Week 4 Course Notes: Chapter 15, Section 16.4, Sections 12.2-12.4
Week 4 Course Notes: Chapter 15, Section 16.4, Sections 12.2-12.4 Biol 2002
U of M
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This 6 page Class Notes was uploaded by Sydney Diekmann on Thursday September 24, 2015. The Class Notes belongs to Biol 2002 at University of Minnesota taught by Dr. Susan Wick, Dr. David Matthes in Fall 2015. Since its upload, it has received 94 views. For similar materials see Foundations of Biology in Biology at University of Minnesota.
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Chapter 15 DNA and the Gene Synthesis and Repair 151 What are Genes made of I scientists originally though genes were composed of proteins 0 many variations in structure and function gt could potentially contain information needed to regulate the many chemical reactions that occur in living organisms 0 DNA only has 4 subunits deoxyribose nucleic acids A The HersheyChase Experiment 1952 I use of the virus Escherichia coli to see what was injected into the host cell to direct the production of the new virus 0 composition of the viral material would determine what type of material genes were composed of gt proteins contain sulfur but not phosphorus gt DNA contains phosphorus but not sulfur I virus proteins and DNA were exposed to radioactivity to easily see what type of material was injected into the cell 0 majority of radioactive protein was outside of the cell in the virus empty capsids gt capsid exterior protein coat of the parent virus that attaches to the outside of the host cell 0 because of this DNA must be the source of heritable information and thus is what genes are composed of B The Secondary Structure of DNA I DNA is double stranded each strand consists of a linear polymer consisted of monomers called deoxyribosenucleotides o deoxyribosenucleotides consist of a deoxyribose sugar a phosphate group and a nitrogenous base gt linked together with phosphodiester bonds between the hydroxyl and phosphate group I the primary structure of DNA consists of a sugarphosphate backbone and nitrogenous bases that project from that backbone 0 each strand of DNA has a directionality gt each strand has an exposed hydroxyl group on the 3 carbon of the sugar and an exposed phosphate group on the 5 carbon I the doublehelix structure of DNA is stable due to the hydrogen bonding between the nitrogenous bases 0 adenine and thymine guanine and cytosine A and T G and C o complementary base pairing hydrogen bonding of certain base pairs 152 Testing Early Hypotheses about DNA Synthesis A Watson and Crick s Hypothesis I existing strands of DNA serve as the template for the production of new strands of DNA I deoxyribonucleotides are added to the new strands by complementary base pairing gt complementary base pairing mechanism for DNA to be copied B Alternative Hypotheses I semiconservative replication when old parental strands of DNA are separated each strand can be used as template for a new daughter strand 0 daughter DNA molecule would consist of one old strand and one new strand I conservative replication bases temporarily turn outward complementary strands don t face each other to serve as template for entirely new double helix I dispersive replication parental double helix is cut wherever one strand crossed over another and DNA is synthesized in short segments gt mix of old and new segments C The MeselsonStahl Experiment I if parent and daughter strands of DNA could be distinguished from one another then the type of replication could be determined 0 parent cells were grown in the presence of different heavier isotopes of nitrogen gt different densities I densitygradient centrifugation separates molecules of DNA based on their density 0 lower density molecules gather in bands high in centrifuge tube 0 higher density molecules gather in bands lower in centrifuge tube after 2 generations centrifugation produced lower density band and higher density band 0 supports hypothesis of semiconservative replication 153 DNA Synthesis I DNA is synthesized by a catalystic protein enzyme called DNA polymerase 0 DNA polymerase can only add deoxyribonucleotides to the 3 end of a growing DNA chain gt 5 gt 3 direction I the DNA synthesis reaction is exergonic releases energy 0 deoxyribonucleoside triphosphates are the monomers used in DNA synthesis gt dNTPs have three close phosphate groups gt high potential energy I DNA synthesis is bidirectional it occurs in both directions at the same time 0 set of proteins are in charge of recognizing sites where replication beings and opening double helix at those points I DNA helicase enzyme that breaks the hydrogen bonds between the base pairs to cause the strands to separate 0 singlestrand DNAbinding proteins attach to separated strands to prevent them from rejoining o topoisomerase enzyme that cuts DNA allows it to unwind and later rejoins it A Lead Strand Synthesis 1 DNA is opened by helicase unwound by topoisomerase and primed by primase gt primase enzyme that synthesizes a segment of RNA that acts as a primer for DNA polymerase 2 synthesis of strand occurs with a sliding clamp holding the DNA polymerase in place and the DNA polymerase synthesizing B Lagging Strand Synthesis occurs in the opposite direction of lead strand synthesis 1 DNA already opened by helicase and unwound by topoisomerase from lead strand synthesis is also primed by primase synthesized RNA primer 2 first Okazaki fragment is synthesized by DNA polymerase a Okazaki fragment short DNA fragments that are linked together into longer fragments as synthesis progresses 3 second Okazaki fragment is synthesized by DNA polymerase 4 DNA polymerase removed the ribonucleotides of RNA primer and replaces them with deoxyribonucleotides 5 DNA ligase closes the gap between the Okazaki fragments in the sugarphosphate backbone a DNA ligase catalyzes the formation of the phosphodiester bonds between deoxyribonucleotides replisome where the enzymes required for DNA synthesis are organized as a macromolecular structure 154 Replicating the Ends of Linear Chromosomes telomere region at the end of a eukaryotic chromosome I the leading strand is synthesized all the way to the end of the parent DNA template 0 leading strand synthesis results in a double stranded copy of parent DNA I the lagging strand primase adds RNA primer close to the tip of the chromosome 0 DNA polymerase synthesizes the last Okazaki fragment on the lagging strand but is UNABLE to add DNA near the tip of the chromosome gt polymerase cannot synthesize DNA without a primer I tip of chromosome is eventually degraded gt shortening of chromosome I telomeres do not contain genes 0 composed of sequences of bases that are repeated continuously I the enzyme telomerase catalyzes the synthesis of its own template for replicating telomeres 1 the RNA primer is removed from the telomere and remains unreplicated 2 telomerase extends the unreplicated end by adding deoxyribonucleotides to the end 3 telomerase moves down the DNA strand and adds additional repeats 4 lagging strand is completed when primase DNA polymerase and ligase synthesize the remaining bases I telomerase is only active in select cells types 0 primarily in cells that produce gametes gt most somatic cells cells not involved in gamete formation lack telomerase 155 Repairing Mistakes and DNA Damage I errors in DNA replication ie mutations can cause defects in the function of cells A Correcting Mistakes in Synthesis I DNA polymerases make limited mistakes in synthesis because 0 correct base pairings are energetically favorable 0 correct pairings have a specific shape I DNA polymerase proofreads o if the wrong base is paired the enzyme will stop and remove it I mismatch repair occurs when mismatched bases are corrected after synthesis is complete 0 proteins recognize the mismatched base remove the section containing the base and fill in the correct bases using the older strand as a template B Repairing Damaged DNA I DNA can be damaged by chemical attack radiation etc o nucleotide excision repair fixes damage that distorts the DNA helix gt defective bases are removed and replaced I if DNA repair enzymes are defective mutation rate increases Section 164 How Can Mutation Modify Genes and Chromosomes mutation any permanent change in an organism s DNA gt change in the genotype gt creation of new alleles A Point Mutation I singlebase change during synthesis 0 missense mutations point mutations that cause changes in the amino acid sequence of proteins 0 silent mutation point mutation that does not change the amino acid sequence of proteins 0 frameshift mutations single additiondeletion mutation that throws the sequence of codons of protein out and alters the meaning of subsequent codons o nonsense mutations codon that specifies an amino acid is changed to one that specifies a stop codon gt early termination of polypeptide chain gt nonfunctioning protein I mutations are divided into 3 categories 1 beneficial increase the fitness of organism 2 neutral no effect on fitness of organism 3 deleterious lowers the fitness of organism B Chromosome Mutations I chromosome inversion segments of chromosome may be flipped and rejoined I chromosome translocation segments of chromosome become attached to a different chromosome I deletion segment of chromosome is lost I duplication additional copies of segment are present Sections 122 through 124 The Cell Cycle 122 M mitotic or meiotic Phase I two main events 0 division of the nucleus gt replicated chromosomes are divided into two daughter nuclei with identicle chromosomes and genes 0 division of the cytoplasm gt cytokinesiscytoplasmic division I chromosomes are DNA wrapped around globular histone proteins called chromatin 0 at the start of mitosis each chromosome consists of two sister chromatids that are attached to each other at the centromere gt centromere area where proteins called cohesins remain attached during mitosis I during mitosis two sister chromatids separate to form independent daughter chromosomes 0 a copy of each chromosome goes to each daughter cell I 5 mitotic subphases 1 prophase chromosomes condense and spindle apparatus forms gt spindle apparatus structure that produces mechanical force that moves replicated chromosomes during early mitosiss and pulls chromatids apart in late mitosis 2 prometaphase nuclear envelope breaks down and microtubules contact chromosomes at kinetochores gt kinetochores specialized structures where kinetochore microtubules attach to chromosomes to prepare for migration to the middle of the cell for separation 3 metaphase chromosomes migrate to the middle of the cell gt metaphase plate imaginary line between the two spindle poles where chromosomes line up 4 anaphase sister chromatids are separated into daughter chromosomes gt pulled apart to opposite sides of the cell gt daughter chromosomes move to opposite side via the connection of kinetochore proteins to the shortening kinetochore microtubules gt poles of the spindle apparatus are pulled farther apart elongating the cell 5 telophase the nuclear envelope reforms and chromosomes decondense gt when two complete nuclei form chromosomes decondense and cytokinesis begins 123 Cell Cycle Checkpoints I G1 cycle will continue if 0 cell size is adequate o nutrients are sufficient 0 social signals are present 0 DNA is undamaged G2 cycle will continue if 0 chromosomes have replicated successfully 0 DNA is undamaged o activated MPF is present gt MPF M phasepromoting factor Mphase cycle will continue if 0 chromosomes have attached to spindle apparatus 0 chromosomes have property separated o MPF is absent 124 Cancer and Cell Division cancer disease caused by cells that divide in an uncontrollable fashion gt invasion of nearby tissue gt spreads to other sites of the body causes disease because the cells use nutrients and space needed by normal cells which disrupts their overall function cancers occur when cellcycle checkpoints see above have FAILED two primary defects 0 defects that make proteins required for cell growth active when they shouldn t be 0 defects that prevent tumor suppressor genes from shutting down the cell cycle Properties of Cancer Cells malignant tumor invasive cancerous mass of cells benign tumor noninvasive noncancerous mass of cells cells become malignant and cancerous when they detach from the tumor and move to other tissues in the body Loss of CellCycle Control social control 0 in multicellular organisms the passage through the G1 checkpoint also depends on response signals from other cells gt Le individual cells should grow when it is in the best interest of the organism as a whole 0 based on growth factors gt polypeptidessmall proteins that stimulate cell division 0 cells can become cancerous when social controls fail gt Le when cell begins to divide without goahead signal from growth factors