Topic A Flashcards
What properties must the genetic information posses?
Four key criteria:
Must encode information
Transmission
Replication
Variation
Who solved DNA structure
Watson and Crick solved the structure of DNA in 1953
Phoebus Levine
Bio chemist, American
Structure = building blocks
“Pure silver Ag”
“Shorter name, bigger structure”
Described how bases put together
3 building blocks
Sugar (pentose)
1 or more phosphate group attached to Nit bases
Nitrogenous base: purine or pyrimidine
Purine —> double rings, A & G
Pyrimidine —> 1 ring, C & T & U
Carbons in sugar numbered normally, in sugar tho are prime
DNA doesn’t have OH on 2’ C but RNA does
Showed how nucleotides attached together = polynucleotide
Joined together by phosphate groups —> polarity to this, free unattached OH 3’ end, free 5’ phosphate group end
OH backbone
Rosalind Franklin
British
X-ray —> determined 3D images of DNA
Crystalogist
Able to determine structure was a double helix based on distance between bases, was a fixed Å and seems to be 10 nucleotides for every 360° turn
Erwin Chargaff
Composition of diff bases for diff organisms
For every organism looked at, all 4 bases present
Patterns of proportion of bases in each species
#G = # C (nG = nC)
#T = #A (nT =nA)
#G + #A = #C + #T (G + A = C + T)
Amount of purine = amount of pyrimidine
Key features of Watson and Crick model of DNA
The polynucleotide chains form a double helix
2. The polynucleotide chains are antiparallel
3. The two polynucleotide chains are complementary to one another
4. The deoxyribose sugar and the phosphate groups form the backbone while the nitrogenous bases face the interior of the helix
5. The diameter of the double helix is 20 Å
6. A purine base is always a cross from a pyrimidine base
7. Nitrogenous bases on opposite strands interact via hydrogen bonds
8. There are two H-bonds between A and T and three between G and C bases.
9. Adjacent nucleotides are joined to each other by a phosphodiester bond
10. There are 10 nitrogenous bases per 360° turn of the double helix.
Conservative model
after one round of replication, half of the new DNA double helices would be composed of completely old, or original, DNA, and the other half would be completely new. Then, during the second round of replication, each double helix would be copied in its entirety.
2 parental strands always stick together
Original double helix: R R
1st replication: R R B B
2nd replication: R R B B B B B B
Tube O: red
Tube 1: red and blue
Tube 2: red and blue
Semi-conservative model
every double helix in the new generation of an organism consists of one complete “old” strand and one complete “new” strand wrapped around each other
Original double helix: R R
1st replication: R B R B
2nd replication: R B B B R B B B
Tube O: Red
Tube 1: purple
Tube 2: red and purple
Dispersive model
the original DNA double helix breaks apart into fragments, and each fragment then serves as a template for a new DNA fragment. As a result, every cell division produces two cells with varying amounts of old and new DNA
Original double helix: R R
1st replication: R&B R&B R&B R&B
2nd replication: R&B R&B R&B R&B R&B R&B R&B R&B
(More blue in 2nd tho)
Tube O: red
Tube 1: purple
Tube 2: purple
Messelson-Stahl Experiment
1958
Objective: Identify the mechanism of DNA replication
Materials and Methods
E. coli (grew quickly —> gens over 1 day)
15N vs 14N (radioactive isotopes of nitrogen, have diff neutrons)
CsCl gradient centrifugation
In a tube, put DNA in it, then centrifuge, DNA would split based on how heavy or light, can then figure out what nit isotope present and how much of it
Initiation of Replication contents
Ori C (where rep starts on E.coli)
Site of initiation
Fixed location
~275 bp (bases)
GATC methylation sites (DNA repair mechanisms)
3 AT-rich 13mers (nucleotide A & Ts, Not strongly held together)
5 DnaA boxes(9 mers)
Initiation of Replication
DnaA proteins bind to DnaA box sequences and to each other.
Additional proteins that cause the DNA to bend also bind. This causes the region to wrap around the DnaA proteins and separates the AT-rich region.
(Need to denature/melt helix in order to open and get to cellular machinery in order to replicate)
Two DNA helicases (DnaB proteins) bind to the origin. DnaC proteins assist this process. (Helicase helps stop helix from binding back together. Have replication bubble)
DNA helicases separate the DNA in both directions, creating 2 replication forks. (DNA actively being replicated/new DNA being made)
Origin of replication in middle of replication bubble, have replication forks on each end of the opening (bi-directly process)
Mechanism of Replication
KEY PLAYERS 1-4
- Helicase (DnaA/DnaB)
- Single Stranded Binding Proteins (hard for DNA to denature, sit outside of DNA)
- Topoisomerase ( sit upstream of fork, job = help unwind DNA, relives supercoiling effect from occurring. Cutting DNA temporarily and then stitching it back together)
- Primase (build RNA polymer)
Mechanism of Replication
KEY PLAYERS 5-7
- DNA PolymeraseIII (bulk of synthesis)
• 5’ ⟶ 3’ Polymerase Function
• 3’ ⟶ 5’ Exonuclease Function (AKA Proofreading Function) (cuts out bad base, does that by going backwards on strand) - DNA Polymerase I
• 5’ ⟶ 3’ Polymerase (cleans everything up)
Function
• 3’⟶5’ Exonuclease Function (AKA Proofreading Function)
• 5’ ⟶ 3’ Exonuclease Function
(removes primer, added nucleotide, proof reads, DNA ligase) - DNA Ligase ( DNA strands binding, phosphodiester bond)
Mechanism of Replication key notes
Remember that DNA replication is bidirectional and initiates at an Ori
One new strand will be synthesized in a continuous fashion
One new strand will be synthesized as a series of Okazaki fragments
Let’s put everything together and look at the entire replication bubble
5’ —————— 3’ | 5’ ——————3’
3’ <———— 5’ | 3’ <—<—<—5’ (lagging)
5’—>—>—> 3’ | 5’ ————> 3’ (leading)
3’ ——————5’ |3’ ——————5’
