After Exam 4 I Chapter 5 a Nucleic acid i Polymers made up of monomers called nucleotides b 2 types of nucleic acids i Deoxyribonucleic acid DNA ii Ribonucleic acid RNA c Gene expression a process including DNA directing RNA synthesis and through RNA controls protein synthesis d mRNA messenger RNA interacts with the cells protein synthesizing machinery to direct production of a polypeptide which folds into all or part of a protein i Conveys genetic instructions for building proteins from the nucleus to the cytoplasm e Flow of genetic information i DNA RNA protein f Ribosomes sites of protein synthesis g Components of nucleic acids i Polynucleotides macromolecules that exist as polymers 1 Consists of monomers called nucleotides a Composed of three parts i A five carbon sugar pentose ii A nitrogen containing nitrogenous base iii One or more phosphate groups b Nucleoside portion of a nucleotide without any phosphate groups i Nitrogenous base sugar ii Two families of nitrogenous bases 1 Pyrimidine has one six membered ring of carbon and nitrogen atoms a Cytosine C thymine T Uracil U 2 Purine larger with a sex membered ring fused to a five membered ring a Adenine A Guanine G iii Adenine guanine and cytosine are found in both RNA and DNA iv Thymine is found only in DNA v Uracil is found only in RNA vi Sugar is then added to the nitrogenous base 1 2 In DNA it is deoxyribose In RNA it is ribose a Difference is deoxyribose lacks an oxygen atom on the second carbon in the ring hence the name deoxyribose vii Next attach phosphate group to 5 carbon sugar now it is a nucleotide h Nucleotide Polynucleotide i The linkage of 2 nucleotides to become a polynucleotide involves ii a dehydration reaction In the polynucleotide adjacent nucleotides are linked by a phosphodiester linkage 1 Consists of a phosphate group that links the sugars of two nucleotides a Bonding results in a repeating pattern of sugar phosphate units called the sugar phosphate backbone i Two free ends of polymer are different 1 One has a phosphate attached to a 5 carbon 5 end 2 The other end has a hydroxyl group on a 3 carbon 3 end iii DNA double helix 1 Two sugar phosphate backbones run in opposite 5 3 directions from each other a Antiparallel arrangement b Two strands held together by hydrogen bonds c A T d G C e A U in RNA i Genomics and proteomics have transformed biological inquiry and applications i DNA sequencing determining the sequence of nucleotides along a DNA strand one by one ii Human Genome Project 1 Came up with more efficient ways to sequence DNA iii Bioinformatics the use of computer software and other computational tools that can handle and analyze these large data sets iv Genomics comparing a whole genome of different species v Proteomics analysis of large sets of proteins II Chapter 16 a Griffith i DNA can transform bacteria ii Transformation a change in genotype and phenotype due to the assimilation of eternal DNA by a cell iii Virus little more than DNA or RNA enclosed by a protective coat 1 Often simply protein 2 To produce more viruses one virus must infect a cell a Phage Chase i Phage DNA entered host cells Hershey and b Chargaff s rules i The base composition of DNA varies between species ii For each species the percentages of A and T bases are roughly equal and the percentages of G and C bases are roughly equal c Double helix the presence of two strands i Antiparallel the two sugar phosphate backbones run in opposite directions A model for DNA replication d Semiconservative model can be distinguished from a conservative model of replication because the two parental strands somehow come back together after the process e Dispersive model all four strands of DNA following replication have a mixture of old and new DNA f Origins of replication where the replication of a chromosome begins i Short stretches of DNA having a specific sequence of nucleotides ii Bacterial chromosome prokaryotic 1 Proteins that initiate DNA replications recognize this sequence and attach to the DNA separating thw two strands and opening up a replication bubble 2 Replication continues in both directions until molecule is copied iii Eukaryotic chromosome 1 May have hundreds of origins a Multiple replication bubble form and then fuse speeding up copying g Replication fork i A Y shaped region where the parental strands of DNA are being unwound 1 Several proteins assist in unwinding a Helicases enzymes that untwist the double helix at the replication forks separating the two parental strands and making them available as template strands b Parental strands separate single strand binding proteins i Bind to the unpaired DNA strands keeping them from re pairing c Topoisomerase helps relieve the stress caused by the untwisting of the double helix ahead of the replication fork by breaking swiveling and rejoining DNA strands 2 Primer the initial nucleotide that is produced during DNA synthesis actually a short stretch of RNA not DNA a Synthesized by primase i Enzyme ii Starts a complementary RNA chain from a single RNA nucleotide adding more RNA nucleotides one at a time using the parental DNA strand as a template h Synthesizing a new DNA strand i DNA polymerases enzymes that catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain 1 DNA polymerase III a In E coli Adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides complimentary to the parental DNA template strand to the growing end of the new DNA strand 2 DNA polymerase I a Replaces RNA nucleotides of the adjacent primer with DNA nucleotides 3 New strands are added to a free 3 meaning all new strands are in 5 to 3 direction ii Leading strand the strand made by the addition of nucleotides to the strand by DNA polymerase III 1 Synthesized continuously iii Lagging strand The DNA strand elongating away from the replication fork 1 Synthesized discontinuously as a series of segments a Okazaki fragments segments i 1000 2000 nucleotides long in E coli and 100 200 nucleotides long in eukaryotes ii Each fragment must be primed separately iv DNA ligase joins the final nucleotide of this replacement DNA segment to the first DNA nucleotide of the adjacent Okazaki fragment 1 Joins the sugar phosphate backbones of all the Okazaki fragments into a continuous DNA strand v Replication overview 1 Helicase unwinding 2 Single strand binding protein stabilization 3 DNA Pol III 4 Primase synthesis of RNA primer for 5th Okazaki fragment 5 DNA pol III finishing
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