SC NATS 1670 LECTURE & WRITTEN NOTES.pdf

Part 2 FROM THE DNA TO THE DNA STRUCTURE F ORGANISM - more cancytoplasm - - - - Venzymes responsible for cell activity - DEFINITIONS a om : smallest molecule : two or chemical more unit atoms of matter held DNA (DEOXYRIBO-NUCLEIC-ACID) together by -> chemical molecule -...

Part 2 FROM THE DNA TO THE DNA STRUCTURE F ORGANISM - more cancytoplasm - - - - Venzymes responsible for cell activity - DEFINITIONS a om : smallest molecule : two or chemical more unit atoms of matter held DNA (DEOXYRIBO-NUCLEIC-ACID) together by -> chemical molecule - bond , ex : Methane CHy largest ↳ Responsible for transmission of Information from one generation to the next in most forms of life on this planet ↳ millions of nucleotides * polurtname I a al going directions Complementary base pairs A-T and G-C through hydrogen bonding Strands have a backbone composed of phosphate to sugars to which the bases are attached Rosallind Franklin • Recognizes that Dna is a double helix, rotating in clockwise rotation • DNA molecule has a diameter of 2nm and that one turn of the helix was 3.4 nm in length • Could not explain how the nitrogenous bases were associated in the centre of the helix Watson and Crick • Take shargraf work and franklin pictures and discovered a double helix • Discovered four different nitrogenous bases (A, T, C, and G) • Chargraff’s ratios of the nitrogenous bases • the phosphate and sugar backbone • Showed that DNA molecule could only be stable if the strands ran antiparralel, that is. - If they ran in opposite directions One DNA strand must have the hydroxyl of the 3’ carbon attached to the deoxyribose sugar at one end and the phosphate attached to the 5’ carbon of the last sugar at the other end - The other strand must wind around the first with its 5’ end opposite the 3’ end of the first strand. ↳The DNA backbone is assembled from repeating deoxyribose sugar unit that are linked through phosphate groups Each phosphate carries a negative charge, make an entire DNA backbone, highly charged and polar a cyclic base is attached to each sugar the bases are planar and extend out perpendicular to the path of the backbone pyrimidine bases are composed of one ring and purine bases of t wo rings adjacent bases are aligned so that their planar rings stack on top of one another base stacking contributes significantly to the stability of the double helix In a double helix each base on one strand is paired to a base on the other strand that lies in the same plane i ⑮ DNA REPLICATION -mem Two functional roles of DNA I Duplication: The molecule must be replicated and transmitted in each cell division • each daughter cell contains almost identical copies of the DNA molecules as compared to its mother cell 2 Information: The molecule contains information expressed in the sequence of the nucleotides • the sequence are transcribed into RNA to release their information - dont ge to 1 . need up I the my opens ~ BNA words ↑ separate between twotrands make phosphodiester bonds ↓ DNA REPLICATION EXPLANATION VIDEO https://www.nagwa.com/en/videos/193135913969/ DNA polymerase is a template- directed enzyme that synthesizes a product with a base sequence complimentary to the template DNA polymerase catalyze efficiently the formation of a phosphorite bond only if the base on the incoming nucleotide is complementary to the base on the template strand The chain-elongation is reaction catalyze by DNA polymerase from 5’ to 3’ of the elongated DNA The t wo strands are “antiparallel” one strand runs 5’ to 3’ while the other runs 3’ to 5’ The chain-elongation reaction catalyze by DNA polymerase from 5’ to 3’ of the elongated DNA • dna replication comes largely from studies of e coli bacteria that are found by the billions in the large intestine • the dna at the origin of replication the t wo strands of dna separate and then ser ve as templates for making new strands • the result is a replication bubble, grows in both directions forming t wo replication forks • at the replication fork are shown here here dna helicase unwinds the t wo strands and dna polymerases type 3 build new strands of dna • a critical component of the dna polymerase 3 protein is the dna clamp protein which prevents the polymerase from dissociating from the template strand thus the process of dna replication is called semiconservative • each new double helix contains one original dna strand and one new DNA strand because strands in a dna double helix run in opposite directions • the new strands must be made in different ways one new strand the leading strand is built continuously and forms from its five prime end to its three prime end the orientation of the other new strand the lagging strand is opposite to the working orientation of dna polymerase three, the lagging strand must be built in fragments called okazaki fragments in the five prime to three prime direction using multiple primers • dna polymerase 3 builds a new strand of dna by adding dna nucleotides one at a time each new nucleotide must pair up with its complementary nucleotide on the parental strand • adding new nucleotides works the same way on both the leading and lagging strands because of the opposite orientation replication of the lagging strand is more complicated to initiate synthesis an enzyme called primase reads the dna strand and produces a short segment of rna which ser ves as a primer • a dna clamp protein surrounds the dna and attaches to dna polymerase 3 which bills the rest of the new fragment of dna until it reaches the previously synthesized okasaki fragment • when the fragment is finished the polymerase releases from the okazaki fragment • DNA polymerase 1 removes rna and replaces it with dna however it cannot finish connecting the okazaki fragments • an enzyme called dna ligase joins the okazaki fragments together • growth of the leading and lagging strands continues at both replication forks until there are t wo identical double-stranded dna molecules METHODS DERIVED FROM DNA REPLICATION First DNA is denatured into single strands at near-boling temperature. At high temperatures, the kinetic motion of the DNA molecule disrupts the weak hydrogen bonds that joins complementary DNA strands together. When the temperature is lowered, the primer binds to its complementary sequence in the template DNA. Kornberg’s earlier work showed that a primer is needed for DNA polymerase to start replication Since billions of DNA molecules are present, the elongation reaction can be terminated at any adenine position • dna strands are in different lengths Sanger method is a process that yields a series of DNA fragments whose size is measures by electrophoresis The last base in each fragment is known, as that dideoxy nucleotide was used to terminate the reaction Ordering the fragments by size tells the base sequence of the DNA An investor can amplify a single copy of a DNA segment into billions of identical copies • Must have a target DNA, determined by primers • • • • A PCR reaction lasts several hours (20 - 35 repeating cycles) A cycle begins by heating the reaction mixture to 95 degrees celsius Heat denatures the DNA After temperature is reduced and the primers can now form hydrogen bonds with their complementary sequences n the target DNA • Temperature then reaches optimal level and begins polymerization, creating t wo double stranded of the target DNA • the PCR contains many copies of prime and nucleotides to perform more cycles, after the second cycle there are four copies of target DNA • REPEATS TRANSCRIPTION AND RNA PROCEESING TWO FUNCTIONAL ROLES OF DNA Replication: the molecule must be replicated and transmitted in each cell division • each daughter cell contains almost identical, copies of the DNA molecules as compared to its mother so Information: The molecule contains information expressed in the sequence of the nucleotides • sequences are transcribed into RNA to release their information In DNA, basic chemicals have been arranged and rearranged in an almost infinite number of combinations to produce a unique score RNA is the information carrier from the nucleus to the cytoplasm CENTRAL DOGMA OF GENETICS DNA is transcribed to RNA RNA translated to form polypeptides (proteins) TRANSCRIPTION Process of releasing information contained in a DNA sequence The sequence of bases in the DNA template is copied into an RNA sequence, which is either used directly or translated into a polypeptide mRNA (messenger) intermediate molecules used for transfer the information DNA to protein rRNA (ribosomal) functional RNA molecules that are components of the ribosome tRNA (transfer) functional RNA molecules that serve as adapters in translation GENE A region of a DNA molecules containing a sequence of bases that transcribed into a functional product Several regions are responsible for the proper function of a gene • regulatory region (promoter) - sequence of bases that control the initiation of transcription • transcribed region - sequence of bases that are read into a functional molecule (RNA and proteins) • termination site - sequence of nucleotides that stops transcription TRANSCRIPTION 1. First step in converting genetic information into proteins • RNA polymerase synthesizes an RNA transcript using one strand of DNA as the template • RNA polymerase synthesizes the RNA strand in the 5'→3' direction - this RNA is complementary to the DNA template strand • transcription begins near promoter sites and ends at terminator sites 3 steps of transcription: INITIATION, ELONGATION, TERMINATION - -is - ELONGATION AND TERMINATION The sequence of the RNA produced is complementary to the base sequence of the DNA template strand Transcription ends with a termination phase. RNA polymerase encounters a transcription termination sequence that causes the RNA to form a unique structure that help it to disassociate from the DNA and from the RNA polymerase POST-TRANSCRIPTIONAL OF mRNA IN EUKARYOTES In eukaryotes, genes consist of coding regions called exons separated with no coding regions called introns After a eukaryotic mRNA is produced, introns must be spliced out The ends of the mRNA receive a cap and tail Initial transcript is known as the pre-mRNA, and before being exported from the nucleus processing must occur. Final processed mRNA is exported to the cytoplasm RNA processing: 1. Addition of cap to the 5’ end 2. Addition of poly-A tail at the 3’ end 3. Removal of introns (splicing) AN ALTERNATIVE RNA SPLICING OTHER ASPECTS OF TRANSCRIPT PROCESSING: CAPS AND TAILS The 5' cap and the poly (A) tail extends the life of an mRNA by protecting it from degradation PROTEIN SYNTHESIS FLOW OF INFORMATION The following series of events defines information flow in the cell: PROTEINS Active players in most cell processes Involved in essentially all sub-cellular, cellular, and developmental functions in living organisms Major classes of proteins: • Enzymatic - catalysts in biochemical reactions (DNA/RNA polymerase) • Regulatory - control of gene expression, inter cell air signaling (transcription factors) • Structural - cellular or organismal anatomy AMINO ACIDS building blocks of protein PROTEIN SYNTHESIS TRANSLATION • converting information stored in nucleus acid sequence into proteins COMPONENTS OF TRANSLATION mRNA - the template used to specify amino acid sequence Ribosomes - complex of proteins and rRNA molecules Transfer RNA (tRNA) - RNA molecule serve as adapters bet ween codons in mRNA and amino acids GENETIC CODE A universal code that is used in a nuclear genome of most organisms Complementary anticodon is present in tRNA molecules, which is specifically linked to an amino acid There are 64 possible codons but only 20 amino acids. The genetic code is redundant were most amino acids are specified by more than one codon (up to 6) TRANSLATION • the sequences of bases in the mRNA is converted to an amino acid sequence in a protein by ribosomes via tRNA • tRNA carry an amino acid and have a three-base anticodon, which binds to an mRNA codon • The amino acid carried by the tRNA is then added to the growing protein via formation of a peptide bond • Each amino acid is specified by three bases (codon) in mRNA MOVING DOWN THE mRNA • translocation - occurs when the ribosome moves down the mRNA in the 5’ -> 3’ direction - ejects the empty tRNA and moves the tRNA containing the growing polypeptide into the P site - opens the A site to a new mRNA codon A • three steps in elongation repeat down the length of the mRNA - arrival of amni acid loaded tRNA - peptide bond formation - translocation 6 Y * g & - - - - - As soon as a messenger RNA molecule is transported from the nucleus to the cytoplasm ribosomes begin to translate the sequence into amino acids. Ribosomes translate the mRNA simultaneously. Each ribosome begins at the five prime end of the mRNA and progresses steadily towards the three prime end. New ribosomes attach to the 5-prime end at the same rate as the previous ones move out of the way. These multiple initiations allow the cell to make much more protein from a single message than if one ribosome had to complete the task before another could begin. When a ribosome reaches a stop codon the ribosome and the new protein dissociate from each other and from the mrna. MUTATIONS THE LENGTH OF THE DNA • human DNA of one cell is 2 meters long • 10^16 cell are produced in human lifetime - 2 x 10^13 km of DNA • speed of light is 300, 000 km/second • The length of the DNA that our body synthesizes is equivalent to 2 light years FROM THE DOUBLE HELIX TO THE CHROMOSOME • In living cells, DNA undergoes chemical changes most mutations are taking place during replication but some not replicating also • most changes are repaired quickly - those that are not result in mutations DNA REPAIR mutations can come from incorporations of incorrect bases during DNA replication Most spontaneous changes in DNA are temporary due to being immediately corrected by DNA repair Most damages to DNA is repaired by the removal of damaged bases - followed by resynthesis of excised region THE MOLECULAR BASIS OF MUTATION • a mutation is any change in an organism’s DNA sequence • proteins, encoded by the genotype, produce the phenotype • DNA mutations affect phenotype only when the mutation is expressed (DNA ->RNA -> protein) and the resulting protein functions abnormally • not all mutations affect the protein's ability to function and thus do not generate a phenotype • point mutation - change in a single nucleotide - can result from errors in DNA replication or from exposure to mutagenic toxics THE GENETIC CODE Silent mutation - do not change the amino acid sequence Missense mutation - a point mutation that causes a change in the amino acid sequence of the protein Nonsense mutation - point mutation that creates a new stop codon Frameshift mutation CONSEQUENCES OF MUTATIONS • selective advantage EVOLUTION • the activity of the protein is reduced - genetic disease - ex: sickles cell anemia • cancers caused by defective repair of DNA • stronger activity of the protein is reduced • activity of the protein is reduced MUTATIONS AND CANCER Smoking and cancer What is cancer? • a genetic disease caused by mutations of genes - mainly somatic non-heritable ORIGINS OF MUTATIONS • spontaneous - undergo chemical changes when it is replicated and spontaneous mutations is the cost we pay for replicating huge genome • Physical induced (uv from the sun, skin cancer), chemically induced - environment EPIDEMIOLOGY OF CANCER • mutated genes are accumulated over time • age -> mutated genes → cancer environment behaviour THE SMOKING GUN • classic mechanism of lung carcinogenesis based on the fact that carcinogens in the tobacco end up causing DNA mutations • Tobacco smoke consist of about 60 known components Primary neoplasms of the lung are among the rarest forms of the disease • lung cancer is like a time bomb that will gain power to be expressed years later • Cancer is about accumulation of mutations • Reasons: - availability, social trends and acceptance k COPD - CHRONIC OBSTRUCTIVE PULMONARY DISEASE • long term disease caused by smoking emphysema - alveoli, a lot of sec that can exchange the oxygen involved with the oxygen delivery TOBACCO AND CANCER • lung cancer is the leading cause of cancer deaths in the US and Canada • In 1992, US Environmental Protection Agency declared tobacco smoke the most dangerous cancer causing agents in humans • In the US, nearly 150 000 people die prematurely each year from tobaccorelated cancers • Lung cancer is almost entirely preventable - most case due to cigarette smoking 30% is all 30% of all Smoking cancer deaths cancer accounts for us due to deaths is due 80% of cases smoking to smoking of lung cancer Second hand smoking • In a pregnant women, at least three generations will be exposed to the same environmental conditions at the same time Spontaneous abortion and other defects in babies brim to smokers (especially mother) If smoking is bad, why is it so common? • Contribution of cigarette company - first they gave soldiers free cigarettes - after the war, they got people paying for cigarettes to satisfy their addiction habits • cigarette companies had a brilliant economical decision - drug dealers • more people killed from tobacco than from bullets When did females start smoking and why? • in the 40s, tobacco companies used physiological manipulations to convince women to smoke - before considered “taboo” “If you can market a product that kills people, you can sell anything” - Chris Reiter IMPLICATORY DENIAL • about denying reality as a way to avoid uncomfortable implications • tobaccos ceo “nicotine is not addictive” 1994 -> Cigarettes toxins -> -> tobacco -> ads filters have pass onto the companies is a is -> not so longs pay physicians powerful tool to participate to looks cool" safe in advertise ads X cigarettes SMOKING WITHIN YOUNG KIDS • tobacco industry has been targeting young children and adolescents as a marketing policy since the 1970s Under the new FDA rules (2010) tobacco companies cannot: • sponsor sporting events and sell items with tobacco brands’ logos go D • Sell tobacco products in vending machines accessible to minors • Some companies helped build/sponsor schools (100 schools) • E-cigarettes used by teens - initially presented as way to stop people from smoking, did not work • tobacco industry used 12.4 million dollars on advertisement and promotion