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Nucleic acid as noted above

1. Nucleic acids
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Freddie Bwanga 04Nov2024
•DNA & RNA
•Plasmids
•Other genetic elements
•Gene structure & Function
•Mutations
•Primers
•Probes

2. Nucleic acids
•DNA
•RNA
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Human DNA is packegdin Chroimosomes

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6. Bacterial DNA and Genome

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Viral DNA/RNA (Genome)

8. Nucleic acids structure scope
1.Primary structure –the components of nucleic
acids
The 5-Carbon sugars
Nitrogenous bases
The Phosphate functional group
Nucleotides and Nucleosides
2.The significance of 5’ and 3’
3.Nomenclature of nucleotides
4.Secondary structure: the double helix
5.Tertiary structure: Supercoiling
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9. Primary structure is composed of
•The 5-Carbon sugars
•Nitrogenous Bases
•The Phosphate Functional group
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10. 5-C Sugars in Nucleic Acids
Sugars differ in Presenceor Absenceof an O2 at 2’-C
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11. The nitrogenous bases
Bases:N2-containing molecules having the chemical properties of a
base (a substance that accepts an H+ ion or proton in solution)
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12. The phosphate functional group
It gives DNA & RNA property of an acid
i.e…..a substance that releases a H+ in solution), hence the
name nucleic acids
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13. Nucleotides and nucleosides
a.Nucleotidesare the monomeric constituents of DNA
and RNA. They are composed of;
5-C sugar
Nitrogenous base
Phosphate group
b.Nucleosidesare composed of;
•A sugar
•Nitrogenous base
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14. Nucleotides vS.Nucleosides
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15. Nucleotides, cont’d
Nucleotides are joined (polymerized)
by condensation reactions to form
chains of DNA and RNA
The –OH on the 3’-Cof a sugar of one
nucleotide forms an ester bond to the
PO4 at 5’-Cof the oncoming
nucleotide to form;
•The 5’ –3’ Phosphodiester bond
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16. The Phosphodiesterbond
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17. Significance of 5’ and 3’
5’ –3’ directionality of nucleic acids is important for understanding;
DNA replication
Transcription
Reading DNA/RNA sequences
Carrying out an experiment in a lab
Genomics / bioinformatics
•By convention DNA sequences are written with the 5’-end to the
left and 3’-end to the right, eg;
….5’-TGGCCCGGGTCGACGGTGACACCGTGTTC -3’
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18. Watson-Crick base-pairing in DNA
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19. The double helix, cont’d
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20. DNA can undergo reversible strand
separation
•Reversible strand separationallows DNA replication, Transcription
and Translation with high fidelity
•Same features make it possible to manipulate DNA in vitro
•Unwinding and separation of DNA strands is referred to as
“Denaturation”
•The temperature at which half the bases in a DNA sample
have denatured is called Melting Temperature (Tm)
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21. RNA
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22. RNA: types & structure
•Polymer of nucleotides
•What is the difference?
•FiveRNA types:
•Ribosomal RNA(rRNA)
•Messenger RNA(mRNA)
•Transfer RNA(Trna)
•Small Nuclear RNA(snRNA)
•small Nucleolar RNAs(snoRNA)
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23. Components of RNA
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•mRNAtakes message from
DNA to proteins
•snRNA-RNA processing
•tRNA-Protein synthesis
•rRNA–Machinery for
Protein synthesis
•RNAcatalyzes chemical certain
reactions in living cells
(ribozymes)
The Role of RNA in gene expression
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25. Messenger RNA (mRNA)
Information in DNA is copied
(transcribed) into mRNA
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mRNA then goes to ribosomes for
translation into proteins
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The Genetic Code -codons in messenger RNA (mRNA) molecule

27. tRNAstructure
Three loops that form a cloverleaf
secondary structure; each loop has
a specific function
1.T-loop: recognizes the ribosome
2.D-loop: recognizes the aminoacyl
tRNAsynthatase
3.Anticodon loop: base pairs with
the codon in mRNA
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T-Loop
D-Loop
Anti-codon -Loop
5’ 3’

28. Functions of tRNA
•Adaptor like molecule that decodes
mRNA codons into amino acids
•Brings amino acid corresponding to the
appropriate mRNA codon
•Each amino acid has unique tRNA
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29. Ribosomal RNA (rRNA)
Type Size Large subunit Small subunit
Prokaryotic 70S
50S
(5S rRNA,23S rRNA)
30S
(16S rRNA)
Eukaryotic 80S
60S
(5S rRNA,5.8S
rRNA,28S rRNA)
40S
(18S rRNA)
Component of theribosome, thesite of protein synthesis in all
livingcells
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30. rRNARoles
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16S/18SrRNAsare used to classify microorganisms; the
Microbiome / Metagenomics
16 rRNAgenes are used in PCR Diagnostics to detect

31. PLASMIDS
•Circular or linear double stranded DNA molecules that replicate autonomously or
outside the bacterial chromosome.
•Vary in length, contain genes that are essential for their function(replication,
inheritance).
•Most of the genes are useful to the host iedrug resistance, virulence factors, toxin
production and degradation of organic compounds.

32. Plasmid incompatibility
•Refers to the inability of two plasmids to be propagated in the same line.
•Plasmids with same replication control> incompatible.
•Plasmids with different replication control > compatible.
•Most of plasmids are found in bacteria, archaeaand multicellular organisms.

33. Types of plasmids
Fertility, F plasmids
•Conjugative plasmids found in make bacterial cells.
•Inserted in chromosomal DNA > episomes.
.

34. Resistance, R plasmids
•Confer resistance to antibiotics and various other growth inhibitors.
•Several antibiotic resistance genes can be carried by a single R plasmid.
•Plasmid R100, for example, is a 94.3-kbp, carries genes encoding resistance to sulfonamides,
streptomycin, spectinomycin, fusidicacid, chloramphenicol, and tetracycline.
•can be transferred between enteric bacteria of the genera Escherichia, Klebsiella, Proteus,
Salmonella, and Shigella.
•Aid in production of pili

36. Virulence plasmids
•Enable pathogenic organisms to colonizehosts and establish infections (attach to
and colonize, PLUS production of toxins, enzymes, and other molecules that cause
damage).
•EPEC colonize the small intestine and to produce a toxin that causes diarrhea
•Colonization factor antigen, encoded by a plasmid.
•2 toxins in EPEC are encoded by plasmids: the hemolysin(lyses RBCs), and
enterotoxin (Secretion of water and salts into the bowel)
•Bacteria containing these plasmids spread among individuals and cause infection
by replicating in the new host

37. pYVplasmid of Y enterocolitica, the genes encoded and the functions of their
protein product

38. Degradativeplasmids
•Aid the host bacterium in digestion of compounds like xylene,
salicylic acid
•They contain genes that code for enzymes that breakdown specific
compounds.

39. Col plasmids
•Many bacteria produce proteins that inhibit or kill closely related species or even
different strains of the same species.
•Contain genes for production of bacteriocins. Named after the species of organism
that produces them. E. coli produces colicins; Yersinia pestisproduces pesticins
etc
•These proteins defend host bacterium through killing other bacteria.
•E.colicontains ColE1 plasmid.

40. Col plasmids
•It contains the gene colicinE1, which produces bacteriocin. It
also codes for immunity against bacteriocinwith the immgene

41. Applications
•Vectors for cloning in biotechnology
•Production of viral particles intended for viral gene and oncolytictherapy
•Transfer of AMR genes.
•Phenotypic changes in genetic engineering.
•Production of genetically modified organism (GMO) in agricultre.

42. Gene Structure

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48. Nucleic Acid Function
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49. MUTATIONS

50. Basic definitions.
Mutation. It is the hereditary change of the nucleotidesequence of the
genome of an organism, virus, extrachromosomal DNA or other genetic
elements
Mutagen. a substance that causes mutation
Mutant. This is strain of any cell or virus carrying a change in nucleotide
sequence. It Is a product of mutation.
Recombination. Is the physical exchange of DNA between genetic
elements.

51. Mutations overview
Mutations can lead to changes—some good, some bad.
It can also be brought about by recombination.
Mutation and recombination fuel the evolutionary process.
May be detected Phenotypically or Genotypically.
Mutations may involve changes in only one or a few base
pairs or even the insertion or deletion of entire genes.
Mutation may occur in the Introns or in the exons.

52. Causesof mutation
•Spontaneouscause.
•Errorpronereplication.
•ErrorsintroducedduetoDNArepair(DNAPolydeltaorEpslon-Euk/DNA
Poly-IandII-Pro)
•Inducedmutation(Chemicals,Radiations,biologicalagents)
•Deliberateintroductionsbyscientists.

53. Consequences of point mutations
•Silence mutation; Changein the base pair doesn’t change the
protein/phenotype produced. Mostly in the 3
rd
base of the codon.
•Misensemutation; Change of base pair changes the proteinproduced
mostly if change is at a critical location in the polypeptide chain.(or may
cause inactivity or have reduced activity)
•Nonsense mutation;Change from sense to nonsense codon. Causes stop of
translation process. Egfrom UAA to UAU leads to stop instead of Tyr.