01 Proteins Structure and Functions.pdf

FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Proteins Structure...

FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Proteins Structure & Functions Lec Module 1 Far Eastern University IAS – Dept. of Mathematics Biochemistry Cluster 1 Outline of the Topics: Amino Acids Levels of Protein Structures Twenty (20) Proteinogenic Primary Amino Acids Secondary Acid-Base Property of Amino Tertiary Acids Quaternary Peptides Functions Peptide Bond Formation Types of Proteins Based on Peptide Drawing Function Peptide Naming Structure-Function Relationship in Proteins 2 1 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Amino Acids 3 Amino Acids Amino acids are the basic unit of proteins. Each amino acid has the following components: a carboxyl group (-COOH/ -COO-) an amino group (-NH2/ -NH3+) an α carbon – carbon adjacent to the carboxyl group an R group – side chain that gives each amino acid a unique property 4 2 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Amino Acids There are twenty-two (22) proteinogenic amino acids, twenty (20) of which can be found in the genetic code. Each amino acid has their own unique side chain. These amino acids are classified based on the characteristics of their R group. Non-Polar amino acids Polar Neutral amino acids Acidic amino acids Basic amino acids 5 Non-Polar Amino Acids Glycine (Gly, G): Alanine (Ala, A): Valine (Val, V): Leucine (Leu, L): Isoleucine (Ile, I): hydrogen methyl group isopropyl group isobutyl group sec-butyl group Methionine (Met, M): Phenylalanine Tryptophan (Trp, W): Proline (Pro, P): thioether group (Phe,F): indole group cyclic benzyl group aromatic aromatic 6 3 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Polar Neutral Amino Acids Serine (Ser, S): Threonine (Thr, T): Tyrosine (Tyr, Y): primary alcohol secondary alcohol phenol group aromatic Asparagine (Asn, N): Glutamine (Gln, Q): Cysteine (Cys, C): β amide group γ amide group thiol group 7 Acidic Amino Acids Aspartic Acid (Asp, D): Glutamic Acid (Glu, E): β carboxyl group γ carboxyl group 8 4 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Basic Amino Acids Lysine (Lys, K): Arginine (Arg, R): Histidine (His, H): ε amino group guanidino group imidazole group aromatic 9 Essential & Non-Essential Amino Acids Essential amino acids are amino acids that are necessary for growth and normal body functions but cannot be synthesized by the body. Hence, they must be obtained through the diet. 10 5 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Chirality of Amino Acids All protein-derived amino acids, EXCEPT glycine, have at least one (1) stereocenter – the α carbon – and are therefore chiral. The most common and naturally accruing configuration of amino acids is the L-configuration. TERM: Chiral- optically-active carbon center; carbon atom that has four different substituents 11 Acid-Base Property of Amino Acids Amino acids may act as weak acids and bases within an aqueous environment. Aside from the carboxyl and amino groups, the side chains may also be ionized at varying pH. Each functional group will gain or lose H atoms at various pH, and therefore have different pKa. Ø At pH lower than the pKa, the functional group is protonated. Ø At pH higher than the pKa, the functional group is deprotonated. 12 6 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Acid-Base Property of Amino Acids At a certain pH, the net charge of an amino acid will become zero (0). At this point, the amino acid is said to be a zwitterion, or is in its zwitterionic form. The pH at which an amino acid becomes a zwitterion is its isoelectric pH (pI). 13 Acid-Base Property of Amino Acids Which ionization state of arginine is its zwitterionic form? 14 7 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Peptides 15 Peptide Bond Formation Amino acids are linked to one another through amide bonds that are called peptide bonds. These bonds are formed between the α-carboxyl group of the first amino acid and the α-amino group of the next amino acid in the chain. 16 8 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Peptide Bond Formation Amino acids bonded together by a peptide bond are generally referred to as amino acid residues. 17 Peptide Chains Short chains of amino acids (up to 50 residues) are referred to as peptides, while longer chains (>50 residues) are called polypeptides. 18 9 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Peptide Drawing and Naming By convention, peptides are written from left to right, starting from the α-amino group (the N-terminal) to the α-carboxyl group (the C terminal). Peptides can be written based on the names of their amino acid residues, their three letter code, or their one letter code. Name: alanyltyrosinylaspartylglycine 3-letter Code: NH3+-Ala-Tyr-Asp-Gly-COO- 1-letter Code: NH3+-AYDG-COO- 19 Peptide Naming What are the amino acid residues present in the pentapeptide below? 20 10 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Peptides vs Proteins Peptides are short chains of amino acids linked together by peptide bonds that can be composed of approximately up to 50 residues. Polypeptides are longer chains of amino acids, greater than 50 residues. Proteins are biomolecules composed of one or more polypeptide chains that have more complex, three-dimensional structures. Other molecules may also be present in their structure in order to function. Ex: Heme group – Hemoglobin Sugar chains – Antibodies 21 Levels of Protein Structure 22 11 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Levels of Protein Structure Protein structures are organized based on their levels of complexity. Primary – the amino acid sequence Secondary – folding in specific areas of the polypeptide Tertiary – 3D folding of the entire polypeptide Quaternary – arrangement of polypeptide chains 23 Primary Structure Primary (1°) Structure - the amino acid sequence of a polypeptide chain held together by peptide bonds and disulfide bonds. A sequence of n number of amino acids can produce 20n number of proteins. 24 12 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Primary Structure Changing the primary structure of a protein can have significant effects on a protein's functions and higher-order structures. This is especially observed when the change involves amino acids of different properties. antidiuretic hormone uterine contraction & milk secretion hormone Amino Acid #2: Arginine Amino Acid #2: Leucine (basic) (nonpolar, aliphatic) Amino Acid #7: Phenylalanine Amino Acid #7: Isoleucine (nonpolar, aromatic) (nonpolar, aliphatic) 25 Primary Structure Changing the primary structure of a protein can have significant effects on a protein's functions and higher-order structures. This is especially observed when the change involves amino acids of different properties. 26 13 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Secondary Structure Secondary (2°) Structure - the 3D arrangements in localized regions of the polypeptide chain. These structures are stabilized by hydrogen bonds between the H atom of the amide group and the O atom of carbonyl group. 27 Secondary Structure There are two common types of secondary structures: α-helix β-pleated sheets 28 14 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Secondary Structure α-Helix Spiral structure stabilized by intramolecular H-bonds C=O of each peptide bond is hydrogen bonded to the N-H of the fourth amino acid away All side chains point outward 29 Secondary Structure α-Helix Turn – complete rotation Pitch – advance within one complete turn Rise – advance per amino acid Turn = 3.6 amino acids Pitch = 0.54nm Rise = 0.15nm 30 15 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Secondary Structure α-Helix Helices can be destabilized by certain factors: Presence of helix breakers – proline and glycine Electrostatic interactions – repulsion or attraction between charged amino acid residues Steric strain – bulkiness of adjacent R-groups 31 Secondary Structure α-Helix α-Keratin – ‘coiled coil’ structure; individual chains of keratin are in α-helix 32 16 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Secondary Structure α-Helix Collagen – triple helix structure; individual chains of collagen are in α-helix 33 Secondary Structure β-Pleated Sheets Zigzag structure stabilized by interchain or intrachain H-bonds of adjacent polypeptide chains Formed when 2 or more polypeptides line side-by-side All side chains extend above or below the sheet in an alternating sequence 34 17 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Secondary Structure β-Pleated Sheets Two types of β-pleated sheets: Anti-Parallel β-pleated sheets – peptide chains run in opposite directions Parallel β-pleated sheets – peptide chains run in the same direction 35 Secondary Structure β-Pleated Sheets Silk Fibroin – has both α-helices and β-pleated sheets 36 18 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Tertiary Structure Tertiary (3°) Structure - 3D conformation of the entire polypeptide. These structures are stabilized by numerous interactions between amino acid side chains. Covalent Bonds H-Bonds Disulfide Bridges Salt Bridges (acid-base interaction) Hydrophobic Interactions Metal Ion Coordination 37 Tertiary Structure 38 19 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Tertiary Structure Myoglobin– monomeric protein with a heme group 39 Quaternary Structure Quaternary (4°) Structure - 3D conformation of multiple polypeptide chains. Not all proteins have quaternary structures. Some proteins are composed of two or more polypeptide chains called subunits. The quaternary structure refers to the arrangement of these subunits. The quaternary structure is stabilized by numerous interactions, similar to the tertiary structure. 40 20 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Quaternary Structure Hemoglobin– a tetrameric protein with 2 α-subunits and 2 β-subunits 41 Protein Classification Proteins can be classified based on their structural shape or their composition. Based on Shape: Fibrous Globular Based on Composition: Simple Conjugated 42 21 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Protein Classification: By Shape Fibrous Proteins Contain 3° structures organized approximately parallel along a single axis Consists of long fibers or large sheets Tend to be mechanically strong α-Keratin Insoluble to water Play structural roles Collagen 43 Protein Classification: By Shape Globular Proteins Folded to a spherical shape Most polar side chains are on the outside while nonpolar side chains are buried inside the structure Hemoglobin Albumin Soluble in water Nearly all have substantial sections of α-helices and β-sheets Varied metabolic functions (catalysis, Myoglobin Lactase transport, etc.) 44 22 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Protein Classification: By Composition Simple Proteins Only composed of amino acids Albumin – a simple protein Conjugated Proteins Contains non-protein components called prosthetic groups Prosthetic groups may be lipids, carbohydrates or metal ions Hemoglobin – a conjugated protein with heme prosthetic group 45 Protein Denaturation A protein in its natural, functional, three-dimensional conformation is said to be in its native state. Denaturation refers to a change in protein native conformation and leads to disruption of protein function. May or may not be permanent. 46 23 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Protein Denaturation Denaturing agents – physical or chemical agents that unfold, alter or destabilize the native conformation of proteins Physical Agents Chemical Agents High temperature Acids and bases (change in pH) Vigorous shaking or agitation Salts (change in ionic strength) Hydrostatic pressure Organic solvents, e.g. urea, UV radiation alcohol Reducing agents, e.g. performic acid, mercaptoethanol Detergents Heavy metals, e.g. Hg2+, Pb2+, Ag+ 47 Protein Hydrolysis Protein hydrolysis refers to the loss of the primary structure. This involves the breakage of the peptide bonds, producing free amino acids or smaller peptide chains. Hydrolysis may be partial or complete, and can be caused by acids, bases or enzymes. 48 24 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Functions of Proteins 49 Protein Functions Proteins serve many functions, including the following: Structure – for support, e.g. collagen, elastin Catalysis – enzymes Storage – for amino acid storage, e.g. casein, ovalbumin Transport – for transport of other substances, e.g. hemoglobin Regulation – for regulating bodily activities, e.g. insulin, glucagon Receptor – for response to external stimuli, e.g. neuron receptors Movement – e.g. myosin, actin Protection – e.g. antibodies, fibrinogen 50 25 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Protein Functions 51 Structure-Function Relationship of Proteins Protein function is highly depended on its structure and amino acid composition. Changes to the amino acid sequence can negatively impact protein function. Examples Proteins for catalysis must have amino acids that can interact and bind with their target molecule for the reaction to take place. 52 26 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 Structure-Function Relationship of Proteins Protein function is highly depended on its structure and amino acid composition. Changes to the amino acid sequence can negatively impact protein function. Examples Proteins meant for transport from one compartment of the cell to another can have its polypeptide chain form a ‘channel’ where molecules can pass through. 53 Structure-Function Relationship of Proteins Protein function is highly depended on its structure and amino acid composition. Changes to the amino acid sequence can negatively impact protein function. Examples Receptor proteins embedded in the cell membrane, e.g. insulin receptors. The cell membrane is largely nonpolar. In order for proteins to remain embedded, they must have nonpolar amino acids in regions that interact with the cell membrane. Regions that interact with the aqueous interior and exterior of the cell should mostly be polar amino acids. 54 27 FEU Biochemistry Cluster Property. Any forms of replication is prohibited. Seek approval from Ms.Jessa Natividad and Ms. Erika Viloria 8/13/24 WORKSHEET! ANSWER WORKSHEET 1: PROTEINS ON CANVAS! 55 END Thank you for listening! 56 28