Chapter 8 DNA: The Chemical Nature of the Gene8.1 Genetic Material Possesses Several Key CharacteristicsA. Genetic material must contain complex information1. Must be capable of storing large amounts of information-instructions for all traits and functions of an organism2. The information must have the capacity to vary because species differ in their genetic makeup3. The genetic material must be stable because most alterations are likely to be detrimentalB. Genetic material must replicate faithfully1. Genetic material must have the capacity to be copied accurately2. At each cell division, the genetic instructions must be transmitted to descendant cells withgreat accuracy3. When organisms reproduce, the coding must be copied with reliabilityC. Genetic Material must encode the phenotype1. The genotype must have the capacity to code for the phenotypic traits2. There must be a mechanism for genetic instructions to be translated into the amino acid sequence of a protein8.2 All Genetic Information Is Encoded in the Structure of DNAA. Early Studies of DNA1. The physical basis of heredity lies in the nucleusa. Chromatin consists of nucleic acids and proteins2. Nucleotides: linked, repeating units containing a sugar, a phosphate, and a base3. Chargaff’s rules: the amount of adenine is always equal to the amount of thymine (A=T) and the amount of guanine is always equal to the amount of cytosine (G=C) B. DNA As the Source of Genetic Information1. Genes reside on chromosomes, which were known to contain both DNA and protein2. Transforming principle: acquiring genetic virulence that causes a permanent, genetic change in the bacteria. Some substance in the polysaccharide coat of the dead bacteria might be responsible. 3. Isotopes: radioactive forms of DNA and proteins. It can be used to identify the location of a specific molecule because any molecule containing the isotope is radioactive4. Experiments confirmed that DNA, not protein, is the genetic material of phagesC. Watson and Crick’s Discovery of the Three-Dimensional Structure of DNA1. X-ray diffraction: X-rays beamed at a molecule are reflected in specific patterns that reveal aspects of the structure of the molecule8.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form a Double HelixA. The Primary Structure of DNAi. A string of nucleotides joined together by phosphodiester linkages1. Nucleotidesa. DNA is typically a very long molecule and is therefore termed a macromoleculeb. It is a polymer, a chain made up of repeating units linked togetherc. The repeating units are nucleotides each comprising three parts: a sugar, a phosphate, and a nitrogen containing base.d. Sugari. The sugars are pentose sugars with five carbon atoms.ii. Ribose: RNA’s sugar has a hydroxyl group (-OH) attached to the 2’carbon chainiii. Deoxyribose: DNA’s sugar has a hydrogen sugar at this position and therefore contains one oxygen atom fewer overall. e. Nitrogenous base: which may be two different typesi. Purine: consists of a six sided ring attached to a five sided ring only1. Both DNA and RNA contain two purinesa. Adenine and Guanine: A and G which differ in the positions of their double bonds and in the groups attached to the six-sided ring.ii. Pyrimidine: a six sided ring 1. Three are common in nucleic acidsa. Cytosine (C), thymine (T), and uracil (U) b. Cytosine is present in both DNA and RNAc. Thymine is found in DNAd. Uracil is only found in RNA iii. Nucleoside: a deoxyribose or a ribose sugar and a base together iv. Phosphate Group: consists of a phosphorus atom bonded to four oxygen atoms.1. They are found in every nucleotide and frequently carry a negative charge making DNA acidic. 2. It is always bonded to the 5’-carbon atomv. Deoxyribonucleotides: DNA nucleotides because there are four types ofbases, there are four different kinds of DNA nucleotides.vi. Ribonucleotides: equivalent with RNA. They sometimes contain additional rare bases which are modified forms of four common bases. f. Polynucleotide strandsi. Phosphodiester linkages: nucleotides connected by covalent bonds, which join the 5’ phosphate group of one nucleotide to the 3’-carbon atom of the next nucleotide. ii. Polynucleotide strand: a series of nucleotides linked together by stron covalent bonds.1. An important characteristic is its direction or polarity. 2. 5’ end: a free phosphate group is attached to one 5’ carbon atom of the sugar in the nucleotide. 3. 3’ end: a free OH group is attached to the 3’ carbon atom. B. Secondary Structures of DNAa. The double helixi. Antiparallel: two polynucleotide strands wound around each other in opposite directions meaning that the 5’ end of one strand is opposite to the 3’ end of the other strand.ii. Held together by hydrogen bonds that link the bases on opposite strands and an interaction between the stacked base pairs. iii. Complementary DNA strands: the two polynucleotide stands of a DNA molecule are not identical but complementaryb. Different secondary structuresi. B-DNA: structure exists when plenty of water surrounds the molecule and there is no unusual base sequence in the DNA- conditions that are likely to be present in cells. 1. Most stable of random sequence of nucleotides2. An alpha helix, clockwise spiral, with 10 b.p. ii. A-DNA: exists if less water is present 1. An alpha helix, short, and wideiii. Z-DNA: forms a left handed helix1. The sugar-phosphate backbone zigags8.4 Large amounts of DNA Are Packed into a CellA. Supercoiling: takes place when the DNA is subjected to strain by being overwound or underwound.B. Relaxed State: The lowest energy state for B-DNA wa. Positive supercoiling: overrotated moleculesb. Negative supercoiling: underrotated moleculesc. Supercoiling takes place when the strain of overrotaing or underrotating cannot be compensated by the turning of the ends of the double helix, which is he case if the DNA is circulard. Topoisomerases: enzymes that add or remove from the DNA helix by temporarily breaking nucleotide strand, rotating ends around each other, and then rejoining the brokenends. i. Can either induce or relive supercoilingC. Most DNA found in cells is negatively supercoiled which has two advantages over nonsupercoiled DNAa. Supercoiling makes the separation of the two strands of DNA easier during replication and transcriptionb. Supercoiled DNA can be packed into a smaller space than relaxed DNA.8.5 A Bacterial Chromosome Consists of a Single Circular
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