DNA Replication Flashcards
Criteria for the function of genetic material (4):
1) Store information
2) Ability to replicate
3) Able to be transmitted (passed down) from parent to offspring (mechanism for inheritance)
4) Allow for variation among individuals of a species
3D Structure of DNA
Double helix
Parts of a nucleotide:
1) Nitrogenous Base
2) Deoxyribose (5 Carbon sugar)
3) Phosphate group
1’ Carbon
Connects to the nitrogenous base
(Upper right corner)
2’ Carbon
Where ribose and deoxyribose differ
–> Deoxyribose = Has an H attached to this carbon
–> Ribose = Has an OH attached to this carbon
3’ Carbon
Bonds to an OH
Where bond forms between nucleotides
–> (Bond to phosphate group of another nucleotide)
4’ Carbon
Last carbon (LEFT) in the main ring of the sugar: Connects to the 5’ Carbon and an H atom
5’ Carbon
The one that sticks out on the left and is attached to:
1) 4’ Carbon
2) Phosphate Group
3) 2 H atoms
Where bond forms between nucleotides
–> (Bonds the phosphate on 5’C to the OH group of another nucleotide)
Phosphodiester Bond
“a chemical bond of the kind joining successive sugar molecules in a polynucleotide.”
–> The connecting bond between nucleotides in which the 3’ end of one nucleotide bonds to the 5’ end of another nucleotide
–> Dehydration/Condensation Synthesis
The DNA “poles”
3’ End = Free OH Group
5’ End = Free phosphate group
DNA strands are ___________ in nature…
anti-parallel
Anti- Parallel
Parallel strands running in opposite directions
DNA replication ALWAYS MOVES TOWARDS the ___________ end…
the 3’ end
The Base Pairs (and their bonds)
A-T –> 2 Bonds (weaker)
G-C –> 3 Bonds (stronger)
Purines
Have TWO rings
–> Adenine and Guanine (A + G)
Pyrimidines
Have ONE ring
–> Thymine and Cytosine (T + C)
Complementary DNA strands
The strands are “opposite matches” –> They predict each other
–> Allows info to be stored in a single strand (important for DNA replication)
DNA Replication
Copying of DNA –> Important for the faithful transmission of genetic info from parent to offspring
Semiconservative DNA Replication Model
The 2 strands of the parental molecule separate abd each functions as a template for the synthesis of a new complementary strand
–> NEW DNA MOLECULE = Old strand + New complementary strand
2 other models for DNA replication
1) Conservative model
2) Dispersive Model
DNA Replication Process
1) Separation of DNA strands
2) Maintaining strand separation
3) Relieving strain on DNA
4) Initiating DNA synthesis (priming)
5) Complementary strand synthesis (leading and lagging)
Helicase
Enzyme that binds to each strand of DNA and breaks the H-bonds between them
–> “Unzips” the DNA at the replication fork
Why is helicase needed?
The enzyme separates the 2 parental strands to make them available as template strands (needed for the creation of the complementary strands)
Why must the DNA strands be held apart from each other once separated?
The 2 strands are attracted to each other –> They have a high affinity for being together and so if left alone, they’d just rejoin (and they must be separated for DNA replication to occur)
Single Strand Binding Protein
Binds to the separated strands of DNA and prevents them from rejoining
–> Coats the strands: stabilizes the unwound parental strands
What helps to maintain strand separation
Single Strand Binding Proteins
What happens as a result of the uncoiling of DNA at the replication bubble?
Supercoiling of the DNA downstream
–> Untwisting of the DNA causes twisting and strain ahead of where the strands are separated
Topoisomerase
An enzyme that breaks, swivels, and rejoins DNA strands to reduce strain/tension on the strands
What are the “molecular scissors”?
Topoisomerase
–> Creates small, reversible cuts in the DNA
What is needed for DNA polymerase to begin DNA synthesis?
A primer –> DNA polymerase needs a scaffold in order to add nucleotides
Limitation of DNA polymerase
Can only add nucleotides to a pre-existing strand
–> CANNOT initiate synthesis on its own
Primer
A short (usually RNA) strand that is base paired to the beginning of the template strand
Primer provides a…
FREE 3’ END
–> for DNA polymerase to begin adding on nucleotides
Primers are usually ____________ long
~5-10 nucleotides
dNTP
Deoxynucleotide triphosphate
–> Nucleotide with 3 phosphate groups (2 of which get hydrolyzed to release energy which is coupled to the formation of phosphodiester bonds)
How does DNA polymerase work (with bonds specifically)?
1) Hydrolyzes a dNTP which releases:
a) 2 inorganic phosphorous
b) ENERGY
c) Nucleotide
2) Coupled rxn to the formation of a phosphodiester bond (connecting the nucleotides together)
DNA Polymerase
Synthesizes the new strand from 5’ end to 3’ end (of the new strand)
–>(or from 3’ end to 5’ end of template strand)
Direction of DNA synthesis in respect to the parental/template/old strand
3’ to 5’
Direction of DNA synthesis in respect to the new strand
5’ to 3’
Replication DOES NOT happen…
End to end
What is the problem with replication happening end to end?
Takes too long for the large genome of humans
Origin of Replication
Short stretches of DNA that have a specific sequence recognized by proteins that initiate DNA replication (by binding to and separating the strands)
Replication Bubble
The unwinding of DNA beginning at the origin of replication and moving out in both directions (creates what looks like a little “bubble”)
Origins of replication are very rich in…
A-T bonds –> since these are weaker, therefore easier to break
Bacteria have __________ chromosomes and contain only ONE ___________________________
1) Circular
2) Origin of Replication
Eukaryotic cells have…
MULTIPLE origins of replication
Replication Fork
The ends of the replication bubble –> Where DNA replication takes place (the site where DNA is actively being unwound)
DNA synthesis goes TOWARDS the…
replication fork in BOTH directions
Why are there two different types of strands during synthesis?
Because DNA polymerase can only go in the 5’ to 3’ direction (in respect to the new strand)
Leading Strand
DNA synthesis occurs in direction of the fork (overall) direction of replication
–> CONTINUOUS strand synthesis
–> ONE primer needed
Lagging Strand
DNA synthesis is occurring in the OPPOSITE direction of the DNA replication fork direction
–> Due to this the strand has to be created in fragments (DISCONTINUOUS STRAND)
–> MULTIPLE primers needed (one for each fragment)
Okazaki Fragments
The segments/fragments making up the lagging strand
Steps for Lagging Strand Synthesis
1) Priming
2) Fragment Synthesis
3) Subsequent Fragments
4) RNA Conversion (“fixing”)
5) Connecting Fragments
Lagging Strand: Priming
Primase adds the first RNA primer to initiate the formation of the first fragment
–> Continues adding other primers up along the old strand
Lagging Strand: Fragment Synthesis
DNA polymerase adds nucleotides to the primer forming the complementary fragment
Lagging Strand: DNA polymerase STOPS adding nucleotides when….
It runs into another primer (or beginning of the adjacent leading strand)
Rate at which DNA replication occurs
Adds 50-500 bases per second
DNA replication error rates BEFORE repair
Every 1 in 10^5 bases are “wrong” during replication
DNA replication error rates AFTER repair
Every 1 in 10^10 bases are an error
DNA polymerase secondary function is…
Proofreading: Has a 3’ to 5’ capability in which it acts as an EXONUCLEASE to remove the error nucleotide
–> Like writing a typo (5’ to 3’) and then going back to fix it (3’ to 5’)
Exonuclease
Enzymes that cleave nucleotides (DNA polymerase’s secondary function)
The “End Problem”
When the last RNA primer of the lagging strand gets removed, DNA polymerase cannot fill the gap as there is no free 3’ end to act as the scaffold for the enzyme
= We lose genetic info
What end of what strand is impacted by the “end problem”?
The 5’ end of the lagging strand cannot be completed
Solution to the “end problem”
Telomeres
Telomere
Units of DNA which are sequences, that DO NOT contain genes, that “cap” the ends of a DNA molecule
–> Made up of many repeats of the same sequence (very long))
–> Provides a buffer between the end of the molecule and where the actual genetic info begins
Telomere Functions (2)
1) Protect the loss of genes –> Telomeres will shorten before the genes themselves can be shortened
2) Prevent the staggered ends from triggering the DNA repair mechanism
Telomere Analogy
Telomeres are like the plastic wrapping on the ends of shoelaces
–> Postpones the unraveling but DOES NOT STOP IT
Telomeres _____________ shortening but DO NOT ___________ gene erosion
1) Postpone
2) Prevent
Telomeres become shorter during…
every round of DNA replication
Telomeres tend to be shorter in…
somatic cells of an older person
OR
a cell that has undergone several (SEVERAL) divisions
Telomerase
An enzyme that helps to repair/lengthens the ends of DNA to reverse the shortening
–> Has an RNA template associated with it that allows DNA polymerase to bind extend the overhanging strand with “junk DNA” (repeating non-important sequences)
–> Primase then comes in and adds a primer to the end of this new junk DNA and then DNA polymerase fill in the shortened lagging strand, base pairing with the added junk DNA at the end and then the last bit of important DNA that had been overhanging initially
Telomerase activity is elevated in…
Germ cells
Telomerase in Cancer
Telomerase activity is abnormally high in many cancers
–> suggests that this increased activity stabilizes telomere length, allowing for uncontrolled cell division
Telomeres as a Cancer Protector
Normal shortening of telomeres may protect from Cancer by limiting the number of divisions a cell can undergo
DNA Polymerase III
The major replicative polymerase
–> Using parental DNA as a template, it synthesizes a new DNA strand by adding nucleotides to an RNA primer or pre-existing DNA strand
DNA Polymerase I
–> Has exonuclease capabilities
–> Removes RNA nucleotides of the primers from the 5’ end and replaces them with DNA nucleotides added to the 3’ end of the adjacent fragment
–> Has functions in proofreading as well
Primase
Synthesizes an RNA primer
–> at 5’ end of the leading strand and at the 5’ end of each Okazaki fragment of the lagging strand
Ligase
Joins Okazaki fragments of lagging strand
–> On the leading strand it joins the DNA replaced by the primer to the rest of the DNA strand
Difference in rates of replication between leading + lagging strands
The leading strand is synthesized at twice the rate of the lagging strand.
