Enzymes Before I get into enzymes let me clarify some terminology Kinases are enzymes that phosphorylate other molecules Phosphorylate is just a phrase that refers to activating different cells in the cell cycle by adding a phosphate group There are a few enzymes we need to look at to help with the cell cycle I covered these in my Chapter 10 Bio Notes but they are Cyclins named so because they are regulatory proteins in a cyclical fashion that increase going into mitosis and degrade coming out of mitosis Cyclin dependent kinases Cdks are a type of kinase that need cyclin Complexes of cdk the enzyme and cyclins the regulator function to trigger different stages of cell cycle by phosphorylating other molecules to activate them Cyclins cyclin dependent kinase This means that when cylins increase in quantity MPF does too I should point out MPF is just one example of cyclins Cdks that occurs during the end of the S phase The anaphase promoting complex is another one and it receives signals to make sure the spindles are at the right spot Cdk cyclin complexes can phosphorylate chromosomal proteins to initiate Mitosis it can phosphorylate microtubule associated proteins to activate the spindle and it can phosphorylate an enzyme that degraded cyclin which leads to cyclin concentrations decreasing Checkpoints Checkpoints are points in the cell cycle where the condition of the cell is assessed to determine if it should move to the next phase If it fails the test cell division is halted for repair Checkpoints are sensitive to internal and external factors The checkpoints are 1 G1 S aka START the start of the restriction point the commitment to divide and begin DNA replication Growth factors are important here 2 G2 M the checkpoint is where MPF comes in to make sure the replication is completed 3 Anaphase the checkpoint where chromosomes separate during anaphase Once separated they must segregate into new cells The anaphase promoting complex above makes sure here These are irreversible steps We need to check to make sure everything is good before DNA replication because if the DNA divides with incompletely replicated DNA it would probably be lethal If it divides with damaged DNA it could be lethal or cancerous Therefore the cell assesses itself with checkpoints DNA and Bases In 1869 Swiss chemist Friedrich Miescher discovered a white substance from the nuclei that was slightly acidic so he called it nucleic acid The two main kinds of nucleic acids are DNA and RNA and nucleic acids are made of nucleotides DNA contains 3 main parts 1 A 5 carbon sugar 2 A phosphate group 3 A nitrogenous nitrogen containing base The big twist of DNA is called the major groove and it is where the backbones of the two strands are far apart The smaller portion of the DNA is called the minor groove and it is where the backbones are close together and the bases are connecting The bases are Large Purines A and G Small Pyrimidines C T DNA only and U RNA only A and T form two hydrogen bonds G and C form three hydrogen bonds and are therefore easier to melt and are therefore harder to melt We refer to the five carbons on a 5 carbon sugar with the prime symbol In DNA the phosphate connects to the 5 carbon atom and the hydroxyl OH connects to the 3 The 5 end has a phosphate and the 3 end has the sugar The phosphodiester bond links the hydroxyl of the 3 atom to the phosphate of the 5 atom It is called that because the phosphate is now linked by way of ester bonds This forms long acid polymers Erwin Chargaff discovered that DNA isn t constant It s complex and it varies a lot but it always has the same amount of A and T and it always has the same amount of C and G Chargaff s rule states C G and A T or A U for RNA The two strands of the helix are made of repeating sugar and phosphate units which we call the phosphodiester backbone A single phosphodiester strand has inherent polarity because the 3 side ends with OH and the 5 side ends with PO4 Thus they are referred to as having 3 to 5 polarity or 5 to 3 polarity DNA strands are antiparallel and run in opposite directions one running 3 5 and the other running 5 3 The H bonds between bases on the interior hold each individual strand together The two strands are then connected by ladders of covalent bonds The new DNA strand is copied by pairing of complementary bases using the old strand as a template AKA semiconservative replication 1 Two sides of the double helix have to separate 2 Each strand is a template for a new strand with complementary bases A T C G 3 New nucleotides only added to existing nucleotides 4 Strands grow from 5 end to 3 end 5 Enzymes link nucleotides at their sugar phosphate groups This will require a lot of enzymes 1 Primase 2 Helicase 3 DNA polymerase 4 Ligase The three stages are Initiation 1 2 Elongation 3 Termination process begins majority of building blocks are added process ends DNA Replication Phases A large protein complex the replication complex replisome interacts with template strands All chromosomes have an origin of replication which is a base sequence in DNA where replication begins The proteins in the replisome bind to the DNA sequence in the origin Side Note A DNA molecule gets copied at several points simultaneously and the copied DNA goes in lots of different directions But for the purposes of this course we only ever focus on one snapshot one copied strand going in one direction DNA replication begins with a short primer a starter strand of RNA made by the enzyme primase The primer is complementary to the DNA template one of the strands that split and the DNA polymerases an enzyme that accelerates this reaction and the primer attracts the polymerase to it This process occurs from the 5 end to the 3 end DNA unwinds at the replication fork where the unwound DNA is exposed to bases with the aid of the enzyme helicase One new strand the leading strand is oriented to grow at its 3 end as the form opens One strand the lagging strand is oriented so that it s exposed 3 end gets farther from the fork After they unwind proteins prevent the DNA template strands from reforming via hydrogen bonds This allows elongation of the leading and lagging strands without the template DNA coming back together DNA polymerases work very fast They are processive meaning they can catalyze many polymerizations each time they bind to DNA Each Okazaki fragment of the lagging strand requires its own primer synthesized by the primase DNA polymerases III adds nucleotides