DNA: Structure and Function

1. DNA: Structure and Function Biology's biggest moment in the 20th century, as heralded (we think) in six paragraphs in The New York Times.

2. Dr. Francis Crick, left, and Dr. James D. Watson at Cambridge in the 1950's, after they discovered the double helix. The two have continued to drive the genetic revolution. Dr. Crick, above right, has been at the Salk Institute since 1976. Dr. Watson worked at Harvard and is now president of the Cold Spring Harbor Laboratory.

3. What is the Structure of DNA? • DNA structure must be compatible with its 4 roles: • Make copies of itself • Encode information • Control cells & tell them what to do • Change by mutation

4. DNA is a Double Helix • Nucleotides that make up DNA have 3 components: • Phosphate group • 5-C sugar (deoxyribose) • Nitrogen-containing organic base

5. Four Bases of DNA Nucleotides • Adenine (A) – purine • Guanine (G) – purine • Thymine (T) – pyrimidine • Cytosine (C) - pyrimidine

6. phosphate base = thymine sugar phosphate base = cytosine sugar phosphate base = adenine sugar phosphate base = guanine sugar

7. Characteristics of Four Bases Watson & Crick • Assumed that the phosphate group & sugar connect the bases together • Thus, nitrogenous bases could occur in any order without changing basic molecular structure • Consistent with role as repository of information

8. 3D Structure of Proteins • L. Pauling made the discovery using X-ray crystallography: • Tiny bit of crystallized sample is bombarded with X-rays • Spots & areas thus formed reveal atomic arrangement in the sample • Some proteins have a regular structure

9. 3D Structure of Proteins • Pauling made paper models to resemble amino acids & assembled them into protein model • Model looked like twisted helix winding around axis (elongated spiral) • Pauling called the model alpha helix

10. Research of DNA Structure • M. Wilkins’ research confirmed DNA was a helix • E. Chargaff found relative amounts of 4 bases conform to rule regardless of DNA source

12. Chargaff’s Rule of Ratios • Amount of adenine always equals thymine • Amount of cytosine always equals guanine • Amount of A+T together is independent of C+G

13. Watson & Crick’s Research • Considered there could be 2 helices with adenine on one & thymine on the other • Proposed pairing relationships – guanine on one & guanine on other

14. Watson & Crick’s Research • Pairing relationship – sequence on one chain is complement of sequence on other • Used Pauling’s model building approach to make a metal model • Their model was sugar-phosphate backbone (like rails on ladder), twisted into helix as predicted by pictures

15. Watson & Crick’s Research • Paired bases projecting from backbone formed rungs of a ladder projecting from rails & satisfied Chargaff’s ratios • Found bonds holding nucleotides together were covalent • Bonds holding base pairs – relatively weak, but many together – strong

16. Watson & Crick’s Research

17. DNA Replication • Replication – process by which DNA copies itself • Precedes cell division • Watson & Crick said replication begins when weak bonds connecting parental strands break • Strands separate as halves of a zipper

18. DNA Replication • Watson & Crick exposed bases attract new mates (T pairing with A, C pairing with G, etc.) • Each strand acts as a blueprint upon which a new partner is assembled • As each new strand forms, nucleotides are lined together to form a complete strand

19. DNA Replication 062A3REP.MOV

20. Double Helix of DNA

21. DNA Replication • Result is two double-stranded daughter helices • Each composed of one parental strand & one newly synthesized strand • This mechanism is called semiconservative replication • Watson & Crick proposed this solely on basis of logic, no scientific evidence

22. How is Info in DNA Expressed? • A. Garrod, 1902, proposed connection between genes & proteins • Proteins – amino acid polymers that fold, twist into 3D structures • Amino acids differ form each other in side group (R group composition) • The genes determine protein primary structure

23. RNA as an Intermediary • DNA codes for protein through related polymer of ribonucleic acid nucleotides or RNA • DNA that encodes protein is copied into sequence of RNA nucleotides • Smaller, more mobile RNA goes to the part of the cell where sequence is decoded into protein

24. Decoding DNA: DNA RNA PROTEIN • Two separate processes involved: • Transcription – DNA used as the template to make RNA • Translation – RNA serves as the template for the sequence of amino acids in a protein

25. Structure of RNA Nucleotides & Polynucleotides • Composed of phosphate group, nitrogenous base (A, G, C, U [instead of T]) & ribose sugar • Nucleotides are joined together into single-stranded molecule by covalent bonds

26. Differences: DNA & RNA • They contain different sugars • DNA contains deoxyribose • RNA contains ribose • Nitrogenous bases • DNA contains A, G, T, & C • RNA contains A, G, U, & C • Uracil (U) replaces thymine (T) in RNA, thus A pairs with U when DNA is used as a template to make RNA

27. Differences: DNA & RNA • DNA – most stable as double helix • RNA most often exists as a single strand of nucleotides • Size • DNA molecules are larger • RNAs are smaller • Mobility • DNAs are basically immobile • RNAs are highly mobile • Life span • DNAs are long-lived • RNAs are broken down soon after their job is done

28. Transcription • Messenger RNA (mRNA) carries genetic info from DNA (nucleus) to cytoplasm where it is translated into protein

29. Transcription • Transfer RNA (tRNA) is interpreter molecule that brings amino acids to site where mRNA translated into protein

30. Transcription • Ribosomal RNA (rRNA) - >80% of RNA in most eukaryotes • Several rRNAs & many proteins combine to form ribosomes • Where translation occurs

31. Transcription • Enzymes involved in and control transcription • The enzyme RNA polymerase catalyzes assembly of RNA & places appropriate complimentary RNA nucleotides into new RNA • Other enzymes separate DNA double helix strands to allow transcription

32. Transcription • What raw materials are required for making RNA? • Ribonucleotides A, U, G, C that are the building blocks of RNA • A template or blueprint of the final product – DNA • Fuel to drive the assembly line linking ribonucleotides – nucleotide triphosphates • Equipment to accomplish actual assembly of the final product

33. Transcription • Transcription from DNA must start & end at specific places on DNA • Certain sequences within DNA (promoter sequences) • Signal RNA polymerase to attach to template and begin transcribing

34. Translation • Proteins are synthesized in translation – assembly of protein from mRNA template • More complex & machinery of translation is far more elaborate than that of transcription

35. Translation • What is needed for translation? • Raw materials (amino acids) • Energy to drive synthesis • Template to determine amino acid sequences • Machinery to do synthesis • Reliable interpreter (tRNA) • Stable synthesis platform (ribosome)

36. Translation • Transfer RNAs carrying amino acids

37. The Genetic Code • 3 RNA nucleotides code for 1 amino acid • The language of genes is written in sequence of nitrogenous base • Can be translated 3 at a time into amino acid words

38. The Genetic Code • Need code to stand for 20 amino acids • Alphabet for code has 4 letters (A, G, C, T or U) • Can only make 4 one-letter words (41), 16 two-letter words (42), 64 three-letter words (43)

39. The Genetic Code • To code unambiguously for 20 amino acids • Need at least 20 words • Three-letter words would be the minimum\ • M. Nirenberg & H. Matthaei, 1960s, developed a technique for cracking code

41. The Genetic Code • Features of code • Code is universal, applies to humans & all other living things • Most amino acids have 2 and many have 4 triplet codons that code for them

42. What Makes Cells Different from Each Other? • During lifetime • A person may manufacture as many as 100,000 different proteins, but • Only ~5000 are found in any one cell at any given time

43. What Makes Cells Different from Each Other? • Eukaryotes regulate genetic expression at many levels • Transcription is important in eukaryotes as well but there are other levels of regulation

44. DNA Mutations • Mutations are essential for life • Mutation is the sudden appearance of a new allele

45. DNA Mutations • Some mutations involve whole chromosomes • Polyploidy arises as genetic accident, but can be advantageous • Aneuploidy is a change in chromosome number involving single chromosome or single homologous pair

46. DNA Mutations • B. McClintock showed that DNA molecules did not always remain intact from generation to generation • Called this genetic rearrangement transposition & • Called moved bits of DNA • Transposable genetic element, later transposons

47. DNA Mutations • While sequences of transposon DNA are not random • Target sites are thought to be random, so that • Transposon can land anywhere • Can create new combinations of genes & can introduce errors in genetic material

48. DNA Mutations • Inversions • Piece of chromosome broken, then reincorporated in chromosome in reversed order • Deletions • Parts of chromosome spontaneously deleted

49. DNA Mutations • Micromutations that involve single DNA bases or just a few bases • Called point mutations • Neutral mutations • Most mutations are harmful, but • Many have little or no impact on recipients