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

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Presentation on theme: "BB10006: Cell & Molecular biology Dr. MV Hejmadi Dr. JR Beeching (convenor) Prof. RJ Scott Prof. JMW Slack."— Presentation transcript:

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

3 Dr. Momna Hejmadi Structure and function of nucleic acids Books (any of these): 1) Biochemistry (2/3e) by D Voet & J Voet 2) Molecular biology of the cell (4 th ed) by Alberts et al 3) Any biochemistry textbook Key websites 1) 2)

4 Outline of my lectures Lecture 1. Nucleic acids – an introduction Lecture 2. Properties and functions of nucleic acids Lecture 3. DNA replication Lectures 4-6. Transcription and translation Access to web lectures at

5 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, structure and forms of DNA Voet and Voet – Chapter 28

6 Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle

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

8 Griffith experiment

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10 What is this transforming principle? Bacterial transformation demonstrates transfer of genetic material

11 Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle Avery, McCleod & McCarty- Transforming principle is DNA 1944

12 Avery, MacLeod, McCarty Experiment

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14 Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle 1949 Avery, McCleod & McCarty- Transforming principle is DNA 1944 Erwin Chargaff – base ratios

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

16 Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle 1952 Avery, McCleod & McCarty- Transforming principle is DNA 1944 Hershey-Chase ‘blender’ experiment Erwin Chargaff – base ratios

17 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 32 P for DNA and 35 S for protein

18 Hershey and Chase experiments

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20 Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle 1952 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 1953 J Watson and F Crick – DNA structure solved

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

22 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: – James Watson and Francis Crick propose their double helix model of DNA structure

23 Human genome project 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 = 3.3 X 10 9 base pairs Number of genes = 26 – 32,000 genes Goal: to sequence the entire human nuclear genome

24 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 - polypeptides made up of individual amino acids linked together - amino acids

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

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

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

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

29 3’ end 5’ end 5’ – 3’ polarity

30 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

31 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

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

33 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

34 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

35 DNA conformations 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 B DNA

36 DNA conformations 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 DNAZ DNA

37 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

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

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

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

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

42 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

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

44 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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