biochemistry 2/e - garrett & grisham copyright © 1999 by harcourt brace & company chapter...

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



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



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.



11.1 Nitrogenous Bases

Know the basic structures

• Pyrimidines – Cytosine (DNA, RNA)

– Uracil (RNA)

– Thymine (DNA)

• Purines – Adenine (DNA, RNA)

– Guanine (DNA, RNA)



Properties of Pyrimidines and Purines

• Keto-enol tautomerism

• Acid/base dissociations

• Strong absorbance of UV light



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



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



11.4 Nucleotides

Nucleoside phosphates

• Know the nomenclature

• "Nucleotide phosphate" is redundant!

• Most nucleotides are ribonucleotides

• Nucleotides are polyprotic acids



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



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



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



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



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



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



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



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!



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



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



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



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



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"



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



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 chapter...

Documents