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Cell Bio (BIO 2600), Week 3

by: Reena Mathew

Cell Bio (BIO 2600), Week 3 BIO 2600

Marketplace > Wayne State University > BIO 2600 > Cell Bio BIO 2600 Week 3
Reena Mathew

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Covers Ch 6- DNA Replication, Repair, and Recombination
Intr To Cell Biology
Dr. Jyoti Nautiyal
Class Notes
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This 7 page Class Notes was uploaded by Reena Mathew on Thursday August 11, 2016. The Class Notes belongs to BIO 2600 at Wayne State University taught by Dr. Jyoti Nautiyal in Fall 2016. Since its upload, it has received 2 views.


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Date Created: 08/11/16
Cells replicate DNA only once A parent cell duplicates DNA to produce two daughter cells but only do this once in its life cycle Growth, Replication, Mitosis There are mechanisms to prevent unlimited replication Recombination occurs, semiconservative, form duplexes with one parent strand each 50% from DNA strand and 50% from newly synthesized strand Forms the basis of replication- base-pairing, each strand acts as a template providing info from new strand In order to start replication- chromatin, DNA is uncoiled/unwound at origin of replication We need RNA primer for DNA replication because DNA polymerase cannot add 2 nucleotides DNA polymerase can only function from 5’ to 3’ 3’ to 5’ DNA polymerase proofreads PO4 to C3 5’ to 3’ Carbon 1 is bound to nitrogenous base 5’ to 3’ synthesis- challenge it creates- 2ndstrand is not able to synthesize continuously, bi-correctional behavior, strand symmetrical Direction of synthesis of Okazaki fragment- 5’ to 3’ 3’ to 5’ direction of synthesis of leading strand Ligase seals the breaks of the DNA strand Once DNA is unwound, they will tend to go back to double helix configuration - You would dissolve this bond by keeping it open from single strand DNA proteins There are many proteins that form this complex There are proteins that detect errors DNA primase- synthesizes RNA primer DNA polymerase- allows polymerization (formation of polymers) Look at new model Parent and lagging strand folded in a way so that one polymerase is ascending and as the DNA passes through this, it is being “stitched” Helicase- unwinds the DNA into 2 strands Replicated chromosomes etched together “chromatin” Telomeres- protect ends of chromosomes from nucleases and maintain the integrity of linear chromosomes, prevent genetic information from being lost Telomerase (one of the major proteins)- synthesizes telomeres - Gradual shortening of chromosomes with each round of cell division o Unable to replicate last section of lagging strand - Specialized structures found on the ends of eukaryotic chromosomes - When the telomere is shortened, it undergoes senescence ***Senescence beneficial- the condition or process of deterioration with age.  loss of a cell's power of division and growth. o Cellular senescence is an important mechanism for preventing the proliferation of  potential cancer cells. Recently, however, it has become apparent that this process entails more than a simple cessation of cell growth - Cancer (uncontrolled cell division) cells generally show activation of telomerase DNA repair Difference between cytosine, guanine, uracil, and adenine and thymine TYPES OF DAMAGE Depurination- nitrogenous base lost Deamination- happens to cytosine base, amino group lost, instead it becomes uracil, will form base pairs with adenine which changes genetic information Due to uncorrected damage, GC base pair changed to UA changes meaning of pair Importance of repair mechanisms- a lot of cells use energy to synthesize repair proteins, photorepair leads to vitamin D synthesis, converts energy from sunlight to form bonds between energy Due to evolution, our system devised a protein called photolyase which creates a bond and tries to fix the damage DNA duplex- only 2 nm wide, allows for base-pairing DNA checked if it was correctly replicated, then it is allowed to move further and complete mitosis Nonhomologous end joining- break repaired with some loss of nucleotides at repair site Homologous recombination- 3’ overhangs are created Cell knows which strand is formed when two strands are damaged because there is a bulge, if it’s a new strand or older strand- parent strand is intact, all in one piece, but newly synthesized strand- parts of it has leading strand & Okazaki fragments, and ligase is still stitching it together, if there is any mismatch, the new strand is the one that needs to be fixed AG  CG Synthesis asymmetric 3’ to 5’ – lagging strand- the backstitching imparts a slight delay to its synthesis - Leading strand- strand that is synthesized continuously At each replication fork, one new DNA strand is being made on a template that runs in one direction (3’ to 5’), whereas the other new strand is being made on a template that runs in the opposite direction, therefore the replication fork is asymmetrical Okazaki fragments- fragments synthesized part of the lagging strand, synthesized from nucleotides, each one needs a primer, when it is completed there is some gap left from the primer, problem resolved by telomere sequences, maintained by enzyme telomerase, KNOW telomerase function - DNA polymerases cannot replicate the 3’ end of linear chromosomes - Telomerase is unique because it contains an RNA molecule - Function of telomerase at the telomere: it adds new DNA to the longer strand of the telomere overhang - Telomeres consist of direct repeat sequences - In the absence of telomerase activity, chromosomes are not shortened slightly after every round of replication At least one nucleotide needs to be bound as a result you need RNA primers New nucleotides arrive as deoxyribonucleotides with three phosphate (triphosphates), leads to the formation of phosphodiester bonds At end of DNA synthesis, error 1 in 10^7 result of polymerase proofreading More complex when there are DNA double strand breaks Nonhomologous end joining- process when DNA strands have a gap joined together by ligase Homologous chromosomes are used and genetic information is copied from other chromosomes Failure to repair DNA damage can have severe consequences for a cell or organism Organs that have become damaged are most likely to get cancer, because it has to heal the inflammation/damage, more damagemore mutationsmay lead to cancer KNOW the difference between the different types of DNA polymerase (delta (main), alpha, beta, upsilon, and epsilon) Sister chromatids, results in two identical daughter cells Do not memorize numbers, but memorize difference between adenine guanine, thymine, and uracil and see the difference it has on base pairing Viruses- present at the boundary of the living and nonliving world Viruses outside the host are nonliving, once they are in the host they are living (ch. 9 pg. 309) - Can be linear or circular - Protein coat- part of genetic material - Special proteins on the coat - Lytic cycle- causes lysis (kills host cell) o Viruses hijack the machinery, retroviruses go against the flow of genetic material - Lysogenic cycle o Hides within the host genome Transcription- synthesis of RNA from DNA Do not need to know viruses that cause human disease know 2 (HIV virus, and influenza virus type A) HIV- as soon as scientists figure out this problem, they will think of new medicine to treat this virus and stop its spread Tamiflu- is an antivirus licensed to prevent or slow the spread of influenza A and influenza B between cells in the body (reading assignment: mechanism) Ch. 6 DNA Replication DNA Repair Homologous Recombination - Every cell originates from pre-existing cells - DNA responsible for transmission of life, not crystallized for a long time because its technique hadn’t evolved Proposed the DNA model, (Watson & Crick) DNA is a duplex helical structure, turns around its central axis - PO4-C5- -- C3 - One group said DNA replication is conserved (maintained as a duplex and the 2 daughter strands form a duplex, model C), One group said not conservative but dispersive, open the parent strand, each daughter gets new daughter strand synthesized with the other strand, other group semiconservative- one strand is completely random from other Based on density- the two types of DNA segregated, heavier on bottom, lighter on top Different bacteria grown in light, medium, and addition 20 min in light medium (equal amount, contains light and dark DNA) So DNA denatured, to break hydrogen bonds, found that one strand corresponded to light strand and one strand corresponded to dark strand SEMICONSERVATIVE proved Base-pairing enables DNA replication 3 R’s (Replication, Repair, & Recombination) - Cells live in “chaotic environment” - Replication o Semi-conservative o Each strand serves as a template for the other one o Base pairing rules dictate which nucleotide to insert o Ensures speed (-8 hrs) and accuracy (10^-7 to 10^-9 errors) - Orange & green pyrimidine C & G - Blue & yellow purine (larger) A & T - One base pair purine formed with pyrimidine Origin(s) of Replication 1. Strand separation- lots of weak H-bonds 2. ID origins- small stretches DNA (AT rich) that can be opened easily [one in bacteria; 10,000 in humans] 3. Initiator, Proteins- open helix, increase access for replication machinery 4. Bidirectional, movement Replication Machinery Rate of extension approx. same both strands Requires energy DNA synthesis begins at replication origins Bidirectional- keep opening the DNA one side and open DNA the other side so the DNA will replicate both sides DNA polymerase- synthesizes DNA using parent DNA as template - Explains semiconservative AT rich sequences is the region of DNA that will serve as origin of replication, because there are fewer hydrogen bonds 5’ to 3’ polarity phosphate (PO4) is linked with carbon Carbon 5 is connected to the phosphate group (5’), 3 carbon position is connected to the next nucleotide (nucleic acid) hydroxyl group (3’) 5’CARBON 5 CONNECTED TO PHOSPHATE 3’ CONTAINS HYDROXYL GROUP 5’ shown by a knob, 3’ shown by a cavity where a nucleotide can form/bind (interlocking sequence), base-pairing is a key feature Phosphodiester bond- covalent bond, requires energy, comes from phosphate (adenosine triphosphate) Move from one energy to the other, adenosine phosphate has 3 phosphate groups, has high energy bonds present and join the phosphate groups, ADP + P  ATP (produced in mitochondria) Energy produced is conserved in the form of chemical bonds Nitrogenous bases allow for bonding of new nucleotides CTP- cytosine triphosphate, will catalyze this reaction to form a covalent bondphosphodiester bond Ch 2 & 5 pay attention to structures and names of the bonds/structures Replication fork is asymmetrical, 5’ to 3’ & 3’ to 5’ For every origin of replication- 2 forks, one goes each way DNA polymerase is the enzyme which is responsible for the synthesis of new strands Cannot synthesize the phosphodiester bond with another strand Must be base paired to another DNA strand To take care of this problem, RNA polymerase formed Important feature of polymerase- can only connect incoming proteins to 3’ cavity and not 5’ end, because its asymmetrical, cannot have interrupted synthesis of strand - To take care of this problem, replication in form of small fragments- Okazaki fragments- synthesizing in reverse steps, as DNA opens up, new primer is laid 5’ to 3’, individual fragments are going in the direction of 3’ to 5’ “backstitching”, as more DNA is unwinding, more fragments are synthesized, overall growth from 3’ to 5’ - Okazaki fragments - DNA ligase- joins “nicks” and breaks - Each strand is being synthesized as leading strand and lagging strand - Adaptation of system because DNA polymerase is restricted - DNA polymerase is self-correcting o Checks its own work, corrects its error, removes it, and corrects pairing of nucleotide o Because of this, very efficient in accurately copying the information o Error 1 nucleotide/10^7 power - There needs to be a 3’ end for addition of nucleotides otherwise there would be a blunt end - Synthesis from 5’ to 3’ - Read questions slowly - Short lengths of RNA act as primers for DNA synthesis - 3’ is base-pair - You need one primer in the beginning and the DNA polymerase picks up the job - Okazaki fragments (size= 200 nucleotides) needs a primer every time


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