Date post: | 01-Apr-2015 |
Category: |
Documents |
Upload: | kylan-audiss |
View: | 227 times |
Download: | 3 times |
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Chapter 11
Nucleotides and Nucleic Acidsto 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 32887-6777
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 NucleosidesLinkage 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 11.29 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