1. 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, Sea Harbor Drive, Orlando, Florida 1

2. 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 2

3. 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. 3

5. Know the basic structures
11.1 Nitrogenous Bases
Know the basic structures
Pyrimidines
Cytosine (DNA, RNA)
Uracil (RNA)
Thymine (DNA)
Purines
Adenine (DNA, RNA)
Guanine (DNA, RNA) 4

10. Properties of Pyrimidines and Purines
Keto-enol tautomerism
Acid/base dissociations
Strong absorbance of UV light 5

14. 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 6

16. Linkage of a base to a sugar
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 7

20. Nucleoside phosphates
11.4 Nucleotides
Nucleoside phosphates
Know the nomenclature
"Nucleotide phosphate" is redundant!
Most nucleotides are ribonucleotides
Nucleotides are polyprotic acids 8

22. 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 9

26. 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 10

27. 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 11

30. Stabilized by hydrogen bonds!
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 12

34. An antiparallel double helix
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 13

37. Transcription product of DNA
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 14

39. 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 15

40. 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! 16

43. 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 17

44. Why does DNA contain thymine?
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 18

47. Why is DNA 2'-deoxy and RNA is not?
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 19

48. 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 20

54. 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" 21

55. 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 22

56. 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 23