introductory terminologies and basic concepts in analysis of genes and genomes

Introductory terminologies and basic concepts in analysis of genes

and genomes

Presented by:Sarbesh D. Dangol

(Genomics Lecture)

05/03/23 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering

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.


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.


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.


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


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


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

HSideChain

Amino Acid


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).


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.


– 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


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.


Exons and CodingWhat’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.


Splicing mechanism


Alternative splicing


Central dogma

Sarbesh D. Dangol, PhD Agricultural Genetic Engineering05/03/23

General structure of a gene

In Prokaryotes

In Eukaryotes


Translation in prokaryotes and eukaryotes

In Eukaryotes

In Prokaryotes05/03/23 Sarbesh D. Dangol, PhD Agricultural

Genetic Engineering

Euchromatin: Lightly packed. Heterochromatin: Tightly packed.


HATs and HMTs


Function of promoter

• RNA polymerase binding site

• Initiation of transcription

• control by regulatory sequences => control the expression of genes


Prokaryotic promoters

• - 35 box and – 10 box ( also called Pribnow box) are consensus sequences.


Prokaryotic promoters

• Possible to have variations in the consensus sequences.


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.


Eukaryotic promoters


• 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


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).


• 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.


Bridging ploidy levels in interspecific crosses

Purpose: For disease resistance, stress resistance, improved traits.

(Wild)


•Thank you.


introductory terminologies and basic concepts in analysis of genes and genomes

Science