Molecules of Life - Bioengineering Lecture Notes PDF

30-08-2023 Molecules of Life Bioengineering(Section A), Instructor: Dr Urmila S...

30-08-2023 Molecules of Life Bioengineering(Section A), Instructor: Dr Urmila Saxena How do you define life or something is alive ? An organism is a life-form—a living entity made up of one or more cells. Although there is no simple definition of life, most agree that organisms share a suite of five fundamental characteristics. Cells: Organisms are made up of membrane-bound units called cells Animal (multi-cellular) Bacteria (Unicellular) Bioengineering(Section A), Instructor: Dr Urmila Saxena 1  30-08-2023 Replication: Process of producing two identical replicas. One of the great biologists of the twentieth century, François Jacob, said: “dream of a bacterium is to become two bacteria.” Almost everything an organism does contributes to one goal: replicating itself Bioengineering(Section A), Instructor: Dr Urmila Saxena Evolution : Organisms are the products of evolution, and their populations continue to evolve today. Favors modification over innovation Cells and organisms must maintain a living line Natural populations of higher organisms take hundreds or thousands of years to make evolutionary changes Evolution does not design anything before starting construction—instead, it builds many, many prototypes Bioengineering(Section A), Instructor: Dr Urmila Saxena 2  30-08-2023 Information: Organisms process hereditary, or genetic, information encoded in units called genes. Bioengineering(Section A), Instructor: Dr Urmila Saxena Energy: To stay alive and reproduce, organisms have to acquire and use energy. Examples: plants absorb sunlight; animals ingest food. Bioengineering(Section A), Instructor: Dr Urmila Saxena 3  30-08-2023 Life is cellular and all organisms are made of cell “Cell is the building block of Life” Where do cell come from and how the cell was built ? Bioengineering(Section A), Instructor: Dr Urmila Saxena The chemical basis of life Life have evolved from nonliving materials at least once early in Earth’s history Four types of atoms—hydrogen, carbon, nitrogen, and oxygen—make up 96 percent of all matter found in organisms today. Many of the molecules found the cells contain thousands, or even millions, of these atoms bonded together Bioengineering(Section A), Instructor: Dr Urmila Saxena 4  30-08-2023 Chemical Evolution Chemical Bond 1. Covalent 2. Ionic Some simple molecules form from C, H, N, O Bioengineering(Section A), Instructor: Dr Urmila Saxena Miller’s Spark-Discharge Experiment: Model system to test chemical evolution Stanley Miller's 1952 Bioengineering(Section A), Instructor: Dr Urmila Saxena 5  30-08-2023 Miller’s Spark-Discharge Experiment: Bioengineering(Section A), Instructor: Dr Urmila Saxena The Start of Chemical Evolution—Two Models 1. The prebiotic soup model proposes that certain molecules were synthesized from gases in the atmosphere or arrived via meteorites. Afterward they would have condensed with rain and accumulated in oceans. This process would result in an “organic soup” that allowed for continued construction of larger, even more complex molecules. 2. The surface metabolism model suggests that dissolved gases came in contact with minerals lining the walls of deep sea vents and formed more complex organic molecules Bioengineering(Section A), Instructor: Dr Urmila Saxena 6  30-08-2023 Water and carbon - chemical basis of life Carbon Life has been called a carbon-based phenomenon. Except for water, almost all of the molecules found in organisms contain this atom. Many molecules that contain carbon bonded to other elements, such as hydrogen, are called organic compounds. 1. it is the most versatile atom on Earth. 2. its four valence electrons, it will form four covalent bonds 3.The formation of carbon– carbon bonds was an important event in chemical evolution: It represented a crucial step toward the production of organic molecules found in living Bioengineering(Section A), Instructor: Dr organisms Urmila Saxena Carbon-Containing Molecules: Bioengineering(Section A), Instructor: Dr Urmila Saxena 7  30-08-2023 Water Why do scientists spend time looking for water on other planets? Why is water so important? 1. Water is one of the more abundant molecules and the one most critical to life on Earth. 2. 71 percent of the Earth's surface is water 3. Approximately 70 percent of the human body is made up of water 4. 75 percent of the volume in a typical cell is water Earth Human Body Cell Bioengineering(Section A), Instructor: Dr Urmila Saxena What makes water so important as molecules of life ? Water is efficient solvent. Water molecule an overall polar in nature. (polar solutes dissolve in water where as non-polar molecules do not dissolve in water) Bioengineering(Section A), Instructor: Dr Urmila Saxena 8  30-08-2023 Water’s Cohesive and Adhesive Properties: High surface tension Water’s States: Gas, Liquid, and Solid : Water is denser as a liquid than as a solid Temperature control Bioengineering(Section A), Instructor: Dr Urmila Saxena Water has a high capacity for absorbing energy Water in acid –base chemical reaction Example of acid–base reaction: 1. 2. Bioengineering(Section A), Instructor: Dr Urmila Saxena 9  30-08-2023 Molecules of Life – Bio-molecules Simple molecules Organic molecules Complex Biomolecules Glycine Protein Bioengineering(Section A), Instructor: Dr Urmila Saxena Molecules of Life – Bio-molecules Four Basic Molecular Plans 1. Protein 2. Nucleic Acids (DNA & RNA) 3. Carbohydrates 4. Lipid Bioengineering(Section A), Instructor: Dr Urmila Saxena 10  30-08-2023 Protein structure and function Stanley Miller and others in life’s origin experiment, repeatedly discovered same molecules as a products—that is amino acids Later scientist found that amino acids are the structural unit of protein Bioengineering(Section A), Instructor: Dr Urmila Saxena Amino Acid: Structure Total Number of amino acid : 20 (share a common core structure) Bioengineering(Section A), Instructor: Dr Urmila Saxena 11  30-08-2023 R- group in amino acid The R-group, or side chain, represents the part of the amino acid core structure that makes each of the 20 different amino acids unique Amino acid R-groups can be grouped into three general types: 1. Charged (acidic and basic) 2. Uncharged polar 3. Nonpolar Bioengineering(Section A), Instructor: Dr Urmila Saxena Bioengineering(Section A), Instructor: Dr Urmila Saxena 12  30-08-2023 The Polarity and Charge of R-Groups Affect Solubility Both polar and electrically charged R-groups interact readily with water and are hydrophilic. Hydrophilic R-groups dissolve easily in water. Nonpolar R-groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving, hydrophobic R-groups tend to coalesce in aqueous solution. Bioengineering(Section A), Instructor: Dr Urmila Saxena How do amino acids link to form proteins? Poly peptide chain Bioengineering(Section A), Instructor: Dr Urmila Saxena 13  30-08-2023 Peptide bond formation Peptide bond is partial double bond Bioengineering(Section A), Instructor: Dr Urmila Saxena Amino acid polymerizes to form polypeptide chain Bioengineering(Section A), Instructor: Dr Urmila Saxena 14  30-08-2023 Peptide bond is partially double bond in nature but amino acid chain is flexible Bioengineering(Section A), Instructor: Dr Urmila Saxena Protein structure Protein structure determine its function 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure Bioengineering(Section A), Instructor: Dr Urmila Saxena 15  30-08-2023 Primary structure of protein The unique sequence of amino acids in a protein is known as primary structure Why is the order and type of residues in the primary structure of a protein important? R-groups present on each amino acid affect its chemical reactivity and solubility. It’s therefore reasonable to predict that the order of the R-groups present in a polypeptide will affect that molecule’s properties and function Bioengineering(Section A), Instructor: Dr Urmila Saxena Secondary structure of protein 1. 𝛂-helix (alpha-helix), in which the polypeptide’s backbone is coiled 2. 𝛃-pleated sheet (beta-pleated sheet), in which segments of a peptide chain bend 180° and then fold in the same plane Bioengineering(Section A), Instructor: Dr Urmila Saxena 16  30-08-2023 Tertiary Structure A protein’s distinctive three-dimensional shape, or tertiary structure, results from interactions between residues that are brought together as the chain bends and folds in space. The residues that interact with one another are often far apart in the linear sequence. In contrast to secondary structures, which involve only hydrogen bonds between backbone components, tertiary structures form using a variety of bonds and interactions between R-groups or between R-groups and the backbone. Five types of interactions involving R-groups to form tertiary structure of the protein 1. Hydrogen bonding 2. Hydrophobic interactions 3. van der Waals interactions 4. Covalent bonding 5. Ionic bonding Bioengineering(Section A), Instructor: Dr Urmila Saxena Tertiary Structure (Covalent bond) Bioengineering(Section A), Instructor: Dr Urmila Saxena 17  30-08-2023 Different types of Tertiary Structure Bioengineering(Section A), Instructor: Dr Urmila Saxena Quaternary Structure Proteins with quaternary structure have multiple polypeptides Bioengineering(Section A), Instructor: Dr Urmila Saxena 18  30-08-2023 Comparison between different protein structure Bioengineering(Section A), Instructor: Dr Urmila Saxena Protein structure and function Molecules diffuse (cell membrane transport) Bioengineering(Section A), Instructor: Dr Urmila Saxena 19  30-08-2023 Nucleic Acid and RNA world Bioengineering(Section A), Instructor: Dr Urmila Saxena Nucleic Acid Nucleic acid stores genetic information of the cell. Nucleic acids are polymers, are made up of monomers called nucleotides. 1. DNA 2. RNA deoxyribonucleic acid ribonucleic acid Bioengineering(Section A), Instructor: Dr Urmila Saxena 20  30-08-2023 Nucleic acids are made up of monomers called nucleotides. Structure of nucleotides Bioengineering(Section A), Instructor: Dr Urmila Saxena Phosphodiester linkage between two nucleotides form polymer Bioengineering(Section A), Instructor: Dr Urmila Saxena 21  30-08-2023 DNA structure and function Nature, 1953 Bioengineering(Section A), Instructor: Dr Urmila Saxena Early Data Provided Cues molecule had a sugar–phosphate backbone Two empirical rules – (1) The number of purines in a given DNA molecule is equal to the number of pyrimidines, and – (2) the DNA molecule has an equal number of T’s and A’s, and it has an equal number of C’s and G’s. DNA molecules had a regular and repeating structure. The pattern of X-ray scattering suggested that the molecule was helical, or spiral, in nature. Bioengineering(Section A), Instructor: Dr Urmila Saxena 22  30-08-2023 First clue about DNA structure Rosalind Franklin Bioengineering(Section A), Instructor: Dr Urmila Saxena DNA is Double stranded DNA is Double stranded, but backbone are antiparallel Bioengineering(Section A), Instructor: Dr Urmila Saxena 23  30-08-2023 A simple structure of Double stranded DNA Bioengineering(Section A), Instructor: Dr Urmila Saxena DNA Double helix Bioengineering(Section A), Instructor: Dr Urmila Saxena 24  30-08-2023 RNA structure and function Structurally RNA differs from DNA Like DNA, RNA has a primary structure consisting of four types of nitrogenous bases extending from a sugar–phosphate backbone. But there are two significant differences between these nucleic acids 1. The sugar in the sugar–phosphate backbone of RNA is ribose, not deoxyribose as in DNA. 2. The pyrimidine base thymine does not exist in RNA. Instead, RNA contains the closely related pyrimidine base uracil. 3. RNA is single stranded , where as DNA is double stranded 4. DNA is more stable than the RNA Bioengineering(Section A), Instructor: Dr Urmila Saxena DNA is more stable than the RNA The hydroxyl group make RNA less stable than DNA because it is more susceptible to hydrolysis. Bioengineering(Section A), Instructor: Dr Urmila Saxena 25  30-08-2023 Secondary Structure of RNA The purine and pyrimidine bases in RNA undergo hydrogen bonding with complementary bases on the same strand. Bioengineering(Section A), Instructor: Dr Urmila Saxena RNA is a versatile molecule RNA is a versatile molecule is terms of structure and function. The structural flexibility of RNA molecules allows them to perform many different function Function of RNA 1. Process information stored in DNA and synthesize proteins tRNA Bioengineering(Section A), Instructor: Dr Urmila Saxena 26  30-08-2023 Function of RNA 2. RNA function as catalytic molecule RNA has a degree of structural and chemical complexity, it’s capable of forming structures that catalyze a number of chemical reactions. The catalytic RNAs are called ribozymes, or RNA enzymes Example of Ribozymes function: 1. Tetrahymena ribozyme This ribozyme involved in both the hydrolysis and the condensation of phosphodiester linkages in RNA Bioengineering(Section A), Instructor: Dr Urmila Saxena Example of Ribozymes function: 2. Ribozymes polymerize amino acids to form polypeptides Observation: Ribozymes could catalyze the formation of a phosphodiester bond raised the possibility that an RNA molecule could polymerize a copy of itself. Such a molecule could qualify as the first living entity. Bioengineering(Section A), Instructor: Dr Urmila Saxena 27  30-08-2023 RNA world : In search of the first life-form The theory of chemical evolution maintains that life began as a naked self- replicator—a molecule that existed by itself in solution, without being enclosed in a membrane. To make a copy of itself, that first living molecule had to 1. provide a template that could be copied 2. Catalyze polymerization reactions that would link monomers into a copy of that template Origin-of-life researchers propose that the first life-form was an RNA Bioengineering(Section A), Instructor: Dr Urmila Saxena First life-form was an RNA 1. RNA contains a sequence of bases so it can function as an information-containing molecule 2. The information stored in RNA can also be used to make copies of itself via complementary base pairing Bioengineering(Section A), Instructor: Dr Urmila Saxena 28  30-08-2023 First life-form was an RNA Replication of RNA strand Bioengineering(Section A), Instructor: Dr Urmila Saxena 29