Reginald H. Garrett Charles M. Grisham Reginald Garrett & Charles Grisham University of Virginia Chapter 10 Nucleotides and Nucleic Acids

Outline What are the structure and chemistry of nitrogenous bases? What are nucleosides? What are the structure and chemistry of nucleotides? What are nucleic acids? What are the different classes of nucleic Acids? Are nucleic acids susceptible to hydrolysis?

Information Transfer in Cells The fundamental process of information transfer in cells.

10.1 What Are the Structure and Chemistry of Nitrogenous Bases? Know the basic structures Pyrimidines Cytosine (DNA, RNA) Uracil (RNA) Thymine (DNA) Purines Adenine (DNA, RNA) Guanine (DNA, RNA)

10.1 What Are the Structure and Chemistry of Nitrogenous Bases? (a) The pyrimidine ring system; by convention, atoms are numbered as indicated. (b) The purine ring system; atoms numbered as shown.

10.1 What Are the Structure and Chemistry of Nitrogenous Bases? The common pyrimidine bases – cytosine, uracil, and thymine – in the tautomeric forms predominant at pH 7.

10.1 What Are the Structure and Chemistry of Nitrogenous Bases? The common purine bases – adenine and guanine – in the tautomeric forms predominant at pH 7.

10.1 What Are the Structure and Chemistry of Nitrogenous Bases? Other naturally occurring purine derivatives – hypoxanthine, xanthine, and uric acid.

The Properties of Pyrimidines and Purines Can Be Traced to Their Electron-Rich Nature

10.2 What Are Nucleosides? Structures to Know Nucleosides are compounds formed when a base is linked to a sugar via a glycosidic bond The sugars are pentoses D -ribose (in RNA) 2-deoxy- D -ribose (in DNA) The difference - 2'-OH vs 2'-H This difference affects secondary structure and stability

10.2 What Are Nucleosides?

The base is linked to the sugar 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 Sugars make nucleosides more water-soluble than free bases

10.2 What Are Nucleosides? The common ribonucleosides.

10.3 What Is the Structure and Chemistry of Nucleotides? Nucleotides are nucleoside phosphates Know the nomenclature "Nucleotide phosphate" is redundant! Most nucleotides are ribonucleotides Nucleotides are polyprotic acids

10.3 What Is the Structure and Chemistry of Nucleotides? Structures of the four common ribonucleotides – AMP, GMP, CMP, and UMP. Also shown: 3’-AMP.

10.3 What Is the Structure and Chemistry of Nucleotides? Figure The cyclic nucleotide cAMP.

10.3 What Is the Structure and Chemistry of Nucleotides?

Nucleoside 5'-Triphosphates Are Carriers of Chemical Energy Nucleoside 5'-triphosphates are indispensable agents in metabolism because their phosphoric anhydride bonds are a source of chemical 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

Nucleoside 5'-Triphosphates Are Carriers of Chemical Energy

Figure Phosphoryl, pyrophosphoryl, and nucleotidyl group transfer, the major biochemical reactions of nucleotides. Nucleotidyl group transfer is shown here.

10.4 What Are Nucleic Acids? Nucleic acids are linear polymers of nucleotides 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

10.4 What Are Nucleic Acids? 3',5'-Phosphodiester bridges link nucleotides together to form polynucleotide chains. The 5'-ends of the chains are at the top; the 3'-ends are at the bottom. RNA is shown here.

10.4 What Are Nucleic Acids? 3’,5’-phosphodiester bridges link nucleotides together to form polynucleotide chains. The 5’-ends of the chains are at the top; the 3’-ends are at the bottom. DNA is shown here.

10.5 What Are the Different 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 for protein synthesis transfer RNA - carries the amino acids for protein synthesis Others: Small nuclear RNA Small non-coding RNAs

10.5 What Are the Different Classes of Nucleic Acids? The antiparallel nature of the DNA double helix. The two chains have opposite orientations.

The DNA Double Helix The double helix is stabilized by hydrogen bonds "Base pairs" arise from hydrogen bonds A-T; G-C Erwin Chargaff had the pairing data, but didn't understand its implications Rosalind Franklin's X-ray fiber diffraction data was crucial Francis Crick showed that it was a helix James Watson figured out the H bonds

The Base Pairs Postulated by Watson

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

The Structure of DNA Replication of DNA gives identical progeny molecules because base pairing is the mechanism that determines the nucleotide sequence of each newly synthesized strand.

Messenger RNA Carries the Sequence Information for Synthesis of a Protein 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

Messenger RNA Carries the Sequence Information for Synthesis of a Protein Transcription and translation of mRNA molecules in prokaryotic versus eukaryotic cells. In prokaryotes, a single mRNA molecule may contain the information for the synthesis of several polypeptide chains within its nucleotide sequence.

Messenger RNA Carries the Sequence Information for Synthesis of a Protein Transcription and translation of mRNA molecules in prokaryotic versus eukaryotic cells. Eukaryotic mRNAs encode only one polypeptide but are more complex.

Eukaryotic mRNA DNA is transcribed to produce heterogeneous nuclear RNA (hnRNA) 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 Provides the Structural and Functional Foundation for Ribosomes Ribosomes are about 2/3 RNA, 1/3 protein rRNA serves as a scaffold for ribosomal proteins The different species of rRNA are referred to according to their sedimentation coefficients rRNAs typically contain certain modified nucleotides, including pseudouridine and ribothymidylic acid Briefly: the genetic information in the nucleotide sequence of mRNA is translated into the amino acid sequence of a polypeptide chain by ribosomes

Ribosomal RNA Provides the Structural and Functional Foundation for Ribosomes Ribosomal RNA has a complex secondary structure due to many intrastrand H bonds. The gray line here traces a polynucleotide chain consisting of more than 1000 nucleotides. Aligned regions represent H- bonded complementary base sequences.

Ribosomal RNA Provides the Structural and Functional Foundation for Ribosomes The organization and composition of ribosomes.

Transfer RNAs Carry Amino Acids to Ribosomes for Use in Protein Synthesis 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-3′-OH. The a.a. is attached in ester linkage to this 3′-OH. Aminoacyl tRNA molecules are the substrates of protein synthesis

Transfer RNAs Carry Amino Acids to Ribosomes for Use in Protein Synthesis Transfer RNA also has a complex secondary structure due to many intrastrand hydrogen bonds. The black lines represent base-paired nucleotides in the sequence.

The Chemical Differences Between DNA and RNA Have Biological Significance Two fundamental chemical differences distinguish DNA from RNA: DNA contains 2-deoxyribose instead of ribose DNA contains thymine instead of uracil

The Chemical Differences Between DNA and RNA Have Biological Significance 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

The Chemical Differences Between DNA and RNA Have Biological Significance

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

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 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 isolated from the R strain of E. coli

Cleavage Sequences of Restriction Endonucleases

Restriction Mapping of DNA

Problems End of Chapter problems 1-14