CHAPTER 7: DNACHARACTERISTICS OF DNA- Overviewo Genome: the complete set of a species genetic code Stored in chromosomes, mostly DNA, some viral RNA Functional unit is a gene The gene encodes an end producto Genetics: the study of geneso Genomics: the analysis of the sequence of DNAo The cell must do 2 things to survive: DNA replication- DNA must be duplicated before the cell division so the encoded information can be passed on to future generations Transcription- The DNA must then be deciphered or expressed- In order to express correct gene products at beset time- Two steps: first is transcription- Copies DNA into RNA (a translational, temp form of DNA) Translation- Intercepts the information encoded in RNA in order to synthesize encoded protein Central Dogma of molecular biology: this process of DNARNAprotein Retrovirus copies RNA into DNA intoprotein- DNAo Composed of nucleuotideso Joined by a covalent bond between the 5’PO4 (5prime phosphate) and one nucleotide and thethree prime hydroxylo The prime numbers refer to the carbon that themolecule is attached to in the pentose sugaro Joining of the sugars in this way creates asugar-phosphate backbone Connected to each sugar is an adenine(A), thymine (T), guanine (G), or cytocine (C)  A DNA strand will always have a five prime phosphate and a 3 prime OH,these ends are referred to as 3’ and 5’ endso Held together by weak hydrogen bonds and nitrogenous bases of opposing strandso Some DNA pieces have weaker bonds, making them more easy to unreavelo Separating the strands is referred to as denaturing or meltingo Complimentary A T (2 Hydrogen bonds) GC (3 Hydrogen bonds) Base pairing allows that 1 side can always code for the other (template)o Antiparallel Oriented in opposite directions, one strand is in the 3’ to 5’ orientation, one is the opposite- RNAo Ribonuecleotides, not deoxynucleotideso A region of RNA, transcript, is synthesized from DNAo Uracil replaces thymine o 3 forms of RNA transcribed from different genes messenger RNA- translated during protein synthesis- correlated 3 nucleotides to form a codon- this forms 1 amino acid Ribosomal RNA or transfer RNA- Never translated, they are the final products- Play role in protein synthesis- Regulating the Expression of Geneso DNA must code for mechanisms to control the expression of geneso Regulate synthesis of mRNA molecules If not transcribed into mRNA, then cannot make the protein Number plays a role as well, reduce the number of mRNA, reduced the expression rapidlybecause mRNA doesnot survive long - Due to theactivity ofRNases thatconstantlydegrade DNA REPLICATION- DNA is biodirectional- From a distinct starting point in DNA,replication proceeds in oppositedirections, creating an ever-expanding bubble of 2 identicalreplicated portions of thechromosomeo Allows for replication in arapid fashion- Replication is also semi-conservativeo Each of the moleculegenerated contains 1 half ofthe original strando One new with 1complementary strand- DNA polymerase are enzymes that synthesize DNA using one strand as a template to generate the complementary protein o These enzymes only add nucleotides onto an existing fragment or DNA or RNAo Thus serve as a primer from which synthesis can continueo DNA is synthesized one nucleotide at a time, by covalently bonding the nucleotide to the 3’ endo Hydrolysis of a phosphate bond provide energy for the reactiono Elongated the chain from the 5’ end tothe 3’ endo DNA polymerase can edit mistakes ofthe replication in order to fix- Initiation of DNA replicationo Origin of replication: in order to start,specific proteins must recognize andbind to this distinct region of the DNAo The binding of proteins initiates melting,from which primase synthesizes RNA toprime for DNA from exposed strandsthat serve as primers for DNA synthesis- The replication fork o The biodirectional nature of DNA creates a Y shaped region in each building molecule: replication forkso The template strands “unzip” at each fork due to activity of helicase o Template read 5’3’o Made 5’3’o the synthesis continues in a 5’ to 3’ direction, as a fresh DNA molecule is exposed  this strand is called the leading strand the oppsing is the lagging strand (more complicated because DNA cannot add nucleotides to the 5’ end)- grows discontinually in fragmentso Since each replication of DNA must be proceeded with RNA primers the synthesis of this series of fragments Okazaki fragments, begins a short stretch of RNAo DNA ligase seals the gaps by catalyzing covalent bonds between nucleotides o DNA gyrase, temporarily breaks the strands of DNA, relieving the tension causeby unwinding of the 2 strands of the helixo By inhibiting function of gyrase, can prevent the growth of bacteria GENE EXPRESSION IN BACTERIA- Transcriptiono The enzyme RNA polmerase catalyzes the process of transcription, producing a single stranded RNA molecule complementary and anitparallel to the DNA templateo To desrcribe the two strands of DNA in a region that is transcribed into RNA:  Minus (-) strand - Serves as the template for RNA synthesis- RNA is the complementary strand to the minus strand plus (+) strand- compliment to the RNA strand- RNA has the same polarity (5’ to 3’) as the complimentary but has U-o mRNA and carrying genes monocistroniccarries the information for 1 gene polycistroniccarries for multiple genes- normally all genes involved in 1 metabolic pathway transcription begins when RNA polymerase recgonisees a nucleotide on the prometer (the mechanism that identifies the region of DNA that should be transcribed into DNA, oriented the strand int one of 2 possible directions)- this dictates which one will be the template - upstream implies that the direction is towards the 5’ end of the +DNA- downstream the direction is towards the 3’ end of - prometer is an upstream of a geneo initiation of RNA synthesis transcription begins after RNA polmerase recognizes and binds to a prometer on the double-stranded DNA molecule in bacteria, a particular subunit of RNA recognizes the prometer region prior to the one that beings transcription- sigma factor can disassociate the enzyme shortly after the transcription begins- the remaining RNA polmerase is the core enzyme that completestransciprtiono Elongation RNA is synthesized in the 5’ to 3’ Once the RNA polmerase