This document discusses protein structure and function. It begins by defining proteins and their essential roles in the body. It then describes the four levels of protein structure - primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structure forms alpha helices and beta sheets via hydrogen bonding. Tertiary structure results from folding influenced by interactions between amino acid side chains. Quaternary structure involves interactions between multiple polypeptide chains. The document also covers different protein classifications and functions, which include enzymes, antibodies, hormones, and more.

1. Protein Structure and Function
Compiled & Edited by
Dr. Syed Ismail
VN Marathwada Agril. University Parbhani

2. DEFINITIONS OF PROTEIN
•Proteins are one of the essential building blocks of the human body.
•They provide amino acids, which are a nutritional requirement of the body to produce its own proteins and a variety of nitrogen-based molecules.
•It is common for programs to recommend a minimum of 50 grams of protein per day to maintain healthy levels.
•Proteins vary in structure as well as function. They are constructed from a set of 20 amino acids and have distinct three-dimensional shapes.

3. General Characteristics of Proteins
•They are the most complex and most diverse in chemical composition, conferring upon the different tissues.
•Protein molecule contains elements of C, H, O,N, S, and P together with traces of Fe, Cu, I, Mn, and Zn.
•It has a molecular weight of 5,000 to 3,000,000
•They are the most important of the biologic substances being the fundamental constituent of cell cytoplasm.
•They supply not only heat and energy but also material for building and repair.
•Unlike carbohydrates and lipids, only small amounts of protein is temporarily stored in the body, and which can be quickly used up upon demand.

4. FUNCTIONS OF PROTEIN

5. FUNCTIONS OF PROTEIN
•Antibodies - are specialized proteins involved in defending the body from antigens (foreign invaders). One way antibodies destroy antigens is by immobilizing them so that they can be destroyed by white blood cells.
•Enzymes - are proteins that facilitate biochemical reactions. They are often referred to as catalysts because they speed up chemical reactions. Examples include the enzymes lactase and pepsin. Lactase breaks down the sugar lactose found in milk. Pepsin is a digestive enzyme that works in the stomach to break down proteins in food.
•Hormonal Proteins - are messenger proteins which help to coordinate certain bodily activities. Examples include insulin, Insulin regulates glucose metabolism by controlling the blood- sugar concentration.

6. FUNCTIONS OF PROTEIN
•Contractile Proteins - are responsible for movement. Examples include actin and myosin. These proteins are involved in muscle contraction and movement.
•Structural Proteins - are fibrous and stringy and provide support. Examples include keratin, collagen, and elastin. Keratins strengthen protective coverings such as hair, quills, feathers, horns, and beaks. Collagens and elastin provide support for connective tissues such as tendons and ligaments.
•Storage Proteins - store amino acids. Examples include ovalbumin and casein. Ovalbumin is found in egg whites and casein is a milk-based protein.
•Transport Proteins - are carrier proteins which move molecules from one place to another around the body. Examples include hemoglobin and cytochromes. Hemoglobin transports oxygen through the blood. Cytochromes operate in the electron transport chain as electron carrier proteins.

7. Classification of Proteins
Based on Composition:
•Simple proteins – composed of entirely amino acids only.
Ex. Albumin, Globulin
•Complex or Conjugated proteins – made up of amino acids and other organic compounds. The non- amino acid group is termed as the prosthetic group.
Ex. Nucleoproteins, lipoproteins,
glycoproteins, metalloproteins

8. Classification of Proteins
Based on Axial Ratio:
Axial ratio is the ratio of the length to the breath.
•Globular proteins – with axial ratio less than 10 but not below 3 or 4. They are compactly folded and coiled.
Ex. Insulin, plasma albumin, globulin,
enzymes
•Fibrous proteins – with axial ratio greater than 10. They are spiral and helical and are cross linked by disulfide and hydrogen bonds.
Ex. Keratin, myosin, elastin, collagen

9. Globular Proteins
•Globular proteins have their axial ratio less than 10 but not below 3 or 4. They are compactly folded and coiled.
•Examples are insulin, plasma albumin, globulin, enzymes

10. Fibrous Proteins
•Fibrous proteins are spiral and helical and are cross linked by disulfide and hydrogen bonds
•Examples are keratin, myosin, elastin, collagen

11. Based on Biological Functions
•Structural proteins: collagen, elastin, keratin, fibroin of silk and webs
•Transport proteins: hemoglobin, myoglobin, lipoproteins
•Protective proteins: immunoglobulins, fibrinogen, thrombin, snake venoms, bacterial toxins
•Contractile proteins: actin, myosin, tubulin
•Catalytic proteins: enzymes
•Regulatory proteins: hormones
•Storage proteins: ferritin, hemosiderin, gluten, casein, ovalbumin
•Reception of Stimuli: rhodopsin, membrane receptor proteins, acethylcholine, insulin
•Germicidal proteins: Polymyxin B1, Gramicidin S

12. Shape = Amino Acid Sequence
•Proteins are made of 20 amino acids linked by peptide bonds
•Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C… in the peptide bond
•The side chain or R group is not part of the backbone or the peptide bond

13. Composed of a chain of amino acids.
R
|
H2N--C--COOH
|
H
Proteins
20 possible groups

14. 0HCOOCNHCOCNHCOOCNHCOOCNH2333     - --  

15. Polar Basic Acid ? Acid
Amine
Different Amino Acid Classes
OH O H H2N C C
R
Generic
Non-polar C C C OH H
H O
H+N H H2N C NH C
C Histidine
H
H2N C C H H
O OH
O
C OH C Aspartic acid C
C C
OH
H H O HS H
H2N
Cysteine
OH
H H O H H
H2N C
C C Alanine

16. Non-Polar Amino Acids OH O
H
H2N
C
C H Glycine Leucine OH
O H
H2N C C H3C CH3 H
C H
H
C Methionine OH O H
H2N C
C H3C H H C H
H
C
S Alanine OH H H O
H H
H2N C C C Valine OH
O H
H2N C C H3C CH3 H
C Phenylalanine
OH
H H O H H2N
C
C
C Tryptophan OH O H H2N
C
C
NH
H C H Isoleucine OH
O H
H2N C C H3C H H
C H
H3C
C Proline OH O H
H2N+ C
C H2C CH2 H2C Protein Structure

17. Polar Amino Acids
Cysteine C
C C OH H H O
HS H
H2N Serine OH O H H2N
C
C
HO CH3 H C Threonine OH
O H
H2N C C H H C
OH
H
C H Tyrosine HO H H
O H
H2N C C C OH Asparagine
H
H2N
C C H H O OH
O
C
NH2
C Glutamine H H2N C
C H
H
O OH O C NH2
C
C
H
H

18. Acidic Amino Acids Aspartic acid H H2N
C C
H
H O OH O C
OH
C
Glutamic
acid H H2N C C H
H
O
OH O C OH C C
H
H

19. Basic Amino Acids Histidine C C C OH
H
H
O
H+N H H2N C NH
C
C
Lysine OH O H H2N C
C +H3N
H
H C H H C
C H
H H H C Arginine OH
O H
H2N C C H H C
H
H
C C H H H N
+H2N
NH2
C Protein Structure

20. Levels of Protein Organization
•Primary Structure - The sequence of amino acids in the polypeptide chain
•Secondary Structure - The formation of  helices and b pleated sheets due to hydrogen bonding between the peptide backbone
•Tertiary Structure - Folding of helices and sheets influenced by R group bonding
•Quaternary Structure - The association of more than one polypeptide into a protein complex influenced by R group bonding

21. Levels of Protein Organization Primary Structure Met-Gly-Ala-Pro-His-Ile-Asp-Glu-Met-Ser-Thr-...
The sequence of amino acids in the primary structure determines the folding of the molecule. Protein Structure

22. Protein Secondary Structure
•The peptide backbone has areas of positive charge and negative charge
•These areas can interact with one another to form hydrogen bonds
•The result of these hydrogen bonds are two types of structures:
 helices
b pleated sheets

23. + - Protein Secondary Structure:  Helix C
O OH
C N H H H C
HO
H
C
H O C N H
H H
C
H H C H N
C
O
C H N O C C
O
C
H
N C H N C
O
C
O C O C O C
H
N
H
N C H N

24. +
-
Protein Secondary Structure:  Helix
C O OH C N H
H H
C
HO H C H O
C N
H H H C H H
C
H
N C O C H N
O
C
C
O C H N C
H
N
C O C O C O
C
O
C
H N H N C
H
N

25. Protein Secondary Structure:  Helix
R R R R R
R R
R
R R R R R
R R groups stick out from the  helix influencing higher levels of protein organization

26. Yeast Cytochrome C Oxidase Subunit IV Leader
MLSLRQSIRFFKPATRTLCSSRYLL R Y P L
T
C
S
R L S T I
K
P
R
F A F M R
Q
L
L
S S
•This would localise specific classes of amino acids in specific parts of the helix The order of the amino acids determines the hydrogen bonding Neutral Non-polar Polar Basic Acidic

27. Protein Secondary Structure: b Pleated Sheet N
H C O C H C
C
N
O N H C O C
H
C
C
N O N H C
O C
H
C C N O N
H C
O C H C C N
O N
H C O C H C
C
N
O N H C O C
H
C
C
N O N H C
O C
H
C C N O N
H C
O C H C C N
O

28. Protein Secondary Structure: b Pleated Sheet
N
H C O C H
C
C
N O N H C O
C
H
C
C N O N H
C O
C
H C C N O
N
H
C O C H C C
N O
N
H C O C H
C
C
N O N H C O
C
H
C
C N O N H
C O
C
H C C N O
N
H
C O C H C C
N O
N
H C O C H
C
C
N O N H C O
C
H
C
C N O N H
C O
C
H C C N O
N
H
C O C H C C
N O

29. Levels of Protein Organization Tertiary Structure
•Tertiary structure results from the folding of  helices and b pleated sheets
•Factors influencing tertiary structure include:
•Hydrophobic interactions
•Hydrogen bonding
•Disulphide bridges
•Ionic bonds

30. Hydrophobic interactions Valine OH O
H
H2N
C
C H3C CH3 H C
Proline OH
O H H2N+ C C H2C
CH2 H2C
OH O H H2N C C
H
Glycine

31. Hydrogen Bonding Asparagine H H2N C C
H
H
O OH O C NH2 C
Glutamine H
H2N C C H H O
OH O
C
NH2 C C H H
N-------H (+) (-) O -------C
slightly slightly

32. Disulphide bridges
Cysteine C C C OH H
H O
HS H H2N Cysteine C C
C OH
H
H O HS H H2N
Cysteine C
C C OH H H O
S H
H2N Cysteine C C C OH
H
H
O
S H H2N

33. Ionic Bonds Glutamic acid
H
H2N
C C H H O OH
O
C
O-
C C H H Arginine
OH O
H
H2N C C H H
C H
H
C C H H H
N +H2N
NH2
C

34. e.g.G-3-P Dehydrogenase Tertiary Structure

35. Levels of Protein Organization Quaternary Structure
•Quaternary structure results from the interaction of independent polypeptide chains
•Factors influencing quaternary structure include:
•Hydrophobic interactions
•Hydrogen bonding
•The shape and charge distribution on amino acids of associating polypeptides

36. G-3-P Dehydrogenase from Bacillus stearothermophilus

37. Protein structure

38. Globular and Fibrous
•e.g. haemoglobin
•3º structure normally folds up in a ball
•hydrophilic R groups point outwards
•Hydrophobic R groups point inwards
•soluble
•metabolic functions
•e.g. collagen
•2º structure does not fold up, form fibres
•not surrounded by hydrophilic R groups
•insoluble
•structural functions

39. Haemoglobin
•Haemoglobin is a globular protein with a prosthetic ‘iron’ group
•In adults, hemoglobin is made up of 4 polypeptides (2  polypeptide chains and 2 b polypeptide chains)
•Each polypeptide surrounds a prosthetic ‘haem’ group
•Hydrophobic interactions between side groups pointing inwards maintain the structure
•Hydrophilic side chains point outwards making it soluble Fe b
b  

40. Polypeptide Backbone

41. Amino Acids (magic 20) You need to know these Hydrophilic Hydrophobic

42. Protein Folding
•The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions
•Weak non-covalent interactions will hold the protein in its functional shape – these are weak and will take many to hold the shape

43. Non-covalent Bonds in Proteins

44. Globular Proteins
•The side chains will help determine the conformation in an aqueous solution

45. Hydrogen Bonds in Proteins
•H-bonds form between 1) atoms involved in the peptide bond; 2) peptide bond atoms and R groups; 3) R groups

46. Protein Folding
•Proteins shape is determined by the sequence of the amino acids
•The final shape is called the conformation and has the lowest free energy possible
•Denaturation is the process of unfolding the protein
–Can be done with heat, pH or chemical compounds
–The chemical compound can be removed and have the protein renature or refold

47. Refolding
•Molecular chaperones are small proteins that help guide the folding and can help keep the new protein from associating with the wrong partner

48. Protein Folding
•2 regular folding patterns have been identified – formed between the bonds of the peptide backbone
•-helix – protein turns like a spiral – fibrous proteins (hair, nails, horns)
•b-sheet – protein folds back on itself as in a ribbon – globular protein

49. b Sheets
•Core of many proteins is the b sheet
•Form rigid structures with the H- bond
•Can be of 2 types
–Anti-parallel – run in an opposite direction of its neighbor (A)
–Parallel – run in the same direction with longer looping sections between them (B)

50.  Helix
•Formed by a H-bond between every 4th peptide bond – C=O to N-H
•The  helix can either coil to the right or the left
•Can also coil around each other – coiled-coil shape – a framework for structural proteins such as nails and skin

51. Protein Structure

52. Domains
•A domain is a basic structural unit of a protein structure – distinct from those that make up the conformations
•Part of protein that can fold into a stable structure independently
•Different domains can impart different functions to proteins
•Proteins can have one to many domains depending on protein size

53. Domains

54. Useful Proteins
•There are thousands and thousands of different combinations of amino acids that can make up proteins and that would increase if each one had multiple shapes
•Proteins usually have only one useful conformation because otherwise it would not be efficient use of the energy available to the system
•Natural selection has eliminated proteins that do not perform a specific function in the cell

55. Protein Families
•Have similarities in amino acid sequence and 3-D structure
•Have similar functions such as breakdown proteins but do it differently

56. Proteins – Multiple Peptides
•Non-covalent bonds can form interactions between individual polypeptide chains
–Binding site – where proteins interact with one another
–Subunit – each polypeptide chain of large protein
–Dimer – protein made of 2 subunits
•Can be same subunit or different subunits

57. Single Subunit Proteins

58. Different Subunit Proteins
•Hemoglobin
–2  globin subunits
–2 b globin subunits

59. Protein Assemblies
•Proteins can form very large assemblies
•Can form long chains if the protein has 2 binding sites – link together as a helix or a ring
•Actin fibers in muscles and cytoskeleton – is made from thousands of actin molecules as a helical fiber

60. Types of Proteins
•Globular Proteins – most of what we have dealt with so far
–Compact shape like a ball with irregular surfaces
–Enzymes are globular
•Fibrous Proteins – usually span a long distance in the cell
–3-D structure is usually long and rod shaped

61. Important Fibrous Proteins
•Intermediate filaments of the cytoskeleton
–Structural scaffold inside the cell
•Keratin in hair, horns and nails
•Extracellular matrix
–Bind cells together to make tissues
–Secreted from cells and assemble in long fibers
•Collagen – fiber with a glycine every third amino acid in the protein
•Elastin – unstructured fibers that gives tissue an elastic characteristic

62. Collagen and Elastin

63. Stabilizing Cross-Links
•Cross linkages can be between 2 parts of a protein or between 2 subunits
•Disulfide bonds (S-S) form between adjacent -SH groups on the amino acid cysteine

64. Proteins at Work
•The conformation of a protein gives it a unique function
•To work proteins must interact with other molecules, usually 1 or a few molecules from the thousands to 1 protein
•Ligand – the molecule that a protein can bind
•Binding site – part of the protein that interacts with the ligand
–Consists of a cavity formed by a specific arrangement of amino acids

65. Ligand Binding

66. Formation of Binding Site
•The binding site forms when amino acids from within the protein come together in the folding
•The remaining sequences may play a role in regulating the protein’s activity

67. Antibody Family
•A family of proteins that can be created to bind to almost any molecule
•Antibodies (immunoglobulins) are made in response to a foreign molecule ie. bacteria, virus, pollen… called the antigen
•Bind together tightly and therefore inactivates the antigen or marks it for destruction

68. Antibodies
•Y-shaped molecules with 2 binding sites at the upper ends of the Y
•The loops of polypeptides on the end of the binding site are what imparts the recognition of the antigen
•Changes in the sequence of the loops make the antibody recognize different antigens - specificity

69. Antibodies