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

2. SEP-SBI074-CP3-02 Introduction Programmes and Courses SEP–SBI074-CP3- U03

3. 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 sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com 3© 2008, YCMOU. All Rights Reserved.

4. School of Science and Technology, Online Counseling Resource… © 2008, YCMOU. All Rights Reserved.4 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.

5. School of Science and Technology, Online Counseling Resource… © 2008, YCMOU. All Rights Reserved.5 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.

6. School of Science and Technology, Online Counseling Resource… © 2008, YCMOU. All Rights Reserved.6 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.

7. School of Science and Technology, Online Counseling Resource…  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. Protein Structure /Anatomy-1 7© 2008, YCMOU. All Rights Reserved.

8. School of Science and Technology, Online Counseling Resource… 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'. 8© 2008, YCMOU. All Rights Reserved.

9. School of Science and Technology, Online Counseling Resource… Protein Structure /Anatomy-3 Bond angles for ψ and ω An α-amino acid 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. 9© 2008, YCMOU. All Rights Reserved.

10. School of Science and Technology, Online Counseling Resource… Two amino acids 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. 10© 2008, YCMOU. All Rights Reserved.

11. School of Science and Technology, Online Counseling Resource…  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. Protein Structure /Anatomy-5 11© 2008, YCMOU. All Rights Reserved.

12. School of Science and Technology, Online Counseling Resource… 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 12© 2008, YCMOU. All Rights Reserved.

13. School of Science and Technology, Online Counseling Resource… 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. 13© 2008, YCMOU. All Rights Reserved.

14. School of Science and Technology, Online Counseling Resource… 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  © 2008, YCMOU. All Rights Reserved.14

15. School of Science and Technology, Online Counseling Resource… 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 C- terminus. 15© 2008, YCMOU. All Rights Reserved.

16. School of Science and Technology, Online Counseling Resource…  This uniform arrangement of bonds confers a polarity on a helix because all the hydrogen- bond 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. The -Helix-2 16© 2008, YCMOU. All Rights Reserved.

17. School of Science and Technology, Online Counseling Resource…  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. The -Helix-3 17© 2008, YCMOU. All Rights Reserved.

18. School of Science and Technology, Online Counseling Resource… 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 © 2008, YCMOU. All Rights Reserved.18

19. School of Science and Technology, Online Counseling Resource… 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. 19© 2008, YCMOU. All Rights Reserved.

20. School of Science and Technology, Online Counseling Resource… 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. 20© 2008, YCMOU. All Rights Reserved.

21. School of Science and Technology, Online Counseling Resource… 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. 21© 2008, YCMOU. All Rights Reserved.

22. School of Science and Technology, Online Counseling Resource… 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 ß- sheet.  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. 22© 2008, YCMOU. All Rights Reserved.

23. School of Science and Technology, Online Counseling Resource… Turns and Loops-1  Many proteins combination of -helix and ß- sheet, 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. 23© 2008, YCMOU. All Rights Reserved.

24. School of Science and Technology, Online Counseling Resource… 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. © 2008, YCMOU. All Rights Reserved.24

25. School of Science and Technology, Online Counseling Resource… 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. 25© 2008, YCMOU. All Rights Reserved.

26. School of Science and Technology, Online Counseling Resource… 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. © 2008, YCMOU. All Rights Reserved.26

27. 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. 27© 2008, YCMOU. All Rights Reserved.

28. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Describe primary structure of protein. 2.Describe different secondary structure of proteins. © 2008, YCMOU. All Rights Reserved.28

29. School of Science and Technology, Online Counseling Resource… 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. © 2008, YCMOU. All Rights Reserved.29

30. 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 30© 2008, YCMOU. All Rights Reserved.

31. 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 31© 2008, YCMOU. All Rights Reserved.

32. 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 32© 2008, YCMOU. All Rights Reserved.

33. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You 33© 2008, YCMOU. All Rights Reserved.