BSCI222 Study Guide Exam II Lectures 8 14 Ch 10 16 o Lecture 8 DNA Chromosomes Transposable Elements o Chapter 10 1 3 5 7 14 18 24 26 27 28 31 33 34 35 36 11 1 2 3 6 7 14 18 21 22 27 28 31 34 36 38 40 42 o Chapter 10 o All genetic information is encoded in the structure of DNA or RNA o The sugars of DNA and RNA are slightly different in structure RNA s sugar called ribose has hydroxyl group OH attached to the 2 carbon atom DNA s sugar called deoxyribose has hydrogen atom H at this position and therefore contains one oxygen atom fewer o A T G C A G T C o Watson and Crick s DNA model DNA consists of two complementary and antiparallel nucleotide strands that form a double helix The repeating units of DNA are nucleotides comprised of o A sugar pentose sugar Five carbon atoms numbered 1 2 3 Sugar of RNA ribose OH DNA deoxyribose H o A phosphate A phosphorus atom bonded to four oxygen atoms Found in every nucleotide and frequently carry a negative charge which makes DNA acidic Always bonded to the 5 carbon atom of the sugar o A nitrogen containing base Purine six sided ring attached to a five sided ring Adenine and Guanine differ in the positions of their double bonds and in the groups attached to the six sided ring Pyrimidine six sided ring only Cytosine Thymine DNA only and Uracil RNA only Differ in the groups attached to the carbon atoms of the ring and in the number of double bonds in the ring Nitrogenous base always forms a covalent bond with the 1 carbon atom of the sugar Deoxyribose ribose base nucleoside Polynucleotide strands The covalent bonds that connect the nucleotides of DNA join the 5 phosphate group of one nucleotide to the 3 carbon atom phosphodiester linkages A series of nucleotides linked in this way constitutes a polynucleotide strand At one end strand a free phosphate group is attached to the 5 carbon atom of the sugar in the nucleotide The end of the strand is therefore referred to as the 5 end The other end of the strand is referred to as the 3 end had a free OH group attached to the 3 carbon atom of the sugar Secondary structures of DNA The double helix antiparallel 5 end is opposite 3 The strands are held together by two types of end molecular forces o Bonds are relatively weak compared with covalent phosphodiester bonds o Several important functions of DNA require the separation of its two nucleotide strands Different secondary structures DNA normally consists of two polynucleotide strands that are antiparallel and complementary B DNA exists when plenty of water surrounds the molecule and there is no unusual base sequence in the DNA B DNA is an alpha helix clockwise spiral 10 bp per 360 degree rotation of the helix A DNA exists if less water is present alpha helix shorter and wider than B DNA Z DNA forms a left handed helix sugar phosphate backbone zigzags back and forth Z Transcription translation replication Central dogma DNA RNA Protein C value the quantity of eukaryotic organisms that differ dramatically in the amount of DNA per cell Special structures can form in DNA and RNA Hairpin Stem consisting of a region of paired bases and a region of unpaired bases between the complementary sequences which form a loop at the end of the stem o Forms when sequences when sequences of nucleotide on the same strand are inverted complements o A hairpin consists of a region of paired bases and sometimes includes intervening unpaired bases The primary structure of DNA can be modified in various ways o DNA methylation a process in which methyl groups are added to certain positions on the nucleotide bases o 5 methylcytosine adenine and cytosine are commonly methylated in bacteria In eukaryotic DNa cytosine bases are often methylated to form 5 methylcytosine o Begin Chapter 11 o Large amounts of DNA are packed into a cell o Supercoiling when the DNA helix is subjected to strain by being overwound or underwound o Relaxed state lowest energy state for B DNA is when it has approx 10 bp per turn of its helix In the relaxed state a stretch of 100 bp of DNA would assume about 10 complete turns o If energy is used to add or remove any turns strain is placed on the molecule causing the helix to supercoil on itself o Molecules that are overrotated exhibit positive supercoiling o Under rotated molecules exhibit negative supercoiling o Topoisomerases enzymes that add or remove rotations form the DNA helix by temporarily breaking the nucleotide strands rotating the ends around each other and then rejoining the broken ends Both induce and relieve supercoiling Packaging problem twisting and turning can only do so much o o The Bacterial Chromosome o Most bacterial genomes consist of a single circular DNA molecule although linear DNA molecules have been found in a few species o When a bacterial cell is viewed with the electron microscope its DNA frequently appears as a distinct clump the nucleoid which is confined to a definite region of the cytoplasm o If a bacterial cell is broken open gently its DNA spills out in a series of twisted loops o The ends of the loops are most likely held in place by proteins o Eukaryotic Chromosomes o Individual eukaryotic chromosomes contain enormous amounts o Each eukaryotic chromosome consists of a single extremely long of DNA molecule of DNA o The chromosomes are in an elongated relatively uncondensed state during interphase of the cell cycle o Chromatin Eukaryotic DNA in the cell is closely associated with proteins chromatin The combination of DNA and proteins is called Euchromatin undergoes the normal process of condensation and decondensation in the cell cycle Heterochromatin remains in a highly condensed state throughout the cell cycle Tightly packed gene off Loosely packed gene on o The nucleosome Chromatin has a highly complex structure with several levels of organization The simplest level is the double helical structure DNA The repeating core of protein and DNA produced by digestion with nuclease enzymes is the simplest level of the nucleosome Core particle consisting of DNA wrapped about two times around an octamer of eight histone proteins Each of the histone proteins that make up the nucleosome core particle has a flexible tail containing from 11 37 amino acids All histones except H1 combine to form nucleosome 2 copies of each Positively charged amino acids in the tails of the histones interact with the negative charges of the phosphates on the DNA keeping the DNA and histones tightly associated Negatively charged DNA readily associates with