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CORE CONCEPTS OF
MOLECULAR
BIOLOGY
AYESHA MAJEED
BSF2000909
BS BOTANY 8th SEMESTER
Molecular Biology:
A branch of biology which study the molecular nature of the gene and its biochemical reactions
such as Transcription and Translation.
Molecular Genetics:
It is the study not only heredity but also molecular nature of genes and gene expression.
Biotechnology:
Managements of a biological system for the benefits of humanity or Industrial use of biological
process for example yeast fermentation for alcohol production.
Cytogenetic:
Study of normal and abnormal chromosome sets and their genetic properties. It has following
steps, taking a cell+ staining + chemical analysis of chromosomes.
Cytochemistry:
Analysis of chemical composition of cell component by staining properties.
Recombinant DNA technology:
A technology which involve construction, study and use of recombinant
DNA molecule.
Genetic Engineering:
❖ A technology which produce DNA molecules containing new genes or
new combination
of genes.
❖ Useful genetic information are transferred from donor to recipient
through vectors (e.g. Plasmids) technology involving man made changes in
the genetic constituents of cells.
Double helix of DNA:
Base paired structure comprising two polynucleotides strands.
Upstream:Towards the 5'end of a polynucleotides. Prime word is used for the C of sugar only, for all other
compounds e.g. nitrogenous bases, prime word not used for its C.
Downstream:
Towards the 3'end of a polynucleotide.
DNA hybridization:
involves hybridizing the DNA from two different species based on complementary base
pairing. A single strand of DNA from each species is combined and allowed to anneal
(recombine).
B-form DNA:
structural form of DNA, in which two
polynucleotides strands are twisted into
a right handed
helix (Watson & crick presentation). It is
metabolically active, bases are attached
perpendicular
(90o) with the main strand having 10
pb/turn.
A-form DNA:
A-DNA is thought to be one of three biologically active double helical
structures along with B-DNA and Z-DNA. It is a right-handed double helix
fairly similar to the more common B-DNA form, but with a shorter, more
compact helical structure whose base pairs are not perpendicular to the helix-
axis as in B-DNA. It was discovered by Rosalind Franklin, who also named
the A and B forms. She showed that DNA is driven into the A form when
under dehydrating conditions. Such conditions are commonly used to form
crystals, and many DNA crystal structures are in the A form DNA.
Z-form DNA:
structural form of DNA, in which two polynucleotides strands
are twisted into a left handed helix. It is metabolically inactive,
bases are attached at slight angle with the main strand having
12 pb/turn.
Chromatin:
Deeply stained material
present in the nuclei of
cells and corresponding
to the chromosomes or
Combination of DNA &
histone proteins.
During cell division
chromatin condense to
chromosome.
Euchromatin:
Regions of eukaryotic
chromatin, which
appeared less deeply
with the DNA specific
dye.
 It is metabolically
active and present in
the centre of the
nucleus.
Heterochromatin:
Regions of the
chromatin, which
appear relatively
more condensed and
stained deeply with
DNA specific dye.
 Metabolically
inactive, found at the
periphery of the
nucleus.
Denaturation :Breakdown of non-covalent interaction between nucleic acid and proteins by using physical and chemical
methods.
Renaturation:
Return of a denatured molecule back into its original state.
Hyperchromicity:
When DNA is a denatured, its absorbance increased at 260 nanometre and which is related is relate to adenine in DNA.
Adenine
(C5H5N5):
• 135.14g/mole is its Molecular mass. Adenine (135.14 g/mol) was detected
in mixtures of HCN (3.73% H, 44.44% C and 51.84% N), ammonia, and
water under conditions that stimulate early Earth. This observation suggests
a possible origin for one of the bases found in DNA.
Guanine
(C5H5N5O):
• 151.27g/mole is its Molecular mass.
Molecular mass of cytosine is 111.1g/mol.
cytosine
Leading strand:
The newly formed strand of the double
helix, which is copied in a continuous
manner during DNA replication, it
moves toward the replicating fork and
its complementary strand runs from 3'-
5' prime end.
Lagging strand:
The newly formed strand of the double
helix, which is copied in a discontinuous
manner having okazaki fragments, it moves
away from the replicating fork and its
complementary strand runs from 5'-3'
prime end.
The polynucleotide of
the double helix
carrying the biological
information of a gene
transcribed by the RNA
polymerase to form
mRNA. Its base
sequence is identical to
base sequence of the
RNA transcript.
The polynucleotide of
the double helix not
carrying the biological
information of the gene
but complimentary to
the coding strand. So
Non-coding or antisense
strand serve as template
to transcribe new
mRNA.
Coding
strand
or
Sense
strand
(5'-3'
prime
end):
Noncoding
strand
or
Antisense
strand
(3'-5'
prime
end):
Trailer segments:
• The untranslated region that lies downstream from the termination code
on mRNA molecule.
Leader segments:
• The untranslated segments that lies upstream of the initial codon on an
mRNA molecule.
Tandem
Repeat:
• A type of Direct repeats, in which
group similar bases are repeated
again and again and present
adjacent to each other with no
intervening DNA.
Inverted
Repeat:
• A single stranded DNA molecule,
having a sequence of nucleotides
which is followed by its reverse
complement, it may be adjacent to
one another or distance apart e.g.5'-
TTACGnnnnnnnnnnCGTAA-3'.
PALINDROME:
A DNA or RNA sequence that read same in
both directions or in nucleic acid, a sequence
in which the base pair read the same on
complimentary strand with respect to template,
responsible for restriction endonuclease
recognition & cutting in transcription
termination. 5’ GGATCC 3’ / 3'-CCTAGG-5'
Transposones:
Retrotransposons:
Spacer DNA:
A region of non-coding DNA
present between genes. Intergenic
spacer (IGS) or Non-transcribed
spacer (NTS) is termed if present
between the tandem repeats of
rRNA genes.
Naked DNA: A DNA
which is not associated
with proteins for
packages, as in bacteria.
Bacterial chromosome is
ds circular DNA.
Linker DNA:
A DNA which
links nucleosome
together.
Promiscuous
DNA:
• A DNA sequence
derived from the
chloroplast genome
but present in
mitochondrial DNA
of a photosynthetic
organisms. The term
'promiscuous DNA'
was coined by Ellis
(1982) to denote
DNA mobility
among the genetic
compartments of
eukaryotic cells.
Repetitive
DNA:
• DNA sequence
repeated a number of
time in a DNA
molecule. They do
not encode
polypeptide.
Satellite
DNA:
• AT-rich, tandemly
repeats, non-coding
DNA, having SSR of
150-400 repeats
• found in Telomere
DNA and
Centromere DNA.
Selfish/Junk
DNA
or
/Parasitic
DNA:
• A DNA having
multiple copies
with no function
present
• between genes
e.g. Transposons
or A DNA
segment (other
organism DNA)
that increase its
• transmission at
the expense of
host DNA.
Probe
DNA:
• Radioactively
labelled DNA
molecules used
to detect the
complementary
nucleic acid
sequence of
• molecules by
molecular
hybridization.
Intermediate
repeated
DNA:
• Genes present in
100-250 copies.
Gene:
Small portion of hereditary material responsible for the formation of
a character.
Constitutive genes or Housekeeping genes:
These genes are transcribed at the same rate
Regardless of metabolic rate of cell because their
product are required by the cells all the time. product
are required by the cells all the time.
Repressible genes:
Found in synthetic pathway. They are on by default but can be turned off
by a small molecule .
Repressible genes are those in which the presence of a substance (a co-
repressor) in the
environment turns off the expression of those genes (structural genes)
involved in the metabolism
of that substance.
Inducible genes:
Found in Degenerative
pathway. Transcribed when
the involved substrate is
available.
Regulatory genes: Code for
proteins that turn other
genes on or off/the control
the functional
genes.
Structural genes: Genes
that encode all proteins in
genome except regulatory
genes, e.g. operon in
prokaryotes, Lac genes.
Discontinuous gene:
A gene in which biological information is
divided between two or more exons
separated by Introns.
Early gene:
Bacteriophage genes expressed at
early stage, during the bacterial cell
infection, it's a product
involved in the phage genome
replication.
Late Gene:
Late Gene:
Bacteriophage genes expressed during
the later stage of the infection cycle.
Late genes code for
the proteins which formed two new
phage particles.
Extrachromosomal genes:
Any Gene not carried by
chromosome e.g. genes
carried by mitochondria,
chloroplast and
plasmids.
Homologous Gene:
Two gene coding for same
gene product from different
organism with different
sequence.
Housekeeping Gene:
The gene whom products are
required by the cell throughout
its life.
Mosaic gene:
A discontinuous gene.
Split Genes:
A Discontinuous Gene.
Multigene family:
A group of genes related
either in function or
nucleotide sequence.
Oncogene:
A mutated gene that has the
potential to cause cancer. Before an
oncogene becomes mutated, it is
called a proto-oncogene and it plays
a role in regulating normal cell
division.
Pseudogene:
A gene similar to functional gene but its
biological information become
scrambled, so Pseudo genes is not
functional.
Tra gene (Transfer gene):
One of a group of a gene carried by
plasmid, coding for proteins, involved
in DNA transfer during conjugation.
OVERLAPPING GENE:
Two genes whom coding regions overlap either completely or partially.
Overlapping genes, also called “dual-coding genes”, are regions of
DNA or RNA that are translated in two different reading frames to yield
two different proteins. Overlapping genes are relatively common in
DNA and RNA viruses. While several examples exist in bacterial and
eukaryotic genomes, overlapping genes appear to be relatively rare in
non-viral organisms and few reports have described overlapping
genes in mammalian genomes. Approximately a quarter of all human
protein-coding genes were overlapping genes. We analysed 19,200
well-annotated protein-coding genes and determined that 4,951
protein-coding genes overlapped with their adjacent genes.
Polygene:
System of genes, in which each gene
individually affects the phenotype in a
minor way e.g.
height, weight, skin, hair and eye
colour.
Pleiotropy:
A condition that, several characteristic
are affected by single gene.
Wild type:
➢ A specific gene predominant in a
controlled population.
➢ A gene or phenotype of an organism
predetermined in the control [stranded
or wild]
population.
Transcription:
RNA synthesis from DNA
template or synthesis of RNA
copy of a gene.
Translation:
Genetic
information in
mRNA directs the
order of assembly
of the specific
amino acid, during
protein synthesis.
Promoter:
A DNA region (100-1000
bases) at which
transcription of gene starts
(sigma factor & RNA
polymerase attached). It is
near the operator.
Operator:
A specific region of the DNA where
synthesis of mRNA is stopped.
Or
A nucleotide sequence element to which
a repression protein attach in order to
stop the gene transcription or operon.
Hogness Box:
A nucleotide sequence which make the
part of the eukaryotic promoter.
TATA Box: Thymine/Adenine rich
sequence. In Bacteria it is called
Pribnow box. It is non-coding DNA
sequence, present 25-30 bp upstream of
the site where transcription starts, found
in core promotor region of a gene in
Archae/Eukaryotes. It define the
direction of transcription and indicate
DNA strand to be read.
Homeobox:
Conserved sequence element involved in
regulating the embryonic development of
eukaryotic organisms.
Operon:
A group of adjacent genes under the
control of same promotor and operator or
a group of linked genes responsible for
regulating other genes involved in protein
synthesis or a cluster of gene whose
expression is controlled by a single
operator.
Genetic code:
The rule that, one nucleotide
triplet encode for one amino
acid during translation.
Codon:
A triplet of nucleotide in
mRNA that code for a single
amino acid and initiation or
termination of
Polypeptide chain.
Anticodon:
A triplet of nucleotide in tRNA
complementary to a codon
triplet in mRNA.
Initiation codon (Gene
starts):
A codon which indicate the
point at which translation of
mRNA should begin usually 5-
AUG-3
Initiation factor:
A protein which play an
ancillary role in the initial
stage of translation.
Termination codon (Gene ends):
One of the three codons which determines
position where translation of mRNA should
stop.
5'-UAA-3', 5'-UGA-3', 5'-UAG-3'
Reading frame:
In molecular biology, a reading frame is a
way of dividing the sequence of
nucleotides in a nucleic acid (DNA or
RNA) molecule into a set of consecutive,
non-overlapping triplets. Where these
triplets equate to amino acids or stop
signals during translation, they are called
codons.
Open reading frame:
A DNA sequence which look like a gene
but no function is assigned to it OR a series
of codons with an initiation codon at the 5'
end, synonymous with gene.
Exon:
Coding region of a discontinuous gene
Intron:
Non-coding region of a discontinuous gene.
Introns are absent in Prokaryotes due to
their small sized genome.
Aminoacylated site (A-site):
It is the first site on rRNA to which aa-
tRNA attached during translation.
Peptidyle site (P-Site):
A second site on the rRNA, which hold the
tRNA linked to growing polypeptide chain
during the translation.
Exit site (E-site): It hold the uncharged
tRNA, after giving its amino acid to
growing polypeptide chain of the protein in
Translation.
Catabolic Activator Protein site (Cap-
site):
A site on DNA template, where
Transcription begins by attaching catabolic
activator proteins.
Replisomes: A complex group of proteins
which help to perform the replication of the
parental strand to the complementary
daughter strands. The replisome is
composed of two replicative
Polymerase complexes, one of which
synthesizes the Leading strand, while the
other synthesizes the Lagging strand.
Primosome:
A protein complex responsible for creating
RNA primers on single stranded DNA
during DNA
RNA splicing: The process of removing
exons from the pre-mRNA catalysed by
Ribozyme enzymes. Spliceosome (Large
RNA-protein complex) catalyse the
removal of intron from pre-mRNA.
Monocistronic mRNA. A mRNA that encode a
single specific gene/protein.
Polycistronic mRNA: A mRNA that encode
many genes.
Polysome:
A cluster of ribosome, translating a single
mRNA molecule, when is product is required in
large quantity.
Transcriptomes: Some total of the all the
mRNA, expressed by all the genes of an
organism.
Cistron: is a sequence of
DNA/RNA that encode a
specific polypeptide in
protein synthesis.
ENZYMES:
• Restriction enzymes, are present in prokaryotes.
Their function is mainly protection against
foreign genetic material especially against
bacteriophage DNA. There are 2 types of
restriction enzymes, exonucleases and
endonucleases. Endonucleases again have their
types; one makes a blunt end that cuts within the
gene, and the other makes sticky ends.
Restriction
Enzymes:
• This enzyme break the
phosphodiester Bond within a
nucleic acid molecule.
Endonuclease:
• This enzyme removes
nucleotide from the end of a
nucleic acid molecule.
Exonuclease:
Sticky end:
An end of the double strand DNA molecule where
there is a single strand extension.
Blunt end:
An end where both strands terminate at the same
nucleotide position within no single strand extension.
Helicase:
An enzyme that break hydrogen bonds during DNA
replication.
Primase:
An enzyme that synthesizes short RNA sequences
called primers. These primers serve as a starting point
for DNA synthesis. Since primase produces RNA
molecules, the enzyme is a type of RNA polymerase.
Protease:
An enzyme that degrade protein
RNA polymerase:
An enzyme which synthesis RNA copy of a DNA
template.
Reverse transcription:
An enzyme which synthesis a DNA copy of a RNA
template.
Topoisomerase:
It adds and subtract turn in DNA helix. .
Ligase:
Enzyme catalysing the formation of bond between two
substrate molecules coupled with hydrolysis of
pyrophosphate Bond in ATP. The pyrophosphate bond,
symbolized by a squiggle (~), is hydrolysed when ATP is
converted to adenosine diphosphate (ADP).
Plant Omics:
The branches of science known informally as Omics are
various disciplines in Biology whose names end in the
suffix-omics, such as Genomics, Proteomics,
Metabolomics, Metagenomics, Phenomics and
Transcriptomics.
Genome:
The complete set of genes or genetic material present in a
cell or organism.
Haplotypes:
Group of genes inherited from a single parent i.e. Haploid.
Genomics: Genomics is an interdisciplinary field of Biology focusing on the structure, function,
evolution, mapping, and editing of genomes.
Proteomics: The study of the structure and function of proteins, including the way they work and
interact with each other inside cell.
Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within
cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a
biological system are known as the metabolome.
Metagenomics: Study of genetic material directly obtained from the environment.
Phenomics: The systematic study of traits that make up a phenotype.
Transcriptomics: The study of transcriptome-the complete set of RNA, also known as Expression
Profiling, as it is a study of the expression levels of mRNAs in a given cell population.
COMPARISON :
Primary & Secondary metabolites:
Primary metabolites responsible for
basic life functions (Growth,
development & reproduction), so
almost similar in all living cells e.g.
Carbohydrates, proteins, lipids, lactic
acids and vitamins etc.
Secondary metabolites; function
not known (Alkaloids, Phenolic,
Steroids, Terpenoids, Lactins, rubber,
gums, cellulose, drugs, pigments,
toxins & Essential oils) produced by
subsidiary pathways like Shikimic
acid pathway (produce folates-
vitamin B and aromatic amino acids,
not found in animals) and indirectly
engage in metabolism, while
performing vital ecological task in
the body.
DIFFERENCE :
Bioinformatics: A field of science that uses
computers, databases, math, and statistics to collect,
store, organize, and analyse large amounts of
biological, medical, and health information or the
science of collecting and analysing complex biological
data such as genetic codes.
Bioinformatics is an interdisciplinary field of science
that develops methods and software tools for
understanding biological data, especially when the
data sets are large and complex. Bioinformatics uses
biology, chemistry, physics, computer science,
computer programming, information engineering,
mathematics and statistics to analyse and interpret
biological data. The subsequent process of analysing
and interpreting data is referred to as Computational
Biology.
Computational Biology: The use of data analysis, mathematical modelling and computational
simulations to understand biological systems and relationships.
Computational simulation: The process of mathematical modelling, performed on a computer, which
is designed to predict the behaviour of, or the outcome of, a real-world or physical system.
Phylogenetic analysis:
A branching diagram showing the evolutionary relationship based on similarities and differences
among various biological species.
Cladogram: A branching pattern showing the cladistics (Clad-group) pattern between a number of
species, however it don’t show evolutionary tree like descend derived from ancestors.
Genetic marker:
An allele whose phenotype is easily recognised and used to follow the inheritance of gene.
Molecular marker (Genetic marker): A fragment of DNA, which has a certain position in a genome.
Direct marker/Indirect marker: Direct marker use coding DNA, which encode protein like different
genes. Indirect marker uses non-coding DNA as a marker like microsatellite, minisatellite etc.
Radioactive marker:
A radioactive atom which become incorporated into a chemical compound and its radioactive emission
can be used to detect the compound during biochemical reaction.
Clone:
Genetically identical individuals produced by vegetative propagation or Population of identical cells
containing similar recombination DNA molecule.
Gene cloning:
A fragments of DNA [containing gene] inserting into cloning vector for propagating recombinant DNA
molecule in a host organisms.
DNA library: A collection of DNA fragments that have been cloned into vectors so that researchers can
identify and isolate the DNA fragments that interest them for further study.
Gene library:
A clone collection carrying a large number of gene from a particular organisms possibly all gene.
Gene pool:
Complete set of unique alleles from a species/population.
Genomic library:
Collection of large number of bacteria/viruses carry a desired segment of foreign DNA, if carrying whole
genome, then called complete genomic library.
Germplasm:
Sum total of all the genes present in a crop, wild/cultivated or genetic material passed on through previous
generation or reproductive body tissue distinct from somatic tissue.
Vector: A DNA molecule (often plasmid or virus) that is used as a vehicle to carry a particular DNA segment
into a host cell as part of a cloning or recombinant DNA technique.
Arabidopsis thaliana: (Mouse ear cress-any plant of Mustard family or Brassicaceae/Model plant genome
sequencing in 2000; 10 chromosomes (n=5), Genome size-125 MB, Number of genes-25500.
Vector: A DNA molecule
(often plasmid or virus)
that is used as a vehicle to
carry a particular DNA
segment into a host cell as
part of a cloning or
recombinant DNA
technique.
Arabidopsis thaliana:
(Mouse ear cress-any plant
of Mustard family or
Brassicaceae/Model plant
genome sequencing in
2000; 10 chromosomes
(n=5), Genome size-125
MB, Number of genes-
25500.
Why Arabidopsis thaliana is called
Drosophila? Since it is used extensively in
genetic studies just like Drosophila
melanogaster.
Arabidopsis thaliana is also known as the
guinea pig of microbiology
As drosophila is the smallest fly as well,
Neurospora crassa is one of the smallest
fungus being extensively used in research
also called Drosophila of plant kingdom.
Site directed mutagenesis:
A mutagenesis in which predetermined alternation is introduced at a specific position in the DNA
molecule.
In-vitro mutagenesis:
It is a technique which produce specific mutation at the predetermined position in the DNA molecule in
the lab.
Somatic or Bud mutation:
A mutation in any cell not destined to become germ cell.
Leaky mutation:
A mutation which results by partial loss of a characteristic.
Lethal mutation:
A mutation which cause death.
Missense mutation:
An altered nucleotide sequence that converts a codon specifying one amino acid into a codon for a
second amino acid.
Nonsense mutation:
An alternation in a nucleotide sequence which converts at triplet coding for an amino acid into
termination codon.
Polar mutation:
A mutation of one gene effecting the expression of other, downstream genes.
Silent mutation:
A mutation which does not affect the expression or function of any gene or gene product.
Back mutation:
It reverse the effect of previous mutation and restores original nucleotide sequence.
Conditional lethal mutation :
A mutation which cause an
individual or Cell to survive under
certain conditions.
Frame shift mutation:
It results from the insertion or
deletion of a group of nucleotide and
it is not multiple of 3 and it changes
the frame by which altered gene is
translated.
Point mutation (change in single
base):
This mutation results from a single
nucleotide alternation in a DNA
molecule. It has two types
Transversion: A point
mutation that result in
purine being replaced by a
pyrimidine or vice versa.
a. Transition:
A point mutation that
result in purine replaced
by purine or pyramids
replaced by pyrimidine.
Insertion
mutation:
Alternation of
DNA molecule
sequence when
one or two
nucleotide is
inserted.
Deletion
mutation:
A mutation
due to
deletion of a
nucleotide
from a DNA
sequence.
Inversion mutation:
Alternation of
DNA molecule
sequence when
one segment is
removed
followed
insertion in the
opposite
orientation.
Spontaneous
mutation:
Mutation
that occurs
naturally in
the absence
of any
artificial
mutagenic
treatment.
Suppression
mutation:
A mutation in
a gene that
reverse the
effect of
mutation in
another
genes.
Temperature
sensitive
mutation:
A condition
lethal
mutation
occurs only
above a
certain
threshold
temperature
Translocation:
The movement of ribosome from one
codon to next on a messenger RNA
molecule during translation.
Transposition:
The movement of a genetic element
from one site to another in a DNA
molecule.
 Interchange of chromosomal
segments between two or more non
homologous chromosome.
Viroid:
An infectious agent causing plant disease and composed only RNA with no protein coat e.g. TMV
Provirus: A virus whose genetic material incorporated and to replicate with the host genome e.g.
integration of DNA copy of retrovirus genome into the host chromosomal DNA.
Temperate phage:
A Bacteriophage that follow a lysogenic mode of infection. While virulent phage follow lytic mode of
infection.
Polyhedrosis:
Any of several diseases of insect, caused by dsDNA viruses.
Positive/Plus sense RNA viruses:
Virus for which the infecting strand serves as an mRNA.
Negative sense RNA viruses:
Infective strand is complimented of the mRNA
Transfection:
Introduction of hybrid DNA of phage into the host.
Prophage: A bacteriophage genome integration into a bacterial DNA of chromosome/plasmid, which is
able to replicate.
Episome/integrative plasmid: Able to replicate by inserting themselves into bacterial chromosome.
Plasmid:
Circular piece of DNA found in bacteria.
PLASMID :
Relaxed plasmid:
A plasmid which can exist
as multiple copies within
the bacterial cell and its
replication is not linked to
the replication of host
genome.
Stringent plasmid:
A plasmid which
present in low copy
number in the bacterial
cell.
SECONDARY STRUCTURE
OF PROTEIN:
α-helix:
Secondary structure of proteins may
twisted in α-helix or β-pleated sheets
forms. The most common ways are
to coil to form alpha helix, found in
keratin present in hair, wool, etc.
Helical shape is maintained by H-
bond and X-rays diffraction analysis
shows that 3.6 amino acids are
present per turn.
β-sheets:
Another secondary protein structure
may be folded into sheets called
(beta pleated sheets). β pleated
sheets mostly occur in flat zigzag
chain present parallel to each other
and H bond formed between the HN
and CO group of the adjacent chains
making zigzag structure e.g. β-
Keratin present in silk formed by silk
worm.
HORMONE ACTIONS :
Auxins Cell elongation
Cytokinins  Cell division
and Cell differentiation.
Gibberellins Cell
elongation  also used to
induce flowering artificially.
Abscisic growth 
previously known as Growth
inhibitor but currently
believed to involve in
stomata movement.
Ethylene involved in
senescence of leaves, fruits
and different floral parts.
NAME OF JOURNALS:
Pakistan Journal of Botany.
Plant Cell, Tissue, Organ culture (Holland Journal).
Science (American Journal). Department of Agriculture, Government of
Punjab, Pakistan.
Nature (American
Journal).

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  • 1. CORE CONCEPTS OF MOLECULAR BIOLOGY AYESHA MAJEED BSF2000909 BS BOTANY 8th SEMESTER
  • 2. Molecular Biology: A branch of biology which study the molecular nature of the gene and its biochemical reactions such as Transcription and Translation. Molecular Genetics: It is the study not only heredity but also molecular nature of genes and gene expression. Biotechnology: Managements of a biological system for the benefits of humanity or Industrial use of biological process for example yeast fermentation for alcohol production. Cytogenetic: Study of normal and abnormal chromosome sets and their genetic properties. It has following steps, taking a cell+ staining + chemical analysis of chromosomes.
  • 3. Cytochemistry: Analysis of chemical composition of cell component by staining properties. Recombinant DNA technology: A technology which involve construction, study and use of recombinant DNA molecule. Genetic Engineering: ❖ A technology which produce DNA molecules containing new genes or new combination of genes. ❖ Useful genetic information are transferred from donor to recipient through vectors (e.g. Plasmids) technology involving man made changes in the genetic constituents of cells.
  • 4. Double helix of DNA: Base paired structure comprising two polynucleotides strands. Upstream:Towards the 5'end of a polynucleotides. Prime word is used for the C of sugar only, for all other compounds e.g. nitrogenous bases, prime word not used for its C. Downstream: Towards the 3'end of a polynucleotide. DNA hybridization: involves hybridizing the DNA from two different species based on complementary base pairing. A single strand of DNA from each species is combined and allowed to anneal (recombine).
  • 5. B-form DNA: structural form of DNA, in which two polynucleotides strands are twisted into a right handed helix (Watson & crick presentation). It is metabolically active, bases are attached perpendicular (90o) with the main strand having 10 pb/turn. A-form DNA: A-DNA is thought to be one of three biologically active double helical structures along with B-DNA and Z-DNA. It is a right-handed double helix fairly similar to the more common B-DNA form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix- axis as in B-DNA. It was discovered by Rosalind Franklin, who also named the A and B forms. She showed that DNA is driven into the A form when under dehydrating conditions. Such conditions are commonly used to form crystals, and many DNA crystal structures are in the A form DNA. Z-form DNA: structural form of DNA, in which two polynucleotides strands are twisted into a left handed helix. It is metabolically inactive, bases are attached at slight angle with the main strand having 12 pb/turn.
  • 6.
  • 7. Chromatin: Deeply stained material present in the nuclei of cells and corresponding to the chromosomes or Combination of DNA & histone proteins. During cell division chromatin condense to chromosome. Euchromatin: Regions of eukaryotic chromatin, which appeared less deeply with the DNA specific dye.  It is metabolically active and present in the centre of the nucleus. Heterochromatin: Regions of the chromatin, which appear relatively more condensed and stained deeply with DNA specific dye.  Metabolically inactive, found at the periphery of the nucleus.
  • 8.
  • 9. Denaturation :Breakdown of non-covalent interaction between nucleic acid and proteins by using physical and chemical methods. Renaturation: Return of a denatured molecule back into its original state. Hyperchromicity: When DNA is a denatured, its absorbance increased at 260 nanometre and which is related is relate to adenine in DNA.
  • 10. Adenine (C5H5N5): • 135.14g/mole is its Molecular mass. Adenine (135.14 g/mol) was detected in mixtures of HCN (3.73% H, 44.44% C and 51.84% N), ammonia, and water under conditions that stimulate early Earth. This observation suggests a possible origin for one of the bases found in DNA. Guanine (C5H5N5O): • 151.27g/mole is its Molecular mass. Molecular mass of cytosine is 111.1g/mol. cytosine
  • 11. Leading strand: The newly formed strand of the double helix, which is copied in a continuous manner during DNA replication, it moves toward the replicating fork and its complementary strand runs from 3'- 5' prime end. Lagging strand: The newly formed strand of the double helix, which is copied in a discontinuous manner having okazaki fragments, it moves away from the replicating fork and its complementary strand runs from 5'-3' prime end.
  • 12.
  • 13. The polynucleotide of the double helix carrying the biological information of a gene transcribed by the RNA polymerase to form mRNA. Its base sequence is identical to base sequence of the RNA transcript. The polynucleotide of the double helix not carrying the biological information of the gene but complimentary to the coding strand. So Non-coding or antisense strand serve as template to transcribe new mRNA. Coding strand or Sense strand (5'-3' prime end): Noncoding strand or Antisense strand (3'-5' prime end):
  • 14.
  • 15. Trailer segments: • The untranslated region that lies downstream from the termination code on mRNA molecule. Leader segments: • The untranslated segments that lies upstream of the initial codon on an mRNA molecule.
  • 16. Tandem Repeat: • A type of Direct repeats, in which group similar bases are repeated again and again and present adjacent to each other with no intervening DNA. Inverted Repeat: • A single stranded DNA molecule, having a sequence of nucleotides which is followed by its reverse complement, it may be adjacent to one another or distance apart e.g.5'- TTACGnnnnnnnnnnCGTAA-3'.
  • 17. PALINDROME: A DNA or RNA sequence that read same in both directions or in nucleic acid, a sequence in which the base pair read the same on complimentary strand with respect to template, responsible for restriction endonuclease recognition & cutting in transcription termination. 5’ GGATCC 3’ / 3'-CCTAGG-5'
  • 19.
  • 20. Spacer DNA: A region of non-coding DNA present between genes. Intergenic spacer (IGS) or Non-transcribed spacer (NTS) is termed if present between the tandem repeats of rRNA genes. Naked DNA: A DNA which is not associated with proteins for packages, as in bacteria. Bacterial chromosome is ds circular DNA. Linker DNA: A DNA which links nucleosome together.
  • 21. Promiscuous DNA: • A DNA sequence derived from the chloroplast genome but present in mitochondrial DNA of a photosynthetic organisms. The term 'promiscuous DNA' was coined by Ellis (1982) to denote DNA mobility among the genetic compartments of eukaryotic cells. Repetitive DNA: • DNA sequence repeated a number of time in a DNA molecule. They do not encode polypeptide. Satellite DNA: • AT-rich, tandemly repeats, non-coding DNA, having SSR of 150-400 repeats • found in Telomere DNA and Centromere DNA.
  • 22. Selfish/Junk DNA or /Parasitic DNA: • A DNA having multiple copies with no function present • between genes e.g. Transposons or A DNA segment (other organism DNA) that increase its • transmission at the expense of host DNA. Probe DNA: • Radioactively labelled DNA molecules used to detect the complementary nucleic acid sequence of • molecules by molecular hybridization. Intermediate repeated DNA: • Genes present in 100-250 copies.
  • 23. Gene: Small portion of hereditary material responsible for the formation of a character. Constitutive genes or Housekeeping genes: These genes are transcribed at the same rate Regardless of metabolic rate of cell because their product are required by the cells all the time. product are required by the cells all the time. Repressible genes: Found in synthetic pathway. They are on by default but can be turned off by a small molecule . Repressible genes are those in which the presence of a substance (a co- repressor) in the environment turns off the expression of those genes (structural genes) involved in the metabolism of that substance.
  • 24. Inducible genes: Found in Degenerative pathway. Transcribed when the involved substrate is available. Regulatory genes: Code for proteins that turn other genes on or off/the control the functional genes. Structural genes: Genes that encode all proteins in genome except regulatory genes, e.g. operon in prokaryotes, Lac genes.
  • 25. Discontinuous gene: A gene in which biological information is divided between two or more exons separated by Introns. Early gene: Bacteriophage genes expressed at early stage, during the bacterial cell infection, it's a product involved in the phage genome replication. Late Gene: Late Gene: Bacteriophage genes expressed during the later stage of the infection cycle. Late genes code for the proteins which formed two new phage particles.
  • 26. Extrachromosomal genes: Any Gene not carried by chromosome e.g. genes carried by mitochondria, chloroplast and plasmids. Homologous Gene: Two gene coding for same gene product from different organism with different sequence. Housekeeping Gene: The gene whom products are required by the cell throughout its life.
  • 27. Mosaic gene: A discontinuous gene. Split Genes: A Discontinuous Gene. Multigene family: A group of genes related either in function or nucleotide sequence.
  • 28. Oncogene: A mutated gene that has the potential to cause cancer. Before an oncogene becomes mutated, it is called a proto-oncogene and it plays a role in regulating normal cell division. Pseudogene: A gene similar to functional gene but its biological information become scrambled, so Pseudo genes is not functional. Tra gene (Transfer gene): One of a group of a gene carried by plasmid, coding for proteins, involved in DNA transfer during conjugation.
  • 29. OVERLAPPING GENE: Two genes whom coding regions overlap either completely or partially. Overlapping genes, also called “dual-coding genes”, are regions of DNA or RNA that are translated in two different reading frames to yield two different proteins. Overlapping genes are relatively common in DNA and RNA viruses. While several examples exist in bacterial and eukaryotic genomes, overlapping genes appear to be relatively rare in non-viral organisms and few reports have described overlapping genes in mammalian genomes. Approximately a quarter of all human protein-coding genes were overlapping genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes.
  • 30. Polygene: System of genes, in which each gene individually affects the phenotype in a minor way e.g. height, weight, skin, hair and eye colour. Pleiotropy: A condition that, several characteristic are affected by single gene. Wild type: ➢ A specific gene predominant in a controlled population. ➢ A gene or phenotype of an organism predetermined in the control [stranded or wild] population.
  • 31. Transcription: RNA synthesis from DNA template or synthesis of RNA copy of a gene. Translation: Genetic information in mRNA directs the order of assembly of the specific amino acid, during protein synthesis. Promoter: A DNA region (100-1000 bases) at which transcription of gene starts (sigma factor & RNA polymerase attached). It is near the operator.
  • 32.
  • 33. Operator: A specific region of the DNA where synthesis of mRNA is stopped. Or A nucleotide sequence element to which a repression protein attach in order to stop the gene transcription or operon. Hogness Box: A nucleotide sequence which make the part of the eukaryotic promoter. TATA Box: Thymine/Adenine rich sequence. In Bacteria it is called Pribnow box. It is non-coding DNA sequence, present 25-30 bp upstream of the site where transcription starts, found in core promotor region of a gene in Archae/Eukaryotes. It define the direction of transcription and indicate DNA strand to be read. Homeobox: Conserved sequence element involved in regulating the embryonic development of eukaryotic organisms. Operon: A group of adjacent genes under the control of same promotor and operator or a group of linked genes responsible for regulating other genes involved in protein synthesis or a cluster of gene whose expression is controlled by a single operator.
  • 34. Genetic code: The rule that, one nucleotide triplet encode for one amino acid during translation. Codon: A triplet of nucleotide in mRNA that code for a single amino acid and initiation or termination of Polypeptide chain. Anticodon: A triplet of nucleotide in tRNA complementary to a codon triplet in mRNA. Initiation codon (Gene starts): A codon which indicate the point at which translation of mRNA should begin usually 5- AUG-3 Initiation factor: A protein which play an ancillary role in the initial stage of translation.
  • 35. Termination codon (Gene ends): One of the three codons which determines position where translation of mRNA should stop. 5'-UAA-3', 5'-UGA-3', 5'-UAG-3' Reading frame: In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons. Open reading frame: A DNA sequence which look like a gene but no function is assigned to it OR a series of codons with an initiation codon at the 5' end, synonymous with gene. Exon: Coding region of a discontinuous gene Intron: Non-coding region of a discontinuous gene. Introns are absent in Prokaryotes due to their small sized genome. Aminoacylated site (A-site): It is the first site on rRNA to which aa- tRNA attached during translation. Peptidyle site (P-Site): A second site on the rRNA, which hold the tRNA linked to growing polypeptide chain during the translation.
  • 36. Exit site (E-site): It hold the uncharged tRNA, after giving its amino acid to growing polypeptide chain of the protein in Translation. Catabolic Activator Protein site (Cap- site): A site on DNA template, where Transcription begins by attaching catabolic activator proteins. Replisomes: A complex group of proteins which help to perform the replication of the parental strand to the complementary daughter strands. The replisome is composed of two replicative Polymerase complexes, one of which synthesizes the Leading strand, while the other synthesizes the Lagging strand. Primosome: A protein complex responsible for creating RNA primers on single stranded DNA during DNA RNA splicing: The process of removing exons from the pre-mRNA catalysed by Ribozyme enzymes. Spliceosome (Large RNA-protein complex) catalyse the removal of intron from pre-mRNA.
  • 37. Monocistronic mRNA. A mRNA that encode a single specific gene/protein. Polycistronic mRNA: A mRNA that encode many genes. Polysome: A cluster of ribosome, translating a single mRNA molecule, when is product is required in large quantity. Transcriptomes: Some total of the all the mRNA, expressed by all the genes of an organism. Cistron: is a sequence of DNA/RNA that encode a specific polypeptide in protein synthesis.
  • 38. ENZYMES: • Restriction enzymes, are present in prokaryotes. Their function is mainly protection against foreign genetic material especially against bacteriophage DNA. There are 2 types of restriction enzymes, exonucleases and endonucleases. Endonucleases again have their types; one makes a blunt end that cuts within the gene, and the other makes sticky ends. Restriction Enzymes: • This enzyme break the phosphodiester Bond within a nucleic acid molecule. Endonuclease: • This enzyme removes nucleotide from the end of a nucleic acid molecule. Exonuclease:
  • 39. Sticky end: An end of the double strand DNA molecule where there is a single strand extension. Blunt end: An end where both strands terminate at the same nucleotide position within no single strand extension. Helicase: An enzyme that break hydrogen bonds during DNA replication. Primase: An enzyme that synthesizes short RNA sequences called primers. These primers serve as a starting point for DNA synthesis. Since primase produces RNA molecules, the enzyme is a type of RNA polymerase. Protease: An enzyme that degrade protein RNA polymerase: An enzyme which synthesis RNA copy of a DNA template. Reverse transcription: An enzyme which synthesis a DNA copy of a RNA template. Topoisomerase: It adds and subtract turn in DNA helix. . Ligase: Enzyme catalysing the formation of bond between two substrate molecules coupled with hydrolysis of pyrophosphate Bond in ATP. The pyrophosphate bond, symbolized by a squiggle (~), is hydrolysed when ATP is converted to adenosine diphosphate (ADP). Plant Omics: The branches of science known informally as Omics are various disciplines in Biology whose names end in the suffix-omics, such as Genomics, Proteomics, Metabolomics, Metagenomics, Phenomics and Transcriptomics. Genome: The complete set of genes or genetic material present in a cell or organism. Haplotypes: Group of genes inherited from a single parent i.e. Haploid.
  • 40.
  • 41. Genomics: Genomics is an interdisciplinary field of Biology focusing on the structure, function, evolution, mapping, and editing of genomes. Proteomics: The study of the structure and function of proteins, including the way they work and interact with each other inside cell. Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a biological system are known as the metabolome. Metagenomics: Study of genetic material directly obtained from the environment. Phenomics: The systematic study of traits that make up a phenotype. Transcriptomics: The study of transcriptome-the complete set of RNA, also known as Expression Profiling, as it is a study of the expression levels of mRNAs in a given cell population.
  • 42. COMPARISON : Primary & Secondary metabolites: Primary metabolites responsible for basic life functions (Growth, development & reproduction), so almost similar in all living cells e.g. Carbohydrates, proteins, lipids, lactic acids and vitamins etc. Secondary metabolites; function not known (Alkaloids, Phenolic, Steroids, Terpenoids, Lactins, rubber, gums, cellulose, drugs, pigments, toxins & Essential oils) produced by subsidiary pathways like Shikimic acid pathway (produce folates- vitamin B and aromatic amino acids, not found in animals) and indirectly engage in metabolism, while performing vital ecological task in the body.
  • 44. Bioinformatics: A field of science that uses computers, databases, math, and statistics to collect, store, organize, and analyse large amounts of biological, medical, and health information or the science of collecting and analysing complex biological data such as genetic codes. Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyse and interpret biological data. The subsequent process of analysing and interpreting data is referred to as Computational Biology.
  • 45. Computational Biology: The use of data analysis, mathematical modelling and computational simulations to understand biological systems and relationships. Computational simulation: The process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. Phylogenetic analysis: A branching diagram showing the evolutionary relationship based on similarities and differences among various biological species. Cladogram: A branching pattern showing the cladistics (Clad-group) pattern between a number of species, however it don’t show evolutionary tree like descend derived from ancestors.
  • 46. Genetic marker: An allele whose phenotype is easily recognised and used to follow the inheritance of gene. Molecular marker (Genetic marker): A fragment of DNA, which has a certain position in a genome. Direct marker/Indirect marker: Direct marker use coding DNA, which encode protein like different genes. Indirect marker uses non-coding DNA as a marker like microsatellite, minisatellite etc. Radioactive marker: A radioactive atom which become incorporated into a chemical compound and its radioactive emission can be used to detect the compound during biochemical reaction.
  • 47. Clone: Genetically identical individuals produced by vegetative propagation or Population of identical cells containing similar recombination DNA molecule. Gene cloning: A fragments of DNA [containing gene] inserting into cloning vector for propagating recombinant DNA molecule in a host organisms. DNA library: A collection of DNA fragments that have been cloned into vectors so that researchers can identify and isolate the DNA fragments that interest them for further study. Gene library: A clone collection carrying a large number of gene from a particular organisms possibly all gene. Gene pool: Complete set of unique alleles from a species/population.
  • 48. Genomic library: Collection of large number of bacteria/viruses carry a desired segment of foreign DNA, if carrying whole genome, then called complete genomic library. Germplasm: Sum total of all the genes present in a crop, wild/cultivated or genetic material passed on through previous generation or reproductive body tissue distinct from somatic tissue. Vector: A DNA molecule (often plasmid or virus) that is used as a vehicle to carry a particular DNA segment into a host cell as part of a cloning or recombinant DNA technique. Arabidopsis thaliana: (Mouse ear cress-any plant of Mustard family or Brassicaceae/Model plant genome sequencing in 2000; 10 chromosomes (n=5), Genome size-125 MB, Number of genes-25500.
  • 49. Vector: A DNA molecule (often plasmid or virus) that is used as a vehicle to carry a particular DNA segment into a host cell as part of a cloning or recombinant DNA technique. Arabidopsis thaliana: (Mouse ear cress-any plant of Mustard family or Brassicaceae/Model plant genome sequencing in 2000; 10 chromosomes (n=5), Genome size-125 MB, Number of genes- 25500. Why Arabidopsis thaliana is called Drosophila? Since it is used extensively in genetic studies just like Drosophila melanogaster. Arabidopsis thaliana is also known as the guinea pig of microbiology As drosophila is the smallest fly as well, Neurospora crassa is one of the smallest fungus being extensively used in research also called Drosophila of plant kingdom.
  • 50. Site directed mutagenesis: A mutagenesis in which predetermined alternation is introduced at a specific position in the DNA molecule. In-vitro mutagenesis: It is a technique which produce specific mutation at the predetermined position in the DNA molecule in the lab. Somatic or Bud mutation: A mutation in any cell not destined to become germ cell. Leaky mutation: A mutation which results by partial loss of a characteristic. Lethal mutation: A mutation which cause death.
  • 51. Missense mutation: An altered nucleotide sequence that converts a codon specifying one amino acid into a codon for a second amino acid. Nonsense mutation: An alternation in a nucleotide sequence which converts at triplet coding for an amino acid into termination codon. Polar mutation: A mutation of one gene effecting the expression of other, downstream genes. Silent mutation: A mutation which does not affect the expression or function of any gene or gene product. Back mutation: It reverse the effect of previous mutation and restores original nucleotide sequence.
  • 52. Conditional lethal mutation : A mutation which cause an individual or Cell to survive under certain conditions. Frame shift mutation: It results from the insertion or deletion of a group of nucleotide and it is not multiple of 3 and it changes the frame by which altered gene is translated.
  • 53. Point mutation (change in single base): This mutation results from a single nucleotide alternation in a DNA molecule. It has two types Transversion: A point mutation that result in purine being replaced by a pyrimidine or vice versa. a. Transition: A point mutation that result in purine replaced by purine or pyramids replaced by pyrimidine.
  • 54. Insertion mutation: Alternation of DNA molecule sequence when one or two nucleotide is inserted. Deletion mutation: A mutation due to deletion of a nucleotide from a DNA sequence. Inversion mutation: Alternation of DNA molecule sequence when one segment is removed followed insertion in the opposite orientation. Spontaneous mutation: Mutation that occurs naturally in the absence of any artificial mutagenic treatment. Suppression mutation: A mutation in a gene that reverse the effect of mutation in another genes. Temperature sensitive mutation: A condition lethal mutation occurs only above a certain threshold temperature
  • 55. Translocation: The movement of ribosome from one codon to next on a messenger RNA molecule during translation. Transposition: The movement of a genetic element from one site to another in a DNA molecule.  Interchange of chromosomal segments between two or more non homologous chromosome.
  • 56. Viroid: An infectious agent causing plant disease and composed only RNA with no protein coat e.g. TMV Provirus: A virus whose genetic material incorporated and to replicate with the host genome e.g. integration of DNA copy of retrovirus genome into the host chromosomal DNA. Temperate phage: A Bacteriophage that follow a lysogenic mode of infection. While virulent phage follow lytic mode of infection. Polyhedrosis: Any of several diseases of insect, caused by dsDNA viruses. Positive/Plus sense RNA viruses: Virus for which the infecting strand serves as an mRNA.
  • 57. Negative sense RNA viruses: Infective strand is complimented of the mRNA Transfection: Introduction of hybrid DNA of phage into the host. Prophage: A bacteriophage genome integration into a bacterial DNA of chromosome/plasmid, which is able to replicate. Episome/integrative plasmid: Able to replicate by inserting themselves into bacterial chromosome. Plasmid: Circular piece of DNA found in bacteria.
  • 58. PLASMID : Relaxed plasmid: A plasmid which can exist as multiple copies within the bacterial cell and its replication is not linked to the replication of host genome. Stringent plasmid: A plasmid which present in low copy number in the bacterial cell.
  • 59. SECONDARY STRUCTURE OF PROTEIN: α-helix: Secondary structure of proteins may twisted in α-helix or β-pleated sheets forms. The most common ways are to coil to form alpha helix, found in keratin present in hair, wool, etc. Helical shape is maintained by H- bond and X-rays diffraction analysis shows that 3.6 amino acids are present per turn. β-sheets: Another secondary protein structure may be folded into sheets called (beta pleated sheets). β pleated sheets mostly occur in flat zigzag chain present parallel to each other and H bond formed between the HN and CO group of the adjacent chains making zigzag structure e.g. β- Keratin present in silk formed by silk worm.
  • 60. HORMONE ACTIONS : Auxins Cell elongation Cytokinins  Cell division and Cell differentiation. Gibberellins Cell elongation  also used to induce flowering artificially. Abscisic growth  previously known as Growth inhibitor but currently believed to involve in stomata movement. Ethylene involved in senescence of leaves, fruits and different floral parts.
  • 61.
  • 62. NAME OF JOURNALS: Pakistan Journal of Botany. Plant Cell, Tissue, Organ culture (Holland Journal). Science (American Journal). Department of Agriculture, Government of Punjab, Pakistan. Nature (American Journal).