Proteins Part 3 2024 PDF

Cellular Biology & Homeostasis AMINO ACIDS & PROTEINS Part 3 VP 2024 Clara Camargo, DVM PROTEIN PRIMARY STRUCTURE Unique sequence of amino acids in polypeptide chain o Amino acids are linked by peptide bonds between α-carboxyl group and α-amino groups Peptide bonds are o Strong covalent bonds o Resi...

Cellular Biology & Homeostasis AMINO ACIDS & PROTEINS Part 3 VP 2024 Clara Camargo, DVM PROTEIN PRIMARY STRUCTURE Unique sequence of amino acids in polypeptide chain o Amino acids are linked by peptide bonds between α-carboxyl group and α-amino groups Peptide bonds are o Strong covalent bonds o Resistant to conditions that denature proteins (i.e. heating & high concentrations of urea) Prolonged exposure to a strong acid or base at elevated temperature is necessary to break these bonds non-enzymatically Molecular Biology of the Cell (© Garland Science 2008) PROTEIN SECONDARY STRUCTURE  Regular, recurring arrangements in Both structures are held in shape by space of adjacent amino acid residues in a hydrogen bonds, formed between the polypeptide chain. carbonyl-O group of one AA and the amino-H group of another Examples of common secondary structures of proteins:  α-Helix  β-Sheet  β-Bends (reverse turns, β-turns) α-HELIX Spiral structure, a tightly packed, coiled polypeptide chain core Hydrogen bonds between carboxy O groups and amino H groups are 4 AA away – spiral structure. Side chains of component amino acids extend outward to avoid interfering with each other From: Alberts. Mol Biol of the Cell α-HELIX Protein Primary Structure αKeratins: fibrous protein component of hair, nails (hoof) and skin, rigidity determined by number of disulfide bonds between α-Helix structures Picture source: Wikiwand Impala or rooibok (Aepyceros melampus) PLEATED BETA SHEET Protein Secondary Structure Antiparallel Parallel Antiparallel Parallel PLEATED BETA SHEET Beta strands are the backbone of the beta-sheets, typically 3 to 10 AAs long Beta sheets consists of various beta strands linked laterally by at least two or three hydrogen bonds. Antiparallel beta-sheets are slightly more stable because of the more optimum hydrogen bonding structure. Protein Secondary Structure PLEATED BETA SHEET Both (parallel and antiparallel structures) are common in nature Protein Secondary Structure Fibroin an insoluble protein present in silk. Made by spiders and certain moths (‘silkworm’ is larvae of moth Bombyx mori). Layers of antiparallel βsheets https://www.researchgate.net/figure/Overview-of-the-origin-and-structures-of-silk-fibroin-A-Popular-silk-sources-include_fig1_337490514 Protein Secondary Structure ß-BENDS β-bends characteristics: o Reverse the direction of a polypeptide chain, helping it form a compact, globular shape o Generally composed of 4 amino acids, one of which is often proline (this causes a kink in the polypeptide chain) o Critical for the protein structure and function, generally occur when the protein chain needs to change direction in order to connect two other elements of secondary structure. ß-BENDS Protein Secondary Structure Roles of β-Turns in Protein Folding: From Peptide Models to Protein Engineering FYI https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904567/#:~:text=Gratifyingly%2C%20the%20turn%20propensities%20of,the%20most%20common%20%CE%B2%2Dturn%2D Protein Structure & Function PROTEIN TERTIARY STRUCTURE TERTIARY refers to  Folding of domains  Final arrangement of domains in the polypeptide  Three-dimensional arrangement of the polypeptide chain in space Domains are the fundamental functional & three-dimensional structural units of proteins  Polypeptide chains ≥ 200 amino acids consist of 2 or more domains Protein Structure & Function The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures → the protein domains The tertiary structure is the structure at which polypeptide chains become functional.  At this level, every protein has a specific 3D shape and presents functional groups on its outer surface, allowing it to interact with other molecules, and giving it its unique function. PROTEIN TERTIARY STRUCTURE Image source: Wikipedia Protein Structure & Function Protein Structure & Function PROTEIN QUARTERNARY STRUCTURE Association of several protein chains or subunits into a closely packed arrangement. Example of a quaternary structure Each of the subunits has its own primary, secondary, and tertiary structure. PROTEIN QUATERNARY STRUCTURE  Subunits are held together primarily by non-covalent interactions Hydrogen bonds, ionic bonds, hydrophobic interactions.  Subunits may function independently of each other or may work cooperatively. i.e hemoglobin(Hb), where binding of oxygen to one subunit increases the affinity of other subunits for oxygen. Protein Structure & Function Protein Quaternary Structure Hemoglobin (Hb) molecule A polymeric protein formed as a symmetric assembly of 4 subunits Contains two copies of α-globin and 2 copies of β-globin Each of four polypeptide chains contains a heme molecule (red) This is the site where oxygen (O2) is bound Each molecule of Hb in blood carries 4 molecules of O2 Molecular Biology of the Cell (© Garland Science 2008) IMPORTANT CHEMICAL BONDS Protein Structure & Function Primary Structure AA’s are joined by peptide bonds  covalent bond 2 atoms sharing electrons between C-atom of carboxyl group of 1 AA and N-atom of amino group of another AA. Strong bond  molecule backbone Secondary Structure 3D shaping (β-sheet, α-helix, β-bends) held in place by → hydrogen bonds Dipole-dipole interaction between a hydrogen H atom and an electronegative atom, such as N or O. Hydrogen bonds are weak bonds! IMPORTANT CHEMICAL BONDS Protein Structure & Function Tertiary Structure  Hydrogen bonds between the side chains of the individual amino acids - WEAK  Ionic bonds between oppositely charged ions (anions - and cations +) - STRONGER THAN Hydrogen bonds  Disulfide bridges S-S-bond between 2 thiol groups (S-H) - STRONG BOND  Hydrophobic interactions between hydrophobic (nonpolar) AA-side chains - CAN BE STRONG  Hydrophilic interactions usually on the outer part of the protein structure, towards the aqueous environment Quaternary Structure is stabilized by hydrogen-bonds and hydrophobic and hydrophilic interactions between amino acids side chains (R groups) of each subunit PROTEIN STRUCTURE Protein Structure & Function A collection of protein molecules, shown at the same scale  Hemoglobin, catalase, porin, alcohol dehydrogenase, and aspartate transcarbamoylase are formed from multiple copies of subunits polymeric Molecular Biology of the Cell (© Garland Science 2008) Protein Structure & Function PROTEIN FOLDING Many proteins don’t fold by themselves, but instead get assistance from chaperone or Heat shock proteins (Hsp) Quality control: protein folded improperly will not leave the ER Chaperones  Heat-stable proteins  High activity at high temperatures  ATPases  Quality Control Hsp70: repairs and refolds damaged proteins, corrects misfolding, prevent protein aggregates, facilitates degradation of aggregates. Protein Structure & Function PROTEIN FOLDING – Folding cycle 1. Chaperone is bound to ADP 2. ADP/Chaperone-complex has a high affinity for unfolded proteins 3. After binding, ADP is released 4. After ATP binding and protein folding, the complex dissociates, and the correctly folded protein is released PROTEIN MISFOLDING Protein Structure & Function Misfolded proteins are usually tagged and corrected by chaperones or degraded in the cell by proteosomes. HOWEVER, quality control systems are not perfect, and intracellular or extracellular misfolded proteins can accumulate, especially as individuals age. Deposits of misfolded proteins are associated with diseases PRION DISEASE Prion diseases are fatal, degenerative brain disorders that occur worldwide in Protein Misfolding Toxic misfolding and clumping of the prion protein – Proteinopathies both humans and animals. Bovine spongiform encephalopathy (BSE) Prions are misfolded proteins that can transmit their misfolded shape onto normal variants of the same protein. FDA Info in cattle - ‘Mad Cow’ disease PROTEIN DENATURATION Unfolding and disorganization of secondary and tertiary structures of a protein. Denaturing agents:  heat  organic solvents  strong acids or bases  Primary structure (generally) remains intact - NO hydrolysis of peptide bonds  May be reversible, so the protein refolds once the denaturing agent is removed  Mostly proteins, once denatured, remain permanently disordered (insoluble, precipitate)  detergents  heavy metal ions (lead) All physiological change is mediated by PROTEINS! Function depends on protein shape and shape changes Proteins can bind to other molecules very specifically, Proteins change shape, which in turn alters their binding properties and their function. The 3D shape of a protein (its conformation), determines protein function. Classification of proteins STRUCTURE Fibrous Linear Tough & Strong Long parallel polypeptide chains cross linked at regular intervals Perform structural functions in the cell Usually do not have a (complex) tertiary structure Globular Spherical/globular shape Polypeptide chain tightly folded into spherical shapes Physically softer Most proteins in cells are globular proteins Functions: form enzymes, antibodies and some hormone Solubility in Water Insoluble Readily Soluble Most Important Structure Secondary Structure Tertiary Structure Examples Collagen, Elastin, Myosin, Keratin, Silk Insulin, Hemoglobin, Albumin, DNA Polymerase and RNA Polymerase Intermediate Intermediate shape, mostly linear Soluble Blood clotting proteins Classification of proteins COMPOSITION Simple proteins Composed of only amino acids, relatively simple structure Examples: Myosin, Collagen, Keratin, Insulin Conjugated proteins: Complex proteins, contain one or more non-amino acid components called prosthetic groups, essential for biological function.  Usually globular and soluble in water  Most enzymes are conjugated proteins  Further classification based on the nature of the prosthetic groups (p.g.): a) Phosphoproteins: p.g. is phosphoric acid (Casein/milk, vitellin/egg) b) Glycoproteins: p.g. is carbohydrate (membrane proteins) c) Nucleoproteins: p.g. is nucleic acid (proteins in chromosomes, ribosomes) d) Chromoproteins: p.g. is pigment or chrome (Hemoglobin) e) Lipoproteins: p.g. is lipid (chylomicrons) f) Flavoproteins: p.g. is FAD- Flavin Adenine Dinucleotide (proteins of electron transport system) g) Metalloproteins: p.g. is metal ions (Hemocyanin – copper containing protein, transport of O2 in crustaceans) FUNCTION 1. Structural proteins Components of connective tissue, bone, tendons, skin, feathers, nail, hair, horn Mostly fibrous proteins, insoluble in water Examples: Collagen, Keratin, Elastin 2. Enzymes Biological catalysts, reduce activation energy of reactants and speed up reactions Can be globular, conjugated proteins, Examples: DNA Polymerase, Lipase… 3. Hormones: Peptide hormones Examples: Insulin, Glucagon, Gastrin, CCK Classification of proteins 4. Respiratory pigments: Colored, conjugated proteins with a pigment (chrome) as their p.g. Examples: Hemoglobin, Myoglobin FUNCTION Classification of proteins 5. Transport proteins: Transport materials in cells and form channels, Example: Serum Albumin 6. Contractile proteins: 7. Can contract muscles with the expense of energy from ATP, Examples: Actin, Myosin Storage proteins: Store metal ions and amino acids in cells, found in seeds and pulses, egg and milk Examples: Ferritin (iron), Casein, Ovalbumin, Gluten 8. Immunoglobulins Antibodies 9. Toxins Toxic proteins Example: snake venom