1. 24 24-1 © 2003 Thomson Learning, Inc. All rights reserved General, Organic, and Biochemistry, 7e Bettelheim, Brown, and March

2. 24 24-2 © 2003 Thomson Learning, Inc. All rights reserved Chapter 24 Nucleotides, Nucleic Acids, and Heredity Nucleotides, Nucleic Acids, and Heredity

3. 24 24-3 © 2003 Thomson Learning, Inc. All rights reserved Introduction each cell of our bodies contains thousands of different proteins how do cells know which proteins to synthesize out of the extremely large number of possible amino acid sequences? chromosomesfrom the end of the 19th century, biologists suspected that the transmission of hereditary information took place in the nucleus, more specifically in structures called chromosomes genesthe hereditary information was thought to reside in genes within the chromosomes histonesnucleic acidschemical analysis of nuclei showed chromosomes are made up largely of proteins called histones and nucleic acids

4. 24 24-4 © 2003 Thomson Learning, Inc. All rights reserved Introduction deoxyribonucleic acids (DNA)by the 1940s it became clear that deoxyribonucleic acids (DNA) carry the hereditary information other work in the 1940s demonstrated that each gene controls the manufacture of one protein thus, the expression of a gene in terms of an enzyme protein led to the study of protein synthesis and its control

5. 24 24-5 © 2003 Thomson Learning, Inc. All rights reserved Nucleic Acids There are two kinds of nucleic acids in cells ribonucleic acids (RNA) deoxyribonucleic acids (DNA) Both RNA and DNA are polymers built from monomers called nucleotides A nucleotide is composed of a base a monosaccharide a phosphate

6. 24 24-6 © 2003 Thomson Learning, Inc. All rights reserved Pyrimidine/Purine Bases

7. 24 24-7 © 2003 Thomson Learning, Inc. All rights reserved Nucleosides Nucleoside: Nucleoside: a compound that consists of D- ribose or 2-deoxy-D-ribose bonded to a purine or pyrimidine base by a  -N-glycosidic bond

8. 24 24-8 © 2003 Thomson Learning, Inc. All rights reserved Nucleotides Nucleotide: Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’ or the 5’-OH

9. 24 24-9 © 2003 Thomson Learning, Inc. All rights reserved Nucleotides deoxythymidine 3’-monophosphate (3’-dTMP)

10. 24 24-10 © 2003 Thomson Learning, Inc. All rights reserved Nucleotides adenosine 5’-triphosphate (ATP) serves as a common currency into which energy gained from food is converted and stored

11. 24 24-11 © 2003 Thomson Learning, Inc. All rights reserved Structure of DNA and RNA Primary Structure: Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA or RNA molecule base sequence is read from the 5’ end to the 3’ end

12. 24 24-12 © 2003 Thomson Learning, Inc. All rights reserved Nucleic Acid - 1° Structure A schematic diagram of a nucleic acid

13. 24 24-13 © 2003 Thomson Learning, Inc. All rights reserved DNA - 2° Structure Secondary structure: Secondary structure: the ordered arrangement of nucleic acid strands the double helix model of DNA 2° structure was proposed by James Watson and Francis Crick in 1953 Double helix: Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right- handed manner about the same axis

14. 24 24-14 © 2003 Thomson Learning, Inc. All rights reserved The DNA Double Helix

15. 24 24-15 © 2003 Thomson Learning, Inc. All rights reserved Base Pairing

16. 24 24-16 © 2003 Thomson Learning, Inc. All rights reserved Higher Structure of DNA histonesDNA is coiled around proteins called histones histones are rich in the basic amine acids Lys and Arg, whose side chains have a positive charge the negatively-charged DNA molecules and positively- charged histones attract each other and form units called nucleosomes nucleosome:nucleosome: a core of eight histone molecules around which the DNA helix is wrapped chromatinnucleosomes are further condensed into chromatin chromosomeschromatin fibers are organized into loops, and the loops into the bands that provide the superstructure of chromosomes

17. 24 24-17 © 2003 Thomson Learning, Inc. All rights reserved Chromosomes

18. 24 24-18 © 2003 Thomson Learning, Inc. All rights reserved Chromosomes

19. 24 24-19 © 2003 Thomson Learning, Inc. All rights reserved Chromosomes

20. 24 24-20 © 2003 Thomson Learning, Inc. All rights reserved Chromosomes

21. 24 24-21 © 2003 Thomson Learning, Inc. All rights reserved DNA and RNA The three differences in structure between DNA and RNA are T UDNA bases are A, G, C, and T; the RNA bases are A, G, C, and U 2-deoxy-D-riboseD- ribosethe sugar in DNA is 2-deoxy-D-ribose; in RNA it is D- ribose double stranded single-strandedDNA is always double stranded; there are several kinds of RNA, all of which are single-stranded

22. 24 24-22 © 2003 Thomson Learning, Inc. All rights reserved RNA RNA molecules are classified according to their structure and function

23. 24 24-23 © 2003 Thomson Learning, Inc. All rights reserved Structure of tRNA

24. 24 24-24 © 2003 Thomson Learning, Inc. All rights reserved Genes, Exons, and Introns Gene: Gene: a segment of DNA that carries a base sequence that directs the synthesis of a particular protein, tRNA, or mRNA there are many genes in one DNA molecule in bacteria the gene is continuous in higher organisms the gene is discontinuous Exon: Exon: a section of DNA that, when transcribed, codes for a protein or RNA Intron: Intron: a section of DNA that does not code for anything functional

25. 24 24-25 © 2003 Thomson Learning, Inc. All rights reserved Genes, Exons, and Introns introns are cut out of mRNA before the protein is synthesized

26. 24 24-26 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication Replication Replication involves separation of the two original strands and synthesis of two new daughter strands using the original strands as templates origin of replicationDNA double helix unwinds at a specific point called an origin of replication bidirectionalpolynucleotide chains are synthesized in both directions from the origin of replication; that is, DNA replication is bidirectional replication forksat each origin of replication, there are two replication forks, points at which new polynucleotide strands are formed

27. 24 24-27 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication DNA is synthesized from its 5’ -> 3’ end (from the 3’ -> 5’ direction of the template) leading strandthe leading strand is synthesized continuously in the 5’ -> 3’ direction toward the replication fork lagging strand Okazaki fragmentsthe lagging strand is synthesized semidiscontinuously as a series of Okazaki fragments, also in the 5’ -> 3’ direction, but away from the replication fork DNA ligaseOkazaki fragments of the lagging strand are joined by the enzyme DNA ligase semiconservative:replication is semiconservative: each daughter strand contains one template strand and one newly synthesized strand

28. 24 24-28 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication

29. 24 24-29 © 2003 Thomson Learning, Inc. All rights reserved Replisomes Replisomes are assemblies of “enzyme factories”

30. 24 24-30 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication Opening up the superstructure during replication, the very condensed superstructure of chromosomes is opened by a signal transduction mechanism one step of this mechanism involves acetylation and deacetylation of key lysine residues acetylation removes a positive charge and thus weakens the DNA-histone interactions

31. 24 24-31 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication Relaxation of higher structures of DNA tropoisomerases (also called gyrases)tropoisomerases (also called gyrases) facilitate the relaxation of supercoiled DNA by introducing either single strand or double strand breaks in the DNA once the supercoiling is relaxed by this break, the broken ends are joined and the tropoisomerase diffuses from the location of the replication fork

32. 24 24-32 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication Unwinding the DNA double helix replication of DNA starts with unwinding of the double helix unwinding can occur at either end or in the middle helicasesunwinding proteins called helicases attach themselves to one DNA strand and cause separation of the double helix the helicases catalyze the hydrolysis of ATP as the DNA strand moves through; the energy of hydrolysis promotes the movement

33. 24 24-33 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication Primer/primases primersprimers are short oligonucleotides of four to 15 nucleotides long they are required to start the synthesis of both daughter strands primasesprimases are enzymes that catalyze the synthesis of primers primases are placed at about every 50 nucleotides in the lagging strand synthesis

34. 24 24-34 © 2003 Thomson Learning, Inc. All rights reserved DNA Replication DNA polymerases DNA polymerases are key enzymes in replication once the two strands have separated at the replication fork, the nucleotides must be lined up in proper order for DNA synthesis in the absence of DNA polymerase, alignment is slow DNA polymerase provides the speed and specificity of alignment along the lagging (3’ -> 5’) strand, the polymerases can synthesize only short fragments, because these enzymes only work from 5’ -> 3’ Okazaki fragmentsthese short fragments are called Okazaki fragments DNA ligasejoining the Okazaki fragments and any remaining nicks is catalyzed by DNA ligase

35. 24 24-35 © 2003 Thomson Learning, Inc. All rights reserved DNA Repair The viability of cells depends on DNA repair enzymes that can detect, recognize, and repair mutations in DNA Base excision repair(BER) Base excision repair (BER): one of the most common repair mechanisms a specific DNA glycosylase recognizes the damaged base Nit catalyzes the hydrolysis of the  -N-glycosidic bond between the incorrect base and its deoxyribose it then flips the damaged base, completing the excision the sugar-phosphate backbone remains intact

36. 24 24-36 © 2003 Thomson Learning, Inc. All rights reserved DNA Repair BER (cont’d) APapapsite endonucleasat the AP (apurinic or apyrimidinic) site thus created, an endonuclease catalyzes the hydrolysis of the backbone exonucleasean exonuclease liberates the sugar-phosphate unit of the damaged site DNA polymerase inserts the correct nucleotide DNA ligase seals the backbone to complete the repair NERner NER (nucleotide excision repair) removes and repairs up to 24-32 units by a similar mechanism involving a number of repair enzymes

37. 24 24-37 © 2003 Thomson Learning, Inc. All rights reserved Cloning Clone: Clone: a genetically identical population Cloning: Cloning: a process whereby DNA is amplified by inserting it into a host and having the host replicate it along with the host’s own DNA Polymerase chain reaction (PCR): Polymerase chain reaction (PCR): an automated technique for amplifying DNA using a heat-stable DNA polymerase from a thermophilic bacterium

38. 24 24-38 © 2003 Thomson Learning, Inc. All rights reserved Cloning

39. 24 24-39 © 2003 Thomson Learning, Inc. All rights reserved End Chapter 24 Nucleic Acids