Download Online Counseling Resource YCMOU ELearning Drive…

Online Counseling Resource
YCMOU ELearning Drive…
School of Architecture, Science and Technology
Yashwantrao Chavan Maharashtra
Open University, Nashik – 422222, India
SEP-SBI074-CP2-01
Introduction
Programmes and Courses
SEP–SBI074-CP02-U02
School of Science and Technology, Online Counseling Resource…
Credits
 Academic Inputs by
Sonali Alkari
 Faculty YCMOU Nagpur Centre,
 Faculty LAD college P.G. D of Biotechnology
 Research officer Ankur Seeds Pvt Ltd
 [email protected]
 [email protected]
School of Science and Technology, Online Counseling Resource…
How to Use This Resource

Counselor at each study center should use this presentation to deliver
lecture of 40-60 minutes during Face-To-Face counseling.

Discussion about students difficulties or tutorial with assignments should
follow the lecture for about 40-60 minutes.

Handouts (with 6 slides on each A4 size page) of this presentation should
be provided to each student.

Each student should discuss on the discussion forum all the terms which
could not be understood. This will improve his writing skills and enhance
knowledge level about topics, which shall be immensely useful for end
exam.

Appear several times, for all the Self-Tests, available for this course.

Student can use handouts for last minutes preparation just before end
exam.
© 2007, YCMOU. All Rights Reserved.
4
School of Science and Technology, Online Counseling Resource…
Learning Objectives
 After studying this module, you should be
able to:
 Describe DNA in details
 Explain physical and chemical propreties of DNA
 Explain Major and minor grooves?
 Explain Base pairing
 Explain Sense and antisense Strand in DNA
© 2007, YCMOU. All Rights Reserved.
5
School of Science and Technology, Online Counseling Resource…
Introduction :DNA:1
 Deoxyribonucleic acid, or DNA, is a nucleic acid that
contains the genetic instructions used in the
development and functioning of all known living
organisms.
 The main role of DNA molecules is the long-term
storage of information and DNA is often compared to a
set of blueprints, since it contains the instructions
needed to construct other components of cells, such as
proteins and RNA molecules.
 The DNA segments that carry this genetic information
are called genes, but other DNA sequences have
structural purposes, or are involved in regulating the
use of this genetic information.
School of Science and Technology, Online Counseling Resource…
Introduction :DNA:2
 Chemically, DNA is a long polymer
of simple units called nucleotides,
with a backbone made of sugars
and phosphate groups joined by
ester bonds.
 Attached to each sugar is one of
four types of molecules called
bases.
 It is the sequence of these four
bases along the backbone that
encodes information.
 This information is read using the
genetic code, which specifies the
sequence of the amino acids
within proteins.
School of Science and Technology, Online Counseling Resource…
Introduction :DNA:3
 The code is read by copying stretches of DNA into
the related nucleic acid RNA, in a process called
transcription.
 Most of these RNA molecules are used to synthesize
proteins, but others are used directly in structures
such as ribosomes and spliceosomes.
 Within cells, DNA is organized into structures called
chromosomes and the set of chromosomes within a
cell make up a genome.
 These chromosomes are duplicated before cells
divide, in a process called DNA replication.
School of Science and Technology, Online Counseling Resource…
Physical and Chemical Properties:2
 The sugar in DNA is 2-deoxyribose, which is a
pentose (five carbon) sugar.
 One of the major differences between DNA and RNA
is the sugar, with 2-deoxyribose being replaced by
the alternative pentose sugar ribose in RNA.
School of Science and Technology, Online Counseling Resource…
Physical and Chemical Properties:3
 The backbone of the DNA
strand
is
made
from
alternating phosphate and
sugar residues.
 The sugars are joined
together by phosphate
groups
that
form
phosphodiester
bonds
between the third and fifth
carbon atoms of adjacent
sugar rings.
School of Science and Technology, Online Counseling Resource…
Physical and Chemical Properties:4
 The DNA double helix is
stabilized by hydrogen
bonds between the bases
attached
to
the
two
strands.
 The four bases found in
DNA
are
adenine
(abbreviated A), cytosine
(C), guanine (G) and
thymine (T).
Pyrimidine Bases:Cytosine and
thymine
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Physical and Chemical Properties:5
 These four bases are
shown in figure and are
attached
to
the
sugar/phosphate to form
the complete nucleotide,
as shown for adenosine
monophosphate.
 Purines are the larger of
the two types of bases
found in DNA
Purine Bases:Adenine and
guanine are purines.
School of Science and Technology, Online Counseling Resource…
Physical and Chemical Properties:6
School of Science and Technology, Online Counseling Resource…
Physical and Chemical Properties:7
 These asymmetric bonds mean a
strand of DNA has a direction.
 In a double helix the direction of
the nucleotides in one strand is
opposite to their direction in the
other strand.
 This arrangement of DNA strands
is called antiparallel.
 The asymmetric ends of DNA
strands are referred to as the 5′
(five prime) and 3′ (three prime)
ends.
School of Science and Technology, Online Counseling Resource…
Major and Minor Grooves:2
 The narrowness of the minor groove means
that the edges of the bases are more
accessible in the major groove.
 As a result, proteins like transcription
factors that can bind to specific sequences
in double-stranded DNA usually make
contacts to the sides of the bases exposed
in the major groove.
School of Science and Technology, Online Counseling Resource…
Base Pairing:1
 Each type of base on
one strand forms a
bond with just one type
of base on the other
strand.
 This
is
called
complementary
base
pairing.
 Here,
purines
form
hydrogen
bonds
to
pyrimidines,
with
A
bonding only to T, and
C bonding only to G.
School of Science and Technology, Online Counseling Resource…
Base Pairing:2
 This arrangement of two
nucleotides binding together
across the double helix is
called a base pair.
 In a double helix, the two strands
are also held together via forces
generated by the hydrophobic
effect and pi stacking, which are
not influenced by the sequence
of the DNA.
School of Science and Technology, Online Counseling Resource…
Sense and Antisense
 A DNA sequence is called "sense" if its
sequence is the same as that of a
messenger RNA copy that is translated into
protein.
 The sequence on the opposite strand is
complementary to the sense sequence and
is therefore called the "antisense" sequence.
 Both sense and antisense sequences can
exist on different parts of the same strand
of DNA (i.e. both strands contain both sense
and antisense sequences).
School of Science and Technology, Online Counseling Resource…
DNA Bending - 1
 DNA bending has been found to affect transcription,
which is the first step in gene expression.
 Several studies have indicated the presence of
bends in DNA upon binding of transcriptional
proteins to DNA, such as the TATA box binding
protein.
 Studies have also shown that DNA bends can be
created without proteins or created with proteins
non-native to the system of interest.
 There have been other studies done where it was
shown that bends induced in DNA that were in the
opposite direction of the naturally occurring bend
inhibited transcription.
School of Science and Technology, Online Counseling Resource…
DNA Bending - 2
 This role of DNA bending in
transcription
leads
to
the
hypothesis that small, man-made
molecules could induce a bend in
DNA,
thus
regulating
gene
expression, and this regulation
could be either activating or
repressing, depending on the
phase (direction) of the bend.
 The
naturally
occurring
polyamides
distamycin
and
netropsin
bind
sequencespecifically to DNA.
School of Science and Technology, Online Counseling Resource…
DNA Bending - 3
 DNA bending is also important for the
regulation of gene expression and protein-DNA
binding.
 It is of fundamental importance therefore to
understand the nature of the forces that govern
the bending of charged DNA molecules into
non-linear
structures
and
quantify
the
magnitudes of their associated energetic
factors.
 Bending is important in DNA packaging and in
regulating diverse cellular processes.
School of Science and Technology, Online Counseling Resource…
DNA Bending - 4
 DNA bending by proteins appears to be the rule rather
than the exception with the topological distortions
ranging from tens of degrees to nearly 720° in the
nucleosome core.
 The Escherichia coli integration host factor (IHF),
discovered as a host protein required for lysogeny by
bacteriophage, plays both of these roles .
 IHF is an excellent model system for analyzing the
mechanism by which proteins bend DNA by virtue of
its cellular functions, sequence specificity, tight
binding, and robust protein-induced DNA bending
School of Science and Technology, Online Counseling Resource…
Integration Host Factor (IHF)
 A depiction of the IHF–DNA
crystal structure showing the
protein subunits in pink (ß) and
white () and the intercalating
prolines in yellow.
 Two segments of DNA from
symmetry-related
complexes
within the crystal are included
at the bottom to accommodate
the full IHF footprint.
 The attachment positions for the
donor and acceptor fluorophores
are indicated by arrows.
School of Science and Technology, Online Counseling Resource…
What You Learn…
 You have learnt :
 DNA, is a nucleic acid that contains the genetic
instructions
 Chemically, DNA is a long polymer of simple
units called nucleotides.
 The DNA double helix is stabilized by hydrogen
bonds.
 The four bases found in DNA are A, C. G,and T.
 There are two grooves twisting around, i.e the
major groove, the other, the minor groove.
 Both sense and antisense sequences can exist
on different parts of the same strand of DNA
School of Science and Technology, Online Counseling Resource…
Critical Thinking Questions
1. Describe in detail what is DNA?
2. Describe in details the physical and
chemical properties of DNA .
3. Describe major groove and minor groove.
4. What is sense and antisense sequences?
© 2007, YCMOU. All Rights Reserved.
25
School of Science and Technology, Online Counseling Resource…
Hints For Critical Thinking Question
1. DNA is structure
role.
composition organization and
2. DNA is a long polymer, sugar backbone, phosphate
diester bonds and base pairing.
3. gaps between each set of phosphate backbones
reposible for groove formation.
4. “sense"
sequence is the same as that of a
messenger RNA copywhere as sequence on the
opposite strand is “antisense”
© 2007, YCMOU. All Rights Reserved.
26
School of Science and Technology, Online Counseling Resource…
Study Tips:1
 Book1
 Title: Molecular Cell Biology
 Author:
Harvey
Lodish,
David
Baltimore
Publisher:Publishers:
W.
H.
Freeman
and
Company
 Book2
 Title: Principles of Biochemistry
 Author: AlbertL Lehninger
 Publisher:CBS Publishers & Distributors
School of Science and Technology, Online Counseling Resource…
Study Tips:2
 Book3
 Title: Biochemistry
 Author: Lubert stryer
 Publishers: Freeman International
 Book4
 Title: Biochemistry
 Author: Keshav Trehan
 Publishers: Wiley Eastern
School of Science and Technology, Online Counseling Resource…
Study Tips
www.en.wikipedia.org
Microsoft Encarta Encyclopedia
http://en.wikipedia.org/wiki/
Wikipedia the free encyclopedia
School of Science and Technology, Online Counseling Resource…
End of the Presentation
Thank You !