Ch. 16 Can Skip 16.5 on cancer if you want, but kinda neat
#DNA
DNA is the heritable material. Book goes into the clever experiments that showed this.
DNA is pretty simple.
- phosphate
- doxyribose sugar
- four nitrogenous bases -- adenine guanine, cytosine, thymine, uracil, and hypoxanthine
- uracil and hypoxanthine mostly in RNA and tRNA
Purines: adenine and guanine Pyrimidines: thymine and cytosine
Nucleotide is the combination of a base (ATGC) a doexyribose sugar, and a phophate group (draw 1)
DNA is double stranded with two strands of nuleotides wound together in double helix. It's a right-handed structure (show fist) although left-handed DNA exists (z-DNA) it is rare. Laugh at people who draw the helix wrong.
Backbone is made of phophate group of one nucleotide linked to ribose of the next. The two strands are held together how ? hydrogen bonding.
A always pairs with T and G always pairs with C
But GC content varies among species. GC content higher in bacteria -- especially in archae living in thermal vents. Why ? B/c G-C 3 H-bonds so are stronger, takes more energy (temp) to separate them
Direction on DNA is important. One end is called 5' and the other end 3' -- these numbers come from the numbering of the carbon atoms of the doxyribose sugar. A molecule of DNA starst with phosphorylated 5' carbon and ends with hydroxyl group on a 3' carbon.
Replication is semiconservative (meaning ?) Each daughter DNA inherits 1 strand of original DNA + 1 new one
The helix is opened and unwound at the replication fork. An enzyme called DNA polymerase III then adds nucloetides at the 3' end. So DNA is syhtnesized 5'->3'.
Draw replication fork. Anyone see problem with this?
Leading strand gets continuous replication Lagging strand cannot. Polymerase has to stop, come back and start again.
But polymerase can't start a new DNA, only extend it. So different enzyme sets down a primer a short strand of DNA that primes DNA sythesis.
DNA pol I removes primer via its exonuclease activity (nculease = ???), and then fills in gaps between Okazaki fragments and an enzyme called DNA ligase does ? joins the bits together.
In total, can do this at ~1Kb/sec!
The whole process actually takes a number of proteins and protein complexes. The replisome Figure 7-20 for bacteria, but very similar in Eukaryotes.
- pol III
- beta clamp to keep pol III attached
- ligase for the okzazaki fragments
- helicase to unwind the DNA. what problems does this cause ?
- single strand DNA could bind: single-stranded binding proteins prevent re-annealing
- overwinding: topoisomerase removes any extra twists
In E. coli, replication starts from one spot, the OriC or origin of replication. In Eukaryotes, DNA replicaiton starts from several origins at once, going in both directions.
What's another difference between Euk and bacteria ? In Eukaryotes, DNA is in chromatin, so replisome has to be able to unwind DNA from nculeosomes to access it. Additional enzymes (e.g. chromatin assembly factor-1) required.
- go back to ch01 and read.
All this is well and good, but there's a problem. DNA gets shorter each time. Why ?
Lagging strand requires addition of primers. Draw part of
Because Pol 1 can only ad to 3' end, it can't fix this problem at the telomere
Telomerase! Telomeres made up of repititve short fragments. Figure 7-28 in book explains details, but because it's repetitive telomerase can use a single known RNA fragment as a template to bind, create new overhang, elongate, repeat. Then finally fill in with normal DNA pol in 5'->3' fashion.
Telomerase also binds to telomeres to form protective cap. Why needed ? So cell doesn't think chromosome end is a DSB!