Nucleic+Acids+(Lecture+Guide)


 * //__Nucleic Acids (Lecture Guide) __//**
 * **__Early DNA Research __**
 * DNA serves as blueprints to build the proteins for our phenotype which is the reason why people are studying so much.
 * __DNA by the Numbers __
 * Each cell has about 2m of DNA
 * The average human has 75 trillion cells
 * The average human has enough DNA to go from the Earth to the sun more than 400 times
 * DNA has a diameter of only 0.000000002m.




 * It all started with Federick Griffith
 * What he did if that was an experiment where if a mouse was injected with the Rough Strain or R -strain bacteria (bacteria with a surface that seemed rough). The mouse was immune and nothing would happen to the mouse.
 * But if a Smooth Strain or S-strain bacteria (viralent and could kill) the mouse died. So what he did was heat up the S-strain to kill the bacteria and put it in and it did not affect the mouse.
 * He then put the R-strain and dead S-strain and it killed the mouse.
 * He then noticed that the dead S-strain began to give the R-strain deadly component that made it deadly showing that it is possible to change one life form into another by changing something in the life form
 * Oswald Avery, Maclyn McCarty, & Colin MacLeod repeated the experiment by extracting every part of the cell including the DNA and just put that into the bacteria making it immediately change proving that it was the DNA and the key.
 * Alfred Hershey & Martha Chase then began studying bacteriophages (virus which attack bacteria, insert their own DNA in the bacteria changing its DNA). They wanted to know what about the virus actually changed the bacteria. They knew that a virus was a capsule that contained genetic material and had leg like objects made of protein to connect to the bacteria. They wanted to know whether the DNA or protein caused the bacteria to change. They did it using molecular tagging and determine whether there was more more of DNA (in this case green) or protein (red) within the cell.
 * Then Erwin Chargaff studied chemical composition of DNA and discovered the DNA pairing rules. 1st he discovered what DNA was made of which was sugar, phosphate groups, nitrogenous bases including adenine, thymine, guanine, & cytosine and he discovered that these were made of different structures; two purines that are double ringed -> adenine & guanine/ and two pyrimidines that are single ringed -> cytosine & thymine. He then notices that the amount of adenine is equal to thymine and the amount of guanine is equal to cytosine and comes up with the idea of base pairing rules which is basically A = T meaning that they must be paired and C = G meaning that these must be paired.
 * <span style="font-family: 'Comic Sans MS',cursive;">Then Maurice Wilkins invented the X-Ray Diffraction Machine which was used to study the molecular structure of small things. Then scientist Rosalinda Frankiln took a picture of a DNA molecule showing that without a doubt that it was a Helical molecule.




 * <span style="font-family: 'Comic Sans MS',cursive;">Then James Watson & Franklin Crick were the first to create a DNA Double Helix Structure model and won the nobel prize
 * <span style="font-family: 'Comic Sans MS',cursive;">Lastly, Matthew Meleson & Franklin Stahl explained a procedure of how DNA was actually copied with semi- conservative model of DNA Replication


 * **__<span style="font-family: 'Comic Sans MS',cursive;">Nucleic Acids __**
 * <span style="font-family: 'Comic Sans MS',cursive;">Monomers are nucleotides and are composed of a nitrogenous base, pentose sugar, & a phosphate group (PO4)
 * __<span style="font-family: 'Comic Sans MS',cursive;">Nitrogenous Bases __
 * <span style="font-family: 'Comic Sans MS',cursive;">//Purines// - have 2 rings
 * <span style="font-family: 'Comic Sans MS',cursive;">Adenine & Guanine
 * <span style="font-family: 'Comic Sans MS',cursive;">//Pyrimidines// - have a single ring
 * <span style="font-family: 'Comic Sans MS',cursive;">Thymine & Cytosine
 * <span style="font-family: 'Comic Sans MS',cursive;">The ATP Connection: ATP is closely related to nucleic acids;similar in structure to the nucleotide based on Adenine fromRNA and is composed of Ribose, adenine and 3 phosphate groups
 * <span style="font-family: 'Comic Sans MS',cursive;">One strand of DNA has the backbone of the molecule is alternating and deoxyribose sugar bound togetherby phosphodiester bonds- The shape of DNA is a long polymer and the basic shape is like a twisted ladder or zipper and is two strands twisted together; double helix
 * <span style="font-family: 'Comic Sans MS',cursive;">Remember, DNA has two strands that fit together like azipper. The teeth are the nitrogenous bases but why do theystick together but why?
 * <span style="font-family: 'Comic Sans MS',cursive;">It goes back to Chargraff's Rule: Adenine and Thyminealways join together (2 bonds) and Cytosine and Guanine always join together (3 bonds)
 * <span style="font-family: 'Comic Sans MS',cursive;">It's all hydrogen bonds. The bonds are weak but there are millions and millions of them in a single DNA molecule.With the bonds C & G always bond and A & T always bond causing a double helix






 * <span style="font-family: 'Comic Sans MS',cursive;">The "legs of the ladder" are the phosphodiester backbone and the "rungs of the ladder" are the nitrogenous base(A, T, G, or C)


 * **__<span style="font-family: 'Comic Sans MS',cursive;">Basic DNA Structure __**
 * __<span style="font-family: 'Comic Sans MS',cursive;">DNA Shape (Twisted Double Helix) __
 * <span style="font-family: 'Comic Sans MS',cursive;">Diffraction X-ray Pictures
 * <span style="font-family: 'Comic Sans MS',cursive;">Base Pairing Rules (10 Base pairs b/n each turn)
 * __<span style="font-family: 'Comic Sans MS',cursive;">DNA Width (2nm or 20A) __
 * <span style="font-family: 'Comic Sans MS',cursive;">Hydrogen Bonds connect the two strands
 * <span style="font-family: 'Comic Sans MS',cursive;">Base pairing (Pyrimidine + Purine = Always 3 rings)
 * __<span style="font-family: 'Comic Sans MS',cursive;">DNA Base-to-Base Length (0.34nm or 3.4A) __
 * <span style="font-family: 'Comic Sans MS',cursive;">Phosphodiester bonds
 * <span style="font-family: 'Comic Sans MS',cursive;">Nucleotide Percentages (A/T = 30; C/G = 20)
 * <span style="font-family: 'Comic Sans MS',cursive;">Base pairing rules
 * <span style="font-family: 'Comic Sans MS',cursive;">that the percentage of A = T making them bond and the percentage of C = G making them bond.
 * <span style="font-family: 'Comic Sans MS',cursive;">//Antiparallel strands//: the orientation of one strand will be the opposite of the other
 * <span style="font-family: 'Comic Sans MS',cursive;">Base Pairing
 * __<span style="font-family: 'Comic Sans MS',cursive;">DNA full turn length (3.4nm or 34A) & Base pairs per twist (layer per turn = 10) __
 * <span style="font-family: 'Comic Sans MS',cursive;">Weak vertical attractions b/n the 3 rings causing it to turn.
 * <span style="font-family: 'Comic Sans MS',cursive;">The twist adds stability to the DNA and makes it stick together better.
 * __<span style="font-family: 'Comic Sans MS',cursive;">Direction of DNA helix twists (B-turn is normal turn) __
 * <span style="font-family: 'Comic Sans MS',cursive;">When manipulated, it may be an A-turn
 * <span style="font-family: 'Comic Sans MS',cursive;">But if turning in opposite direction or the left, it is a Z-DNA or Southpaw DNA and may lead tomutations during copying.

<span style="font-family: 'Comic Sans MS',cursive;">If more information needed watch the Nucleic Acids videos at: []
 * **__<span style="font-family: 'Comic Sans MS',cursive;">DNA Replication __**
 * <span style="font-family: 'Comic Sans MS',cursive;">The point of replication is to make to identical copies of DNA polymer. The old strands are used as a template for the newDNA- S phase: during interphase of cell cycle in the nucleus of eukaryotes to make the sister chromatids
 * <span style="font-family: 'Comic Sans MS',cursive;">Y-Fork (Replication Fork): the funny little structure that forms when the DNA strand unzips.
 * <span style="font-family: 'Comic Sans MS',cursive;">Replication Bubbles: it is not much a fork but a bubble that the DNA copies itself; Analagy: If you are building a road,the fastest way of building a road is have th road start construction at different locations then have several teams build the road at once and is completed when the two areasmeet. One section of the bubble has the DNA has the replicating and when it meets the other end, it creates one strand of DNA.
 * <span style="font-family: 'Comic Sans MS',cursive;">Nucleoside Triphosphates: molecules that ressemble ATP going into DNA. One of the molecules with go within the Y-Fork area to be able to get a nitrogenous base. The bonds on the phosphate groups break releasing energy. The energy will beused to connect the nucleotide to the DNA strand.
 * <span style="font-family: 'Comic Sans MS',cursive;">Replication Point of Origin: area in which DNA replication will begin and is farthest away from the Y-Fork and copied into the direction of the Y-Fork (3-5)
 * <span style="font-family: 'Comic Sans MS',cursive;">Leading Strand: a new strand being built in a 5-3 direction;DNA polymerase can only add to the 3' end of the DNA.The strand is synthesized as a single strand from thepoint of origin toward the open in replication fork <span style="background-color: #00ff00; color: #ff0000; font-family: 'Comic Sans MS',cursive;">
 * <span style="font-family: 'Comic Sans MS',cursive;">Lagging Strand: synthesized discontinuously against overall direction of replication and is made of many short segments from the fork to the origin in a 3-5 direction
 * <span style="font-family: 'Comic Sans MS',cursive;">Okazaki Fragment: series of segments on the lagging strand; must be joined by an enzyme called ligase together to make one strand.
 * __<span style="font-family: 'Comic Sans MS',cursive;">Enzyme/Steps __
 * <span style="font-family: 'Comic Sans MS',cursive;">//Topoisomerase// -> Uncoil/Untwist & Stabalize
 * <span style="font-family: 'Comic Sans MS',cursive;">//Helicase// -> Unzips the genes and creates Y-Fork
 * <span style="font-family: 'Comic Sans MS',cursive;">Single Strand Binding Proteins -> Stabalizes unpaired strands
 * <span style="font-family: 'Comic Sans MS',cursive;">//Primase// -> Marks starting spot of DNA copy process
 * <span style="font-family: 'Comic Sans MS',cursive;">//RNA Primers// -> Markers for starting spot laid down by Primase.
 * <span style="font-family: 'Comic Sans MS',cursive;">//DNA Polymerase// -> Copy Machine.) Replication Direction reads on a 3-5 directionmeaning it is building the new strand on a 5-3direction (reads at 3-5 and creates at 5-3)b.) Leading vs. Lagging.) Y-Fork vs. DNA Polymerase Size (Polymerase won't be able to fit on Y-Fork and cannot copy the very inner area of the Fork and wil not becopied until it moves more forwardd.) Pieces in the Lagging strand that are createdone at a time are Okazaki fragments
 * <span style="font-family: 'Comic Sans MS',cursive;">//Ligase// -> one creating bridge between Okazaki fragments and building a continuous strand
 * <span style="font-family: 'Comic Sans MS',cursive;">//Mismatch Repair// -> Sometimes, Polymerase accidentally pairs the the wrong purine and pyrimidine causing a mutation damaging the nucleotide and the enzymelocates the incorrect area
 * <span style="font-family: 'Comic Sans MS',cursive;">//Excision Repair// (Nuclease) -> Will do excision repair and pick up the incorrect area and cut it out and the gap created will then be marked by Primase.Polymerase will then come and repair it and then Ligase will come and stitch what is not filled in
 * <span style="font-family: 'Comic Sans MS',cursive;">//Telomerase & Telomeres// -> The ends of thechromosomes or the ends of the genes have aproblem. Since this whole Okazaki business,the last piece will not be copied leaving the piece out and is just a special ending to the DNA molecule protecting the actual DNA from degredation b/c a special enzyme known as telemerase and add the special piece to protect the DNA. We age b/c as the more wegrow, the more the telemres begin to detereorate andthe telemerase tries to replace it but sometimes itcannot. Creation of offspring there is little DNA being lost.) Senescence: a cell that kills itself b/c it has no purpose over time.) Apoptosis: a cell self-destructs b/c it does notwant to develop problems of not having telemeres such as cancer- Copy Process Accuracy
 * __<span style="font-family: 'Comic Sans MS',cursive;">Mutation Incedence __
 * <span style="font-family: 'Comic Sans MS',cursive;">Why Mutation
 * <span style="font-family: 'Comic Sans MS',cursive;">Semi-conservative Model of DNA Replication
 * <span style="font-family: 'Comic Sans MS',cursive;">Idea that DNA is half new and half old
 * <span style="font-family: 'Comic Sans MS',cursive;">Mathew Meselson & Franklin Stahl