DNA Replication and Chromosomes Flashcards
What did the 3-dimensional crystal structure *proposed by Watson ad Crick suggested?
How DNA could be replicated to maintain the genetic information.
What could each strand of DNA do?
Separated.
Used as the template for second strand production.
What should DNA duplex be before any synthesis begins?
Unwound.
Melted apart.
With what do enzymes need to deal?
With the 5’-3’ orientation of each of the DNA strands.
In what do the 3 replication models of DNA differ?
In terms of how much old and new DNA daughter cells contain.
What were the thoughts of DNA helix unwound and replication?
Unclear if it would happen along the entire bacterial chromosome in one go.
If it had to be done in multiple smaller sections.
How could the 3 competing models of DNA replication be tested based on Meselson and Stahl?
By labelling Escherichia coli DNA during replication with nitrogen isotopes.
Where did incorporation of 14N resulted?
In light DNA.
Where did use of 15N resulted?
In heavier DNA.
How could light and heavy DNA be separated?
By ultra-centrifugation.
Where is DNA centrifuged?
In a CsCl gradient.
What happens to DNA when it is centrifuged in a CsCl gradient?
It moves towards neutral buoyancy point.
Which are the 3 models of DNA strands?
Conservative.
Semi-conservative.
Dispersive.
What happened in Meselson-Stahl experiment?
Several generations of bacteria went through it.
Chromosomal DNA became increasingly ‘light’.
When is replicating/synthesising DNA simple?
When a single template strand is provided.
What happens while the double-stranded DNA is replicated?
One strand is in the opposite direction to the other.
The 2 DNA Polymerases collide.
How do the cells avoid the 2 DNA Polymerases from colliding?
By flexing one of the 2 strands around.
What happens to the 2 DNA Polymerases when the cells flex one of them around?
They move in the same direction as a single ‘DNA synthesis/replication machine’.
For what is a replication complex/machine responsible?
DNA replication in vivo.
What does the replication complex/machine generate?
Copies of whole chromosomes in each cell cycle.
What does DNA Polymerase synthesize?
New DNA.
What does DNA Polymerase catalyse?
Formation of phosphodiester bond between 3’-OH of DNA strand synthesized and incoming 5’-triphosphate (dNTP).
What does the parental DNA strand provide?
The template for base pairing.
From where does the energy for the parental DNA providing the template come from?
The removal of pyrophosphate from incoming dNTP.
What must be free for the parental DNA providing the template?
3’OH group.
In which direction does polymerisation always occur?
In 5’–>3’.
What does DNA Polymerase test?
Each new dNTP.
What does DNA Polymerase required?
The correct base pairing before moving to the next base.
What is the direction of DNA Polymerase activity?
3’-5’.
How is the activity of DNA Polymerase named?
Exonuclease.
What does the exonuclease activity 3’-5’ of DNA Polymerase allow it to do?
Remove a mistake.
Replace the wrong nucleotide with the correct one.
What do RNA primers initiate?
DNA synthesis.
What does DNA Polymerase need to begin polymerisation?
A 3’-OH group.
What can DNA Primase start, without requiring starting point?
An RNA-based polynucleotide chain.
What does DNA Primase provide?
A ‘primer’ for DNA Polymerase.
What does primases uses instead of deoxyribonucleotides?
Ribonucleotides.
For how long does Primase function?
For only very short time.
Why does primase function for only a very short time?
Because RNA is unstable.
NTPs are limited.
How long is the primer?
Around 10 nucleotides long.
What does primase incorporate?
dNTPs.
Why does primase incorporates dNTPs?
To provide a stronger synthesis scaffold.
By what can DNA Polymerase synthesize DNA?
From the leading strand.
What is the characteristic of the other/lagging strand of DNA?
It is in the ‘wrong’ orientation than the leading strand.
How is the problem of wrong orientation of lagging strand synthesis fixed?
By breaking down the synthesis into small sections.
Which are the small sections lagging strand break down to?
Okazaki fragments.
How are Okazaki fragments linked together?
By DNA ligase.
What do helicases unwind?
The parental double helix.
What do single-strand binding proteins stabilise?
The unwound parental DNA.
From what are the 2 parental strands of DNA replicated?
By 2 DNA Polymerases.
Where are the 2 parental strands of DNA while they are replicated by 2 DNA Polymerases?
In a single replication machine.
Where does e single replication machine travel during DNA replication by DNA Polymerases?
Along the parental DNA duplex.
What does the single replication machine do to the parental DNA duplex?
Unwinding.
Melting as goes.
In what are origin (Ori) sequences rich?
AT base pairs.
Where does a family of initiator proteins gather?
At Ori sites of DNA.
When does a family of initiator proteins gather at Ori sites of DNA?
At beginning of S-phase.
Why does a family of initiator proteins gather at Ori sited of DNA at the beginning of S-phase?
To trigger synthesis.
=Activate replication machine.
Which chromatin is replicated first in DNA?
The least condensed chromatin.
Where does DNA replication start?
At Ori sequences of DNA.
Where does DNA replication move after Ori sequences?
Out in both directions.
What do large chromosomes have?
Multiple origins .
Why do large chromosomes have multiple origins?
To reduce the time of replication in all the DNA before cell division.
What is DNA?
A very long polymer.
Where does DNA need to be packaged?
Inside the cell.
Why does DNA need to be packaged inside the cell?
For safety.
How else does DNA need to be?
Readily unpacked.
Why does DNA need to be readily unpacked?
For replication.
Gene expression.
Where is DNA wrapped?
Around specialised proteins.
How are the specialised proteins, DNA is wrapped around, called?
Histones.
What does DNA form when it is wrapped around histones?
Nucleosomes + ‘beads on a string’.
What happens to nucleosomes and ‘beads on a string’ formed by DNA wrapped around histones?
It is further coiled and folded.
Why is nucleosomes + ‘beads on a string’ further coiled and folded?
To reduce size.
To regulate gene expression.
In what does higher order packing result?
In chromosome structures.
How can the chromosome structures be visualised?
By light microscopy.
Into what are the ‘beads on a string’ supercoiled?
Into a helical fibre.
On what is the helical fibre, formed by supercoiled ‘beads on a string’, looped?
On a chromosome protein scaffold.
What happens to the helical fibre after it is looped on a chromosome protein scaffold?
It is coiled agai.
Why is a helical fibre coiled again after it is looped on a chromosome protein scaffold?
To form the chromosome.
What is the Histone H1?
A ‘Locking unit’.
What does Histone H1 do?
It locks a loop of DNA around the main body of the nucleosome.
Of what is the main body of the nucleosome composed?
An octamer of 4 different histones.
Which are the 4 different histones of what the main body of the nucleosome is composed?
H2A.
H2B.
H3.
H4.
What do specific DNA sequences determine?
Which sections of DNA are associated with histones.
Which parts of DNA form the links between nucleosomes.
When do nucleosomes repeat?
Approximately every 200bp.
Why do nucleosomes repeat approx. every 200bp?
To form the ‘beads on a string’.
Of what does one nucleosome consist?
A DNA segment –> wrapped around a drum-shaped nucleosome core –> containing 8 histones –> locked in place by a 9th histone.
How can nucleosomes be removed and repositioned?
By replacing/modifying H1 linker protein.
Why can nucleosomes be removed and repositoned?
To expose/hide particular DNA sequences –> effect gene expression.
What can the effect of gene expression, due to hidden/exposed DNA sequences by nucleosome remodelling, be?
Cross-generational.
Inherited.
Is the nucleosome remodelling encoded by DNA?
No.
What must happen to a newly replicated DNA?
It must be repackaged.
Where are histone proteins made?
During S-phase.
Where are nucleosomes gathered?
Behind the replication machine.
What are the parental histone proteins?
Re-cycled.
How are the re-cycled parental histone proteins used?
New histones –> mixed with –> parent histones: in new nucleosomes.
What do new histones mixed with parental histones produce?
Completely new, mixed, and old nucleosomes.
How is the production of completely new nucleosomes from new histones mixed with parent histones called?
Effectively semi-conservative and conservative replication.
What does the highest order of DNA packing produce?
The ‘classical’ chromosome structure.
Where is the ‘classical’ chromosome structure seen?
Only during cell division.
Why is the ‘classical’ chromosome structure seen only during cell division?
Replicated chromosomes –> separated inot –> daughter cells.
What is used to identify chromosomes?
Chromosome size.
Banding patterns.
Where to genetic problem lead some times?
To disease.
How many autosomal chromosome pairs and sex chromosome pairs do humans normally have?
22 autosomal.
2 sex.
Between which organisms does the number of autosomal and sec chromosome pairs vary?
Mammals.
Animals.
Eukaryotes.
Is DNA always found in the ‘classical’ chromosomes?
No.
How is the DNA packed in the nucleus for most of the cell cycle?
Less well-packed.
What does the less well-packing of DNA in the nucleus for most of the cell cycle form after staining?
Light and dark bands.
What is chromatin?
The relaxed structure chromosomal DNA adopts in nucleus.
When does DNA adopt chromatin relaxed structure?
When DNA it is not in the condensed chromosomes form.
What happens during DNA replication to each chromosome?
They are duplicated.
What does each chromosome form once it is dulicated?
‘X’ chromosome structure.
What does an individual have?
A copy of chromosomes from each parent.
How are the copies of chromosomes form each parent called?
‘Chromosome pairs’.
What do ‘chromosome pairs’ have?
Very similar sequences.
What can the very similar sequences of ‘chromosome pairs’ do?
Recombine.
What can the very similar sequences of ‘chromosome pairs’ give when they recombine?
Allele combinations.
What is ‘Karyotyping’?
A diagnostic technique.
What can the ‘Karyotyping’ identify?
Genetic disorders.
Developmental abnormalities.
Cancers.
Where do genetic disorders identified by ‘karyotyping’ occur?
Through large-scale re-arrangement of chromosomal sections.
What is the characteristic of the ‘Edwards syndrome’?
Trisomy at chromosome 18.
How else is he ‘Edwards syndrome’ called?
Trisomy 18.
Where does ‘Edwards syndrome’ result?
In severe developmental problems.
Neonatal death.
How can ‘a-thalassaemia mental retardation syndrome’ called?
(ATR-16).
Based on which characteristics can chromosomes be identified?
Size.
Shape.
Banding patterns.
What did recombination and physical maps allow?
Isolation of specific sequences.
Investigation of gene function.
Mutations’ effect.
Why can chromosomes not be manipulated to investigate gene structure and function?
They are far too big.
What did they need to do to investigate gene structure and function?
Produce smaller segments of chromosome with 1/few genes for experiments in a model organism like E. coli.
When did the multi-disciplinary study of gene function begin?
In 1970.
How did the multi-disciplinary study of gene function begin?
Through collaboration of biochemistry and genetic.
How do we know the multi-disciplinary study of gene function, today?
‘Molecular biology’.
What did key enzymes allow?
Gene cloning.
DNA sequencing.
PCR development.
Where was PCR used?
Genetic engineering.
Genetic diagnostics.
Forensic profiling.
