Proteins: Structure and Function 2/8/2017 1

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1 Proteins: Structure and Function 2/8/2017 1

2 outline Protein functions hemistry of amino acids Protein Structure; Primary structure Secondary structure Tertiary structure Quaternary structure 2/8/2017 2

3 Overview Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells. They occur in great variety; thousands of different kinds, ranging in size from relatively small peptides to huge polymers with molecular weights in the millions, may be found in a single cell. Simple monomeric subunits (amino acids) provide the key to the structure of the thousands of different proteins. All proteins, whether from the most ancient lines of bacteria or from the most complex forms of life, are constructed from the same set of 20 amino acids They are the molecular instruments through which genetic information is expressed. Proteins exhibit enormous diversity of biological function and are the most important final products of the information pathways 2/8/2017 3

4 Biological Functions 1. Enzyme catalysts Almost all chemical reactions in biological systems are catalyzed by enzymes Nearly all known enzymes are proteins. 2. Transport and storage Many small molecules and ions are transported by specific proteins e.g aemoglobin transports oxygen. Iron is stored in the liver as ferritin. 3. oordinated motion Muscle contraction is accomplished by sliding motion of two kinds of protein filaments; myosin and actin 2/8/2017 4

5 4. Mechanical support Tensile strength of the skin and bone is due to the presence of collagen 5. Immune protections Antibodies and most Antigens are proteins 6. Generation and transmission of nerve impulses Receptor proteins at the nerve endplate play a role in transmission of impulses 7. ontrols growth and differentiation Growth factor proteins i.e Growth ormone coordinate activities of different cells in multicellular organisms. 2/8/2017 5

6 Properties key to their Function 1. Are linear polymers of amino acids. Protein function is directly dependent on its 3 dimensional structure which is determined by the linear sequence of amino acids in the protein polymer 2. ontain a wide range of functional groups. includes alcohols, thiols, thioethers, carboxylic acids, carboxylamides, and a variety of basic groups. When combined in various sequences, this array of functional groups accounts for the broad spectrum of protein function. E.g at active sites of enzymes. 2/8/2017 6

7 3. an interact with one another and with other biomolecules to form complex assemblies. In these assemblies proteins act synergistically to generate capabilities not afforded by the individual component proteins. These assemblies include macro-molecular machines that carry out the accurate replication of DNA, the transmission of signals within cells, and many other essential processes. 4. Some are quite rigid, whereas others display limited flexibility. Rigid units can function as structural elements in the cytoskeleton or in connective tissue. Parts of proteins with limited flexibility may act as hinges, springs, and levers that are crucial to protein function, to the assembly of proteins with one another and with other molecules into complex units, and to the transmission of information within and between cells 2/8/2017 7

8 Amino Acids: Structure Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type of covalent bond. The term residue reflects the loss of the elements of water when one amino acid is joined to another. All mammalian proteins are built from 20 amino acids. These are the one that are coded for in the genetic code. But the are more than 300 different amino acids in nature. All the 20 amino acids have an α carbon to which a carboxyl group, an amino group and a distinctive side chain (R- group) is attached. Except 2/8/2017 proline. 8

9 Amino acids: lassification 1. Non polar side chains: Aliphatic and Aromatic Do not bind, give protons, or participate in hydrogen or ionic bonds. Are important in hydrophobic interactions In proteins found in aqueous solutions, these non polar R groups cluster together in the interior of the protein. Fill up the interior of the folded protein and help give the protein its 3 D shape. Proline; the side chain and the amino group form a ring structure called an imino group. Tyrosine has a O group and can lose protons at alkaline p. O group makes tyrosine polar 2/8/2017 9

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12 2. Uncharged Polar Side chains ave zero net charge at neutral p ysteine and Tyrosine can lose proton at alkaline p Serine, theronine and tyrosine contain O group that participate in hydrogen bonding. Asparagine and glutamine used their carbonyl and amide groups to form hydrogen bonds. ysteine form disulfide bonds when two sulfhydrl group become oxidized to form a cystine dimer Side chains are site for attachment eg O for attachment of the phosphate group. Also for attachment of oligosaccharides in glycoproteins. 2/8/

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14 3. Acidic side chains At neutral p, they are fully ionized; containing a negatively charged carboxyl group ( _coo-) Are proton donors at physiological p and hence are negatively charged. 2/8/

15 4. Basic side chains Are proton acceptors Lysine and arginine are fully ionized and positively charged at physiological p. But istidine is weakly basic and in proteins, it can be positively charged or neutral depending on the p. This is important in the functioning of proteins such as myoglobin. 2/8/

16 The α-r groups determine the properties of amino acids Glycine the smallest amino acid often occurs where peptides bend sharply. ydrophobic R groups of alanine, valine, leucine and isoleucine and aromatic R groups of phenylalanine, tyrosine, and tryptophan occur primarily in the interior of cytosolic proteins. Proline often found on bends of folded proteins. The charged R groups of basic and acidic amino acids stabilize specific protein conformation via ionic interactions, or salt bonds. istidine plays an important role in enzymatic catalysis. 2/8/

17 Functional groups dictate the chemical reactions of amino acids Each functional group of an amino acid exhibits all its characteristic chemical reactions; For carboxylic acid groups : formation of esters, amides and acid anhydrides For amino groups acylation, amidation and esterification For O and S groups oxidation and esterification The most important reaction of amino acids is the formation of peptide bonds 2/8/

18 Amino acids are linked by peptide bonds to form polypeptide chains + 3 N R 2 R 2 R 1 O O O O N 3 N N 2 O O O O R 1 Peptide bond 2/8/

19 Two amino acids may be joined by a peptide bond to form a dipeptide Three two peptide bonds to form a tripeptide Peptides with more than 10 amino acid residues are termed polypeptides and when few amino acids are joined, peptides are referred to as oligopeptides -An amino acid unit in a chain is a residue -By conversion the amino end is taken to be the beginning of a polypeptide chain. O Aminoterminal end O N + 3 O N O N O N O O arboxyterminal end The tetrapeptide with seryltyrosylalanylleucine or Ser-Tyr-Ala-Leu 2/8/

20 - A polypeptide chain consists of a regularly repeating part, the main chain (backbone) and a variable part consisting of distinctive side chains (R 1, R 2 and R 3 R 1 O R 2 O R 3 O N N N Amino acid sequence determines the primary structure -Amino acids present in peptides are termed aminoacyl residues - the suffixes ate or ine are replaced with -yl (eg alanyl, aspartyl, tyrosyl) - peptides are named as derivatives of the carboxyl terminal aminoacyl residue (eg lysyl-leucyl-tyrosyl-glutamine). The ine ending of glutamine indicates that the carboxyl group is not involved in peptide bond formation 2/8/

21 Some proteins contain chemical groups other than amino acids Simple proteins contain only amino acid residues and no other chemical groups onjugated proteins contain permanently associated chemical groups in addition to amino acids The non amino acid part of a conjugated protein is called the prosthetic group - onjugated proteins are classified on the basis of the chemical nature of the prosthetic group -lipoproteins contain lipid -glycoproteins contain sugar groups -metalloproteins contain a specific metal -Usually the prosthetic group plays a role in the protein s biological activity A protein without its characteristic prosthetic group is termed as apoprotein 2/8/

22 Levels of Protein Structure Primary structure A description of all covalent bondss (mainly peptide bonds and disulfide bonds) linking amino acid residues in a polypeptide chain. The most important element of the primary structure is its amino acid sequence which determines; how a protein folds up into its unique three-dimensional structure and this in turn determines the function of the protein cellular location certain sequences serve as signals that target proteins for export or tissue distribution Attachment sites for prosthetic groups an also elucidate evolutionary trees

23 Types of non covalent bonds in primary structure; 1. ydrogen Bonds 2. ydrophobic interactions 3. Electrostatic (Ionic) Bonds

24 Protein Secondary structure Is a stable arrangement of amino acid residues giving rise to recurring structural patterns The α helix is a common protein secondary structure The simplest structure the polypeptide chain can assume with its rigid peptide bonds (other bonds free to rotate) is a helical structure The helix is stabilized by hydrogen bonds between the N and O groups of the main chain The O group of each amino acid is hydrogen bonded to the N group of the amino acid that is located four residues ahead in the linear sequence All the main chain N and O groups are hydrogen bonded (except those close to each end of the helix)

25 O O N R 1 O N R 2 N R 3 O N R 4 N R 5 O In the α-helix the O group of residue n is hydrogen bonded to the N group of the residue (n+ 4) The helix can be right handed (counter clock wise) or left handed (clock wise) The α- helices found in protein are right-handed

26 The β-pleated sheets -The pleated sheet is extended into a zig zag (pleated) formation rather the being tightly coiled as in the α helix. - the β pleated sheet is stabilized by hydrogen bonds between N and O groups in different polypeptide strands where as in the α helix the hydrogen bonds between N and O groups are on the same strand. -R groups of adjacent amino acids protrude from the zigzag structure in opposite directions

27 Adjacent chains in a β pleated sheet can run in the same direction (parallel β sheet) or in the opposite direction (antiparallel β sheet) Individual segments that form a β sheet are: usually nearby on a polypeptide chain can be distant from each other in the linear sequence of the polypeptide they may be segments in different polypeptide chains

28 Supersecondary structure Refers to clusters of secondary structures -Eg a β strand separated from another β strand by an α helix to form a motif (β-α-β unit) -Such motifs are intermediate between secondary and tertiary structures

29 Protein structure showing α-helix and β sheet conformations α-helix β sheets Random coils

30 Protein Tertiary Structure -Refers to the entire three dimensional conformation of a polypeptide - - In contrast to secondary structure which refers to the spatial arrangement of amino acid residues that are adjacent in the primary structure, tertiary structures include longer - range aspects of amino acid sequence -It indicates in three-dimensions how secondary structural features - helices, sheets, bends, turns and loops - assemble to form domains and how these domains relate spatially to one another -A domain is a section of protein structure able to perform a particular chemical or physical task such as binding to substrate -other domains may - anchor a protein to a substrate - interact with a regulatory molecule

31 Protein Quaternary Structure Quaternary structure comprises 2 or more polypeptide chains united by forces other than covalent bonds ( ie not peptide or disulfide bonds) -The forces that stabilize these aggregates are hydrogen bonds and electrostatic bonds formed between residues on the surface of the polypeptide chains -Such proteins are called oligomers and the individual polypeptides of which they are composed are protomers ( monomers,or subunits) 31

32 -Two major groups -Fibrous proteins - polypeptide chains arranged in long strands or sheets -Usually consist largely of a single type of secondary structure -Provide support, shape and external protection to vertebrates -Insoluble in water due to a high concentration of hydrophobic amino acids both in the interior of the protein and on its surface -eg α-keratin, collagen etc - Globular proteins polypeptide chains folded into spherical or globular shape -Often contain several types of secondary structure -Most enzymes, regulatory proteins, immunoglobulin, transport proteins, motor proteins are globular proteins play a special role in intracellular regulation because the protomers can assume different spatial arrangement relative to each other with resulting changes in the properties of the oligomer eg haemoglobin 32