Transcript Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India.

Online Counseling Resource
YCMOU ELearning Drive…
School of Architecture, Science and Technology
Yashwantrao Chavan Maharashtra
Open University, Nashik – 422222, India
SEP-SBI074-CP3-02
Introduction
Programmes and Courses
SEP–SBI074-CP3- U03
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]
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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.
© 2008, YCMOU. All Rights Reserved.
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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.
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School of Science and Technology, Online Counseling Resource…
Learning Objectives
 After studying this module, you should be able
to:
 Describe Protein anatomy.
 Discuss primary structure proteins.
 Describe secondary protein structure.
 Discuss motif, turns and loops.
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School of Science and Technology, Online Counseling Resource…
Protein Structure /Anatomy-1
 Proteins are amino acid chains, made up
from 20 different L-α-amino acids, also
referred to as residues, that fold into unique
three-dimensional protein structures.
 The shape into a which a protein naturally
folds is known as its native state, which is
determined by its sequence of amino acids.
Below about 40 residues the term peptide is
frequently used.
 A certain number of residues is necessary to
perform a particular biochemical function.
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Protein Structure /Anatomy-2
 Protein sizes range 40-50 residues to several
thousand residues in multi-functional or
structural proteins.
 The current estimate for the average protein
length is around 300 residues.
 Very large aggregates can be formed from
protein
subunits,
for
example
many
thousand actin molecules assemble into an
actin filament.
 Large protein complexes with RNA are found
in the ribosome particles, which are in fact
‘ribozymes'.
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Protein Structure /Anatomy-3
An α-amino acid
Bond angles for ψ and ω
The rigid peptide dihedral angle, ω (the bond between C1 and
N) is always close to 180 degrees. The dihedral angles φ (the
bond between N and Cα) and psi ψ (the bond between Cα and
C1) can have a certain range of possible values.
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Protein Structure /Anatomy-4
 Two amino acids can be
combined
in
a
condensation reaction.
 By repeating this reaction,
long chains of residues
(amino acids in a peptide
bond) can be generated.
 This reaction is catalysed
by the ribosome in a
process
known
as
translation.
 The peptide bond is planar
due to the delocalization of
the electrons from the
double bond.
Two amino acids
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Protein Structure /Anatomy-5
 The primary structure is held together by covalent
peptide bonds, which are made during the process of
translation.
 The secondary structures are held together by
hydrogen bond.
 The tertiary structure is held together primarily by
hydrophobic interactions but hydrogen bond, ionic
interactions, and disulfide bonds are usually involved
too.
 The two ends of the amino acid chain are referred to
as the carboxy terminus (C-terminus) and the amino
terminus (N-terminus) based on the nature of the
free group on each extremity.
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Protein Structure /Anatomy-6
 The polypeptide chain of a protein
seldom forms just a random coil.
 Protein structure is discussed in terms
of four levels of organization.




Primary structure
Secondary structure
Tertiary structure
Quaternary structure
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Secondary Structures-1
 Secondary structure is the spatial arrangement of
the polypeptide backbone, ignoring the conformation
of the side chains.
 Many of the interesting biological properties of
protein are due to tightly coiled polypeptide chain
producing helical shape.
 The functions of the proteins arises from their
conformation, which is represented
by the
secondary structure and certain other structure
because these represents the three-dimensional
arrangement of atoms.
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Secondary Structures-2
 Many of the physicochemical properties of the
proteins are due to fact that the polypeptide chain
is held in a coiled shape by forces other than those
in the primary structure.
 The two most common secondary structure
arrangement are the right-handed -helix and the
ß-sheet, which can connect into large tertiary
structure(or folds) by turns and loops of a variety
of types.
 The secondary structure elements satisfy a strong
hydrogen bond network within the geometric
constraints of the bond angle ,  and 
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The -Helix-1
 In 1950s, Linus Pauling and
Robert
Corey
stated
that,
polypeptide
segments
composed of certain amino
acids tend to assume a regular
spiral, or helical, conformation,
called the -helix .
 In -helix, the carbonyl oxygen
of
each
peptide
bond
is
hydrogen bonded to the amide
hydrogen of the amino acid four
residues
towards
the
Cterminus.
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The -Helix-2
 This uniform arrangement of
bonds confers a polarity on a
helix because all the hydrogenbond
donars
have
same
orientation .
 The peptide backbone twists
into a helix having 3.6 amino
acid per turn .
 Each “step” up this spiral
staircase of amino acids (axial
rise per residue) represents a
distance of about 0.15 nm along
the axis.
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The -Helix-3
 The inflexible, stable arrangement of amino
acid in the -helix holds the backbone as a
rod like cylinder from which the side chains
point outwards.
 A important consequence of this arrangement
is that the hydrophobic quality of the helix is
determined by the side chains.
 The polar groups of the peptide backbone are
already involved in hydrogen bonding in the
helix and thus are unable to affect the
hydrophobicity or hydrophilicity of the helix.
 Alpha helix may be considered the default
state for secondary structure.
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The -Helix-4
 Although the potential energy is not as low as for
beta sheet, H-bond formation is intra-strand, so
there is an entropic advantage over beta sheet,
where H-bonds must form from strand to strand,
with strand segments that may be quite distant in
the polypeptide sequence.
 The main criterion for alpha helix preference is that
the amino acid side chain should cover and protect
the backbone H-bonds in the core of the helix. Most
amino acids do this with some key exceptions:
Prolein, Glycine
alpha-helix preference
Ala,Leu,Met,Phe,Glu,Gln,His,Lys,Arg
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The -Helix Functions
 The -helix as a rod like element of protein
structure, performs purely structural function.
 Interaction between helice leads to formation of
core called as globin fold.( ex. Oxygen binding
proteins like hemoglobin and myoglobin.
 In some proteins, -helix functions as binding
sites, especially for other proteins and DNA.
 Fibrous proteins contains chains of the -helix
segements, which span long distance or form
tough, sturdy structures when twisted about
each other like a rope.
 Many -helix are amiphipathic are important
structural element in proteins that act as pores
or channels, in the cell membrane.
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ß-sheet-1
 The ß-sheet, consists of laterally
packed ß strands.
 Each ß strand is a short (5-8
residue),
fully
extended
polypeptide chain.
 The backbone atoms in adjacent
ß strands, either within the same
or different polypeptide chains,
can hydrogen bonds, forming ß
sheets.
 ß-sheet have a polarity defined
by the orientation of the peptide
bond.
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ß-sheet-2
 The planarity of the peptide
bond forces the sheet to be
pleated, hence this structure
is called ß pleated sheet.
 Adjacent ß strands can be
oriented
antiparallel
or
parallel with respect to each
other.
 But antiparallel array is the
most stable one.
 In either orientation, the side
chains projects from both
faces of sheet .
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ß-sheet Functions
 ß-sheet form the floor of a binding
pocket.
 In
many
structural
proteins,
multiple layers of pleated sheet
provide toughness.
 Silk fibers , consists almost
entirely of stacks of antiparallel ßsheet.
 The fibres are flexible because of
ß-sheet can slip over each other.
 However ß-sheet also resistant to
breakage because the peptide
backbone is aligned parallel with
the fibre axis.
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Turns and Loops-1
 Many proteins combination of -helix and ßsheet , which are connected by Loops.
 Turns Composed of three or four residues,
turns are compact, U-shaped secondary
structures stabilized by
Hydrogen bond
between their end residue.
 Turns are located on protein surface and form
sharp bend that redirects the polypeptide
backbone towards the interior.
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Turns and Loops-2
 Glycine and Proline are commonly present in
turns. The lack of a large side chain in the
case of glycine and the presence of built –in
bend in case of Proline allow the polypeptide
backbone to fold into a tight U-shaped
structure.
 Without turns, a protein would be large,
extended, and loosely packed.
 If a polypeptide contain a long bend, it is
called as Loop.
 Loops have irregular lengths and shapes and
are on the surface of the protein .
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Motif-1
 A Motif has a characteristic sequence and
usually is associated with particular function.
 Motif is a recurring thematic element, i.e. it is
found in many molecules not uniquely in just
one and it is a dominant or central theme.
 Motif can be seen in both molecular sequence
and structure.
 Generally protein contain motif of two or
three secondary structures usually -helix
and ß-sheet , and Loops.
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Motif-2
 The presence of the same motif in different
proteins
with
similar
functions
clearly
indicates
that
nature
reuses
certain
combinations of secondary structures rather
than inventing new ones.
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School of Science and Technology, Online Counseling Resource…
What You Learn…
 You have learnt :
 The primary structure is held together by covalent
peptide bonds, which are made during the process
of translation.
 Secondary structure is the spatial arrangement of
the
polypeptide
backbone,
ignoring
the
conformation of the side chains.
 The two most common secondary structure
arrangement are the right-handed -helix and the
ß-sheet, which can connect into large tertiary
structure(or folds) by turns and loops of a variety
of types.
 A Motif has a characteristic sequence and usually
is associated with particular function.
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Critical Thinking Questions
1. Describe primary structure of protein.
2. Describe different secondary structure of
proteins.
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Hints For Critical Thinking Question
1. The primary structure is held together
by covalent peptide bonds, which are
made during the process of translation.
2. Secondary structure is the
spatial
arrangement
of
the
polypeptide
backbone, ignoring the conformation of
the side chains.
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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
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Study Tips:2
 Book3
 Title: Biochemistry
 Author: Lubert stryer
 Publishers: Freeman International
 Book4
 Title: Biochemistry
 Author: Keshav Trehan
 Publishers: Wiley Eastern
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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
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End of the Presentation
Thank You
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