CHAPTER 3.pptx structure and function of amino acid and protein

This chapter provides the brief discussion on amino acid and protein

1. CHAPTER 3 PROTEIN STRUCTURE AND FUNCTION Contents of the chapter Introduction Structure, classification and function of amino acids Amino acids as buffers Peptide bond formation Structure and function of proteins Primary structure of proteins 1 Secondary structure of proteins Tertiary structure of proteins Quaternary structure of proteins Denaturation of proteins Uses of proteins

2. 3.1. Introduction Amino acids are the building blocks of proteins. Among the thousands of amino acids available in nature, proteins contain only 20 different kinds of amino acids, all of them are L-alpha-amino acids , The same 20 standard amino acids make proteins in all the living cells, may it either be a virus, bacteria, yeast, plant or human cell. These 20 amino acids combine in different sequences and numbers to form various kinds of proteins. 2

3. Cont. The number of proteins that can be had from these 20 amino acids can be calculated from 20 factorial i.e. 20 x 19 x 18 x 17 x 16 x........... x 2 x 1 = 2.4 x 10 18 . In human beings alone there are more than 100,000 different types of proteins. 3

4. 3.2. Structure, classification and function of amino acids Structure of amino acids: Four different groups are attached to α- carbon: amino group COOH group Hydrogen atom and side Chain (R). 4

5. Cont. At physiological pH (7.4), COOH group is dissociated forming a negatively charged carboxylate ion (COO - ) and amino group is protonated forming positively charged ion (NH 3 + ) forming Zwitter ion . 5

6. Name of Amino Acids The twenty common amino acids are often referred to using three-letter abbreviations. The structures, names, and abbreviations for the twenty common amino acids are shown below. Note that they are all α -amino acids . 6

7. Cont. A codon consisting of three base pairs determines each amino acid The codon table shows the 64 different codons, in RNA language, alongside the amino acids they encode. Three of the codons act as stop signals. 7

8. Classification of Amino Acids: Three classification of Amino acid: Depending upon the charge they contain Depending upon the solubility in water Depending upon their nutritional requirements: Depending upon the charge : Amino acids can be broadly classified into three major groups: (1) Neutral (2) Acidic and (3) Basic 8

9. Classification of Amino Acids: Neutral amino acids: Those amino acids that do not contain any charge on the 'R' group. They are further classified into the following categories (a) Aliphatic: a group of aa with R group consisting of only carbon and hydrogen atoms in a linear or branched chain– Ala, Ser, Thr , Val, Leu, Ile, Asn , Gln. (b) Aromatic: Those amino acids whose 'R' group has a benzene ring - Phe , Tyr, Trp. (c) Heterocyclic: The "R" group has a heterocylic ring i.e. any of the ring structures which contain different atoms - Pro, His. (d) Sulphur containing: Those amino acids which contain a sulphur atom - Cys, Met. 9

10. Cont. 10

11. Classification of Amino Acids: 2) Acidic amino acids: Those amino acids that contain a negative charge or an acidic group - Asp, Glu. 3) Basic amino acids: Are those amino acids that contain a positive charge or a basic group - Arg, Lys and His. 11

12. Cont. II. Depending upon the solubility in water: The amino acids can also be grouped into two different categories, depending upon their solubility in water. They are:- Hydrophobic amino acids: amino acids that have nonpolar side chains that repel water. They are - Ala, Val, Leu, Ile, Pro, Met, Phe , Tryp. Hydrophilic amino acids: amino acids that have polar or charged side chains that attract water. They are - Gly, Ser, Thr , Cys, Tyr, Asp, Asn , Glu, Gln, Lys, Arg, His. 12

13. Cont. II. Depending upon their nutritional requirements: Essential aa : Are those which cannot be synthesized by the animal/human body and hence they should be taken through the diet. Methionine, Valine, Phenylalanine, Isoleucine, Threonine, Leucine, Lysine, Tryptophan Semi-essential aa : formed in the body but not in sufficient amount for body requirements especially in children. Arginine and Histidine Non essential : aa Are those that can be synthesized in the human body and are not required in the diet. These include gly , ala, ser, pro, tyr , cys , asp, asn , glu , gln . 13

14. Cont. Functions of Amino Acids Apart from being the monomeric constituents of proteins and peptides, amino acids serve variety of functions. (a) Some amino acids are converted to carbohydrates and are called as glucogenic amino acids . ( alanine, glutamate, glutamine, aspartate, and valine ) (b) Specific amino acids give rise to specialized products, e.g. Tyrosine forms hormones such as thyroid hormones , (T3, T4), epinephrine and norepinephrine and a pigment called melanin . Tryptophan can synthesize a vitamin called niacin . Glycine, arginine and methionine synthesize creatine . 14

15. Cont. Glycine and cysteine help in synthesis of Bile salts . Glutamate, cysteine and glycine synthesis glutathione . Histidine changes to histamine on decarboxylation. Tryptophan form Serotonin . Glycine is used for the synthesis of haem . Pyrimidines and purines use several amino acids for their synthesis such as aspartate and glutamine for pyrimidines and glycine, aspartic acid, Glutamine and serine for purine synthesis 15

16. Cont. c) Some amino acids such as glycine and cysteine are used as detoxicants of specific substances. (d) Methionine acts as “active” methionine (S-adenosylmethionine) and transfers methyl group to various substances by transmethylation. (e) Cystine and methionine are sources of sulphur 16

17. 3.3.Amino acids as buffers Amino acids act as buffers because their carboxyl and amino groups can donate or accept protons to resist pH changes. This is possible due to their amphoteric nature, where they can act as both an acid and a base, forming a buffer system around their  pKa (aa dissociation conistant )values. For example, the carboxyl group acts as a buffer in the acidic pH range near its pKa , while the amino group acts as a buffer in the alkaline pH range near its pKa .  17

18. Cont. Zwitterionic nature : At a specific pH (the isoelectric point), the amino acid is a zwitterion with a net charge of zero, but it still has a carboxyl group (COOH)  and an amino group (NH 2 ) that can be protonated or deprotonated. When acid is added : The amino group (NH 2 )  can accept a proton (H + ) to form a protonated amino group(NH 3 + ), neutralizing the added acid and keeping the pH stable. When base is added : The carboxyl group (COOH) can donate a proton (H + ) to neutralize the added base, preventing the pH from rising too high. Buffering ranges : Each ionizable group (carboxyl and amino) has a pKa value, and the amino acid can act as a buffer in the pH range around these values. For example, glycine has pKa values of approximately 2.34 and 9.60 meaning it can buffer solutions in those two pH ranges. 18

19. 3.4. Peptide bond formation Twenty amino acids are commonly found in protein. These 20 amino acids are linked together through “peptide bond forming peptides and proteins The chains containing less than 50 amino acids or whose molecular weight is less than 5000 Daltons are called “peptides”, while those containing greater than 50 amino acids or whose molecular weight is more than 5000 Daltons are called “proteins”. This differentiation is based upon the immunological property of the two units - peptides are non-immunogenic, whereas proteins are immunogenic. 19

20. Cont. Peptide bond formation : -carboxyl group of one amino acid (with side chain R1) forms a covalent peptide bond with amino group of another amino acid (with the side chain R2) by removal of a molecule of water. The result is: Dipeptide (i.e. Two amino acids linked by one peptide bond). By the same way, the dipeptide can then form a second peptide bond with a third amino acid (with side chain R3) to give Tripeptide. Repetition of this process generates a polypeptide or protein of specific amino acid sequence. 20

21. Cont. 21

22. Cont. Each polypeptide chain starts on the left side by free amino group of the first amino acid enter in chain formation. It is termed (N-terminus). Each polypeptide chain ends on the right side by free COOH group of the last amino acid and termed (C-terminus). 22 Full name: Alanyl tyrosyl aspartyl glycine

23. 3.5. Structure and function of proteins The structure of a protein is critical to its function. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary. 23

24. 3.5.1.Primary structure of protein Primary structure denotes the number and sequence of amino acids in the protein. The higher levels of organization are decided by the primary structure. Each polypeptide chain has a unique amino acid sequence decided by the genes. The primary structure is maintained by the covalent bonds of the peptide linkages. At one end is an amino acid with a free amino group the (the N-terminus) and at the other is an amino acid with a free carboxyl group the (the C-terminus). 24

25. Cont. Branched and Circular Proteins i . Generally, the polypeptide chains are linear. However branching points in the chains may be produced by interchain disulphide bridges. The covalent disulphide bonds between different polypeptide chains in the same protein (interchain) or portions of the same polypeptide chain (intrachain) are also part of the primary structure. 25

26. Cont. ii. Rarely, instead of the alpha COOH group, the gamma carboxyl group of glutamic acid may enter into peptide bond formation, e.g. Glutathione ( gammaglutamyl -cysteinyl-glycine) The term pseudopeptide is used to denote such a peptide bond formed by carboxyl group, other than that present in alpha position. iii. Very rarely, protein may be in a circular form, e.g. Gramicidin. 26

27. Cont. Primary Structure of Insulin As an example of the primary structure of a protein, that was originally described by Sanger in 1955 who received the Nobel prize in 1958. 1 -Insulin has two polypeptide chains. The A chain (Glycine chain) has 21 amino acids and B (Phenylalanine) chain has 30 amino acids. 2 -They are held together by two interchain disulfide bonds. A chain 7 th cysteine and B chain 7 th cysteine are connected. Similarly, A chain 20 th cysteine and B chain 19 th cysteine are connected. There is another intrachain disulfide bond between 6 th and 11 th cysteine residues of A chain. 27

28. Cont. 3 -The species variation is restricted to amino acids in position 8, 9 and 10 in A chain and in C-terminal of B chain. The amino acid sequence has been conserved to a great extent during evolution. 4 -Human insulin required for replacement therapy, is now produced by recombinant DNA technology. 28 Fig. Primary structure of human insulin

29. Cont. Primary Structure Determines Biological Activity A protein with a specific primary structure will automatically form its natural three-dimensional shape. So, the higher levels of organization are dependent on the primary structure. Even a single amino acid change (mutation) in the linear sequence may have profound biological effects on the function. 29

30. Cont. For example, in the human genetic disease sickle cell anemia, the hemoglobin  β  chain (a small portion of which is shown in  Figure   below ) has a single amino acid substitution (valine for glutamic acid). This change of one amino acid in the chain causes hemoglobin molecules to form long fibers that distort red blood cells into a crescent or “sickle” shape, which clogs arteries and leads to serious health problems such as breathlessness, dizziness, headaches, and abdominal pain 30

31. Cont. 31 A single amino acid substitution in the beta chain of hemoglobin leads to sickle cell anemia. In this blood smear, visualized at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped.

32. 3.5.2 Secondary Structure Results from hydrogen bond formation between hydrogen of –NH group of peptide bond and the carbonyl oxygen of another peptide bond. According to H-bonding there are two main forms of secondary structure: α-helix: It is a spiral structure resulting from hydrogen bonding between one peptide bond and the fourth one. β-sheets: when two or more polypeptides (or segments of the same peptide chain) are linked together by hydrogen bond between H- of NH- of one chain and carbonyl oxygen of adjacent chain (or segment). 32

33. Cont. 33 Figure The α-helix and β-pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone.

34. 3.5.3 Tertiary Structure The unique three-dimensional structure of a polypeptide is its  tertiary structure  ( Figure ). This structure is primarily due to interactions among R groups. For example, R groups with like charges are repelled by each other and those with unlike charges are attracted to each other via ionic bonds. When protein folding takes place in a watery environment, such as that found inside cells, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, while the hydrophilic R groups face out. 34

35. Cont. Hydrophobic R groups also interact with each other through van der Waals forces. Interaction between cysteine side chains forms disulfide linkages, which are the only covalent bond formed during protein folding. All of these interactions determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it may no longer be functional. 35

36. Cont. 36 Figure The tertiary structure of proteins is determined by a variety of chemical interactions, including hydrophobic interactions, ionic bonding, hydrogen bonding and disulfide linkages.

37. 3.5.4 Quaternary Structure Some proteins contain two or more separate polypeptide chains or subunits which may be identical or different. The arrangement of these protein subunits in three dimensions is known as quaternary structure which is biologically functional. These subunits or polypeptide chains may be similar or different thus produce homogeneous and heterogeneous quaternary structures respectively. The hemoglobin proteins possess heterogeneous quaternary structure because it is made up of 2 α chains and two β-chains (Figure). 37

38. Cont. 38 Fig. Quaternary structure of haemoglobin Based on higher level of structure, proteins are classified as fibrous globular, and membrane . Fibrous proteins contain single type of secondary structure such as strands or sheets and their tertiary structure is relatively simple where as in globular proteins, the polypeptide chains are arranged into spherical or globular shape and it often contain several types of secondary structures.

39. 3.6.Denaturation of proteins Denaturation:- is a process in which a protein loses its native shape due to the disruption of weak chemical bonds and interactions, thereby becoming biologically inactive. 39 In case of proteins: A loss of three-dimensional structure, sufficient to cause loss of function. Loss of secondary, tertiary and quaternary structure of proteins. Change in physical, chemical and biological properties of protein molecules .

40. Cont. Cause of protein denaturation 40 Method Effect on Protein Structure Heat above 50°C or ultraviolet (UV) radiation Heat or UV radiation supplies kinetic energy to protein molecules, causing their atoms to vibrate more rapidly and disrupting relatively weak hydrogen bonding and dispersion forces. Use of organic compounds, such as ethyl alcohol These compounds are capable of engaging in intermolecular hydrogen bonding with protein molecules, disrupting intramolecular hydrogen bonding within the protein. Salts of heavy metal ions, such as mercury, silver, and lead These ions form strong bonds with the carboxylate anions of the acidic amino acids or SH groups of cysteine, disrupting ionic bonds and disulfide linkages. Alkaloid reagents, such as tannic acid (used in tanning leather) These reagents combine with positively charged amino groups in proteins to disrupt ionic bonds.

41. Cont. Anyone who has fried an egg has observed denaturation. The clear egg white turns opaque as the albumin denatures and coagulates. No one has yet reversed that process. However, given the proper circumstances and enough time, a protein that has unfolded under sufficiently gentle conditions can refold and may again exhibit biological activity. Such evidence suggests that, at least for these proteins, the primary structure determines the secondary and tertiary structure. A given sequence of amino acids seems to adopt its particular three-dimensional arrangement naturally if conditions are right. 41

42. Cont. 42 The primary structures of proteins are quite sturdy. In general, fairly vigorous conditions are needed to hydrolyze peptide bonds. At the secondary through quaternary levels, however, proteins are quite vulnerable to attack, though they vary in their vulnerability to denaturation. The delicately folded globular proteins are much easier to denature than are the tough, fibrous proteins of hair and skin.

43. 3.7. Uses of proteins The main functions of proteins in animal/human body are They serve a s body building units. Ex. Muscle proteins. They provide support and protection to various tissues. Ex. Collagen and keratin. All chemical reactions in the body are catalyzed by proteinacious enzymes. Ex. Trypsin. They transport various molecules and ions from one organ to the other. Ex. Haemoglobin , serum albumin. 43

44. Cont. They store and provide nutrients. Milk casein, ovalbumin. They defend the body from harmful foreign organisms. Ex. Immunoglobulins, fibrinogen. They help to regulate cellular or physiological activity. Ex. Hormones viz. insulin, GH. 44