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Weekly notes

by: Meghan Cooper Mendes de Oliveira

Weekly notes BSC 2010

Meghan Cooper Mendes de Oliveira
Biological Science
Dr. Steven Marks

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Hey Guys! I'm an elite note taker with study soup and I'm posting my notes for BSC 2010 with Dr. Marks! This set is on the lectures from this past week! Please feel free to use them!
Biological Science
Dr. Steven Marks
Class Notes
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This 15 page Class Notes was uploaded by Meghan Cooper Mendes de Oliveira on Sunday October 25, 2015. The Class Notes belongs to BSC 2010 at Florida State University taught by Dr. Steven Marks in Fall 2015. Since its upload, it has received 48 views. For similar materials see Biological Science in Biological Sciences at Florida State University.


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Date Created: 10/25/15
Exam 3 Notes Thursday September 17 2015 BSC 2010 0001 Chapter 16 Molecular Basis of lnhcritancc DNA Replication Background Importance Control Mechanism Initiation Elongation Termination Other Considerations Different types of genomes Replication errors Why does a cell make copies of its DNA DNA contains more information that RNA or Protein Exam 3 Notes Thursday September 17 2015 It is the only biological molecule that can copy itself SemiConservative Replication 5 3 iii9iii iii9iii9 yTAACCTGTACATGGCATTGC 5 5 3 hydrogen ATTGGACATGTACCGTAACIJCIB bonds I I I I I I I I I I I I I I I I I I TAACCTGTACATGG CATTG C 3 5 5 3 T GGACATGTACCGTAACG I I I I I I I I I I I I I I I I I I A 1 Parent First Second 3 cell replication replication a Sggiervative lt m W m m mltm b S 39 t39 meDrg clonservaive lt gt gt c Dispersive model Conservative model the original DNA is completely conserved Semiconservative model Exam 3 Notes Thursday September 17 2015 DNA split in half Dispersive model Original DNA is not preserved in anyway Matthew Meselson and Franklin Stahl performed experiments at Cal Tech supported the SemiConservative model labeled nucleotides of the old strands with Nitrogen 15 new nucleotides labeled with Nitrogen 14 Control of DNA Replication Speci c amount of DNA in each cell Diploid cells 2 copies of each chromosome More or less than the original DNA is not tolerated by the cell Cell division is the only time cells replicated DNA Replication DNA sequences recruit proteins needed for replication Proteins create a starting point for replication Proteins recruited Helicase Unwinds DNA Exam 3 Notes Thursday September 17 2015 Single Strand Binding Protein Stabilizes Single Strand DNA Primase Adds an RNA primer Topoisomerase induces supercoils in DNA to counteract supercoils created by unwinding Polymerase catalyze elongation of new DNA Ligase New DNA Strand synthesis DNA Polymerase an enzyme catalyzes the elongation of new DNA DNA polymerase requires a primer and a DNA template add nucleotides only to free 3 end of a growing strand new DNA can only be elongated only in the 5 to 3 direction Leading Strand Synthesis Leading strand synthesis is continuous in the 5 to 3 direction lagging strands strand copied in the opposite direction DNA polymerase works away from the replication fork to elongate the other new strand Exam 3 Notes Thursday September 17 2015 Primase assembles new primers Synthesized by DNA polymerase III as series of segments or Okazaki Fragments Resolution of DNA RNA Hybrid RNA primers have to be replaced by DNA To Remove RNA nucleotides DNA Polymerase removes RNA and fills the gap with DNA nucleotides DNA Ligase joins the 5 end of one DNA molecule to the 3 end of another Termination of Replication Only Prokaryotes have termination sequences Ter sites 23bp sequences cause termination in Vitro Protein bound to the ter site stops the replication fork from proceeding Different Genomes Different Replication Bacteria prokaryotic circular genome single DNA molecule 1 origin of replication Humans eukaryotic linear genome Multiple linear chromosomes Exam 3 Notes Thursday September 17 2015 Multiple origins of replication on each chromosome How do Eukaryotes Protect Chromosome Ends Eukaryotic Chromosomal DNA molecules have noncoding nucleotide sequences at their ends called telomeres Telomeres do not prevent shortening of the DNA molecules they stop the erosion of genes at the end of DNA molecules Telomere Shortening and Aging Telomeres are generally shorter in older individuals in somatic cells somatic cell telomeres gene turned off In germ cells telomeric shortening cannot be tolerated Telomerase in germ cells maintain telomeres at their original length protective against cancer by limiting cell division telomerase activity within tumor cells may be oncogenic Proofreading replication errors once every 100000 nucleotides DNA polymerase will add the wrong nucleotide DNA Pol l and DNA Pol 111 have 3 and 5 exonuclease activity allows them to remove mistaken nucleotide when it s added Extraordinary fidelity considering rate of nucleotide incorporation 50 nucleotides sec Human polymerase 500 nucleotides sec Bacterial polymerase Exam 3 Notes Thursday September 17 2015 Important Replication Proteins Helicase Unwinds DNA to create two single strands Single Strand Binding Protein SSB Binds to and stabilizes the single stranded DNA Primase Provides an RNA primer to start new DNA strand synthesis Topoisomerase Travels ahead of helicase nicking and swiveling the DNA to relieve torsional strain on the molecule Polymerase Ill Assembles new DNA strand in the 5 3 direction Polymerasel Can remove RNA nucleotides as it adds new DNA in a 5 3 direction Ligase Joins two DNA strands together at their ends Telomerase Maintains telomere length in germline cells to protect the health of gametes Chromosomes have a DNA molecule packed with Proteins Bacteria chromosomes are doublestranded circular DNA molecules small amount of protein Eukaryotic chromosomes have linear DNA large amount of histone proteins In bacterium DNA is supercoiled found in the part of the cell call the nucleoid Chromatin DNA and protein complex found in eukaryotic nucleus undergoes changes in packing during cell cycle Exam 3 Notes Thursday September 17 2015 organized into 10nm ber compacted into 30 nm ber by folding and looping must be pack more tightly into pairs of chromatids in preparation of cell division loosely packed during interphase and condenses in mitosis loosely packed chromatin called euchromatin during interphase few regions are highly condensed into heterochromatin dense backing makes it difficult for the cell to express genetic information in these regions EXAM 3 Thursday October 15 2015 BSC 2010 Chapter 5 amp 16 39 Overview The doublehelical model for DNA was introduced by James Watson and Francis Crick in 1953 DNA deoxyribonucleic acid the substance of inheritance is considered the most celebrated molecule of our time DNA contains hereditary information and it is reproduced in every cell of the body DNA Programs direct the development of biochemical anatomical physiological and behavioral traits DNA the material of genetics relatively new discovery occurred Within the last 100 years How do we know discover thats DNA makes up heredity Thomas Hunt Morgan discovered that genes are located on chromosomes looked at fruit ies gene that makes red eyes white located on the X chromosome genes are responsible for inherited traits rst to say genes are located on chromosomes Therefore Chromosomes are inherited material passed from one generation to the next Chromosomes are built up of two molecule types Protein EXAM 3 Thursday October 15 2015 DNA If chromosomes are made of protein and DNA which is responsible for inheritance main thought Protein was the likely carrier of hereditary proteins were more complex 20 monomer polymer DNA is a polymer with 4 monomers 1928 Fredrick Grif th researched this question worked with two bacterium strains Streptococcus pneumoniae one was pathogenic and the other was harmless introduced bacteria cells into mice Scells killed the mice Rcells the mice remain healthy Heat killed S cells mice stays healthy heat destroys protein function but does not destroy DNA Heat killed S cells nonfunctional proteins functional DNA are mixed with living Rcells nonpathogenic mouse dies EXPERIMENT Mixture of Heatkilled heatkilled Living 8 cells Living R cells 8 cells 8 cells and control control control living R cells 00 Mir RESULTS 1 Mouse dies Mouse healthy Mouse healthy Mouse ies Living 8 cells EXAM 3 Thursday October 15 2015 Experiment suggests that DNA was the carrier of heredity described the phenomenon as transformation de ned as a change in genotype and phenotype due to assimilate of foreign DNA studies of viruses that are able to infect bacteria provided more evidence of DNA as the genetic material bacteriophages or phages commonly used in molecular genetics research can pass their inherited material to infected cells made up of a combination of DNA and Protein Which was passed to the infected cell how to distinguish between Proteins and DNA Radioactive Sulfer labeled proteins Radioactive Phosphorus labeled DNA which ever infected the bacteria must be the viral genetic material EXPERIMENT Radioactive 9 prOtei y r Radioactivity Phage Shequot phage protein quot in liquid Bacterial cell i 9 Batch 1 3 Radioactive 6 DNA i a Sgl lfur y Phage f M S 39 DNA l I lt3 39 l 4 amp r quot Centrifuge r Radioactive Pellet bacterial ff 1 DNA 1 cells and contents Batch 2 O7 Radioactive phosphorus 32p L I 2011 Pearson Education lnc Centrifuge Radioactivity Pellet phage DNA in pellet EXAM 3 Thursday October 15 2015 Erwin Chargaff reported that DNA make up varied from one species to another in 1950 DNA is doublestranded making Chargaff s data not perfect for every A there is a T on the opposite strand Every C has a G on the opposite strand well known that DNA is a polymer consisting of a nitrogenous base a sugar and a phosphate group Two findings became known as Chargaff s rules The base composition of DNA varies between species In any species the number of A and T bases are equal and the number of G and C bases are equal the rules were not completely understood until the discovery of DNA as a double helix Rosalind Franklin Rosalind Franklin took a Xray crystallographic image of DNA allowed for the observation that DNA is a double helix Watson and Crick what did they know before their discovery DNA is made of a collection of 4 nucleotides The overall molecule looks like a double helix One turn of the double helix is 34 nm long The diameter of the double helix is 1 nm wide If you link nucleotides together in a chain through the phosphate groups you have a linear molecule The sugarphosphate side of the molecule would be hydrophilic The nitrogenous bases are relatively hydrophobic EXAM 3 Thursday October 15 2015 built models of the double helix their model is made of backbones that were antiparallel subunits ran in opposite directions Hydrogen bonds between nitrogenous bases A T G C Nucleic Acids What are their roles Two types of nucleic acids Deoxyribonucleic acid DNA Ribonucleic acid RNA DNA provides direction for its own replication DNA directs synthesis of messenger RNA mRNA and controls protein synthesis Protein Synthesis occurs on Ribosomes Protein Sequence Gly Pro Thr Gly Thr Corresponding RNA Sequence CCU GGA UGC CCG UGA Corresponding DNA Sequence GGA ccr ACG GGC ACT 5 Part of a Gene EXAM 3 Thursday October 15 2015 Read Protein sequence from left to right write DNA sequence from 5 to 3 5 T G C A 3 we know each is attached to a ribose sugar Structure of Nucleic Acids Nucleic acids are polymers the polymers are called polynucleotides polynucleotides are made up of monomers called nucleotides Nucleotides consist of a nitrogenous base a pentose sugar and one or more phosphate groups the portion of the nucleotide without a phosphate group is called a nucleoside 5 end Sugarphosphate backbone Nucleoside Nitrogenous base group Sugar pentose b Nucleotide 3 end 0 a Polynucleotide or nucleic acid Nucleoside nitrogenous base sugar two types of nitrogenous bases Pyrimidines cytosine thymine and uracil single sixmembered ring EXAM 3 Thursday October 15 2015 Purines adenine and guanine sixmembered ring fused to a ve membered ring In DNA sugar is deoxyribose In RNA sugar is ribose Nucleotide nucleoside phosphate group Nucleotide Polymers Nucleotide polymers can be linked together to form a polynucleotide nucleotides are joined together by covalent bonds formed between OH group 3 carbon of a nucleotide and the phosphate 5 carbon of a nucleotide linllt creates a sugarphosphate backbone with a nitrogenous bases as appendages DNA or mRNA sequences of bases is unique for each gene Difference between DNA and RNA Molecules RNA single polypeptide chain DNA Doublestranded form of a double helix two backbones run in opposite directions One molecule has many genes


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