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BIOL 302 2/2/16, 2/4/16, and 2/11/16

by: Michaela Sanner

BIOL 302 2/2/16, 2/4/16, and 2/11/16 BIOL 302

Marketplace > University of South Carolina > Biology > BIOL 302 > BIOL 302 2 2 16 2 4 16 and 2 11 16
Michaela Sanner
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First set of notes post exam 1 and the notes from the week prior to exam 1 (can be used to study for final)
Cell and Molecular Biology
Erin Connolly
Class Notes




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This 7 page Class Notes was uploaded by Michaela Sanner on Thursday February 4, 2016. The Class Notes belongs to BIOL 302 at University of South Carolina taught by Erin Connolly in Spring 2016. Since its upload, it has received 73 views. For similar materials see Cell and Molecular Biology in Biology at University of South Carolina.


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Date Created: 02/04/16
Chromosomes: A functional chromosome must: -carry genes -ability to replicate -have its 2 copies separated and partitioned into 2 daughter cells during cell division Chromosomes- 3 DNA Elements Important for Replication and Segregation (into 2 daughter cells) -replication origins: location where DNA replication begins -many per chromosome -centromere: important for separation of the 2 copies of a duplicated chromosome during the process of mitosis -one per chromosome -constricted region of a mitosis chromosome -holds together 2 sister chromatids -telomeres: 2 per chromosome -repeated DNA sequences found at the ends of chromosomes -important for replication of ends of chromosomes Centromere: DNA sequence -site of chromosome where kinetochore forms Kinetochore: protein complex attaches sister chromatids to mitotic spindle -allows the 2 sisters to be pulled apart with one copy going to each daughter cell Chromosome structure is dynamic -proteins (histones and nonhistones chromosome proteins) serve to fold up the DNA into a more compact form Interphase VS Mitotic -less folded -tightly folded -500-1000 fold -10,000 fold -different regions are unpacked for -replication -repair of DNA -gene expression Levels of Chromatin Packing: -"beads-on-a-string" form of chromatin -involves nucleosomes :nucleosome core particle and linker DNA -nucleosomes core particle : piece of double stranded DNA (~147base pairs) wrapped ~2 times around a protein complex of 8 histone molecules (histone octomer) -histone octomer: 2 molecules each of 4 different histones: H2A, H2B, H3, & H4 -histones are basic (positively charged) -attracted to negatively charged DNA -each of the core histones has a tail (flexible extension from the wheel) -tails can be chemically modified by addition of various chemical groups** -30nm (nanometer) fiber -folding of "beads-on-a-string" in a zig-zag fashion -requires a 5th histone- histone H1 -H1 helps to pull nucleosomes together into 30nm fiber -String of loops -loops of the 30nm fiber that radiate out from a central axis Interphase Chromosomes (above):"beads-on-a-string", 30nm fiber, string of loops -Mitotic Chromsome: most highly condensed form -~10,000 fold compaction An interphase chromosome: varying levels of condensation along length -some regions are more folded (less accessible to proteins) -some regions are less folded *( more accessible to proteins) *more likely to see gene expression in those regions 2 Types of Interphase Chromatin -Heterochromatin: most highly condensed form of interphase chromatin -usually near the centromere and telomeres -not many genes -genes found in Heterochromatin are usually not expressed -Euchromatin: more extended form of interphase chromatin -genes located in Euchromatin are more accessible and can be expressed Chromatin remodeling: cells can rapidly alter local structure of a region of a chromosome -proteins are involved -chromatin remodeling complex: use ATP hydrolysis to change the structure or spacing of nucleosomes -makes the DNA more accessible to proteins -histone modifying enzymes: covalent lay modify the N-terminal tails of histones -modifications: can attract or repel proteins involved in gene expression -methyl, acetyl, phosphate, etc. CHAPTER. 6: DNA Replication -each strand of DNA contains a sequence of nucleotides (nts) that is complementary to the nt sequence of the partner strand -each of the two strands of DNA, in a double stranded DNA molecule, can act as a template (mold) for the synthesis of a new complementary strand Chapter 6: DNA Replication and DNA repair DNA Replication: 1) General process A) replication origins B) replication forks C) DNA polymerase 2) Detailed look A) primase B) nuclease C) DNA repair polymerase D) DNA Ligase E) Helicase F) single-strand binding protein G) Sliding clamp 3) Put this all together = molecular mechanism of DNA replication DNA Repair: 1) Mutations A) DNA replication errors B) DNA damage 2) DNA mismatch repair -repairs mistakes made during replication 3) DNA repair mechanisms -repair DNA damage DNA Replication: -see 2/2 ch 6 notes* -semi-conservative: each product of DNA replication consist of one parental strand ("old") and one newly synthesized strand -one double helix is replicated to form 2 identical double helices -original DNA strands remain intact through many generations of DNA replication A) Replication Origins: DNA Replications begins at replication origins -bacterial cells-single origin on a single circular chromosome -human genome-~10,000 origins spread out over the set of chromosomes -origin contains a particular sequence of nucleotides -origin is recognized by a set of proteins that bind to the nucleotide sequence at the origin **DNA replication begins when these "initiator proteins" bind to the origin** -"Initiator Proteins" - pull apart the 2 strands of DNA by breaking hydrogen bonds between complementary bases --> this opens up a short stretch of DNA --> exposes the bases of single strands --> attracts a second set of proteins that start replication of DNA -"replication machinery" B) Replication Forks -Y shaped junctions in the DNA as it is being replicated -at each origin there are 2 replication forks that move away from each other in opposite directions as replication proceeds -at the forks, DNA is unzipped as the forks move -replication is bidirectional -replication fork is asymmetrical -one DNA strand is **growing overall** at 3' end while other strand is growing overall at its 5' end (does not mean adding at the 5' end) **DNA is only synthesized in the 5'-->3' direction** always add at the 3' end -the 2 new DNA strands are constructed in different ways -leading strands: DNA synthesized continuously from 5'-- >3' end -lagging strands: DNA synthesized discontinuously in separate, small pieces called Okazaki fragments -Okazaki fragments are synthesized 5'-->3' but, overall, on the lagging strand, DNA is growing in the 3'-->5' direction -at lagging strand, DNA polymerase is moving backwards from the form (back stitching) C) DNA Polymerase -enzyme that synthesizes DNA -adds nucleotides at the 3' end*** of a GROWING DNA Strand ** using old/parental strand as a template -catalyzes formation of phosphodiester* bonds (strong covalent bonds) between 3' OH of last nucleotide in the strand with the 5' phosphate of the incoming nucleotide -can only add nucleotides to a growing DNA strand (can't start a new strand from scratch) -after adding a nucleotide, DNA polymerase stays attached to chain -self-correcting: has a proof reading activity -it detects its own errors -after adding a nucleotide, DNA polymerase checks to make sure the correct nucleotide was added -if added correct nucleotide: DNA polymerase adds next nucleotide -if added incorrect nucleotide: DNA polymerase removes incorrect nucleotide by cleaving the phosphodiester bond and then adds the correct nucleotide -DNA polymerase has a 3'-->5' exonuclease activity 2/11/16 Chapter 6 part 2 detailed look A) Primase: required to start synthesis of new DNA strand -can begin a new strand by joining 2 nucleotides together -makes a short stretch of RNA about 10nucleotides long, that is base- paired to template strand -short stretch of RNA is called a PRIMER because it provides a 3' end for DNA polymerase to use for DNA synthesis Leading strand-only need 1 primer Lagging strand-requires many primers; 1 primer for each Okazaki fragment (each needs its own primer); every ~200 nucleotides --> DNA Polymerase will add nucleotides onto 3' end of primer until it runs into primer of previous Okazaki fragment B, C, D) Nucleases, DNA Repair Polymerase, and DNA Ligase -primer is later removed by Nucleases -Nucleases that recognize RNA in a RNA/DNA duplex and excises it -gap left by removal of primer is filled in by DNA repair polymerase uses adjacent Okazaki fragments as a primer -DNA Ligase-joins together the completed fragments -catalyzes formation of phosphodiester bonds -3' OH of one DNA fragment and 5' phosphate of adjacent DNA fragment Replication Machine: a large, multi-subunit protein complex -present at replication fork -contains: primase, DNA polymerase, Helicase, single strand binding protein, and sliding clamp -complex moves along the DNA to allow DNA synthesis on both strands in a coordinated manner E,F,G) Helicase, single strand binding protein, and sliding clamp Helicase- uses ATP hydrolysis to move along DNA helix and open it up --> separates the 2 strands to expose the 2 single stranded DNA templates Single-strand binding protein: binds to the single strands and prevents reformation of the base pairs Sliding clamp: keeps DNA polymerase firmly attached to the DNA, forms a ring around DNA On the lagging strand: DNA polymerase is temporarily released each time an Okazaki fragment is completed -DNA polymerase and sliding clamp are released and may then reassociate with DNA template stand to synthesize the next Okazaki fragment Replication of ends of eukaryotic chromosomes -problem: synthesis of the end of lagging strand (end of chromosomes) -no place to put down RNA primer that is needed to start last Okazaki fragment -if this DNA can't be replicated, chromosomes would get shorter with each round of replication -"end replication problem" -Problem is solved by *telomeres* and *telomerase* -telomeres are special repeated sequences found at the ends of chromosomes that allow the ends to be replicated -telomerase: enzyme that binds to telomeres -adds additional copies of the same DNA sequence to the end of the template strand -humans : (GGGGTTA) -telomerase contains a short RNA that is complementary to the telomere DNA repeat sequence -it produces a template DNA sequence need to complete synthesis of lagging strand DNA Repair: Genetic stability: cells have elaborate mechanisms to correct errors in DNA -DNA replication -DNA damage (UV, Chemicals, etc) -changes to DNA sequences: -necessary for evolution -individual prospective- almost always detrimental **individuals have to be genetically stable to reproduce and divide** How is genetic stability achieved? 1) accurate mechanisms for DNA replication DNA polymerase without proofreading, error rate ~1 in 10^5 nucleotides DNA polymerase with proofreading, error rate ~ 1 in 10^7 nucleotides 2) Repair mechanisms A) errors that do occur during replications -fixed by DNA mismatch repair B) errors that arise via DNA damage (UV, chemicals) -fixed by DNA repair Mutations: a permanent change in the nucleotide sequence of DNA -effects of mutation depends on location Ex: mutation that results in an amino acid change that affects protein structure and protein function Germ cells: mutation will be passed along to next generation Ex: sickle cell anemia Somatic Cells (body cells; non germ cells): will not be passed on Ex: cancer Mutations in Somatic Cells: -not passed on to progeny -can result in cells that reproduce in an **uncontrolled fashion** -sometimes leads to cancer -cancer usually results from the gradual accumulation of mutations over time -If an individual has a slightly higher mutation rate, this may result in an increased likelihood of cancer


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