CHAPTER 7 DNA CHARACTERISTICS OF DNA Overview o 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 product o Genetics the study of genes o Genomics the analysis of the sequence of DNA o 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 into DNA protein o Composed of nucleuotides o Joined by a covalent bond between the 5 PO4 5 prime phosphate and one nucleotide and the three prime hydroxyl o The prime numbers refer to the carbon that the molecule is attached to in the pentose sugar Joining of the sugars in this way creates a sugar phosphate backbone o 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 ends o Held together by weak hydrogen bonds and nitrogenous bases of opposing strands o Some DNA pieces have weaker bonds making them more easy to unreavel o Separating the strands is referred to as denaturing or melting o Complimentary A T 2 Hydrogen bonds G C 3 Hydrogen bonds Base pairing allows that 1 side can always code for the other template Oriented in opposite directions one strand is in the 3 to 5 orientation o Antiparallel RNA one is the opposite o Ribonuecleotides not deoxynucleotides o A region of RNA transcript is synthesized from DNA o 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 Regulating the Expression of Genes Play role in protein synthesis o DNA must code for mechanisms to control the expression of genes o 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 rapidly because mRNA does not survive long Due to the activity of RNases that constantly degrade DNA REPLICATION DNA is biodirectional From a distinct starting point in DNA replication proceeds in opposite directions creating an ever expanding bubble of 2 identical replicated portions of the chromosome o Allows for replication in a rapid fashion Replication is also semi conservative o Each of the molecule generated contains 1 half of the original strand o One new with 1 complementary 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 RNA o Thus serve as a primer from which synthesis can continue o DNA is synthesized one nucleotide at a time by covalently bonding the nucleotide to the 3 end o Hydrolysis of a phosphate bond provide energy for the reaction o Elongated the chain from the 5 end to the 3 end o DNA polymerase can edit mistakes of the replication in order to fix Initiation of DNA replication o Origin of replication in order to start specific proteins must recognize and bind to this distinct region of the DNA o The binding of proteins initiates melting from which primase synthesizes RNA to prime for DNA from exposed strands that 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 forks o 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 fragments o 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 RNA o DNA ligase seals the gaps by catalyzing covalent bonds between nucleotides o DNA gyrase temporarily breaks the strands of DNA relieving the tension cause by unwinding of the 2 strands of the helix o By inhibiting function of gyrase can prevent the growth of bacteria GENE EXPRESSION IN BACTERIA Transcription o The enzyme RNA polmerase catalyzes the process of transcription producing a single stranded RNA molecule complementary and anitparallel to the DNA template To desrcribe the two strands of DNA in a region that is transcribed into RNA o Minus strand plus strand Serves as the template for RNA synthesis RNA is the complementary strand to the minus 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 gene 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 completes transciprtion o initiation of RNA synthesis o Elongation RNA is synthesized in the 5 to 3 Once the RNA polmerase advance enough to clear the prometer another RNA polymerase binds o Termination When RNA encounters a terminator it Translation falls off the DNA and release the newly synthesized DNA Therminator is a sequence of nucleotides that