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) by Alberts et al
Any biochemistry textbook
Key websites

3. 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

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

5. Timeline F Miescher - nucleic acids
1928
F. Griffith - Transforming principle

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

7. Griffith experiment
Figure 6.3 a

8. Griffith experiment
Figure 6.3 b

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

10. Timeline F Miescher - nucleic acids
1928
F. Griffith - Transforming principle
Avery, McCleod & McCarty- Transforming principle is DNA
1944

11. Avery, MacLeod, McCarty Experiment
Figure 6.4 a

12. Avery, MacLeod, McCarty Experiment
Figure 6.4 c

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

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

15. Timeline F Miescher - nucleic acids
1928
F. Griffith - Transforming principle
Avery, McCleod & McCarty- Transforming principle is DNA
1944
1949
Erwin Chargaff – base ratios
1952
Hershey-Chase ‘blender’ experiment

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
Figure 6.5 a,b

18. Hershey and Chase experiments
Figure 6.5 c

19. Timeline F Miescher - nucleic acids
1928
F. Griffith - Transforming principle
Avery, McCleod & McCarty- Transforming principle is DNA
1944
1952
Hershey-Chase ‘blender’ experiment
1952
Erwin Chargaff – base ratios
1952
R Franklin & M Wilkins–DNA diffraction pattern
J Watson and F Crick – DNA structure solved
1953

20. X-ray diffraction patterns produced by DNA fibers – Rosalind Franklin and Maurice Wilkins
Figure 6.6

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. Human genome project Public consortium Headed by F Collins
Goal: to sequence the entire human nuclear genome
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 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 - polypeptides made 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
adenine
cytosine
guanine
thymine
Note:
Base carbons denoted as 1 etc
Sugar carbons denoted as 1’ etc
uracil

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

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
Figure 6.9 d

31. Maybe because RNA but not DNA is prone to base-catalysed hydrolysis
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: A-DNA Z-DNA 4 stranded 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. both form right-handed double helices
DNA conformations
B DNA
A 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.

35. DNA conformations Z DNA B 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
Parvoviruses are among the smallest, simplest eukaryotic viruses and were only discovered in the 1960's. They are widespread in nature; human Parvovirus infections were only recognised in the 1980's. Essentially, they fall into two groups, defective viruses which are dependent on helper virus for replication and autonomous, replication-competent viruses. In all, >50 parvoviruses have been identified
Parvovirus

38. Genetic material may be RNA
Double stranded RNA
Single stranded RNA
Parvoviruses are among the smallest, simplest eukaryotic viruses and were only discovered in the 1960's. They are widespread in nature; human Parvovirus infections were only recognised in the 1980's. Essentially, they fall into two groups, defective viruses which are dependent on helper virus for replication and autonomous, replication-competent viruses. In all, >50 parvoviruses have been identified
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