BIOL 302 1st EditionExam # 2 Study Guide Lectures: 8 - 13Lecture 8 Structure of nucleotides:1. 3 components:a. 5-carbon ribose sugari. Sugar carbons are numbered 1-5.1. #1: where the base attaches2. #2, #3, #4: are in the ring3. #5: not included in the ring and is attached to the triphosphate – high energy binds lots of oxygen molecules because of negative charges (unstable).a. Alpha (nearest carbon to #5)b. Betac. Gama (farthest)ii. Nucleoside: sugar + base. NO PHOSPHATEiii. DNA: deoxyribose, missing an –OH group from the #2 carboniv. RNA: ribose sugar, oxygen is reactive and carries out functions b. 5 different basesi. 2 families:1. Pyrimidines: 6 member rings, C.U.T.,2. Purines: double ringed, A.G.3. **Uracil and Thymine are identical but thymine include an extra –CH3 groupc. Phosphate groupII. How do they come together?a. 3 prime hydroxyl on the #3 sugar creates a bond between oxygen and alpha (phosphodiester bond- the linkage of 2 sugars/nucleotides) then releases beta and gamma b. During DNA synthesis – polymerase adds nucleotides together at the 3-prime hydroxyl from the bottom. i. NH -------------------------------------- COOHii. 5’ ------------------------------------- 3’ [SAME RESEMBLENCE & VERY SPECIFIC]c. 5 prime triphosphate stays the same; 3 prime hydroxyl is where the extension occursd. Chains are acidic because it gives off a protein and is very polar because it contains many oxygen moleculese. RNA sequences are typically the same wayi. 2-prime hydroxyl can cut the phosphodiester bond and create a new bond. This undergoes auto-hydrolysis: which bonds with any new phosphate; the RNA cuts itself whereas the DNA does not – proves that RNA has a lot of different activities and also that RNA is more unstableStructure and differences of DNA and RNA, phosphodiester bondsI. DNA: a. Stores genetic informationb. Sizes ~3,000 nucleotidesc. Human chromosomes have over 100 million link together and way much larger than proteinsII. RNAa. Have very different activities and functions and are really tinyb. Few 100,000’s RNA (largest). mRNA: 2,000 i. Three types of RNA: messenger, transfer, and ribosomal: standard RNA wemissed a lot of information which resulted in missing the important fact that RNA has enormous amounts of functions which play into a role in thephysiology of the cellc. Stores information (HIV, flue virus, polio)d. Gene expression regulatione. Protein synthesis – which are involved in the construction of proteinsf. Enzymatic functions and propertiesChargaff’s RuleI. 1940s – 1960sII. Broke down components and found that the moles of A + G = to the moles of T + C. The moles of A = T and the moles of G = CIII. Some kind of symmetry and base composition of DNA varies from one species to the otherIV. The G and C pairs (3 hydrogen bonds) are stronger than A & T (2) due to the amount of hydrogen bondsV. Structure fit together and always paired; genetic information has to be able to replicate in order to pass down through generationsa. Genetic information comes from the basesVI. Anti-parallel strands with bases that are perpendicularGenetic Code: Lecture 9DNA Replication: a. Site of replication on thousands of sights – telomeres (ends of chromosomes)b. Normal cells have limited life span corresponds to telomeresc. Demonstrates multiple sites on every chromosomesd. Pulse Labelinga. Labeling takes place in culture & adds in media. Thymidine: precursor (sugar and base) – it can get in the cell  dttp (radioactive)a. When its being synthesized it takes into the new strandb. Same x-ray but liquid formc. Can see the DNA and sees the radioactived. Bubbles represent the DNA.e. Corners is where the radioactive material isb. Fork: where replication is being placese. Pulse-Chase Labelingc. Adds 20 minutes for labeling. d. Radioactive is being placed original DNA.e. The next DNA material is being more into the center which allows us to make the same conclusions a. Both replication forth is moving outward equally – bidirectional – 50 nucleotides per secondGenetic code: a lot of base pairs but only 2% encodes proteinsI. 98% does everything elseII. Information is divided into units. Each codon specifies each amino acida. ATG: start codonb. UAA, UGG, UAG: stop codonsIII. Transcription (DNA  RNA)a. Huge amount of DNA identifies where the gene is and unwinds it, opens and the RNA polymerase copies DNAIV. Translation (RNA  protein) a. Same sequence because they are complimentsb. Top strand - copying strand (template)V. Information is stored in the nucleus, protein is synthesized in the cytoplasm by copying and sending it off – like a printerVI. RNA comes off and carriers into translation (2nd step)VII. Wobble position: doesn’t matter what the 3rd one is, it’ll have the same amino acid – there are 20 different amino acids but 64 different combinationVIII. Neutral Mutation: change in the sequence but no change in the amino acidi. Universal1. Central Dogma: flow of information from one form to anotherii. Chromosome: how DNA replicates1. Histone, 2 copies of each chromosomes2. Bacteria has one single chromosomea. No way to keep that on one long lineb. 23 pairs – 2 copies of eachi. Autosomes Chromosomes (1-22)ii. Sex Chromosomes – last twoLecture 9I. Centromeresa. Some kind of restriction referred to centromere because they each have different locationsb. These hold sister chromatids together required for portioning, it helps chromosomes be pulled apartc. Centromeres is a DNA sequence that act as binding sitesd. Centromere Binding Sequences: once bounded to a sequence it is called contecticori. Functions in binding the DNA sequence and microtubulese. ATP generator are considered dynein-like structures and move down the tubules whichact like a platform and pull the chromosomes apartf. DNA carrying information; if you change the sequenceg. It is required for stabilityII. Chromatina. DNA + a lot of proteins (Histones) – very difficult to explain and describe the amount ofDNA in the nucleus b. DNA has to be packed in the nucleus and is highly organizedc. Took protease and digested all the proteinsd. Extract and spread out – visualizinge. 30 nm ~ considered thickf. detergent breaks down weak bonds by relaxing – referred to as ‘beads on a string’ (nucleosomes – basic subunit – made up of proteins that get spooled around with DNA)Lecture 11I. Gene Structure:a. 2% of genome that cells generate different symbols in different parts =