BSCI222 Study Guide Exam IILectures 8-14; Ch. 10-16o Lecture 8: DNA, Chromosomes, Transposable Elementso 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 10o All genetic information is encoded in the structure of DNA or RNAo The sugars of DNA and RNA are slightly different in structure RNA’s sugar called ribose has hydroxyl group –OH attachedto the 2’-carbon atom DNA’s sugar called deoxyribose has hydrogen atom –H at this position and therefore contains one oxygen atom fewero 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 frequentlycarry a negative charge which makes DNA acidic Always bonded to the 5’-carbon atom of the sugaro 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 andin 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 thecarbon atoms of the ring and in thenumber of double bonds in the ring Nitrogenous base always forms a covalent bond with the 1’ carbon atom ofthe 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 attachedto 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’ end- The strands are held together by two types of molecular forceso 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 per360-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 wayso DNA methylation: a process in which methyl groups are added to certain positions on the nucleotide baseso 5-methylcytosine: adenine and cytosine are commonly methylated in bacteria. In eukaryotic DNa, cytosine bases are often methylated to form 5-methylcytosineo Begin Chapter 11o Large amounts of DNA are packed into a cello 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 turnso If energy is used to add or remove any turns, strain is placed on the molecule, causing the helix to supercoil on itselfo Molecules that are overrotated exhibit positive supercoilingo Under rotated molecules exhibit negative supercoilingo Topoisomerases: enzymes that add or remove rotations form theDNA 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 doso muchoo The Bacterial Chromosomeo Most bacterial genomes consist of a single circular DNA molecule, although linear DNA molecules have been found in a few specieso 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 cytoplasmo 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 proteinso Eukaryotic Chromosomeso Individual eukaryotic chromosomes contain enormous amounts of DNAo Each eukaryotic chromosome consists of a single, extremely longmolecule of DNAo The chromosomes are in an elongated, relatively uncondensed state during interphase of the cell cycleo Chromatin Eukaryotic DNA in the cell is closely associated with proteins - The combination of DNA and proteins is called chromatin 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 ono 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