BIOL 2012 Week 2 Notes
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This 7 page Class Notes was uploaded by Chris Bonty on Wednesday January 13, 2016. The Class Notes belongs to BIOL 2012 at a university taught by Bethany Zolman in Spring 2016. Since its upload, it has received 18 views.
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Date Created: 01/13/16
Chapter 1 & 7 + main lecture high lights - First information for making an organism is encoded in the nucleotide bases making the DNA strands -Due to complimentary base pairs 1 strand decides the sequence of the other - Each strand of the original DNA serves as a template -Know about Frederick Griffiths experiment on mice with the smooth and rough bacteria - Transformation: converting an organism from one form to a completely different one. - Heredity material must have 3 key parts - Every cell must have the same genetic makeup (allow faithful replication) - Must encode for proteins (informational content) - Must be able to change/mutate - DNA is simple and made up of three main components - Shape double helix - Held together by hydrogen bonds between the bases of each pair - Deoxyribose sugar units connected by phosphodiester linkages - 5’ carbon deoxyribose is connected to the 3’ carbon atom of the adjacent deoxyribose - Each sugar backbone is said to have 5’ to 3’ polarity or direction - The two backbones are opposite/antiparallel - Major Groove is larger one - Minor Groove is the smaller one - Phosphate - Deoxyribose (a sugar) - 4 nitrogenous bases (A, T, C, G) - 2 bases A & G are purines (double ringed structures) - 2 bases C & T are pyrimidines (single ring structure) - Chemical components of DNA called nucleotides made of: phosphate, deoxyribose sugar, & a base (1 of 4) - G-C base pairs have 3 H bonds while A-T pairs have only 2 - Chargaff’s rule: # of A’s = # of T’s & # of C’s = # of G’s - X-ray diffraction Analysis of DNA (X-rays fired at DNA fibers) - Watson & Crick believed in semi- conservative replication. (old DNA splits in half and is used for a template for 2 new strands) - Conservative method of Replication (old DNA is conserved & a single double helix daughter is produced) - Dispersive replication (Daughter molecules are made and each consist of new and old segments from the parental molecule) - Mathew Meselson & Franklin Stahl: Ran an E. coli DNA experiment two isotopes of Nitrogen to discover DNA replication is Semiconservative - Replication fork is the segment of DNA where the double helix is unwound then duplicated - Building a DNA polymer is endergonic - 5 known DNA polymerases - pol 1 does 3 things in different parts of the molecule: catalyzes chain growth 5’ to 3’ direction(polymerase activity), removes mismatched bases in a 3’ to 5’ direction(exonuclease activity), in 5’ to 3’ direction degrades single strands of DNA or RNA(exonuclease activity) - pol 3 acts at the replication fork and extends the RNA chain composing of the primer - DNA polymerases only add nucleotides at the 3’ growing tip - Newly synthesized strand is called the leading strand. - short 1000-2000 nucleotide segments are Okazaki fragments - Okazaki fragments must be initiated by a primer(short chain of nucleotides that binds with the template to form a segment of duplex nucleic acid) each fragment needs its own primer - Primers are synthesizes by a protein known as a primosome - Primase(synthesizes short 8-12 nucleotides stretch of RNA complementary to the chromosome) primosomes central component and a type of RNA polymerase - DNA ligase joins 3’ end of gap filling DNA to 5’ end of the downstream okazaki fragment forming a new strand known as the ligand strand - catalyzes the formation of phosphor diester bonds between the 5’ phosphate and adjacent 3’ OH group of different fragments - Both DNA pol 1 & 3 possess exonuclease activity for proof reading helping account for its less than one error per 10^10 nucleotides inserted - Tautomerization: addition of the wrong base into a sequence - Tautomers are base isomers that differ in the positions of their atoms and bonds between atoms - Normally DNA bases are found in Keto form abut occasionally can shift into imino or enol form causing them to potentially pair with the wrong base pair - Replisome large nucleoprotein complex that coordinates activity at the replication fork - pol 3 holoenzyme: 2 catalytic cores and many accessory proteins - one catalytic core handles leading strand synthesis and the other ligand strand synthesis - Accesssory protiens form a bridge between the two cores keeping them cooridinated - know about Beta clamp and replisome - Distributive enzyme adds a few nucleotides then falls off - Processive enzyme stays adds tens of thousands of nucleotides - Single Strand Binding proteins(SSBs): - Helicases: - Topoisomerases: - Difference between Eukaryotic and Prokaryotic replication: - Daughter molecules - Cell phases - Origin Recognition process ORC’s: - Telomeres: - Telomerase: Class Notes 1/25/2016 - DNA in itself does not do anything - DNA translated into RNA inter mediate - Mutations occur during replication and due to environment - No one has the same genome as you!! - Can have identical sequence but different regulatory molecules - Proteins made by DNA can be considered enzymes - Poly morphisms/Differences in DNA sequences - Why aren’t we all the same? - Alleles alternative forms of gene encoding proteins - Often lead to altered Amino acid sequence/ gene expression - Located on same chromosome loci - Geno type is the genes you have inherited in your DNA - Phenotype way the genes are expressed - Albinism is an example of a single gene change -Tyrosinase is enzyme involved in production of pigment for skin -Mutation in DNA is carried into the RNA - Mutated albino tyrosine cannot bind to its substrate -Most recessive mutated enzyme is usually fully covered for by the one dominant allele (heterozygotes) Lecture 2 notes -Albinism is categorized trait. Either you have it or you do not distinct categories - Single gene traits have low Environmental influence -Type 2 diabetes is a threshold trait, subset of categorical either yes or no but not affected solely by 1 gene. - If # of genetic/environmental risk is above the threshold you will get it disease/trait -Bracka alleles (Repair DNA) and relationship to breast cancer - Stature/Continuous trait: unbroken range of phenotypes, Individuals to be intermediate and not on the extreme ones shoe size, weight, wing span, head circumference ect. - We will discus developmental or physical genotypes mostly - Mendelian genetics, 1 particular gene in that 1 particular context - WE can do genetic counseling for diseases. (don’t mix 2 carrying parents) - Use knowledge to recommend environmental control -Genetics in the news ?s on the exam just 1 for 5pts and send her an article u can skip that ? it has to be new ( Title, link, and why it connects to our class) -( use new York times, news week) -How long is your DNA 1.052 meters - 3,095,693,981 bp or 3,095,693 kb or 3.095 Gb - Not important to class its google able - Wants us to have a reference/perspective for genome size - Early 1900s they believed Proteins must carry the hereditary material - DNA must be diverse with high specificity, Replicate fast, occasionally be mutable, possess diverse structures, must hold info, and be translate able - Mentioned bacteria injected into mice, different strands - Transformation phenomenon - Hershey and Chase(1952): - Found 4 phases connected to DNA - Figure out amount of bases through math - Franklin and Wilkens structure of the double helix - Watson and Crick DNA structure in depth: grooves, spacing, and bases - Why DNA is helical - 3` OH and 5` phosphate group - Strands are ANTI Parallel, H bonds aid in making the shape possible - What DNA replication is - Parent copy is the original strand of DNA - 3 methods on how DNA replicates dispersive(more random), semi conservative(, and conservative - Meselson & Stahl (1958) Nitrogen experiment - DNA is not the conservative model - DNA uses Semi-conservative form found in gel experiment - Replication forks replication occurring In more than one place - DNA splits and enzymes come to copy until they hit other enzymes also copying - Faster than using just one enzyme from front to back - Origin of replication (ori) - Base addition done by polymerase in DNA and RNA - Can add a new base pair to an existing strand of DNA - Nucleotide triphosphates are key to new base reaction attachments - Polymerase adds on base pairs to the daughter strand as it is replicated at the replication fork. - One synthesized toward fork the other away - 2 proteins come together as one unit (dimer) to do work - DNA must curve In order for dimer to properly do work - Continuous strand adds new pairs at the fork point and is continuously edited - Discontinuous is edited in spurts away from the replication fork always adding to the 3 prime oxy group - Okazaki fragment growing helps keep the ligand strand caught up with the leading strand then is glued on by ligase - Topoisomerase acts just a head of DNA replication relaxing the coiled DNA by cutting holes in it. - Helicase is the (unzipper) it disrupts the H bonds between the bases. Forming single strands - SSBP (single stranded binding protein) bind to keep the DNA strands separated
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