Nucleotides and Nucleic Acids

1
Nucleotides and Nucleic Acids

• Dr. W. McLaughlin

2
Learning Objectives

• The types of nucleic acids
• The structure and components of nucleic acids
• The conformations of DNA
• The base composition of DNA
• Function of nucleic acids

3
Why learn about Nucleic Acids?

• Knowledge of the anatomy of the gene is as
  important in medical practice as knowledge of the
  anatomy of the heart

4

• There have been numerous advances in the areas of
  molecular biology and biotechnology in medicine
  but the biggest could be the Human Genome Project
  
• The information, it is hoped will revolutionize
  the detection, prevention and treatment of
  conditions from cancer to depression to old age
  itself

5
The Future Medical Doctors

• will drip droplets of our genes onto a biochip
  to figure out if we have the kind of prostrate
  cancer that will kill or not, or to figure out if
  ours is the kind of leukaemia that respond to
  this drug rather than that one
• medical records will include the complete
  genome
• ..treat patients as a biochemical and genetic
  individual

6
THE STRUCTURE OF NUCLEIC ACIDS

• Both DNA and RNA are known as nucleic acids
• Nucleic acids are high-molecular-weight polymeric
  compounds
• On complete hydrolysis yields pyrimidine and
  purine bases, a sugar component and phosphoric
  acid.
• Partial hydrolysis yields compounds known as
  nucleosides and nucleotides

7
Structure of Nucleotide

• A nucleotide consists of three things
• A nitrogenous base, which can be either adenine,
  guanine, cytosine, or thymine (in the case of
  RNA, thymine is replaced by uracil).
• A five-carbon sugar or pentose sugar
• One or more phosphate groups

8
Cyclic 5-carbon sugar

• D-ribose in RNA
• 2'-deoxyribose in DNA

9
(No Transcript)
10
Purine Bases

• Adenine Guanine
• Other naturally occurring derivatives
• Hypoxanthine
• Xanthine
• Uric acid

11
(No Transcript)
12
Pyrimidine Bases

• Thymine, cytosine and uracil
• 5-methylcytosine
• 5-hydroxymethylcytosine.
• N4-methylcytosine
• N6-methylcytosine

13
(No Transcript)
14
Phosphate group

• a molecule of Phosphoric acid, PO43

15
Nucleosides

• Purine or a Pyrimidine base ribose or
  deoxyribose Nucleoside.
• ribose ribonucleosides
• 2-deoxyribose deoxyribonucleosides

16
Nucleotides

• Purine or a pyrimidine linked to ribose or
  deoxyribose and phosphoric acid Nucleotide

• ribose ribonucleotides
• 2-deoxyribose deoxyribonucleotides

17
Nucleotide
18
Nucleotide
19
Components of Adenosine Triphosphate
20
Nucleic Acids

• Nitrogenous base attached to the sugar by
  N-glycosidic bonds to carbon 1 of the sugar
• Sugar is attached at position N-1 of the
  pyrimidine base
• Sugar is attached at position N-9 of the purine
  base
• Phosphate forms a bond with the sugar through
  phosphodiester linkages between 5' OH of the
  sugar and the negatively charged oxygen group

21
Purine Linkage N9 to C1
22
Pyrimidine Linkage N1 to C1
23
(No Transcript)
24
Primary structure of nucleic acids

• Nucleotides join through phosphodiester linkages
  between 5 and 3 carbon atoms to form nucleic
  acids
• When many nucleotides subunits combine, the
  result is the large single-stranded
  polynucleotide or Nucleic Acid

25
Primary structure of DNA
26
Secondary structure of DNA

• DNA exists as a double helix
• In April 1953, Watson and Crick proposed the
  structure of DNA

27
Secondary structure of DNA

• two complementary polymeric chains forming a
  regular right-handed double helix
• the two stands run in opposite directions
• (antiparallel alpha-helices), and are of
  opposite polarity
• the rails of the ladder runs in opposite
  direction and contain alternating units of
  deoxyribose sugar and phosphate.

28
2 structure of DNA

• the sugar and phosphate groups are always linked
  together by 3 - 5 phosphodiester linkages.
• the purine and pyrimidine bases are flat
  (planar), are relatively water-insoluble and are
  stacked tightly on top of one another like a pile
  of plates, forming the steps of the helical
  ladder.
• the bases are arranged at right angles to the
  long axis of the polynucleotide chain.

29
2 structure of DNA

• each step is composed of a pair of nucleotide- a
  base pair held together by weak hydrogen bonds.
• the order of the purine and pyrimidine bases
  along the chain is highly irregular, varying from
  one molecule to the other.
• the chain is not straight but is wound helically
  around a central axis, one full turn ( the pitch)
  of the helix extending 3.4 nm (34 Å), and there
  are 10 bases per turn

30
2 structure of DNA

• the bases are separated by a spacing of 0.34 nm
  (3.4 Å).
• the width of the double helix is 2 nm (20 Å).
• the chains are complementary, the sequence of
  bases on one strand is the exact complement of
  the other strand.
• Adenine always pair with thymine and cytosine
  always pair with guanine.

31
(No Transcript)
32
Hydrogen bonds

• Essential for 3-D structure of DNA
• Not the main contributor of DNA stability
• Important for the specificity of the helix
• Allow for only complementary strands to pair
• AT GC
• Complementary nature allow DNA to carry
  information

33
Hydrogen bonds
34
Bases pair in a Specific way

• Purines are larger structures than pyrimidine, if
  two purine are paired their dimensions are too
  great to fit the constant diameter of the double
  helix (2 nm) while the dimensions of the two
  pyrimidine are too small
• The specificity of position of the H atoms that
  can participate in bonding. It is essential that
  the hydrogen bonds have relatively stable
  positions to have the biological functioning of
  DNA.

35
Tautomeric Shifts

• H-atoms do undergo shift to other positions to
  form new pairing interactions
• the nitrogen atoms attached to the purine and
  pyrimidine rings are usually in the amino (NH2)
  form and only rarely assume the imino (NH)
  configuration
• the oxygen atoms attached to C6 atoms of guanine
  and thymine normally have the keto (C-O) form and
  rarely take up the enol (COH) configuration.

36
Tautomeric Shifts

• if the H-atom normally present at the 6-amino
  position in adenine shifts to the N1 position,
  Adenine will pair with Cytosine instead of with
  Thymine

37
Base composition of DNA

• Chargaff described fundamental features of DNA as
  revealed by chemical analysis.
• Chargaff was the first to draw attention to
  certain regularities in the composition of DNA
• Chargaffs Rule is true because of the strict
  H-bond forming rules

38
Chargaffs Rules

• ? purines ? pyrimidines
• ? amino bases (A C) ? keto bases (G T)
• ? between the amounts of A T, and between the
  amounts of G and C, ( A T and G C).
• Wide variations in the molar proportions of bases
  although DNA from different organs and tissues of
  any one species are essentially the same.
• AT/GC, (base ratio) may vary widely between
  species, and remains constant for any one
  species.

39
Molar Proportion of Bases in DNA from various
sources __________________________________________
__ Source A G C T AT/GC _______________________
______________________ Bovine thymus
28.2 21.5 21.2 27.8 1.3 Bovine spleen 27.9 22.7 20
.8 27.3 1.3 Bovine sperm 28.7 22.2 20.7 27.2 1.3 W
heat germ 27.3 22.7 16.8 27.1 - Yeast 31.2 18.7 1
7.1 32.9 1.8 E. coli 26.0 24.9 25.2 23.9 1.0 E.
aerogenes 21.0 28.0 29.0 22.0 0.7 C. perifringens
34.0 15.0 16.0 35.0 2.2 M. tubercolosis
15.1 34.9 35.4 14.6 0.4 ?X174 24.3 24.5 18.2 32.3
- _____________________________________________
40
DNA Conformations

• The major forms of DNA are
• the B-form, basically describes the Watson and
  Crick model
• the A-form DNA

41
B-form DNA

• Represent the conformation of most DNA found in
  cells
• Exists under most physiological conditions
• The main features are the pitch, the angle of
  tilt, the distinct major and minor grooves
• Pitch 3.4 nm
• 10 bases/full turn
• Long and thin

42
B-form DNA
43
Major and Minor Grooves

• Two asymmetrical groves
• Larger Major Minor Minor
• Arise because of the geometrical configurations
  of the bonds
• The groves expose the bases
• Recognised by proteins

44
A-form DNA

• The base pairs tilt some 30? so that successive
  base pairs occur every 0.28 nm
• Adopted by DNA under low humidity
• 11 bases/full turn
• Is short and broad and has deeper and narrow
  major grooves
• he 2-OH of ribose prevents RNA from forming the
  classic B-helix

45
Z-form DNA

• Alternating purine and pyrimidine residues
  (dinucleotides CGCGCGCGCGC) can fold up into
  left-handed as well as right handed helices.
•  
• One deep helical groove

46
50 Yrs after the discovery of DNA

• Deciphering of the human genome
• Genetic engineering of animals and crops
• Use of gene therapy to treat human diseases
• Designing better drugs
• Admissibility in courts in criminal cases
• DNA chips

47
Properties of DNA

• Denaturation Renaturation of DNA
• The DNA double helix can unwind to form
• single strands when subjected to
•  extremes of pH
• increased temperature
• decreased dielectric constant by alcohols,
  ketone, etc.
• exposure to amides or urea

48
DNA denaturation

• denature when the DNA changes from a double helix
  to a random coil
• melting or transition temperature Tm
• measured at 260 nm
• hyperchromic effect

49
Denaturation of DNA

• The nature of the melting transition is affected
  by 3 factors
• The GC content of the DNA
• The nature of the solvent.
• The nature of the DNA.

50
GC Content

• DNA with higher GC is more stable and have a
  higher melting temperature
• G?C
• AT

51
Relative GC content of DNA from various sources
________________________________________ Source
of DNA GC ___________________________________
_____ Bacillus cereus 37 Haemophilus
influenzae 39 Rat liver 40 Chicken
liver 43 E. coli 51 Herpes simplex
virus 72
52
Nature of the solvent

• Low conc of ions, denaturation occurs a
  relatively low temperatures over a broad range
• High conc of ions, the Tm is raised and the
  transition is sharp

53
Nature of the DNA

• Most DNA are mosaics of varying regions of GC and
  AT rich regions
• AT regions will melt abut GC regions will be held
  together
• On cooling the GC regions will allow for rapid
  re-annealing

54
Renaturation of DNA
55
Secondary Tertiary Structure of RNA

• RNA are single stranded molecules
• Contains ribose instead of de-oxyribose
• Contains the base uracil instead of thymine
• Retains all the information of the DNA sequence
• Has base pairing properties of DNA

56
RNA

• RNA performs a variety of functions within the
  cell and for each function a specific type of RNA
  is required
• RNA differ in chain length and secondary and
  tertiary structures

57
Types of RNA

• mRNA carry genetic information
• rRNA the site for protein synthesis
• tRNA carriers specific amino acids to the
  ribosomes
• Small RNA molecules enzymatic activities

58
Secondary Structure -RNA

• Do not possess regular H-bonded structure
• In some RNA molecules about 70 of the bases are
  involved in secondary structure interactions e.g.
  tRNA
• Structure similar to A-form of DNA

59
tRNA
60
Triple standed regions

• Occurs in RNA in which two chains run in parallel
  with one another
• Third strand anti parallel with one strand
• Unusual arrangement found in myxobacterium

61
RNA triple structure
Hoogsteen Base pairs
62
Functions of Nucleic Acids

• To direct its own replication during cell
  division
• To direct transcription of complementary
  molecules or RNA

63
Functional requirements

• The genetic material is the blueprint for the
  cell and carries the information necessary to
  direct all its specific activities. The
  information necessary is coded in the 4 bases
  ATGC
• The genetic material replicates, reproduces
  itself, so that the information it carries is
  inherited in a very precise way by daughter
  cells. The two intertwining strands of
  complementary bases suggests that one strand
  serves as a template upon which the other strand
  is synthesized.
• The genetic material can undergo mutations so
  that the message is altered in a specific
  heritable way.

64
Functions of RNA

• mRNA formed by DNA transcription, directs
  ribosomal synthesis of polypeptides in a process
  known as translation.
• RNAs of the ribosomes have functional as well as
  structural roles rRNA is composed of about 2/3
  RNA and 1/3 protein.
• During protein synthesis a.a are delivered to the
  ribosome by molecules of transfer RNA.
• Certain RNAs are associated with specific
  proteins to form ribonucleoproteins that
  participate in post-transcriptional processing of
  other RNAs.
• In many viruses, RNA, and not DNA is the carrier
  of genetic information

65
Cricks Central Dogma