Nucleic acids Flashcards
(66 cards)
1
Q
What is meant by the central dogma?
A
shows the flow of genetic information
2
Q
Describe the structure of DNA
A
- a five carbon sugar (deoxyribose)
- a nitrogenous base
- a phosphate group
3
Q
What are the purines and pyrimidines present in DNA
A
purine - adenine, guanine
pyrimidine - cytosine, thymine
4
Q
What is a nuceloside?
A
formed when a base is linked to the 1’ carbon of a deoxyribose/ribose molecule
5
Q
Describe the charge on nucleic acids
A
negatively charged
6
Q
Describe the polarity of nucleic acids
A
have a 5’ –> 3’ polarity
7
Q
List the properties of the double helix
A
- right handed
- sugar-phosphate backbone on the outside
- hydrophobic interactions between adjacent base-pairs
- bases lie flat inside helix and perpendicular to the sugar-phosphate backbone
- diameter of 2nm
- height of 3.4nm per turn
- 10 base pairs per turn
- has major and minor grooves
8
Q
What is A-DNA?
A
- double stranded RNA
- 11 bp per turn
- right-handed
- slanted base pairs
- forms when DNA is dehydrated
9
Q
What is Z-DNA?
A
- 12 bp per turn
- left-handed
- zig-zag backbone
- may form if DNA contains long runs of alternating G and C
10
Q
Describe supercoiling in DNA
A
- underwinding –> negative supercoil
- overwinding –> positive supercoils
11
Q
Describe denaturation in DNA
A
- occurs between 70-110 degrees or exposed to alkaline conditions
- strands separate
- strands can re-anneal if left to cool slowly
12
Q
What is meant by the ‘hyperchromic shift’
A
UV absorbance rises as DNA denatures
13
Q
What is meant by the melting temperature (Tm)?
A
the temperature needed to denature 50% of the DNA molecules in a sample
14
Q
What is Tm increased in?
A
- DNA with high content of GC base pairs due to more H-bonds
- presence of cations - reduce repulsion between phosphate groups
15
Q
List the three key structural differences between DNA and RNA
A
- RNA has ribose not deoxyribose –> RNA is denser and more reactive and versatile
- RNA contains uracil
- Usually single stranded
16
Q
List some functions of RNA
A
- messenger RNA
- transfer RNA
- act structurally or catalytically (ribosomal RNA)
- acts as a regulator of gene expression
17
Q
List some properties of plasmids
A
- accessory circular DNA molecules separate from the chromosome
- carry non-essential genes
- readily passed from cell to cell
- have an origin of replication
- can be exploited in genetic manipulation
18
Q
Write an equation for the packing ratio
A
packing ratio = length of DNA/length of structure DNA packed into
19
Q
What are eukaryotic chromosomes made of?
A
1/3 DNA
1/3 histone protein
1/3 non-histone proteins
20
Q
List the five types of histone proteins
A
histone H1
histone H2A
histone H2B
histone H3
histone H4
21
Q
Describe the structure of the nucleosome
A
2 molecules of histone H2A
2 molecules of histone H2B
2 molecules of histone H3
2 molecules of histone H4
22
Q
What do chromsomes visible at mitosis and meiosis consist of?
A
a scaffold and non-histone proteins
23
Q
What is condensin?
A
a ring-shaped protein that can anchor the ends of a loop of DNA
24
Q
What is topoisomerase II
A
an enzyme that can remove or add supercoils within DNA
25
How does acetylation regulate histone proteins?
- removes positive charge from side-chain and weakens interactions between histones and DNA
- makes it easier to transcribe a gene
26
Describe the Meselson-Stahl experiment
1. grew E.coli in growth medium containing 15N - DNA is therefore denser than normal
2. switched E.coli to medium containing 14N - all DNA synthesised after switch will be less dense
3. measured density of DNA after replication
4. all replicated DNA was of intermediate density --> semi-conservative
27
What does DNA polymerase need to synthesise DNA?
1. all four deoxynucleoside triphosphates
2. a template
3. a primer
28
What is the function of 5'-->3' exonuclease
combines with DNA polymerase activity to allow nick translation
29
What is the function of 3'-->5' exonuclease
allows DNA polymerase I to remove incorrect nucleotides made from DNA
30
Where do the primers used in DNA replication come from?
- made of RNA
- synthesised by primase
31
What removes positive supercoils?
- DNA gyrase
- type II topoisomerase
32
List the events of DNA replication in E.coli
1. partial unwinding by helicase
2. synthesis of primers by primase
3. DNA synthesis by DNA pol III
4. removal of RNA primers by nick translation by DNA polymerase I
5. sealing gaps between okazaki fragments by DNA ligase
33
Describe the initiation stage of transcription
- RNA polymerase binds to promoter
- DNA strands partially unwind
- RNA synthesis begins
34
Describe the elongation stage of transcription
RNA polymerase moves along the DNA molecules synthesising an RNA copy
35
Describe the termination stage of transcription
RNA polymerase dissociates from DNA releasing new RNA molecule
36
What are consensus sequences?
'average' sequences found in association with many different genes
37
What is the holoenzyme?
- hexamer
- carries out initiation but not elongation
38
What is the core enzyme?
- a pentamer
- carries out elongation but not initiation
39
List the 3 types of RNA polymerase present in eukaroytes
- RNA polymerase I - synthesises rNA
- RNA polymerase II - synthesises mRNA
- RNA polymerase III - synthesises tRNA
40
What is meant by capping?
addition of a methylated G to the 5' end of the 1 transcript - stabilises mRNA and is required for translation
41
What is the purpose of cleavage and polyadenylation?
the 3' end of the 1 transcript is cleaved and a poly A tail is added - stabilises mRNA molecule
42
What is meant by RNA splicing
splits genes into exons
43
List some features of the genetic code
- it is non-overlapping
- it is degenerate - amino acids can be coded for by more than one codon
- almost universal
44
List some features of tRNAs
- small
- contains some unusual bases - arise from post-transcriptional modifications
- all have an anitcodon
- have the unpaired sequences CCA at their 3' end
- have a 'clover leaf' secondary structure with 3/4 loops and 4 double stranded stems
45
What is meant by the term base wobble
the ability of some bases at the 5' end of anticodon to pair with more than one base at the 3' end of the codon (GCC, GGC, GGU)
46
What are the enzymes that link tRNAs to amino acids called
aminoacyl-tRNA synthetases
47
List the two steps in the aminoacyl tRNA synthetase reaction
step 1:
AA + ATP ----> AA-AMP + PPi
step 2:
AA-AMP + tRNA ----> AA-tRNA + AMP
48
List the three tRNA binding sites in ribosomes
- the E site (exit)
- the P site (peptidyl)
- the A site (aminoacyl)
49
What are ribosomes comprised of?
protein and ribosomal RNA (rRNA) --> 2:1 ratio of rRNA to protein
50
What are the functions of the small unit and the large unit?
small unit - binds mRNA
large unit - catalyses peptide bond formation
51
What is the first amino acid is prokaryotes?
N-formyl-methionine
52
List the process of translation initiation in E.coli
1. small ribosome subunit binds to ribosome binding site on mRNA
2. f-met-tRNA binds to initiation codon
3. 50S subunit binds, generating complete ribosome
53
List the process of translation initiation in eukaryotes
1. first amino acid is methionine
2. 40S subunit and Met-tRNA combine prior to binding to mRNA
3. no ribosome binding site on the mRNA - 40S subunit recognises cap at 5' end of mRNA
4. 40S subunit and Met-tRNA migrate along mRNA until AUG reached
5. 60S subunit binds generating intact ribosome with first tRNA in the P site
54
What does the elongation cycle consist of?
- binding of aminoacyl-tRNA
- peptidyl transferase reaction
- translocation
55
How many ATP molecules are used for each amino acid incorporated?
3
1 ATP to link amino acid to tRNA
1 GTP used when aminoacyl tRNA binds to ribosome
1 GTP used during translocation
56
What is the peptidyl transferase reaction?
peptide bond synthesis
- catalysed by the 23S rRNA
57
List the elongation factors and their function
- EF-Tu - delivers aminoacyl tRNAs to ribosome
- EF-G - uses energy provided by hydrolysis to GTP to move ribosome along mRNA
58
Describe the target and action of erythromycin and clarithromycin
- prokaryotic large ribosomal unit
- inhibits peptidyl transferase reaction and translocation
59
Describe the target and action of chlorampthenicol
- prokaryotic and mitochondrial large subunit
- inhibits peptidyl transferase reaction
60
Describe the target and action of ricin
- eukaryotic 60S subunit
- catalytic, removes a base from rRNA
61
List the functions of the Lac genes
1. Lac Z - encodes B-galactosidase (lactose ---> glucose + galactose)
2. Lac Y - encodes galatoside permease (uptake of lactose)
3. Lac A - encodes galactoside transacetylase
62
What is the function of the CAP site?
binding site for (CAP)-cAMP complex, stimulates transcription of the lac genes
63
What is an operon?
a cluster of several genes transcribed into a single mRNA
64
What happens to the lac operon when lactose is present?
- some lactose converted to allolactose
- binds to lac repressor protein inducing conformational change
- lac repressor cannot bind to operator
- lac genes can be transcribed
65
What is meant by catabolite repression?
when both glucose and lactose are present in the environment, lac operon genes are transcribed weakly
66
What does the removal of catabolite repression require?
- CAP
- cAMP
