Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Chapter 11 Nucleotides and Nucleic Acids to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, 6277 Sea Harbor Drive, Orlando, Florida
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Outline 11.1 Nitrogenous Bases 11.2 The Pentoses of Nucleotides and NA 11.3 Nucleosides are Formed by Joining a Nitrogenous Base to a Sugar 11.4 Nucleotides - Nucleoside Phosphates 11.5 Nucleic Acids are Polynucleotides 11.6 Classes of Nucleic Acids 11.7 Hydrolysis of Nucleic Acids
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Information Transfer in Cells See Figure 11.1 Information encoded in a DNA molecule is transcribed via synthesis of an RNA molecule The sequence of the RNA molecule is "read" and is translated into the sequence of amino acids in a protein.
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company 11.1 Nitrogenous Bases Know the basic structures Pyrimidines –Cytosine (DNA, RNA) –Uracil (RNA) –Thymine (DNA) Purines –Adenine (DNA, RNA) –Guanine (DNA, RNA)
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Properties of Pyrimidines and Purines Keto-enol tautomerism Acid/base dissociations Strong absorbance of UV light
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company 11.2 Pentoses of Nucleotides Know these structures too D-ribose (in RNA) 2-deoxy-D-ribose (in DNA) The difference - 2'-OH vs 2'-H This difference affects secondary structure and stability
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company 11.3 Nucleosides Linkage of a base to a sugar Base is linked via a glycosidic bond The carbon of the glycosidic bond is anomeric Named by adding -idine to the root name of a pyrimidine or -osine to the root name of a purine Conformation can be syn or anti Sugars make nucleosides more water-soluble than free bases
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company 11.4 Nucleotides Nucleoside phosphates Know the nomenclature "Nucleotide phosphate" is redundant! Most nucleotides are ribonucleotides Nucleotides are polyprotic acids
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Functions of Nucleotides Nucleoside 5'-triphosphates are carriers of energy Bases serve as recognition units Cyclic nucleotides are signal molecules and regulators of cellular metabolism and reproduction ATP is central to energy metabolism GTP drives protein synthesis CTP drives lipid synthesis UTP drives carbohydrate metabolism
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company 11.5 Nucleic Acids - Polynucleotides Polymers linked 3' to 5' by phosphodiester bridges Ribonucleic acid and deoxyribonucleic acid Know the shorthand notations Sequence is always read 5' to 3' In terms of genetic information, this corresponds to "N to C" in proteins
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company 11.6 Classes of Nucleic Acids DNA - one type, one purpose RNA - 3 (or 4) types, 3 (or 4) purposes –ribosomal RNA - the basis of structure and function of ribosomes –messenger RNA - carries the message –transfer RNA - carries the amino acids
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company The DNA Double Helix Stabilized by hydrogen bonds! "Base pairs" arise from hydrogen bonds Erwin Chargaff had the pairing data, but didn't understand its implications Rosalind Franklin's X-ray fiber diffraction data was crucial Francis Crick knew it was a helix James Watson figured out the H-bonds
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company The Structure of DNA An antiparallel double helix Diameter of 2 nm Length of 1.6 million nm (E. coli) Compact and folded (E. coli cell is only 2000 nm long) Eukaryotic DNA wrapped around histone proteins to form nucleosomes Base pairs: A-T, G-C
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Messenger RNA Transcription product of DNA In prokaryotes, a single mRNA contains the information for synthesis of many proteins In eukaryotes, a single mRNA codes for just one protein, but structure is composed of introns and exons
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Eukaryotic mRNA DNA is transcribed to produce heterogeneous nuclear RNA –mixed introns and exons with poly A –intron - intervening sequence –exon - coding sequence –poly A tail - stability? Splicing produces final mRNA without introns
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Ribosomal RNA Ribosomes are about 2/3 RNA, 1/3 protein rRNA serves as a scaffold for ribosomal proteins 23S rRNA in E. coli is the peptidyl transferase!
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Transfer RNA Small polynucleotide chains - 73 to 94 residues each Several bases usually methylated Each a.a. has at least one unique tRNA which carries the a.a. to the ribosome 3'-terminal sequence is always CCA-a.a. Aminoacyl tRNA molecules are the substrates of protein synthesis
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company DNA & RNA Differences? Why does DNA contain thymine? Cytosine spontaneously deaminates to form uracil Repair enzymes recognize these "mutations" and replace these Us with Cs But how would the repair enzymes distinguish natural U from mutant U? Nature solves this dilemma by using thymine (5-methyl-U) in place of uracil
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company DNA & RNA Differences? Why is DNA 2'-deoxy and RNA is not? Vicinal -OH groups (2' and 3') in RNA make it more susceptible to hydrolysis DNA, lacking 2'-OH is more stable This makes sense - the genetic material must be more stable RNA is designed to be used and then broken down
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Hydrolysis of Nucleic Acids RNA is resistant to dilute acid DNA is depurinated by dilute acid DNA is not susceptible to base RNA is hydrolyzed by dilute base See Figure for mechanism
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Restriction Enzymes Bacteria have learned to "restrict" the possibility of attack from foreign DNA by means of "restriction enzymes" Type II and III restriction enzymes cleave DNA chains at selected sites Enzymes may recognize 4, 6 or more bases in selecting sites for cleavage An enzyme that recognizes a 6-base sequence is a "six-cutter"
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Type II Restriction Enzymes No ATP requirement Recognition sites in dsDNA usually have a 2-fold axis of symmetry Cleavage can leave staggered or "sticky" ends or can produce "blunt” ends
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Type II Restriction Enzymes Names use 3-letter italicized code: 1st letter - genus; 2nd,3rd - species Following letter denotes strain EcoRI is the first restriction enzyme found in the R strain of E. coli
Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company