Nucleic Acids and Gene Expression Flashcards
What does DNA stand for
deoxyribonucleotide acid
What is the difference between deoxyribose and ribose
Deoxyribose = -O2
Draw the structure of a nucleotide
3 P on the 5’, OH on the 3’, base on the 1’
Which bases are purines
A and G
Which bases are pyrimidines
C and T
Which bases have NH2
A and C
which bases have =O
G and T
How do bases pair
A and T, C and G
What is a nucleoside
A nucleotide without phosphates. Includes adenosine, guanosine, cytidine and thymidine (uridine)
What are the structural features of DNA
3’ and 5’ leads to asymmetry
Right hand helix
Major and minor groove
How many bonds between base pairs
A-T = 2 H bonds C-G = 3 H bonds
How many bp per turn
10
How can DNA be denatured
Lowering salt content or increasing heat
Describe the structural organisation of DNA
2nm double helix 11nm Nucleosome (-ve backbone and +ve histone) with 8 core proteins 30nm fibre 700nm 1400nm chromosome
Which enzymes are involved in DNA replication
Topoisomerase
DNA helicase (needs ATP)
DNA polymerase
What are the names of the two strand on the replication fork
Leading and lagging strand
What is the process of replication on the lagging strand
- DNA primase creates and RNA primer which binds to the DNA
- dNTPs form an Okazaki fragment
- Ribonuclease removes the previous primer using 5’-3’ exonuclease activity
- Repair DNA polymerase replaces the primer
- DNA ligase joins the Okazaki fragments, requiring ATP
What are the accessory factors for replication
Single strand binding protein to prevent folding
Sliding clamp to prevent polymerase falling off
3’-5’ exonuclease activity by DNA polymerase to fix mutations
How does E. coli replicate
Origin is OriC
Bi-directional with 2 replication forks
How do eukaryotes replicate
Multiple replication origins
Bi-directional
Describe the cell cyle
G1 - 10hrs
S - DNA synthesis 9 hrs
G2 - 2-4hrs
M - mitosis 1 hrs
What is the difference between early and late prophase
early - pairing of chromosomes and crossing over
late- condensing and spindle formation
Give examples of nucleoside analogues
Acyclovir - Herpes
AZT - HIV
Cytosine arabinose - Chemo
ddC - HIV
What are the types of RNA polymerase
Type 1 - rRNA
Type 2 - mRNA
Type 3 - tRNA
What is the promoter region
DNA sequence where the initiation complex forms
What are transcription factors
TFs are proteins that regulate genes, acting collectively to bring expression
What is the effect of acetylation
hyperacetylation = expression Hypoacetylation = repression
What are some determinants of expression
hormones, heat, stress, voltage, light etc.
What are the pre initiation complex and describe its formation
TF II D binds to TATA
TF II B and A binds to TF II D
RNA polymerase binds to TF II B
TF II E, F, H, J binds
What is special about TF II D
Causes asymmetrical unwinding of the DNA leading to unidirectionality ]
Widens the minor groove
contains TBP and TAF
What is special about TF II H
further unwinds the DNA helix
How is pre-mRNA processed
Removal of intron using snRNPs
intron starts with GU and ends in CAG
u1 binds to GU while U2,4,5 binds to the chain and U6 binds to CAG
breaking of the GU and binding to the branch point (A)
DNA ligase joins axons
What structure are introns removed as
Lariat
What is added to processed mRNA
CAP which protects mRNA and enhances translation
PolyA
