Important Information Flashcards
What are phosphodiester bonds?
2
Covalent bonds that link adjacent nucleotides together in both DNA and RNA
Formed between the OH group on the 3’ C of one nucleotide and phosphate on the 5’ C of the next nucleotide
What are hydrogen bonds between nucleotides?
They join nitrogen bases of nucleotides together in complementary base pairs in the centre of DNA
This holds the 2 antiparallel strands together
What is a replication “bubble” in DNA replication?
2
Where the two separate strands open up from the origin of replication
A replication fork is found at either end of the bubble
DNA replication is semi-conservative, what does this mean?
Each of the 2 daughter molecule will have one of the old parent strands and 1 newly made strand
What is a replication fork?
3
A Y-shaped region found at each end of a replication bubble
This is where the new strands of DNA are elongating
They move away from the origin of replication
What is the Origin of Replication?
The position in DNA where the helix is first opened
What is the leading strand?
2
The new strand that can be synthesised continuously
The new strand in the 5’ to 3’ direction strand (complementary to the 3’ to 5’ parent strand)
What are okazaki fragments
Short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by DNA ligase to create the lagging strand during DNA replication
What is an exonuclease?
An enzyme which removes successive nucleotides from the end of a polynucleotide molecule
What happens if DNA pol finds out the previous nt is incorrect?
(3)
DNA pol removes the incorrect nt by cutting the phosphodiester bond
This releases the nt
DNA pol tries again to add the correct nt
What four proteins cooperate to form the replication machine?
Helicase
Topoisomerase
Sliding clamp
Single strand binding proteins
How does helicase work?
Uses energy of ATP hydrolysis to speed along DNA and separate the strands of parental DNA ahead of polymerase
It breaks the hydrogen bonds between base pairs
How does ligase work?
Joins 5’ phosphate end of one DNA fragment to 3’ OH end of the next (ATP required for ligase activity)
How does topoisomerase work?
Prevents DNA helix upstream from becoming supercoiled by relaxing it
How does the sliding clamp work?
2
Keeps DNA polymerase firmly attached to DNA template
On the lagging strand it releases polymerase from the DNA each time an Okazaki fragment is completed
What are the four key players in DNA replication?
Ligase
Helicase
Primase
DNA polymerase
What does nuclease do?
Removes any incorrect nucleotides - by cleavage of phosphodiester bonds
Classify DNA damage.
Single strand
Double strand
What causes single strand damage?
3
Endogenous replication errors
Oxidative chemicals
Non-ionising radiation e.g. UV
What are the two classifications of agents that can damage DNA?
Exogenous
Endogenous agents
Give three examples of exogenous agents
Toxins
Chemicals
UV radiation
What causes double strand damage?
2
Antitumor agents e.g. Cisplatin
Ionising radiation e.g. Gamma rays
Define DNA damage
Any alteration to DNA that distorts its geometry
What are the five types of single strand damage?
Base Mismatch
Depurination
Deamination
Thymine dimers
Bulky adducts
What does DNA pol I primarily do?
2
Exonuclease activity (nuclease activity at end of chain)
Nick translation
What does DNA pol II primarily do?
DNA repair
What does DNA pol III primarily do?
DNA synthesis
What is a mutation?
Randomly produced permanent change in a sequence of DNA
What are the three repair processes for SSD?
Mismatch repair (MMR) for repairing
Base excision repair (BER)
Nucleotide excision repair (NER)
What is meant by 5’ and 3’?
2
The 5’ and 3’ indicate the carbon numbers in the DNA’s sugar backbone.
The 5’ carbon has a phosphate group attached to it and the 3’ carbon a hydroxyl (-OH) group
How do you draw deoxyribose?
7
Draw a pentagon - O at the top with four carbons
Label each carbon in a clockwise direction 1’ to 4’
1' = OH on top and H on bottom 2' = H on top and H on bottom 3' = H on top and OH on bottom 4' = 5' on top and H on bottom 5' = (HOCH2)
What is the structural difference between deoxyribose and ribose?
2’ and 3’ of ribose have a H on top and an OH on bottom
To which C of ribose is the nitrogenous base attached?
1’
To which C of ribose is the phosphate attached?
5’
Define transcription
A portion of DNA nucleotide sequence (gene) is copied into a RNA nucleotide sequence
Define translation
2
The synthesis of polypeptide under direction of RNA
Formation of amino acid chains - proteins
What are transcription factors?
A collection of proteins that mediate the binding of RNA pol II to promoter in eukaryotes
What is RNA polymerase called when it is comprised of all five of it’s subunits?
Haloenzyme
What are the three main steps in transcription in prokaryotes?
Binding and initiation
Elongation
Termination
How does initiation of transcription work in eukaryotes?
4
A collection of proteins called transcription factors are needed
They mediate the binding of RNA pol II to promoter
A promoter DNA sequence (TATA box) is crucial for forming the transcription initiation complex
Complex then moves Pol II to start site of gene and begins to polymerise
What is the spliceosome?
2
Small nuclear RNAs (snRNA)
Combined with proteins (snRNP)
What does mRNA need to be bound to in order to be transported?
(3)
Poly-A-binding protein
Cap-binding complex
Nuclear transport receptor
What is an operon?
A set of adjacent genes in a bacterial genome, transcribed from a single promoter into a single mRNA
Write a note on the trytophan operon
4
5 genes which encode for enzyme which manufacture trytophan
These genes are arranged in a cluster on the genome (form an operon)
Genes transcribed from one promoter as 1 long mRNA molecule from which 5 proteins are translated
This operon isn’t needed if bacteria can get trytophan from their environment so it’s shut off
Define a repressor protein.
A protein that switches genes off or represses them
Define an activator protein
A protein that switches genes on or activates them
Write a note on the lac operon
4
Operon that encodes proteins required to import and digest lactose
Consists of 3 genes: lacZ, lacY and lacA
All genes under control of 1 promoter
Allolactose - lactose digestion intermediate - binds to repressor to inactivate it
What is the genetic code?
The rules by which nucleotide sequence of a gene is translated into an amino acid sequence of a protein
What do ribosomes do in translation?
They add each amino acid brought to it by tRNA to the growing end of a polypeptide chain
