HL Chemistry - Option B : Human Biochemistry

1. HL Chemistry - Option B : Human Biochemistry Nucleic Acids

2. DNA, RNA, & Flow of Genetic Information DNA & RNA are long linear polymers, called nucleic acids. Genetic information is stored in a sequence of 4 kinds of bases along the chain, and is passed from one generation to the next • A nucleic acid consists of 4 kinds of bases linked to a sugar-phosphate backbone • A pair of nucleic acid chains with complimentary sequences • can form a double-helical structure • DNA is replicated by polymerases that take instructions from • templates • Gene expression is the transformation of DNA information into functional molecules • Amino acids are encoded by groups of three bases starting from a fixed point • Most eucaryotic genes are mosaics of introns & exons

3. Polymeric structure of nucleic acids Linear polymers of covalent structures, built from similar units Sequence of bases uniquely characterizes nucleic acids Represents a form of linear information Backbone is constant: repeating units of sugar-phosphate

4. Different pentose sugars in RNA & DNA RNA Sugar carbons have prime numbers, to distinguish them from atoms in bases DNA

5. Backbone of DNA & RNA 3’-to-5’ phosphodiester linkages Sugar, red. Phosphate, blue

6. Purines & Pyrimidines DNA Note: ring atom #s RNA

7. Sugar - base linkage Base above plane of sugar, linkage is  Nucleoside RNA: adenosine, guanosine, cytidine, & uridine DNA: deoxyadenosine, deoxyguanosine, deoxycytidine, & thymidine

8. Nucleotides: monomeric units of nucleic acids Deoxyguanosine 3’ monophosphate Adenosine 5’-triphosphate 5’ nucleotide - most common 3’ nucleotide Nucleotide: nucleoside joined to one or more phosphate groups by an ester linkage

9. Adenosine 5’-triphosphate Adenosine linked to sugar C1’ Triphosphate linked to sugar C5’

10. Deoxyguanosine 3’-monophosphate

11. Structure of DNA chain 5’ end, phosphate attached 3’ end, free hydroxyl group

12. X-ray diffraction of DNA hydrated fiber Shows double-helix structure Meridian arcs - stack of nucleotide bases, 3.4 A apart Central X - indicates helical structure R. Franklin & M. Wilkins photograph

13. Watson-Crick model - DNA double helix Axial view Features: Bases separated by 3.4 Å 10 bases / turn Rotation: 36 degrees / base Helix pitch: 34 Å Helix diameter: 20 Å Two helical polynucleotide chains, coiled around common axis, run in opposite directions Sugar-phosphate backbones outside, bases inside Bases nearly perpendicular to helix axis

14. DNA double helix - radial view Looking down the helix axis

15. Watson and Crick base pairs Essentially the same shape

16. Axial view of DNA Base pairs stacked on top of one-another, contributes stability to double helix in 2 ways: Base attraction: van der Walls forces Hydrophobic effect of base stacking, exposure of polar surfaces to surrounding water

17. Semiconservative replication of DNA Parental DNA, blue Newly synthesized DNA, red

18. Hypochromism of DNA Used to detect separation of single strands, DNA melting

19. DNA melting At Tm ,50% of helix is separated Below Tm, DNA is renatured or annealed Separation by by helicases inside cells

20. EM of circular DNA, mitochondria Relaxed form

21. EM of circular DNA, mitochondria Supercoiled form

22. Single stranded nucleic acids: elaborate structures Stem & loop structures

23. RNA stem & loop

24. RNA complex structure Base pairing & loops Long-rang interaction

25. Long-range interaction W & C base pairing, dashed black lines Other base pairing, dashed green lines

26. DNA polymerization reaction By DNA polymerase Step by step addition of deoxyribonucleotide units to a DNA chain New DNA chain assembled directly on a preexisting DNA template Primer & template required Activated precursors required: dATP, dGTP, TTP, dCTP Also required: Mg2+ ion

27. DNA replication, phosphodiester bridge Nucleophilic attack by 3’ -hydroxyl group of primer on innermost phosphorus atom of deoxynucleotide triphosphate (dNTP) Elongation proceeds, 5’ -to- 3’ Hydrolysis of pyrophosphate (PPi) helps drive polymerization

28. Retroviruses reverse flow of information Reverse transcriptase brought into cell by the virus (eg. HIV-1) ssRNA genome Incorporated into host DNA

29. Roles of RNA in gene expression Messenger RNA: template for translation (protein synthesis) Transfer RNA: carriers of activated AAs to ribosomes (at least one kind for each of 20 AAs) Ribosomal RNA: major component of ribosomes (play structural and catalytic roles)

30. mRNA & DNA complementarity mRNA sequence is the compliment of that of the DNA template & is the same as that of the coding DNA strand, except for T in place of U

31. Genetic code, nonoverlapping

32. Genetic code, no punctuation Sequence of bases is read in blocks of 3 bases from a fixed starting point (64 combinations of 4 bases)

33. Genetic code, degenerate (64 codons, 20 aas) Trp & Met, one codon each, other 18 aas, two or more codons, Leu, Arg, & Ser, six codons each, Synonyms, codons for same aa, Synonyms differ in last base, 3 stop codons, designate translation termination

34. DNA Profiling (part 1) • Every human has a unique genetic “fingerprint” • The genetic fingerprint can be obtained by looking at how many pieces DNA can be broken into using one of two different methods • Method #1: Restriction Enzymes Cleave DNA between known base sequences and compare fragment lengths from the sample to the person in question

35. DNA Profiling (part 2) • Method #2: VNTR - VNTR stands for “Variable Number of Tandem Repeats” - DNA contains repetitive base patterns (function unknown) that varies from person to person - use enzymes to reproduce these sections millions of times and compare lengths of fragments

36. DNA Profiling - Electrophoresis • A gel (agar, agarose) is created between 2 plates of glass • A solution of the aforementioned DNA fragments is loaded into the gel, and an electric current applied • The negatively charged DNA (phosphates) attracts the fragments to the + end of the gel • Smaller fragments move faster than the larger fragments • A fluorescent dye is added (ethidium bromide) which causes the DNA to glow under UV light • The gel is photographed and the number and position of DNA fragment bands is compared to a sample from the human donor (suspect?)

37. DNA Profiling – What it Shows • The techniques discussed in the previous slides are used to identify people and solve crimes • DNA-containing material at the scene of a crime is compared to samples obtained from suspects (Forensics) • VNTR can also be used to identify the father of a child in paternity cases