Introduction to Biochemistry PDF

Summary

This document provides an introduction to biochemistry, covering chemical bonds, reactivity, and the structure of living organisms. The material is designed for an undergraduate level audience and explores fundamental concepts related to the study of life.

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Introduction to Biochemistry Chemical Bonds and Reactivity Prof. Dr. Özlem Dalmızrak Department of Medical Biochemistry Faculty of Medicine Near East University Biochemistry is the study of chemistry of life. Biochemistry describes the structure, organization, and funct...

Introduction to Biochemistry Chemical Bonds and Reactivity Prof. Dr. Özlem Dalmızrak Department of Medical Biochemistry Faculty of Medicine Near East University Biochemistry is the study of chemistry of life. Biochemistry describes the structure, organization, and functions of living matter in molecular terms What are the chemical structures of the components of living matter? How do the interactions of these components give rise to organized supramolecular structures, cells, multicellular tissues, and organisms? How are the chemical reactions controlled inside living cells? How does living matter extract energy from its surroundings in order to remain alive? How does an organism store and transmit the information it needs to grow and reproduce itself accurately? What chemical changes accompany the reproduction, growth, development, aging, and death of cells and organisms? Distinguishing features of living organisms: A high degree of chemical complexity and microscopic organization. Systems for extracting, transforming and using energy from the environment. Defined functions for each of an organism’s components and regulated interactions among them. Mechanism for sensing and responding to alterations in their surroundings. A capacity for precise self-replication and self-assembly. A capacity to change over time by gradual evolution. Cells are the Structural and Functional Units of All Living Organisms Eukaryotes-Prokaryotes Organisms can be classified according to how they obtain the energy and carbon they need for synthesizing cellular material. Bacterial cells Monomeric Units of Complex Macromolecules Molecular Organization of Cell Essential Elements for life and health Three-Dimentional Structure of Molecules Stereochemistry: Arrangement of the molecule’s constituent atoms in three-dimentional space. A carbon containing compound commonly exist as stereoisomers (Molecules with the same chemical bonds but different configuration). Perspective form Ball-and-stick model Structure of amino acid alanine Space-filling model Configuration is conferred by the presence of either (1) double bonds, around which there is no freedom of rotation or (2) chiral centers, around which substituent groups are arranged in a specific orientation. Geometric isomers (cis-trans isomers) Number of stereoisomers: 2n n = Number of chiral carbon Stereoisomers are the mirror images of each other are called enantiomers. Pairs of stereoisomers that are not mirror images of each other are called diastereomers. Conformation: The position of atoms in space that can be changed by rotation about single bonds, without breaking any bonds. Interactions between Biomolecules are Stereospecific Three-dimentional structures of biomolecules: Configuration and conformation Enzyme-substrate Antigen-antibody Hormone-receptor In living organisms, chiral molecules are usually present in only one of their chiral forms. Amino acids – L isomers, glucose – D isomers. Physical Foundations Living cells and organisms must perform work to stay alive and to reproduce themselves. The synthetic reactions that occur within cells require the input of energy. Living organisms exist in dynamic steady state, never at equilibrium with their surroundings. Organisms transform energy and matter from their surroundings. System: All the constituent reactants and products and solvent that contains them and immediate atmosphere in short everything within a defined region of space (Isolated / Closed / Open Systems). Universe: The system and surroundings together constituent the universe If the system exchanges neither energy nor matter with its surroundings , it is isolated. If the system exchanges energy but not matter with its surroundings, it is a closed system. If it exchanges both energy and matter with its surrounding, it is an open system. A living organism is an open system Cellular energy conversions=Thermodynamic The first law of thermodynamics explains the principle of the conservation of the energy: in any physical or chemical change, the total amount of energy in the universe remain constant, although the form of the energy may change. The second law of thermodynamics: The total entropy of the universe is continually increasing. Entropy (Randomness / Disorder) C6H12O6 + 6O2 → 6CO2 + 6H2O Whenever a chemical reaction results in an increase in the number of molecules-or when a solid substance is converted into liquid or gaseous products, which allow more freedom or molecular movement than solids-molecular disorder, and thus entropy, increases. Entropy change: S Free-energy content: G Enthalpy: H, the number and kinds of bonds Absolute temperature: T (in Kelvin) The definition of free energy is G = H – TS Free energy change G = H – T S IF G IS NEGATIVE, A PROCESS TENDS TO OCCUR SPONTANEOUSLY. Energy requiring reactions are called endergonic. Energy releasing reactions are called exergonic. Aminoacids → Protein ATP → AMP + P-P (or ADP + P) Major Chemical Bonds and Functional Groups in Biological Molecules Formation and Stabilization of Biological Molecules Major biological molecules are macromolecules with very high molecular weight. Macromolecules are stabilized by various types of chemical bonds: 1. Non-covalent interactions 2. Covalent bonds Non-Covalent Interactions-1 Strength of interaction 1. Charge-Charge + - -NH3+ -OOC- 1/r 2. Charge-Dipole q+ q- + H 2O +H 3N- 1/r2 3. Dipole-Dipole q+ q- q+ q- H 2O H 2O 1/r3 4.Charge-Induced -NH3+ dipole q+ q- + - + 1/r4 5.Dipole-Induced q+ q- q+ q- H 2O - + 1/r5 dipole Non-Covalent Interactions-2 6. Dispersion q+ q- - + 1/r6 q- q+ + - 7. Van der Waals interactions: a. Attraction b. Repulsion 1/r12 8. Hydrogen bonds q- q+ C=O H-N Acceptor donor Covalent Bonds The chemistry of living organisms is organized around carbon. Geometry of carbon bonding Tetrahedral structure Covalently linked carbon atoms in biomolecules can form linear chains, branched chains and cyclic structures. Common functional groups in biomolecules C = NH Imino O Phenol R OH R S OH O Sulpho O O Pyrophosphate R P O P OH OH OH Ether Bonds R-OH + HO-R’ R O R’ + H2O Glycosidic Bonds a) O-Glycosidic Bonds b) N-Glycosidic Bonds R-NH2 + HO-R’ R NH R’ + H2O R-OH + HO-R* R O R* + H2O Ester Bonds O O R-C-OH + HO-R’ R-C-O-R’ + H2O O O R-OH + HO-P-O- R-O-P-O- + H2O O- O- Thioester Bond O O R-SH + HO-C-R’ R-S-C-R’ + H2O Amide Bond H O O + R- N-H + HO-C-R’ R-N-C-R’ + H2O H H Dehydrogenation of amines, via the formation of an imine, results in deamination: HH -2H + H2O R-C-N-H R-C=NH R- C=O + NH3 R’ R’ R’ H H -2H + H2O R-C-N-H R-C=NH R- C=O + NH3 H H H Dehydrogenation of aldehyde hydrate produces carboxylic acids: O H -2H R-C-H + H2O R-C-OH R-C= O OH OH Hemiacetal and Hemiketal Formation Despite the presence of reactive group in biological molecules, rarely spontaneous reactions take place. All of the chemical reactions are catalyzed by biocatalysts, enzymes. Further Reading 1. Lehninger Principles of Biochemistry 2. Harper’s Illustrated Biochemistry

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