BCHM 3010 Nucleic Acids, Chromosome Structure, & DNA Replication
BCHM 3010 Nucleic Acids, Chromosome Structure, & DNA Replication 3010
Popular in Biochemistry
verified elite notetaker
Popular in Department
verified elite notetaker
This 4 page Class Notes was uploaded by Morgan Dimery on Wednesday March 2, 2016. The Class Notes belongs to 3010 at a university taught by Dr. Cheryl Ingram-Smith in Spring 2016. Since its upload, it has received 19 views.
Reviews for BCHM 3010 Nucleic Acids, Chromosome Structure, & DNA Replication
Report this Material
What is Karma?
Karma is the currency of StudySoup.
Date Created: 03/02/16
Nucleotides and Nucleic Acids Continued • Sometimes there are palindromic sequences in DNA-‐ they read the same forward and backward. o This allows you to get base pairing within a single strand and can cause hairpins (stem loops) • Cruciforms are weird structures and they involve both strands of DNA • Hoogsteen base pairs are when 3 strands are interacting with one another-‐ the double strand interacts with another strand from a different helix • Tetraplex DNA can form whenever there are four strands of DNA interacting together • All of these weird things are found in cells that are having some kind of issue! • RNA has a lot of important roles-‐ can be single stranded or double up on themselves to be double stranded o Double stranded RNA is very complex o Messenger RNA-‐ used when you want to copy a small section-‐ translated into protein o Ribosomal RNA-‐ involved with putting amino acids together-‐ translation machinery o Transfer RNA-‐ also involved with putting amino acids together-‐ transfer amino acids to growing polypeptide chains o There are other small RNAs that are involved with determining what genes need to be turned on/off to make proteins RNA can make secondary structures that form together to make 3D structures-‐ this happens through base pairing Chromosome Structure • Really big • Cells hold a lot of DNA • Eukaryotic cells have more chromosomes than bacteria-‐ must be compacted into the cell • Different species have different amounts of chromosomes • Mitochondria and chloroplasts also have DNA-‐ much smaller than genomic DNA • Supercoiling is the first level of compaction for DNA-‐ the helix is being wound up even tighter • Underwinding is when the DNA is turned the other way (abnormal way)-‐ it will start to strain the helix and it could pop open, it is then easier to separate strands o DNA is usually underwound-‐ supercoiling has to relieve the strain caused by underwinding • Topoisomerases release the supercoiling and relieve the strand from strain o Plays a role in DNA replication o Type I-‐ cut in one DNA strand and pass unbroken strand through the break o Type II-‐ cut in both DNA strands and then allow another intact strand to pass through Chromosome structure changes throughout the eukaryotic cell cycle • Histones are positively charged proteins for wrapping DNA o Have roles in gene regulation o They form nucleosomes-‐ DNA naturally likes to wrap around these, the nucleosome can form higher order structures and the DNA will be compacted even more o Areas that do not have a lot of nucleosomes are more transcriptionally active! Proteins can move nucleosomes around DNA Replication • Making a new copy of your DNA • There is ALWAYS base pairing across the two strands • A new strand is built on each old strand-‐ there will be one parental and one daughter strand • Replication is semiconservative o One strand is conserved, the other one is new o Meselson-‐Stahl experiment showed this using N and N 14 § There had to be a mixture of strands in the first generation daughter tubes § They never got back both parental strands together • Replication is bidirectional o Two replication forks, one going in each direction o If it were only unidirectional then it would be a much slower process • Replication is semidiscontinuous o If they were both continuous then one would have to be in the 3’ to 5’ direction and this does not happen o One strand is made as a straight shot, the other is made in chunks o Both go 5’ to 3’ and the same DNA polymerase does both • DNA synthesis is not random, things must fit perfectly in the active site o 3’ –OH group o 5’ phosphate group o Each nucleotide coming in has 3 phosphate groups and when the nucleotide adds, two of them are released • There are two metal ions (Mg ) that help keep the DNA strands separated o They are held in place by Asp groups o The top metal (Metal A) starts the attack of the 3’ –OH on the phosphate o The bottom metal (Metal B) helps to stabilize the phosphate leaving group o These groups are absolutely required in order for DNA polymerase to work! • DNA polymerase requires a template and a primer-‐ RNA o There must be a free 3’ site already there-‐ it cannot start from nothing o RNA polymerase is able to start from zero • DNA polymerase wraps around DNA-‐ DNA becomes double stranded as it exits DNA polymerase • DNA polymerase is able to detect incorrect base pairing o If the correct things are coming in then they fit the architecture really well o If it is incorrect then it just doesn’t fit right o Every 10,000-‐100,000 bases there will be a wrong base put in-‐ some can be lethal! You don’t want to pass this on to your daughter cells o If the incorrect base is inserted then DNA polymerase can go back and correct the errors § It cuts the wrong base out and allows for it to try again § Not just reversing the reaction, it’s a separate reaction-‐ improves replication by 1,000 fold! o There are also enzymes that come along and look at the genome to see if things are accurate • Initiation requires many proteins o DNAa-‐ origin recognition and opening o DNAb-‐ aka helicase, unwinds DNA and makes a big open bubble o DNAc-‐ puts helicase on the DNA and clamps it on o DNAg-‐ adds primers o Gyrase-‐ relieves strain from DNA unwinding • In a nutshell: o Open up DNA o Ensure it is open enough o Add primer • Initiation occurs at origins of replication o There is a downstream unwinding element-‐ contains a lot of A-‐T base pairs so it is weaker and can break easier § The area next to this is strained and this causes the DNA to pop open and a bubble forms (helicase causes this bubble to get even bigger) • Multiple origins make replication even faster-‐ circular chromosomes only have one origin • There are a lot of proteins present at the replication fork • DNAc puts the helicase on ssDNA and holds it there • Helicase unwinds the strands from each other-‐ a ring wraps around the DNA and it is able to move freely, not in a fixed position on the DNA • SSB protects the DNA as it is waiting on the DNA polymerase to come • Primase is what makes the primer DNA Polymerase • DNA polymerase I: no ring to hold it on DNA, involved with proofreading, helps in taking the RNA primer out (removes primers and fills gaps) • DNA polymerase II: no ring to hold it on DNA, mostly just involved with proofreading DNA • DNA polymerase III: ring holds it on DNA, involved with proofreading, goes very fast and is able to remain on the DNA (responsible for synthesizing new strands) Proofreading DNA: 3’ à 5’ (referred to as exonuclease activity) • DNA polymerase III has many different subunits that have different functions o The core is the section that has 3 subunits and that makes DNA and catalyzes the reaction, it is also able to proofread o There are 2 cores, one for each strand of DNA o The τ subunit holds the cores together o The β clamp holds the core onto the DNA-‐ it circles around the DNA and holds it there o The γ clamp is the loader and unloader o The fact that there are two cores allows you to replicate two strands at once! • Each Okazaki fragment has its own RNA primer-‐ must have primase to be able to do this! o Each of the primers are taken off later o DNA gets looped around and fed in the proper direction o There is a primer and a β clamp that will remain there until the DNA polymerase gets on o When the strain becomes too great the core will separate o When the old primer is reached the strand dissociates and leaves the clamp behind-‐ a new clamp and primer are waiting for the DNA polymerase to come and start working with them