New Material as of March 10

Telomere – region of repetitive sequences on the end of chromosome. Doesn't code for protein so an organism can afford to lose them. Telomere: the region of DNA the RNA primers attach to. Help chromosomes from breaking apart. Are needed because wherever RNA primer was on end of linear chromosome, DNA can’t be replicated. Chromosome gets shorter with each round of replication because DNA can’t be replicated where RNA primers are located – new primer has to be formed with each round of replication. Enzymes can’t copy end of chromosomes because of RNA primers. After too many rounds of replication, the DNA strand gets too short, and the cell commits apoptosis (kills itself off) – if DNA gets too short, it can’t code for proteins properly anymore. DNA polymerase can only move in 5 prime to 3 prime direction

Why haven’t things with linear chromosomes gone extinct?
Sex cells have the ability to regenerate telomeres. No somatic cells have this ability. Telomerase (enzyme) in gametes regenerates telomeres.
Why can bacteria divide indefinitely?
Bacteria have circular chromosomes. DNA polymerase can go all around chromosome in 5 prime to 3 prime direction without stopping. There is no loss of DNA during bacteria cell replication.
Repair to errors in DNA replication
3 ways to correct errors of DNA replication: DNA proofreading, mismatch repair, excision repair
Because DNA polymerase is copying DNA strand really fast, sometimes wrong base paired between new and original strand
Mismatch repair system/Excision repair:
Enzymes scan length of DNA, identifying mismatched swatches (look for missing hydrogen bonds between bases – kink in double stranded DNA)
On new DNA strand, enzymes snip out (break sugar-phosphate backbone) swatch of DNA which contains mismatched base (bases surrounding mismatched base are snipped out). New swatch is synthesized. Then, DNA ligase comes in to make the strand whole (like with Ozaki fragments)
How does the enzyme know which strand is the original strand and which is the old strand? methylation
Methylated DNA is older
Methylation: methyl (carbon with 3 hydrogen atoms) groups are added to some bases of the DNA. Happens after every other step of DNA replication. Because of methylation, enzyme can tell which strand is the original. Methylated strand is original strand.

DNA polymerases usually have “proofreading” abilities. While copying strand, might synthesize wrong base. DNA polymerase can “tell” if they’ve placed an incorrect base on the new strand – hydrogen bonds don’t form (forming a “kink”). If an incorrect base has been placed, DNA polymerase stops and backs up 1 base, “snips out” wrong base, and then continues on by replacing wrong base with correct base.
Because of proofreading ability, spontaneous mutation rate is only about 1 mutant base pair per 10 billion base pairs copied (really low)
DNA polymerases without proofreading ability have a spontaneous mutation rate of about 1 X 10^5 bases copied
DNA polymerase – enzyme (ase). Makes new DNA strand. Polymer = many parts / molecules connected together
Size of genomes (genome - all of the DNA within one cell)
Prokaryotes – range in size of 500 thousand base pairs (bp) to 8 million base pairs
Ex E. coli has 5 million base pairs (bp) in genome
Ex Humans 80 million bp
How many spontaneous mutations would occur after 1 human cell divides one time? 80 million/10 billion = .008
How many rounds of replication would have to occur for 1 mutation to occur? 125 (How is this determined?) (If DNA polymerase didn’t have proofreading ability, mutations would occur more often and in greater numbers)
PCR (polymerase chain reaction)
Technique we’re going to use in lab
Relies on the fact that DNA polymerase will copy strand of DNA given other correct circumstances (DNA polymerase needs a RNA primer or enzyme that makes primer, strand to be replicated (template DNA), and a pool of nucleotide triphosphates)
DNA strands will unzip themselves if they’re heated to 95 degrees C
EX: heat up double strand of DNA to 95 degrees C, strands unzip. Let strands cool to 50 degrees C. If you have DNA polymerase, ntps, primers, and a template DNA, new strands will be synthesized. Proteins don’t like being heated so high – they die

Thanks for posting this; I ran out of room on my sheet to keep taking notes.

Ya thanks!! I swear I never get everything written down in class.

Good notes for sure!

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