DNA replication Flashcards
what is the big idea of DNA replication?
DNA replication copies the entire chromosome and occurs during the S-phase (synthesis) of the cell cycle
what does it mean by replication is semi-conservative?
it uses an existing parent
strand as the template
Who are the people you know in timeline order?
Levene
Chargaff
Franklin & Wilkins
Pauling
Watson & Crick
what did Phoebus Levene determine correctly about DNA
- DNA is made up of chains of nucleotides
- a nucleotide is a phosphate linked to a sugar linked to one of four nitrogenous bases
- nucleotides link in series phosphate to sugar
What did Phoebus Levene get wrong about DNA?
the tetranucleotide hypothesis, which is the idea of a repeating tetramer, order of bases exist in a fixed pretitive sequence, thus all bases appear in equal ratio
What did Erqin Chargaff discover about DNA?
isolated DNA from different organisms and measured numbers of each base present and found the number of A=T and the number of C=G
What did Linus Pauling propose? Right or wrong?
proposed the alpha helix secondary structure in proteins, but made it the idea of a triple helix which was wrong
what else did Linus Pauling get wrong?
- phosphate groups were shown as neutral molecules
- phosphates organized in the core for the helix negative charges on oxygen would repel
- bases facing outwards
What did Rosalind Franklin & Maurice WIlkins do?
x-ray diffraction of crystalline DNA fiber
what is x-ray crystallography?
a physics approach to examining biological molecules where a pure crystallized sample of the molecule is isolated, Xrays bombard the crystal sample and refract the rays in multiple directions and the diffraction pattern is analyzed to determine the moldecule’s 3D structure
what did the X-ray ‘expose’
- a double helix structure
- with a backbone of alternating phosphate and sugars
- nitrogenous bases are in the middle of the molecule
- bases are at right angles to the backbone
- molecule is a uniform helix with consistency in helical dimensions
what are the 4 measurements the x-ray interpretation of DNA was able to yield?
diameter
- distance between one helical turn
- distance between one stacked base pair
- angle of helical turns
what did James Watson and Francis Crick find?
- determined rules for base pairing, hydrogen bonding between AT, GC and the width of a purine and pyrimidine pair
What is Chargaff’s ratio?
the idea that the ratio of AT is 1:1 and the ratio of CG is also 1:1
How does Chargaff’s ratio dispute Levene’s tetranucleotide hypothesis
Leven’s idea was that all bases repeat equally as 1 of each base is in the tetranucleotide. But Chargaff found that there were different ratios of C to T so it was wrong
Describe the error in Pauling’s triple helix model
- phosphate groups were shown as neutral
- phosphates were in the core of the helix as the negative charges on the oxygen would repel
- bases faced outwards
what technique that Franklin and Wilkins used in determining the DNA structure
x-ray diffraction of crystalline DNA fiber
what are the three methods of DNA replication?
conservative, semi-conservative and dispersive
describe the conservative DNA replication model
the parental double helix remains intact and an all new copy is made
describe the semi-conservative DNA replication model
the two strands of the parental molecule separate and each functions as a template for synthesis of a new complementary strand
describe the dispersive DNA model
each strand of both daughter molecules contains a mixture of old and newly synthesized parts
What was the first step of Meselson and Stahl experiment?
Grew E.Coli cells in heavy nitrogen. centrifuge the DNA - it shows up heavy as DNA contains nitrogen atoms.
What was the second step of the Meselson & Stahl Experiment
transfer the E.Coli cells into a medium with light nitrogen (N14) where they went 1 round of replication, were centrifuged again
What was the third step of the Meselson & Stahl Experiment
second round of replication in light medium the centrifuged
if DNA underwent conservative replication, what can be expected after the second step?
2 bands
if DNA underwent semi-conservative replication, what can be expected after the second step?
1 band
if DNA underwent dispersive replication, what can be expected after the second step?
1 band
what did meselson and Stahl observe after the second step?
1 band
if DNA underwent conservative replication, what can be expected after the third step?
2 bands
if DNA underwent semi-conservative replication, what can be expected after the third step?
2 bands
if DNA underwent dispersive replication, what can be expected after the third step?
1 band
What did Meselson and Stahl observe after the third step
2 bands relatively closer together than compared to the conservative ( + conservative already disproven)
how does DNA replication initiation differ between prokaryotes and eukaryotes
prokaryotes: replication begins at one fixed origina -> bidirectional until all DNA is replicated
eukaryotes: multiple origins of replication
ori
origins of replication
sites on DNA where replication begins
contains specific sequence recognized by replcation machinery (enzymes)
often high in A-T base pairs
describe replication initiation
origin sites are separated and separate outwards forming bubbles with replication forks at each end. Separates until there are two daughter DNA molecules
primer
a short segment of RNA needed to initiate DNA replication
why is priming needed?
RNA polymerase and DNA polymerase are different - have different abilities:
RNAP can start a new chain without an existing end all required is a template
DNAP can only add nucleotides to the end of an existing chain
primase
and RNA polymerase (RNAP) which synthesizes the primer by adding ribonucleotides that are complementary to the DNA template
polymerase
enzyme that makes polymers
helicase
enzyme that disrupts H bonds between two strands of DNA to separate the template DNA strands at the replication fork
single strand binding proteins (SSBPs)
proteins that bind to unwound single stranded regions of DNA to keep the template strands apart during replication
topoisomers/topoisomerase
enzymes that can break bonds in DNA and the reform the bonds - can release the twists made in DNA replication like DNA gyrase
DNA polymerase
enzyme which synthesizes nucleotide chains
how do the roles of DNAP I and DNAP III differ?
DNAP III catalyzes the elongation of DNA molecules by adding nucleotides to the 3’ end of a pre-existing nucleotide whereas DNAP I replaces the RNA primer with DNA complementary to the template
summar:
DNAP III elogates DNA strand
DNAP I replaces RNA with DNA
where are DNAP I and II found?
eukaryotes
What is the problem at the replication fork caused by the antiparallel nature of DNA
one parental strand has its 3’ end while the other has 5’ end at the fork but DNA synthesis can only proceed in a 5’ to 3’ direction to DNA before the 5’ end aren’t synthesized
describe leading strand
synthesized continuously and polymerizes int he same direction as the replication fork
Describe the lagging strand
synthesized in short, discontinuous segment of 1000 to 2000 nucleotides called Okazaki fragments
polymerization is in the opposite direction of the replication fork
okazaki fragments
the discontinuous segments of DNA on the lagging strand
name and describe the enzymes on the lagging strand
DNAP III synthesizes DNA
DNAP I replaces the RNA primer with DNA complementary to the template
DNA ligase joins broken pirces of DNA by catalyzing the formation of phosphodiester bonds
When does DNA replication reach termination for prokaryotes and eukaryotes?
for prokaryotes: reaches the end of the chromosome
for eukaryotes: replication bubble or fork meets another replication bubble or fork
whats the replication problem at the ends of linear DNA
DNA gets progressively shorter with each round of replication
what is a telomere and its purpose
it protects the chromosomes from being eroded, serves as a protective cap to prevent unwinding
telomere structure
consists of multiple repeats of short genetic sequence in humans TTAGGG at the ends of eukaryotic chromosomes that are noncoding
cellular aging - the two types and their name
senescence - where cells stop growing and dividing
OR
apoptosis - programmed self-destruction
telomerase + its mechanism
enzyme responsible for adding telomeres to chromosomes extends the chain by reverse transcribing off its internal RNA template (repeats) binds to 3’ end of parental strand
ribonucleoprotein
an enzyme that contains RNA and protein, in humans has an RNA component that contains the internal sequence AAUCCC
reverse transcriptase
synthesis of complementary DNA from an RNA template, extends the 3’ end of the chromosome
what happens if telomere is not long enough
conding DNA gets damaged
what cell types have telomerase activity
germ line cells
cancer cells
