The document provides an overview of key concepts in genomics and molecular biology. It defines important terms like genome, DNA, RNA, proteins, genes, alleles, exons, introns and more. It describes the central dogma of DNA to RNA to protein. It also explains gene structure in prokaryotes versus eukaryotes, transcription, translation, splicing, polyploidy and gene regulation elements like promoters.

1. Introductory terminologies and
basic concepts in analysis of genes
and genomes
Presented by:
Sarbesh D. Dangol
(Genomics Lecture)
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

2. Genome
• The genome is all the DNA in a chromosome of
the cell.
– Includes genes, intergenic sequences, repeats.
• Eukaryotes can have nuclear genome,
mitochondrial genome, plastid genome.
• If not specified, “genome” usually refers to the
nuclear genome.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

3. Genomics
• Genomics is the study of genomes, including
large chromosomal segments containing many
genes.
• Map and sequence an initial set of entire
genomes.
• Functional genomics aims to deduce
information about the function of DNA
sequences.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

4. Central dogma of molecular biology:
DNA  RNA  Protein
1. Genetic information is stored in DNA.
2. Segments of DNA that encode proteins or other
functional products are called genes.
3. Gene sequences are transcribed into messenger
RNA intermediates (mRNA).
4. mRNA intermediates are translated into proteins
that perform most life functions.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

5. DNA
• Deoxyribonucleic Acid
• 4 Bases
– Purines
• Adenine
• Guanine
– Pyrimidines
• Cytosine
• Thymine
• Sugar is Deoxyribose
Adenine
OH
P
H
CH2O
H
O
NH2
N
N
N
N
O
O
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

6. RNA
• Ribonucleic Acid
• 4 Nucleotides
– Purine
• Adenine
• Guanine
– Pyrimidines
• Cytocine
• Uracil*
• Sugar is Ribose
OHOH
P
H
CH2O
H
O
NH2
N
N
N
N
O
O
Adenine
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

7. Proteins
• Polymer made of monomers –
Amino Acids
• 20 Naturally occurring amino acids
• Grouped by Side Chain:
– Hydrophobic
– Hydrophilic
• Acidic
• Basic OH
O
C C
H
N
H
H
Side
Chain
Amino Acid
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

8. Genes
• Genes are the basic physical and functional
units of heredity.
• Each gene is located on a particular region of a
chromosome and has a specific ordered
sequence of nucleotides (the building blocks
of DNA).
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

9. The same gene can have many versions called
alleles.
• An allele is any alternative form of a gene.
• It occurs at a specific locus on a chromosome.
• Alleles are often represented by letters.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

10. – Each parent donates one
allele for every gene.
– Homozygous describes two
alleles that are the same at a
specific locus.
– Heterozygous describes two
alleles that are different at a
specific locus.
– Dominant allele.
– Recessive allele.
RR
Rr
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

11. Exons vs Introns
• Eukaryotic genes have introns and exons.
• Exons contain nucleotides that are translated into
amino acids of proteins.
• Exons are separated from one another by intervening
segments of junk DNA called introns.
• Introns do not code for protein.
• They are removed when eukaryotic mRNA is
processed.
• Intron-free mRNA is used as a template to make
proteins.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

12. Exons and Coding
What’s the difference between exons and coding sequence?
Portions of exons or even entire exons may contain sequence
that is not translated into amino acids.
These are the untranslated regions or UTRs.
UTRs are found upstream and downstream of the protein-coding
sequence.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

13. Splicing mechanism
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

14. Alternative splicing
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

15. Central dogma
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering
3/2/2016

16. General structure of a gene
In Prokaryotes
In Eukaryotes
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

17. Translation in prokaryotes and
eukaryotes
In Eukaryotes
In Prokaryotes
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

18. 3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

19. Euchromatin: Lightly packed.
Heterochromatin: Tightly packed.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

20. 3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

21. 3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

22. HATs and HMTs
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

23. Function of promoter
• RNA polymerase binding site
• Initiation of transcription
• control by regulatory sequences
=> control the expression of genes
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

24. Prokaryotic promoters
• - 35 box and – 10 box ( also called Pribnow box) are consensus
sequences.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

25. Prokaryotic promoters
• Possible to have variations in
the consensus sequences.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

26. Eukaryotic promoters
• There are two parts:
- The core promoter or basal promoter
- Upstream promoter element ( one or more)
• Core promoter is constituted by the TATA box and the transcriptional start site
(TSS)
• Initation complex bind to the core promoter.
• Upstream elements are responsible for the regulation of the transcription.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

27. Eukaryotic promoters
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

28. • Polyploidy = the addition of one or more complete sets of
chromosomes to the original set.
• Two copies of each autosome = diploid
• Four copies of each autosome = tetraploid
• Six copies of each autosome = hexaploid
Polyploidy
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

29. Polyploidy
• Polyploidy permits greater expression of
genetic diversity.
• Unreduced gametes.
• Triploids/ Pentaploids are generally infertile.
• Used to genetically deseed certain plant
cultivars (eg-Triploid watermelon, banana).
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

30. • Polyploidy refers to a numerical change in a
whole set of chromosomes.
• Polyploidy may occur due to abnormal cell
division, either during mitosis, or commonly
during metaphase I in meiosis.
• Use of Colchicine or oryzaline.
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

31. Bridging ploidy levels in
interspecific crosses
Purpose: For disease resistance, stress
resistance, improved traits.
(Wild)
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering

32. •Thank you. 
3/2/2016
Sarbesh D. Dangol, PhD Agricultural Genetic
Engineering