Lecture 19 Structure of Nucleic Acids Be able to describe and interpret the experiment on the replication of the bacterial virus in which it was demonstrated that DNA is the genetic material Know the roles of radioactive sulfur and phosphorus in this experiment o Mix radioactively labeled phage with bacteria The phage infects the bacterial cells Agitate in a blender to separate phage outside the bacteria from the cells and their contents Centrifuge and measure the radioactivity in the pellet and supernatant o The phage is either marked with radioactive protein 35S or radioactive DNA 32P o So when the phages protein was marked with 35S and centrifuged the radioactive protein was found in the supernatant not the pellet where the bacterial cell remains When the phages DNA was marked with 32P and centrifuged the radioactive DNA was found in the pellet o When viruses infect E coli DNA but not protein enters the bacterial cell Thus DNA has the information to produce new phage particles Know the components of a nucleotide and how nucleotides are joined together to make nucleic acids phosphodiester bonds are formed between the 5 carbon on sugar of one nucleotide with 3 carbon on the sugar of the next nucleotide know how the 5 and 3 ends of a nucleic acid differ o oDNA is a linear polymer of nucleotide subunits joined together by phosphodiester bonds covalent bonds between the phosphate group at 5 C and 3 C of next nucleotide uses oxygen as bridges phosphate components Nitrogenous bases stick off backbone at regular intervals chain of nucleotides with alternating sugar and o Sugar phosphate backbone o Any linear chain of nucleotides has a free 5 PO4 on one end and a free 3 OH on the other A chain of DNA thus has polarity o Different DNA molecules differ only in the identities of the nitrogenous bases at any given position they have different DNA sequences Be able to state the names of the nucleic acid bases and know the chemical composition of DNA and RNA o In DNA there is a H attached to the 2 C In RNA there is an OH attached to the 2 C o o RNA sugar is ribose nitrogenous bases are A G C U RNA is single stranded o DNA sugar is deoxyribose nitrogenous bases are A G C T DNA almost always exists as a double helix Be able to describe the Watson and Crick model for the structure of DNA double stranded antiparallel helix held together by complementary base pairing and know which bases pair with each other o Double Helix Two strands of DNA are wrapped around each other in a shape of a helix Strands are held together by hydrogen bonding between nitrogenous bases Only pairing that works are A with T and G with C Strands held at constant distance from one another because of the similar geometry aof A T and G C base pairs Only way pairing will work is if strands have opposite polarity 5 to 3 antiparallel o Complementary base pairing A bonds with T 2 H bonds G bonds with C 3 H bonds A T and G C base pairs both contain a purine and a pyrimidine due to similar geometry same overall diameter If two chains can form proper base pairs when oriented with opposite polarity the chains are said to be complementary to each other Because the two strands are complementary if you know the sequence of one strand you can determine the sequence of the other ex 5 ATCCGCT 3 3 TAGGCGA 5 The cell replicates duplicates DNA by simply synthesizing new strands of DNA complementary to old strands Lecture 20 DNA Replication Know that DNA polymerase requires a DNA template a primer synthesizes 5 to 3 and uses deoxynucleotide triphosphates understand what 5 3 synthesis means the polymerase adds a nucleotide to the hydroxyl on the 3 end of the growing nucleotide chain o DNA polymerase attaches to the RNA primer and begins DNA replication The RNA primer is at the 5 end of the new strand so the synthesis of the new strand goes from 5 to 3 Know that DNA replication begins at sites called origins and proceeds bidirectionally away from the origin This produces two replication forks that move away from the origin and both strands of DNA are replicated simultaneously at each fork Know what the leading strand and the lagging strand are o The leading and lagging strands run antiparallel Leading strand Lagging strand strand replicated continuously strand replicated in small pieces Know the roles of the following enzymes in DNA replication Helicase Primase DNA polymerase III and DNA polymerase I binds the origin and unwinds the DNA attaches and makes a short primer RNA o Helicase o Primase o DNA Polymerase III most of the replication of DNA primers o DNA polymerase I attaches to the primer and begins DNA replication does completes lagging strand synthesis by removing the RNA Know that DNA polymerases have proofreading function and what the significance of proof reading is o The proofreading function of DNA polymerase reduces the error rate from about one in a million base pairs to about one in a hundred million base pairs o DNA polymerases use their 5 to 3 exonuclease activity to remove a mismatched base pair o Proofreading by DNA polymerase involves the removal of several bases on the newly synthesized strand of DNA Improper base pairing during DNA replication causes a pause in chain elongation following base removal DNA polymerase can add nucleotides in the 5 to 3 direction again o Know why linear DNA molecules shorten with each round of replication and be able to explain how cells solve this problem o During chromosome replication the enzymes that duplicate DNA cannot continue their duplication all the way to the end of a chromosome so in each duplication the end of the chromosome is shortened this is because the synthesis of Okazaki fragments requires RNA primers attaching ahead on the lagging strand The telomeres are disposable buffers at the ends of chromosomes that are shortened by cutting off an end during cell division their presence protects the genes before them on the chromosome from being cut instead Know the importance of DNA repair and be able to explain how it works repair enzymes identify unpaired bases or damaged bases and cut them out from one side of the double helix then DNA polymerase I fills in the correct bases used complementary base pairing with the DNAs undamaged strand o DNA polymerase makes an error every 10 5 10 6 bases copied o Radiation and certain chemicals can damage DNA bases o DNA repair enzymes polymerases ligase find unpaired bases and damaged bases cut them out and DNA polymerase 1 fills in the
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