FUNBIO 2 2024 RCSI Biological Molecules Proteins PDF

Biological molecules: Proteins Class: Foundation Year Course: Fundamentals of Human Biology Code: FUNBIO 2 Lecturer: Dr. Kulwinder Kaur Date: 24-09-2024 Learning Outcomes: Describe amino acid structure and the nature of the peptide bond. Explain polypeptide primary, secondary and tertiary struc...

Biological molecules: Proteins Class: Foundation Year Course: Fundamentals of Human Biology Code: FUNBIO 2 Lecturer: Dr. Kulwinder Kaur Date: 24-09-2024 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 PROTEINS Protein word is derived from Greek word proteios meaning holding 1st place. Proteins are the most abundant organic molecules of the living system (100,000 different protein). They occur in every part of the cell and constitute about 50% of the cellular dry weight. They form the fundamental basis of the structure and function of life. Proteins largely determine what a cell looks like and how it functions  FUNCTION Static function (structural) Collagen, elastin, keratin Dynamic Function Enzymes, hormones, muscle contractions Elemental Composition Proteins are predominantly constituted by 5 major elements; Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur And traces of P, Fe, Cu, I, Mg, Mn, Zn etc. *Mulder (Dutch chemist) in 1983 used the term proteins for higher molecular weight nitrogen rich and most abundant substances present in living system.  Amino Acid- Building Block of Proteins Proteins are polymers of amino acids. Amino acids are a group of organic compounds containing two functional group Amino (-NH2)-Basic Carboxyl (-COOH)-Acidic Out of 300 amino acids occur in nature only 20 known as standard amino acids, repeatedly found in the structure of proteins  Amino Acid- Structure All Amino acids have a fundamentally similar structure. Termed as a-amino acids if both the carboxyl and amino groups are attached to the same carbon atom. The a carbon atom binds to side chain represented by R which is different for each of the 20 amino acids.  Classification Based on Polarity NON-POLAR These are refereed as hydrophobic They have no charge on ‘R’ group. POLAR They posses groups such as hydroxyl, amide and participate in hydrogen bonding of protein structure They have no charge on ‘R’ group.  Classification Based on Polarity Electrically Charged Polar amino acids with positive R group Polar amino acids with negative R group  Peptide Bond A covalent chemical bond, which joins two amino acids by removing a water molecule (H2O) from an amino group (–NH2) of one amino acid and a carboxyl group (–COOH) of the adjacent amino acid. The bond between the two amino acids is called the peptide bond. Free N-terminal and C-terminal of dipeptide available to react with further amino acids to make larger polypeptides and eventually proteins (starts from N terminal). Peptide bond is quite rigid but adjacent R groups etc can rotate.  Structure of Proteins The structure of proteins can be divided into four levels of organisation: 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 The linear unique sequence of amino acids within a protein is considered the primary structure of the protein. Its largely responsible for functioning of protein. Example: first six amino acids in hemoglobin  Secondary Structure The primary sequence of the protein must organize itself to form a compact structure through hydrogen bonding. This is done in an elegant fashion by forming secondary structure elements. The two most common secondary structure elements are a helix and β sheets, formed by repeating amino acids with the same angles Example: keratin a Helix b Sheet  a Helix Hydrogen bond forms between the oxygen of the carboxyl group of one amino acid; the hydrogen is part of the fourth amino acid down the chain. Complete turn of the helix is only 3.6 amino acid residues. Basic structural unit of some fibrous proteins that make up hair, skin and nails. Elasticity due to helical shape and hydrogen bonding  b Sheet The hydrogen bonding takes place between different polypeptide chains or different regions of a polypeptide chain that has turned back on itself. Each chain is fully extended as each has a zigzag structure Strong and flexible but not elastic as the distance between the plates https://www.researchgate.net/figure/a-Two-forms-of-the-b-sheet- is fixed. structure-the-antiparallel-and-the-parallel-b-sheet- b_fig1_242461912 (diagram) Fibroin, the protein of silk  Tertiary Structure The complete 3-dimensional conformation of the protein, including its backbone atoms and all its side chains with hydrogen and ionic bonding. Example: RNA  Quaternary Structure The association of several protein chains into a closely packed arrangement. Each of the chain has its own primary, secondary, and tertiary structure. The subunits are held together by hydrogen bonds and van der Waals forces between nonpolar side chains. Example: Hemoglobin Protein Structure  Why do proteins have different conformations? Conformation is dictated by the amino acid sequence. Each protein normally folds up into a single stable conformation. However, the conformation often changes slightly when the protein interacts with other molecules in the cell. Environment factors: pH, temperature (causing the protein to lose its 3D structure and turn back into an unstructured string of amino acids).  Molecular Chaperones Specialised proteins that assist the conformational folding or unfolding of large proteins. Facilitate and regulate protein conformational change within cells. Assist others to fold properly during or after synthesis, to refold after partial denaturation. Denaturation: Disrupts hydrogen and ionic bonding leads to unfolding, change in shape and loss of biological activity  What determines the biological role / activity of a protein? The entire protein structure determines its role. Different regions of a single protein can have different functions Proteins differ from one another primarily in their sequence of amino acids, and which folded into a specific 3D structure that determines its activity. Function of Proteins  Enzymes Enzymes are proteins that help speed up metabolism, or the chemical reactions in our bodies such as respiration, digesting food, muscle and nerve function. They build some substances and break others down. All living things have enzymes. Each cell in the human body contains thousands of enzymes. Synthesis enzymes: Building proteins (tyrosinase: involves the linking together of amino acids in correct sequence). Digestive enzymes: Breaking down molecules: Amylase (made in the mouth and pancreas; breaks down complex carbohydrates) Catalyst enzymes: speed up reactions: Diastase (conversion of starch into maltose)  Enzymes Each enzyme is the specific helper to a specific reaction – each enzyme needs to be the right shape for the reaction – enzymes are named for the reaction they help sucrase breaks down sucrose proteases breakdown proteins lipases breakdown lipids DNA polymerase builds DNA  Enzymes Enzymes are not changed by the reaction Used only temporarily Re-used again for the same reaction with other molecules Only a very small quantity of an enzyme is needed to catalyze a reaction. A typical enzyme molecule can convert 1,000 substrate molecules per second. product substrate active site enzyme  Enzymes Lock & Key model The active site of an enzyme is structured to fit a specifically shaped substrate. Once the substrate binds to the active site, the enzyme will facilitate the reaction and release products of the reaction. Specific enzyme for each specific reaction  Reading Chapter 3 ‘The Chemistry of Life’ Organic Compounds Solomon 11th Ed. p59-68 Thank you F O R M O R E I N F O R M AT I O N P L E A S E C O N TA N T NAME SURNAME EMAIL: [email protected]