FUNBIO.3_Proteins 2023 WT.pptx

RCSIRoyal RoyalCollege CollegeofofSurgeons SurgeonsininIreland Ireland- Medical Coláiste Ríoga naofMáinleá University Bahrainin Éirinn Biomolecules: Proteins Class Course Code Title Lecturer Date Foundation Year Fundamentals of Human Biology FUNBIO.3 Biomolecules: Proteins Prof Warren Thomas 28th...

RCSIRoyal RoyalCollege CollegeofofSurgeons SurgeonsininIreland Ireland- Medical Coláiste Ríoga naofMáinleá University Bahrainin Éirinn Biomolecules: Proteins Class Course Code Title Lecturer Date Foundation Year Fundamentals of Human Biology FUNBIO.3 Biomolecules: Proteins Prof Warren Thomas 28th September 2023 Learning Outcomes • Describe amino acid structure and the nature of the peptide bond • Explain polypeptide primary, secondary and tertiary structure • Describe the role of structural and functional domains in protein tertiary structure • Discuss the role of molecular chaperones in protein synthesis • Explain the role of specialised proteins termed ‘enzymes’ in the body 12/22/2023 Biology RCSI-MUB PROTEINS..... • Proteins • Proteins are macromolecules composed of amino acids Folded linear un-branched polymers of amino acids • Approximately 100,000 different proteins in human body • Most versatile cell components 12/22/2023 Biology RCSI-MUB Proteins • Most enzymes are proteins – important for catalyzing metabolic processes • Proteins are major structural components of cell –Growth, repair and maintenance of the cell depends on proteins • Protein component of cells largely determines what a cell looks like and how it functions –Muscle cell – actin/myosin, –Red Blood Cell - Haemoglobin 12/22/2023 Biology RCSI-MUB AMINO ACID- BUILDING BLOCK OF PROTEINS • All Amino acids have a fundamentally similar structure: • Central Carbon and Hydrogen • Amino functional group • Carboxylic acid functional group / or carboxylate • Distinctive side chain or R group – gives each amino acid its unique characteristics and identity You should be able to draw this! Proteins – Amino Acid Structure • The simplest, and smallest Amino Acid is glycine for which the R group is a hydrogen (H) • Alanine has a methy (-CH3) group You should be able to draw these! Proteins – Amino Acid Structure • Amino acids differ from one another on the basis of their side chain (R group). • The R group can vary in size, charge, polarity and reactivity • Amino acids are grouped according to the polarity and charge of their side chains – Polar – Non-polar – Acidic – Basic • The groups include amino acids with a wide range of properties • Only 20 amino acids commonly found in proteins 12/22/2023 Biology RCSI-MUB Side chains which have functional groups such as acids, amides*, alcohols, and amines* will impart a more polar character to the amino acid. They are generally soluble in water (i.e. hydrophilic) You should know some examples by name! *An amine consists of a nitrogen-carbon single bond (C-N). In an amide, the carbon that is bonded to the nitrogen is also double bonded to an oxygen (N-C(=O)). .. 12/22/2023 Biology RCSI-MUB • Side chains which have pure hydrocarbon alkyl groups (*alkane branches) or aromatic (benzene rings) are nonpolar. Examples include valine, alanine, leucine, isoleucine, phenylalanine. • Generally insoluble in water (hydrophobic) *any of the series of saturated hydrocarbons including methane, ethane, propane, and higher members HC3 CH2 CH3 You should know some examples by name! Biology RCSI-MUB If the side chain contains an acid functional group, the whole amino acid produces an acidic solution. If the side chain contains an amine functional group, the amino acid produces a basic solution Both acidic and basic side chains are ionic at cell pH and therefore hydrophilic - COO + NH NH+ 3 You should know some examples by name! Levels of Protein Organisation/Structure The polypeptide chains making up a protein are twisted or folded to form a macromolecule with a specific conformation (or 3-D shape). • Some polypeptide chains are long fibres • Globular proteins are tightly folded into compact, roughly spherical shapes. A protein’s conformation affects its function. Four levels of protein organization are recognised: 1. Primary structure - amino acid sequence 2. Secondary structure - results from hydrogen bonding between amino acids 3. Tertiary structure - depends on interactions among side chains 4. Quaternary structure - results from interactions among polypeptides PRIMARY STRUCTURE & PEPTIDE BOND REVISION The amino group from one amino acid (with side group R) can react with the carboxylic acid from a 2nd amino acid (with side group R’) to form a dipeptide. This is called a condensation reaction or dehydration synthesis. The bond between the two amino acids is called the peptide bond (which is a covalent bond). • Free N-terminal and Cterminal of dipeptide available to react with further amino acids to make larger polypeptides and eventually proteins • Peptide bond is quite rigid but adjacent R groups etc can rotate Proteins - Secondary Structure • The backbone of the polypeptide chain does not extend in a straight line for its entire length. • Instead, the chain repeatedly folds in a number of distinct forms to give rise to a 3-D structure (or conformation). • The secondary structure of a protein refers to the conformation of a short stretch of the polypeptide chain which can fold into 2 commons forms known as the alpha ( -) helix and the beta ( -) pleated sheets • In both forms of the secondary structure the protein is stabilized by hydrogen bonding, between amino acids at regular intervals along the polypeptide backbone, and neighbouring elements such as oxygen (e.g. R-H----O=C) Biology RCSI-MUB Secondary Structure: α-Helix and β-Pleated Sheet a Helix b Sheet The hydrogen bond is a form of non-covalent bond between a hydrogen atom with a partial positive charge and an oxygen (or nitrogen) atom with a partial negative charge. Although weaker than covalent bonds, the considerable number of bonds between hydrogen and oxygen atoms in peptide units allows sufficient force for the secondary structure of proteins to be stabilized. THE ALPHA HELIX • Each hydrogen bond forms between an oxygen with a partial -ve charge and a hydrogen with a partial +ve. • The oxygen is part of the remnant of the carboxyl group of one amino acid; the hydrogen is part of the remnant of the amino group of the fourth amino acid down the chain • The typical α-helix is about 11 amino acids long. • Basic structural unit of some fibrous proteins that make up wool, hair, skin and nails. • Provides elasticity due to unwinding of helical coil and breaking of hydrogen bonds THE BETA PLEATED SHEET • The hydrogen bonding takes place between different polypeptide chains OR different regions of a polypeptide chain that has turned back on itself • The resulting “sheet” has an overall pleated conformation • Strong and flexible but not elastic because the distance between the pleats is fixed, by the strong covalent bonds of the polypeptide backbones. • Fibroin, the protein of silk has a β-pleated sheet structure. It is not uncommon for a single polypeptide to include both α-helix regions and β-pleated regions Proteins – Tertiary Structure • Tertiary structure of a protein molecule is the overall 3-D shape assumed by EACH individual polypeptide chain (i.e. bonding between the secondary structure) – Amino acids that were far apart in the primary structure may now be in close proximity. • It is only when the protein has folded to its tertiary structure that it is able to function. 12/22/2023 Biology RCSI-MUB Proteins – Tertiary Structure • The 3-D tertiary structure is determined by 4 main factors that involve interactions among R groups belonging to the same polypeptide chain. 1. Hydrogen bonds formed between R groups of certain AA subgroups (weak interactions) 2. Ionic bonds formed between – and + charged R groups (weak interactions) 3. Hydrophobic interactions with nonpolar R groups (weak interactions) Van der waals interactions 4. Covalent bonds – disulfide bonds or bridges (-S-S-) (strongest interactions). Disulfide bridges are formed between two monomers of the AA cysteine. 12/22/2023 Biology RCSI-MUB Tertiary structure of a protein Side chain interactions Neutral molecules may be held together by weak electric force (van der Waals bond). It results from the distortion of a molecule so that a small positive charge develops on one end and a corresponding negative 12/22/2023develops on the other Biology RCSI-MUB charge Tertiary Structure – Bonding Between 2o Structure Proteins – Quaternary Structure Some proteins are composed of more than one polypeptide chain, and in these cases, the protein is now considered to have a quaternary structure (i.e. 3-D structure). • The quaternary structure is defined as the structural arrangement of each polypeptide chain (or subunit) relative to each other. • The bonds that hold each subunit together are similar to those in the tertiary structure (i.e. hydrogen and ionic bonding, hydrophobic interactions and disulfide bridges) 12/22/2023 Biology RCSI-MUB Quaternary structure of a protein Four polypeptide chains/subunits: 2 alpha and 2 beta Linear coiled triple helix Why do proteins have different conformations? • The AA sequence of a protein determines its conformation overall shape) and thus its biological activity. • Environment In vitro or ex vivo (i.e. outside of the cell; in the lab setting): a polypeptide can spontaneously undergo folding processes that result in its normal, functional conformation. In vivo (in the cell) however, the cytoplasm is a crowded place, filled with many other macromolecules capable of interacting with a partially folded protein. Inappropriate associations with nearby proteins can interfere with proper folding and cause large aggregates of proteins to form in cells e.g. experiments with myoglobin molecule (1996). MOLECULAR CHAPERONES • In vivo, proteins are assisted in (post-translational) folding by molecular chaperones (which are specialized proteins themselves)  Similar to a catalyst, chaperones do not become part of the product but aid its development  Hsp60 (chaperonins), Hsp70 and Hsp90 are three main classes • For example, Hsp70 recognizes exposed, unfolded regions of new protein chains - especially hydrophobic regions  It binds to these regions, protecting them until productive folding reactions can occur https://www.youtube.com/watch?v=b39698t750c What determines the biological role / activity of a protein? • Entire protein structure determines its role • Different regions of a single protein can have different functions • Many proteins are modular: 2 or more globular regions – domains connected by less compact regions of polypeptide chain • In turn each domain can have different functions e.g. one domain could act as an enzyme while the other docks in a membrane • The biological activity of a protein can be disrupted by a change in amino acid sequence that results in a change in conformation… Change in Amino Acid Sequence in Sickle Cell Anemia Haemoglobin (Hb) • Consists of 4 polypeptide chains (2 x α and ß chains) • 2 genes (one for α and ß chains) responsible for haemoglobin type Change in Amino Acid Sequence in Sickle Cell Anemia Sickle cell anaemia • Inherited disease • Single point gene mutation or SNP (single nucleotide polymorphism) results in a single AA substitution in the ß chains • Glutamic acid (which has a charged side chain) is replaced by valine (which has a nonpolar side chain) at 6th position from amino end The single AA substitution makes haemoglobin less soluble and more likely to form crystal-like structures. This gives red blood cells a crescent or sickle shape At low O2 levels, sickle cells carry oxygen poorly. Their structure can cause clots and this may result in death particularly during childhood DENATURATION The biological activity of a protein may be affected by change in its 3-D structure. Changes in environment / conditions affect protein function • Disrupts hydrogen and ionic bonding • Leads to unfolding, change in shape • Loss of biological activity Such changes in shape and the accompanying loss of biological activity are called “DENATURATION” of the protein. • Generally, denaturation cannot be reversed (e.g. albumin in eggs turns white and solid when fried), but under some circumstances, proteins can return to their original shape and activity when normal environmental conditions are restored. Heat Chemical Exposure pH Change Enzymes One of the most important functions of proteins is to act as enzymes – biological catalysts that speed up the rate of chemical reactions (up to millions of times) without being directly modified themselves. 12/22/2023 Biology RCSI-MUB Each enzyme is the specific helper to a specific reaction Enzyme needs to be the right shape for the job Enzymes are named for the reaction they help • • • • Sucrase breaks down sucrose Proteases breakdown proteins Lipases breakdown lipids DNA polymerase builds DNA Enzymes are not changed by the reaction Used only temporarily Re-used again for the same reaction with other molecules Very little enzyme needed to help in many reactions substrate active site product enzyme Lock & Key Model Shape of protein allows enzyme & substrate to fit together Specific enzyme for each specific reaction Recommended Reading Chapter 3 ‘The Chemistry of Life’ Organic Compounds Solomon 11th Ed. p59-68