhibits the breakdown of IkB so NFkB remains in the cytoplasm so cannot initiate transcription of cytokine genes

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33
Q

What is the structure of pre-mRNA

A

GU at the start
A in the middle
15 pyrimidines, random nucleotide, CAG at the end

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34
Q

What does RNA processing use

A

ribonucleic proteins snRNPs

35
Q

Explain the events that take place in pre-mRNA processing

A
  1. U1 binds to the splice donor sequence (GU)
  2. U2, U4, U5, U6 binds to form the spliceosome (U5 binds to CAG)
  3. Cleavage of the splice donor sequence and formation of a branch point (phosphodiester bond) at A between 5’ P on G and 2’Oh on A
  4. PD bond between intron and exon at the end is cleaved to release lariat intermediate
  5. DNA ligase joins the exons together
36
Q

What is the purpose of the CAP and PolyA tail

A

CAP protects the mRNA and enhances translation

PolyAAA = added 11-30 bases from AAUAAA

37
Q

What are the splice donor and acceptor sites

A

splice donor = GU where U1 binds

spice acceptor = CAG where U5 binds

38
Q

Explain how mutations in splice sites feature in polio

A

Polio interferes with the recognition of CAP and invades the nervous system to cause total paralysis

39
Q

What proportion of mutations are in splice donor sequences

A

1/3

40
Q

Explain how mutations in splice sites feature in thalassaemia

A

Inherited disorder where there is an imbalance in globin chains

41
Q

Explain how mutations in splice sites feature in DMD

A

Duchenne muscular dystrophy

Dystrophin gene is mutated (most deletion of axons) causing prematurely aborted dystrophin protein synthesis

42
Q

How is DMD treated

A

Alternative splicing sp that exons are purposefully skipped but the dystrophin remains functional

43
Q

Does genome size = complexity

A

No

44
Q

What is ENCODE

A

Encyclopaedia of DNA elements

Identifies all regions of transcription factor association, chromatin structure and histone modification

45
Q

What proportion of introns are functional

A

20% of introns = functional

60% = unknown function

46
Q

What is ncRNA

A

non-translated RNA that is highly abundant and important

e.g. tRNA, rRNA, microRNA, sn, pi, long ncRNA

47
Q

Explain X-inactivation

A

1/2 X chromosomes in females are inactivated (packaged so one is transciptionally inactive) - heterochromatin
choice of which X chromosome is random
Controlled by long ncRNA

48
Q

What is long ncRNA

A

ncRNA >200 n

used in C inactivation/lyonisation

49
Q

What is the experimental support for small ncRNA

A

Nematode Caenorhabditis elegans is a free living nematode(worm) that is one of the simplest organisms with a nervous system
Used to map the connectome and fate map
dsRNA is a silencing trigger to C. elegans

50
Q

What is antisense RNA

A

Transcribing the reverse of a gene
It forms H bonds with the sense RNA to prevent translation
Forms dsRNA
Used in plants against viruses

51
Q

What is RNAi

A

A small single stranded RNA that anneals to viral RNA to cause degradation (microRNA + siRNA operate via RNAi)

52
Q

Explain how RNAi is developed and works

A
  1. siRNA or microRNA enter the cytoplasm
  2. Break down into fragments by DICER and endonuclease
  3. Creates 3’ overhangs
  4. Ago proteins attach to the overhangs
  5. Formation of RNA induced silencing complexes (RISC) with ATP
  6. Attachment to complementary RNA
  7. cleavage and silencing of the RNA
53
Q

what is the difference between siRNA and microRNA

A

siRNA is made exogenously and cuts mRNA at 1 point

microRNA is made endogenously and cuts at multiple points + hairpin structure

54
Q

Describe microRNA

A

genetically encoded siRNA which was first seen in C. Elegans (Lin4)
3’ overhang by 2 nucleotides

55
Q

Explain how microRNA works

A
  1. miRNA is transcribed by RNA polymerase II into a pre-mRNA
  2. Processing by RNase III endonuclease (Dresha) complex with DIGeorge syndrome critical region
  3. Transport to the cytoplasm
  4. RISC formation
  5. Binding via the seed region (rest is not complementary)
  6. Permanent binding
56
Q

Give an example of how miRNA is involved in human disease

A

E.g. chronic lymphoid leukaemia (CLL)
Deletion of part of a gene on chromosome 14 leads to loss of miRNA. Supplementing the miRNA to nude mice that have CLL, you can get rid of the cancer

57
Q

Why is analysis of DNA important

A

Used for personalised mediciein e.g. and increase in HER2 can lead to breast cancer
Herceptin can be used for those with HER2

58
Q

What are restriction endonuclease

A

Enzymes that cleave DNA at specific sequences
Only cuts unmethylated DNA
Produces blunt or sticky ends

59
Q

What is electrophoresis

A

Technique to separate DNA fragments
-ve DNA is attracted to a +ve charge at the anode
Smaller fragments will travel faster and further

60
Q

Describe the process of in vivo cloning

A
  1. cut the target DNA using REs
  2. Cut the replicon (replicates out of the host e.g. plasmid bacteriophage) with the same RE
  3. combine fragments using DNA ligase
  4. transformation of the recombinant DNA
  5. Selective propagation of the colonies
  6. expansion via culturing
61
Q

Explain one technique for selective propagation in in vivo cloning

A

Antibiotic resistance in the recombinant gene so exposure to the antibiotic will kill those who did not take up the gene

62
Q

Describe the process for in vitro cloning

A

Uses polymerase chain reaction (PCR)
Primer must be 20N and tandem repeats should be avoided
A non-complementary end to 3’ so it binds to 5’
1. denaturation at 94 to break H bonds
2. annealing at 50-60 to allow annealing between strands and dNTPs
3. Elongation at 72 for tax polymerase to form PD bonds

63
Q

What are the 3 things required for PCR

A

Oligonucleotide primer
dNTP
Taq polymerase

64
Q

What can DNA cloning be used for

A 
sequence DNA
Detect point mutation
DNA microarrays
cDNA cloning
Typing genetic markers
65
Q

What are microarrays

A

Monitors expression levels for genes
Collection of dots that represent single genes sprayed on a surface e.g. a glass slide
Expression profiling
SNP detection array - SNP in genomes of the population

66
Q

How does hybridisation work

A
  1. denature the nucleic acid
  2. single-strand reacts with nylon or nitrocellulose to immobilise
  3. complementary nucleic acid (probe)
  4. H-bonds form between the target and probe
  5. electrophoresis
  6. probes show radioactivity or fluorescentivity
67
Q

What are the different types of hybridisation

A 
Southern blot - DNA, RNA
Northern blot - RNA, DNA
Coloney blot - Bacterial DNA, DNA 
Tissue in situ - RNA x 2
Chromosome in situ - chromosome, DNA
reverse - DNA x 2
68
Q

What is hybridisation stringency

A

precision to which the hybridisation procedure can distinguish between similar nucleic acid sequences

69
Q

How can hybridisation stringency be increased

A

Increase in temperature and a low salt concentration

70
Q

What is the entry point for a ribosome during translation

A

7MetG cap

71
Q

What 3 materials are required for translation

A

mature mRNA, charged tRNA, ribosome

72
Q

What are the start and stop codons

A 
Start = AUG = Met
Stop = UAA, UAG, UGA
73
Q

Describe the structure of tRNA

A

Clover shaped
Carries and amino acid (Charged)
anticodon (anti-parallel)
64 RNAs

74
Q

Explain how tRNA becomes charged

A
  1. Amino acid binds to aminoacyl tRNA synthase
  2. Aminoacyl tRNA synthase cleaves pyrophosphate from ATP and binds remaining AMP to AA
  3. Amino acids is adenylated
  4. Adenylated AA is attached to tRNA
  5. Aminoacyl tRNA synthase and AMP then detaches leaving the charged tRNA
75
Q

What are the 3 stages of translation

A

Initiation
Elongation
Termination

76
Q

Explain the process of initiation in translation

A
  1. ribosomal unit dissociates into 40S and 60S units
  2. initiation factor 4G and 4E bind to the cap
  3. Charged tRNA, eIF2, GTP, 40S recognise the structure
  4. Reads until AUG to form the pre-initation complex
  5. GTP is converted to GDP which then binds to 60S
  6. met-tRNA binds to the P-site on ribosomes
77
Q

Explain the process of elongation in translation

A
  1. The next tRNA binds to the A site
  2. peptide transferase creates a peptide bond
  3. elongation factors move along the strand using GTP (translocation)
78
Q

What is the function of GTP hydrolysis in elongation during translation

A

gives time for dissociation of incorrect amino acids

79
Q

What doe ribosomes split into during translation in prokaryotes

A

30S and 50S

80
Q

Explain the process of termination in translation

A
  1. Stop codon attracts release factors (no tRNA for stop codon)
  2. binding to the A site of the ribosome
  3. peptide transferase binds water to the final amino acid (carboxyl group)
  4. Translocation complex dissociates
81
Q

What molecules are involved in modification after translation

A

signal sequence or signal recognition proteins (20-24AA)

82
Q

Explain the process of modification after translation

A
  1. SRP is detected by the SRP receptor in the RER to stop translocation
  2. SRP binds to the receptor
  3. Translocation resumes
  4. Polypeptide moves to the lumen of the RER
  5. SRP degraded
  6. Polypeptide folded and cleaved
  7. Further modification or transmembrane (further hydrophobic groups added)§
83
Q

Describe insulin modification

A

undergoes disulphide bond formation in the ER and golgi body
Proteolytic cleavage in secretory vesicle
Chain C is released into the cytoplasm and then the blood so it can be used to detect insulin levels

MCD (13 decks)

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