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BB10006: Cell & Molecular biology

BB10006: Cell & Molecular biology. Dr. MV Hejmadi Dr. JR Beeching (convenor) Prof. RJ Scott Prof. JMW Slack. Dr. Momna Hejmadi (bssmvh@bath.ac.uk). Structure and function of nucleic acids Books (any of these) : Biochemistry (2/3e) by D Voet & J Voet

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BB10006: Cell & Molecular biology

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  1. BB10006: Cell & Molecular biology Dr. MV Hejmadi Dr. JR Beeching (convenor) Prof. RJ Scott Prof. JMW Slack

  2. Dr. Momna Hejmadi (bssmvh@bath.ac.uk) Structure and function of nucleic acids Books (any of these): • Biochemistry (2/3e) by D Voet & J Voet • Molecular biology of the cell(4th ed)byAlberts et al • Any biochemistry textbook Key websites • http://www.dnai.org/lesson/go/2166/1994 • http://molvis.sdsc.edu/dna/index.htm

  3. Outline of my lectures Lecture 1. Nucleic acids – an introduction Lecture 2. Properties and functions of nucleic acids Lecture 3. DNA replication Lectures4-6. Transcription and translation Access to web lectures at http://www.bath.ac.uk/bio-sci/hejmadi/teaching%202004-05.htm

  4. Lecture 1 - Outline • How investigators pinpointed DNA as the genetic material • The elegant Watson-Crick model of DNA structure • Forms of DNA (A, B, Z etc) • Types of nucleic acids (DNA and RNA) References: History, structureand forms of DNAhttp://www.dnai.org/lesson/go/2166 Voet and Voet – Chapter 28

  5. 1800’s Timeline F Miescher - nucleic acids 1928 F. Griffith - Transforming principle http://www.dnai.org/lesson/go/2166/1994

  6. Discovery of transforming principle • 1928 – Frederick Griffith – experiments with smooth (S) virulent strain Streptococcus pneumoniae and rough (R) nonvirulent strain

  7. Griffith experiment

  8. Griffith experiment

  9. What is this transforming principle? • Bacterial transformation demonstrates transfer of genetic material

  10. 1800’s Timeline F Miescher - nucleic acids 1928 F. Griffith - Transforming principle Avery, McCleod& McCarty- Transforming principle is DNA 1944 http://www.dnai.org/lesson/go/2166/1994

  11. Avery, MacLeod, McCarty Experiment

  12. Avery, MacLeod, McCarty Experiment

  13. 1800’s Timeline F Miescher - nucleic acids 1928 F. Griffith - Transforming principle Avery, McCleod& McCarty- Transforming principle is DNA 1944 Erwin Chargaff – base ratios 1949 http://www.dnai.org/lesson/go/2166/1994

  14. E. Chargaff’s ratios A = T C = G A + G = C + T % GC constant for given species

  15. 1800’s Timeline F Miescher - nucleic acids 1928 F. Griffith - Transforming principle Avery, McCleod& McCarty- Transforming principle is DNA 1944 Erwin Chargaff – base ratios 1949 1952 Hershey-Chase ‘blender’ experiment http://www.dnai.org/lesson/go/2166/1994

  16. Hershey and Chase experiments • 1952 – Alfred Hershey and Martha Chase provide convincing evidence that DNA is genetic material • Waring blender experiment using T2 bacteriophage and bacteria • Radioactive labels 32P for DNA and 35S for protein

  17. Hershey and Chase experiments

  18. Hershey and Chase experiments

  19. 1800’s Timeline F Miescher - nucleic acids 1928 F. Griffith - Transforming principle Avery, McCleod& McCarty- Transforming principle is DNA 1944 Hershey-Chase ‘blender’ experiment 1952 Erwin Chargaff – base ratios 1952 R Franklin & M Wilkins–DNA diffraction pattern 1952 J Watson and F Crick – DNA structure solved 1953 http://www.dnai.org/lesson/go/2166/1994

  20. X-ray diffraction patterns produced by DNA fibers – Rosalind Franklin and Maurice Wilkins

  21. The Watson-Crick Model: DNA is a double helix • 1951 – James Watson learns about x-ray diffraction pattern projected by DNA • Knowledge of the chemical structure of nucleotides (deoxyribose sugar, phosphate, and nitrogenous base) • Erwin Chargaff’s experiments demonstrate that ratio of A and T are 1:1, and G and C are 1:1 • 1953 – James Watson and Francis Crick propose their double helix model of DNA structure

  22. Public consortium Headed by F Collins Started in mid 80’s Working draft completed in 2001 Final sequence 2003 Nature: Feb 2001 Celera Genomics Headed by C Venter Started in mid 90’s Working draft completed in 2001 Science: Feb 2001 Human genome project Goal: to sequence the entire human nuclear genome Humangenome = 3.3 X 109 base pairs Number of genes = 26 – 32,000 genes

  23. DNA, gene, genome? DNA = nucleic acid Gene = segments of DNA that encode protein Genome = entire nucleic acid component of any organism Nucleic acids:made up of individual nucleotides linked together Protein- polypeptidesmade up of individual amino acids linked together -

  24. Nucleotides Originally elucidated by Phoebus Levine and Alexander Todd in early 1950’s Made of 3 components 1) 5 carbon sugar (pentose) 2) nitrogenous base 3) phosphate group 1) SUGARS DNA RNA 2’-deoxy-D-ribose 2’-D-ribose)

  25. 2) NITROGENOUS BASES planar, aromatic, hetercyclic derivatives of purines/pyrimidines purines pyrimidines adenine cytosine guanine thymine Note: Base carbons denoted as 1 etc Sugar carbons denoted as 1’ etc uracil

  26. Nucleotide monomer nucleotide = phosphate ester monomer of pentose dinucleotide - Dimer Oligonucleotide– short polymer (<10) Polynucleotide – long polymer (>10) Nucleoside = monomer of sugar + base

  27. 5’ – 3’ polynucleotide linkages 2) N-glycosidic bonds Links nitrogenous base to C1’ pentose in beta configuration • 1) Phosphodiester bonds • 5’ and 3’ links to pentose sugar

  28. 5’ – 3’ polarity 5’ end 3’ end

  29. Essential features of B-DNA • Right twisting • Double stranded helix • Anti-parallel • Bases on the inside (Perpendicular to axis) • Uniform diameter (~20A) • Major and minor groove • Complementary base pairing

  30. Structurally, purines (A and G pair best with pyrimidines (T and C) • Thus, A pairs with T and G pairs with C, also explaining Chargaff’s ratios

  31. Why DNA evolved as the genetic material but not RNA? Maybe because RNA but not DNA is prone to base-catalysed hydrolysis

  32. B-DNA Biologically dominant Right-handed double helix planes of base pairs are nearly perpendicular to the helix axis. helix axis passes through the base pairs and hence B-DNA has no internal spaces B-DNA has a wide and deep major groove and a narrow and deep minor groove

  33. DNA conformations B-DNA: • right-handed double helix with a wide and narrow groove. A-DNA • major groove is very deep and the minor groove is quite shallow Z-DNA • consists of dinucleotides, each with different conformations 4 stranded DNA • Telomeric DNA

  34. DNA conformations B DNA both form right-handed double helices B-DNA helix has a larger pitch and hence a smaller width than that of A In B-DNA, the helix axis passes through the base pairs and hence B-DNA has no internal spaces, whereas that of A-DNA has a 6 Angstrom diameter hole along its helical axis. The planes of the base pairs in B-DNA are nearly perpendicular to the helix axis, whereas in A-DNA, they are inclined from this. Therefore, B-DNA has a wide and deep major groove and a narrow and deep minor groove, whereas A-DNA has a narrow and deep major groove, but a wide and shallow minor groove. A DNA

  35. DNA conformations Z DNA B-DNA forms a right-handed double helix in which the repeating unit is a nucleotide, whereas Z-DNA forms a left-handed double helix in which the repeating unit is a dinucleotide. The Z-DNA helix has a larger pitch and is therefore narrower than that of B-DNA. B-DNA has a wide and deep major groove and a narrow and deep minor groove, whereas Z-DNA has a narrow and deep minor groove but a nonexistent major groove. B DNA

  36. Types of RNA • Messenger RNA (mRNA): Codes for proteins • Transfer RNA (tRNA): Adaptor between mRNA & amino acids • Ribosomal RNA (rRNA): Forms ribosome core for translation • Heterogenous nuclear RNA (hn RNA) • Small nuclear RNA (sn RNA): involved in post-transcriptional processing

  37. Genetic material may be DNA Double stranded DNA Single stranded DNA linear linear human chromosomes adeno-associated viruses circular Prokaryotes Mitochondria Chloroplasts Some viruses (pox viruses) circular Parvovirus

  38. Genetic material may be RNA Double stranded RNA Single stranded RNA Retroviruses like HIV reoviruses

  39. RNA / DNA hybrids e.g. during retroviral replication

  40. What is the base found in RNA but not DNA? ?   A) Cytosine B) Uracil       C) Thymine       D) Adenine E) Guanine

  41. What covalent bonds link nucleic acid monomers?   A) Carbon-Carbon double bonds B) Oxygen-Nitrogen Bonds    C) Carbon-Nitrogen bonds    D) Hydrogen bonds E) Phosphodiester bonds

  42. What sugar is used in in a DNA monomer? A) 3'-deoxyribose B) 5'-deoxyribose C) 2'-deoxyribose D) Glucose

  43. Each deoxyribonucleotide is composed of   A) 2'-deoxyribose sugar, Nitrogenous base, 5'- hydroxyl B) 3'-deoxyribose sugar, Nitrogenous base, 5'- hydroxyl C) 3'-deoxyribose sugar, Nitrogenous base, 5'- Phosphate D) Ribose sugar, Nitrogenous base, 5'-hydroxyl E) 2'-deoxyribose sugar, Nitrogenous base, 5'- phosphate

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