1. Chapter 10 Nucleotides and Nucleic Acids Biochemistry by
Reginald Garrett and Charles Grisham

2. Essential Question
What are the structures of the nucleotides? How are nucleotides joined together to form nucleic acids? How is information stored in nucleic acids? What are the biological functions of nucleotides and nucleic acids?

3. Outline What Is the Structure and Chemistry of Nitrogenous Bases?
What Are Nucleosides?
What Is the Structure and Chemistry of Nucleotides?
What Are Nucleic Acids?
What Are the Different Classes of Nucleic Acids?
Are Nucleic Acids Susceptible to Hydrolysis?

4. Information Transfer in Cells
See Figure 10.1
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.

5. This information transfer system is encapsulated in the dogma:
Figure The fundamental process of information transfer in cells. Information encoded in the nucleotide sequence of DNA is transcribed through synthesis of an RNA molecule whose sequence is dictated by the DNA sequence.
As the sequence of this RNA is read (as groups of three consecutive nucleotides) by the protein synthesis machinery, it is translated into the sequence of amino acids in a protein.
This information transfer system is encapsulated in the dogma:
DNA  RNA  protein.
Figure 10.1

6. 10.1 – What is 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)

7. Figure (a) The pyrimidine ring system; by convention, atoms are numbered as indicated. (b) The purine ring system, atoms numbered as shown.

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

9. Know these structures too
10.2 – What Are Nucleosides?
Know these structures too
Nucleosides are compounds formed when a base is linked to a sugar. 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. Figure 10.9   Furanose structures—ribose and deoxyribose.

11. 10.2 – What Are Nucleosides? 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.
Nucleosides are relatively stable in alkali, but purine nucleosides are easily hydrolyzed in acid to yield the free base and pentose.

12. Figure 10.10 b-Glycosidic bonds link nitrogenous bases and sugars to form nucleosides.

13. Figure The common ribonucleosides—cytidine, uridine, adenosine, and guanosine. Also, inosine drawn in anti conformation.

14. Adenosine: a nucleoside with physiological activity
High [Ado] promotes sleepiness. Caffeine blocks the interaction of extracellular Ado with its neuronal receptors.
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15. 10.3 – What Is the Structure and Chemistry of Nucleotides?
Nucleoside phosphates
Know the nomenclature
"Nucleotide phosphate" is redundant!
Most nucleotides are ribonucleotides
Nucleotides are polyprotic acids.

16. 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.

17. 10.4 - What Are Nucleic Acids?
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.
The base sequence of a nucleic acid is its distinctive characteristic.
pGpApCpU, GpApCpUp, pGpApCpUp, GACU,
dGACT

18. 10.5 - What Are the Different Classes of Nucleic Acids?
DNA - one type, one purpose:
a single DNA molecules in virus and bacteria
Eukaryotic cells have many diploid chromosomes mainly in nucleus, but also mitochondria and chloroplasts.
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
Small nuclear RNA
Small non-coding RNAs

19. Stabilized by hydrogen bonds!
The DNA Double Helix
Stabilized by hydrogen bonds!
DNA: Genetic material: Typically double stranded
dsDNA: Strands antiparallel
Interchain H bonds form base pairs.
Chargaff’s rules: A=T, G=C, Purines = Pyrimidines
X-ray diffraction of Franklin and Wilkins and model building of Watson and Crick

20. The DNA Double Helix "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.

21. The sequence of bases in one strand is complementary to the sequence of bases in the other strand.
Figure Replication of DNA gives identical progeny molecules because base pairing is the mechanism determining the nucleotide sequence synthesized within each of the new strands during replication.

22. The information in DNA is encoded in digital form.
DNA contains two kinds of information:
The base sequences of genes that encode the amino acid sequences of proteins and the nucleotide sequences of functional RNA (rRNA and tRNA).
The gene regulatory networks that control the expression of protein-encoding (and functional RNA-encoding) genes.

23. An antiparallel double helix
The Structure of DNA
An antiparallel double helix
diameter of 2 nm
circular in prokaryotic cells.
length of 1.6 million nm (E. coli)
Compact and folded (E. coli cell is only 2000 nm long)
The linear eukaryotic DNA is wrapped around histone proteins to form nucleosomes.
Base pairs: A-T, G-C

24. RNA: Typically single stranded: Produced during transcription
mRNA: Carries information encoded in genes to direct protein synthesis on ribosomes
Derive from heterogeneous nuclear RNA (hnRNA)
RNA processed by splicing (removal of introns and joining of exons), capping (5’ end), and polyA tail addition (3’ end)
rRNA: Components of ribosome: Protein synthesis
Small subunit of ribosome: Single rRNA
Large subunit of ribosome: Large subunit rRNA, 5S rRNA, and in eukaryotes 5.8S rRNA
tRNA: Carriers of activated amino acids used by ribosome for protein synthesis
snRNA: Small nuclear RNAs
siRNAs: Small interfering RNAs: Degrade mRNAs
miRNAs: Bind to mRNA and block translation
snoRNAs: Required for certain RNA modification

25. 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.

26. Eukaryotic mRNA
DNA is transcribed to produce heterogeneous nuclear RNA (hrRNA).
mixed introns and exons with poly A
intron - intervening sequence
exon - coding sequence
poly A tail - stability?
Splicing produces final mRNA without introns.

27. Ribosomal RNA Ribosomes are about 2/3 RNA, 1/3 protein.
rRNA serves as a scaffold for ribosomal proteins. rRNA has a characteristic secondary structure due to many intramolecular H-bonds.
23S rRNA in E. coli is the peptidyl transferase!

28. Ribosomal RNA rRNA: Components of ribosome: Protein synthesis
Small subunit of ribosome: Single rRNA
Large subunit of ribosome:
Large subunit rRNA, 5S rRNA, and in eukaryotes 5.8S rRNA

29. Transfer RNA Small polynucleotide chains - 73 to 94 residues each
Several bases are usually methylated.
Carriers of activated amino acids used by ribosome for protein synthesis.
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.

30. Structure of a tRNA molecule

31. Small RNAs
Altering gene expression in response to stressful environmental situations
snRNA: Small nuclear RNAs: Important in converting hnRNA to mature mRNA.
siRNAs: Small interfering RNAs: Degrade mRNAs — post-transcriptional gene silencing
miRNAs: micro RNAs: Bind to mRNA and block translation
snoRNAs: small nucleolar RNAs: Required for certain RNA modifications

32. 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 uracils with cytosines.
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.

33. 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.

34. 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.

35. Peptide Nucleic Acids (PNAs) are synthetic mimics of DNA and RNA
Poor substrates for proteases
Neutral charge; facilitate penetration into negatively charged cell membranes.
Note the repeating six bonds (in blue) between base attachments and the three-bond linker between base (B) and backbone.
p.331

36. 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“.

37. 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.
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.