Chapter 17: Outline

1. Chapter 17: Outline • DNA • Mutation Chromosomes and • Variations Chromatin • Supercoiling Genome Structure • RNA • Transfer, Ribosomal, Messenger • Heterogeneous and Small Nuclear • Viruses

2. Definitions • DNA stands for deoxyribonucleic acid. It is the genetic code molecule for most organisms. • RNA stands for ribonucleic acid. RNA molecules are involved in converting the genetic information in DNA into proteins. In retroviruses, RNA is the genetic material.

3. 17.1 Nucleic Acids, DNA • DNA and RNA are polymers whose monomer units are called nucleotides • A nucleotide itself consists of: • a nitrogen containing heterocyclic base • a ribose or deoxyribose sugar ring • a phosphoric acid unit

4. Nucleobases • The bases found in nucleic acids are derived from either the purine or the pyrimidine ring systems. Examples follow on the next screen.

5. Major Purine Bases guanine in DNA and RNA adenine in DNA and RNA

6. Major Pyrimidine Bases uracil in RNA cytosine in DNA and RNA thymine in DNA and some RNA

7. Some less common bases 5-methylcytosine 5,6-dihydrouracil hypoxanthine

8. Nucleosides base deoxyribose sugar • A nucleoside is a compound in which the DNA/RNA base forms a glycosidic link to the sugar molecule. The sugar molecule is numbered with primed numbers. glycosidic link

9. Nucleotides-1 base phosphate ester deoxyribose sugar • A nucloetide is the repeating unit of the DNA or RNA polymer. The nitrogen base is attached b to the ribose (RNA) or deoxyribose (DNA) ring. The sugar is phosphorylated at carbon 5’

10. Nucleotides-2 • Nucleotides are named after the parent nucleoside. Examples follow. Deoxythymidine 5’-monophosphate

11. Nucleotides-3 2-deoxy Deoxycytidine 5’-monophosphate Deoxyadenosine 5’-monophosphate

12. Nucleotides-4 Uridine 5’-monophosphate Guanosine 5’-monophosphate

13. DNA/RNA Chains • When nucleotides polymerize, the 5’ phosphate on one unit esterifies to the 3’ OH on another unit. The terminal 5’ unit retains the phosphate. An example of a three nucleotide DNA product is shown on the next slide .

14. Segment of DNA Chain 5’-end guanine thymine cytosine 3’-5’ link 3’-end

15. Abbreviated DNA • DNA and RNA chains are abbreviated using a structure where vertical lines represent the sugars, diagonal lines with P at the midpoint represent the 3,5-phosphodiester bonds, and horizontal lines the ends of the chain. • The structures are always written with the 5’ end to the left. • Single letter abbreviations are also used.

16. Abbreviated DNA-2 Or: pdGpdTpdC Or: pd(GTC) RNA abbreviations lack the d (for deoxy)

17. DNA-Secondary Structure • The most common form of DNA is the B form . Its structure was determined by Watson and Crick in 1953. • This DNA consists of two chains of nucleotides coiled around one another in a right handed double helix. • The chains run antiparallel and are held together by hydrogen bonding between complimentary base pairs: A=T, G=C.

18. DNA-Secondary Structure: 2 Hydrogen bonding between A and T or G and C helps to hold the chains in the double helix The strands are said to be complimentary

19. DNA-Secondary Structure: 3 • In addition to hydrogen bonding between bases, other important noncovalent interactions contribute to helical stability. • 2. Hydrophobic interactions among the bases. • 3. Base stacking results in weak van der Waals attractions • 4. Electrostatic interactions with Mg2+, histones, etc.

20. DNA: Mutations • If tautomers form during replication, base mispairing can occur. E. g. purine for purine: a transition mutation

21. DNA: Mutations-2 • Hydrolysis of purine-sugar bond can occur and purine base is lost. • Bases can spontaneously deaminate. • (cytosine  uracil) • Ionizing radiation can cause strand breaking and base modifications, esp. thymine dimers.

22. Xenobiotics • Base analogues • Caffeine can pair with guanine causing a transition mutation. • 2. Alkylating agents • Adenine and guanine are especially liable to alkylation (e. g. methylation). • Transversion mutations (purine for pyrimidine or reverse) are possible.

23. Xenobiotics-2 • 3. Nonalkylating agents • Nitrous acid deaminates bases. • Polyaromatic hydrocarbons are mutagenic and prevent base pairing. • 4. Intercalating agents • Some planar molecules can insert between base pairs. Adjacent pairs may be deleted or new ones inserted resulting in a frame-shift mutation.

24. DNA: Variations on a Theme • The Watson-Crick form of DNA (B-DNA) is not the only one possible. A and Z forms also exist. • The forms differ in helical conformation.

25. B DNA segment Sugar-phosphate backbone Chain 2 Chain 1 Hydrogen bonded base pairs in the core of the helix

26. B DNA: 2 Major groove Outside diameter, 2 nm Interior diameter, 1.1 nm Minor groove Length of one turn of helix is 3.4 nm and contains 10 base pairs.

27. A DNA and Z DNA • A second form of DNA is the A form. • It has 11 base pairs per turn of the helix and the bases lie at an angle of about 20o relative to the helix axis. It, too, is a right hand double helix. • A third form of DNA is the Z form. It is a left handed helix. • A picture of A DNA is on the next slide.

28. A DNA segment Base pairs not perpendicular to helix axis. 11 pairs per turn.

29. DNA, Higher Order Structure • Examples of higher order structures include cruciforms, triple helices, and supercoils. • Cruciforms are cross-like structures likely to form when the DNA sequence contains a palindrome, a sequence providing the same information read forward or backward. • E. g. MADAM I’M ADAM

30. Cruciforms • Inverted repeats form palindromes within DNA. Palindromes play an important role in the function of restriction enzymes.

31. Triple Helix • A polypurine strand hydrogen-bonded to a poly pyrimidine strand can form a triple helix (H-DNA) involving Hoogsteen base pairing.

32. Supercoiling • Prokaryotic DNA is circular. If the circular loop of right-handed DNA is twisted in a left-handed manner the DNA is said to be negatively supercoiled. Cruciforms and H-DNA can result. • Extra right-handed twists results in a positively supercoiled loop of DNA. This is found when DNA coils around a protein core to form a supercoil.

33. Chromosomes (Prokaryote) • In the nucloid the E. coli chromosome (circular DNA) is attached to a protein core in at least 40 places. • The protein HU binds DNA. Polyamines (+ charge) bound to DNA help neutralize DNA charge for denser packing of the DNA. • A diagram of the E. coli chromosome is on the next slide.

34. The E. coli Chromosome Fig 17.16

35. Chromosomes (Eukaryote) • Eukaryotic chromosomes have two unique structural elements: • Centromere: AT-rich, associated with nonhistome protein to form kinetochore which interacts with spindle fibers during cell division. • Telomeres: CCCA repeats at the end of DNA that postpone loss of coding on replication.

36. Chromosomes (Eukaryote)-2 • Each chromosome has one linear DNA complexed with histone proteins to form nucleosomes. Histones regulate access to DNA of transcription factors. • Cells not undergoing cell division have partially decondensed chromosomes called chromatin which looks like a beaded chain. • As chromatin packs to form chromo-somes, 30nm and 200 nm fibers appear. Chromosomes have multiple levels of supercoiling.

37. Chromosomes (Eukaryote)-3 • The figure below shows levels of coiled structure for nuclear chromatin.

38. Genome • The genome of each living organism is the full set of inherited instructions required to sustain all living processes. • Size varies: 1x106 to 1x1010 base pairs • Eukaryotes have larger and more complex information-coding capacity than prokaryotes.

39. Genome: Prokaryotes • Size. Most prokaryotic genomes are smaller: E. g. E. coli 4.6 Mb, 4300 genes. • Coding capacity. Genes are compact and continuous. Little, if any, noncoding DNA. • Gene expression. Higher percentage of operons, sets of linked genes. • Prokaryotes often contain plasmids, nonchromosome DNA.

40. Genome: Eukaryotes • Genomic size. Larger than prokaryotes but many have vast amounts of noncoding DNA. • Coding capacity. Enormous capacity but only about 1.5% codes for proteins. • Coding continuity. Most are dis-continuous and contain noncoding introns.

41. Genome: Eukaryotes-2 • About 45% of human genome is “repeated sequences.” • Tandem repeats (satellite DNA) have multiple copies arranged next to each other and can vary from 10 to 2000 bp repeating to 105 to 107 bp. • Interspersed genome-wide repeats are scattered in the genome. Many result from transposition whereby DNA sequences are duplicated and moved in the genome.