Objectives for Exam 3 Chromatin and DNA Sequence Organization Chapter 11 Be able to de ne chromatin and describe its structure nucleosomes histone proteins plus associated DNA chromatin complex of DNA RNA histones and nonhistone proteins that make up uncoiled chromosomes characteristic of the eukaryotic interphase nucleus as the cell cycle progresses most cells reenter mitosis where the chromatin coils into visible chromosomes once again the associated proteins are divided in basic positively charged histones and less positively charged histones histones contain large amounts of the positively charged AA s lysine and arginine making it possible for them to bind to the phosphate groups of the nucleotides which are negatively charged nucleosome beads on a string a nuclear complex consisting of 4 pairs of histone molecules an octamer of H2a H2b H3 and H4 wrapped by 2 turns of a DNA molecule The major structure associated with the organization of chromatin in the nucleus each repeating nucleosome is associated with about 200bp DNA Know the difference between euchromatin and heterochromatin in terms of its structure composition cytosine methylation of DNA histone tail modi cation and transcriptional activity euchromatin uncoiled true chromatin or chromosomal regions that are relatively uncoiled during the interphase portion of the cell cycle capable of transcription uncondensed heterochromatin condensed the heavily staining late replicating regions of chromosomes that are prematurely condensed in interphase Thought to be devoid of structural genes condensed DNA transcription is repressed Heterochromatic areas are genetically inactive because they either lack genes or contain genes that are repressed heterochromatin also replicates later than euchromatin does constitutive heterchromatin heterochromatic DNA in all cells centromeres and telomeres facultative heterochromatin heterochromatic in some cells X inactivation Modi cation of histone tails regulates chromatin structure and function histone acetylation is associated with euchromatin and transcription cytosine is methylated in many inactive genes ex X inactivation involves formation of facultative heterochromatin inactive X has deacetylated histones and methylated cytosines see above genome in eukaryotes stranded Know the difference between constitutive and facultative heterochomatin and be able to name two places on chromosomes where constitutive heterochromatin is found Be able to interpret a Cot curve for the renaturation of eukaryotic DNA and know which part of the curve is due to the renaturation of repeated DNA sequences in the the renaturation kinetics of DNA showed the existence of repeated DNA sequences the curves with multiple slopes have repeated DNA sequences remember that the x axis is C0t and the y axis is the fraction remaining single Differences between simple sequence DNAs satellite DNA sequences and interspersed repeats and the percentage of the human genome that is composed each of these classes of repeated DNA sequences satellite DNAs or Simple Sequences not transcribed long tandem arrays of long repeats short sequences 5 100bp often in large s of copies localized sites on chromosomes basically short sequences repeated many times in the genome Interspersed Repeats longer sequences 300 5000 variable of copies not in tandem array repeats are not identical dispersed over the chromosome 5 10 of the genome sometimes transcribed about 40 of the human genome 40 60 of the genome of eukaryotes is repetitive sequences most repetitive DNA has no known function except telomeres and Know the size of the human genome and the approximate percentage of the genome centromeres that codes for proteins genes that code for proteins only account for 5 10 of the genome we have about 25 000 genes and 3 x 109 bp Genetic Code Transcription Chapter 12 Transcription process by which base sequence in DNA is converted into RNA The enzyme responsible is RNA polymerase the linear sequence of deoxyribosenucleotides making up DNA ultimately dictates the components constituting proteins the end product of most genes the question is how much information stored as a nucleic acid is decoded into a protein in the rst step of of gene expression info on one of the strands template strand is transferred into an RNA complement through transcription once synthesized this molecule acts as a messenger molecule bearing the coded information hence its name messenger RNA mRNA the mRNAs then associate with ribosomes where decoding into proteins takes Understand how the genetic code was deciphered using synthetic mRNAs and in vitro place translation Nirednberg and Matthaei used in vitro cell free protein synthesizing system and an enzyme called polynucleotide phosphorylase to decipher the code the in vitro mixture contained all the necessary things for protein synthesis ribosomes tRNAs AA s etc one or more of the AA s was radioactively labeled in order to follow the synthesis nally an mRNA is added to serve as a template the polynucleotide phosphorylase enzyme catalyzed the reaction each addition of a ribonucleotide is random based on the concentrations added the probability of insertion is proportional to its availability relative to the other to the mixture ribonucleotides Using Homopolymers RNA homopolymers UUU AAA CCC only one type of ribonucleotide they had added a mRNA molecule only like UUUUUU AAAAAA etc to get these and then would see what the RNA homopolymers coded for Be able to determine possible codon assignments in experiments involving repeating copolymers as the mRNA pg 245 246 this was another technique use to decipher the genetic code di tri and tetra nucleotides that are replicated many times and then enzymatically joined together to form long polynucleotides depending upon the point of initiation you can get several different repeating triplets from the copolymers Know what base transition and base transversions are Know that adenine and guanine are purines and that cytosine of thymine are pyrimidines base transitions mutations where a purine is switched with another purine A with G or a pyrimidine is switched with another pyrimidine U with C base transversions a purine is switched with a pyrimidine or vice versa base transition mutations are 5 10 times more common than base transversions Know the organization of the genetic code and its important features degenerate universal and understand how the genetic code is organized to protect
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