Biochemistry Lecture 1: Introduction Biochemistry Deals with the study of the chemistry of living organisms Biochemical substances which are found in living organisms and the chemical interactions of these substances with each other Divided into 2 groups Application of the principles and methods of chemistry to the field of biology and physiology Concerned with the physio-chemical processes underlying Digestion, absorption, circulation, respiration, metabolism, growth, and reproduction Why study Biochemistry? To describe and explain in molecular terms all chemical processes of living cells Knowledge in biochemistry is essential to all life sciences A reciprocal relationship between biochemistry and medicine has stimulated mutual advances in health concepts, discovery of diseases, and treatment of diseases Biochemistry and medicine works hand in hand E.g. Louis Pasteur – Discovered fermentation Fermentation – Conversion of sugar to alcohol For years, it has been known that yeasts can ferment sugars to ethyl alcohol but the cell needs to be intact In 1899, the Buchner brothers found out that fermentation can also occur without intact cells More investigations in Biochemistry reveal the importance of biochemical substances (Phosphate, ADP, ATP, and enzymes) Normal biochemical processes are the basis of health Biochemical research has impact on nutrition and preventive medicine Understand the importance of nutrition and maintain health Optimal dietary intake of vitamin, certain amino acids, minerals, and water Will help us understand diseases Most and perhaps all disease has biochemical basis Two-Way Street: Medicine and Biochemistry In the medical field, it has been important to maintain a patient’s health and provide effective treatment of diseases Scientists research on basic substances that may have caused diseases and lead to treatment In Biochemistry, we understand more fundamental concepts which impacts both maintenance of health and treatment of diseases Knowledge of nucleic acids, proteins, lipids, carbohydrates, and other concepts of Biochemistry is important because it clarifies our understanding of diseases such as: Genetic diseases Sickle cell anemia Atherosclerosis Diabetes mellitus E.g. Archibald Garrod (English Physician) – Studied patients and genetic diseases such as albinism Albinism – Results from abnormalities of nucleic acids With the presence of genetic diseases, scientists go back to the more basic molecules (nucleic acids) Scientists also investigated that problems in lipids (fats), such as Familial Hypercholesterolemia (too much cholesterol), prevents the body to remove LDL (low density lipoprotein – bad cholesterol) Inability to remove LDL from the blood results to Atherosclerosis Investigation of protein structure and function led to the discovery of diseases (sickle cell anemia) Patients with sickle cell anemia have an abnormal hemoglobin “S” (HbS) Hemoglobin – Main component of red blood cells HbS causes the RBC’s to look like the C-shape farm tool called sickle and the RBC’s become very hard and they die early which results to poor oxygen delivery in the body Human Genome Project Major advances to biochemistry and health is related to this A rough draft is complete, > 90% sequenced (human genome) DNA structure – Double helix After 50 years, in 2003 – Sequence of human genome was completed Represents approximately 75,000 human genes (Estimated range: 30,000 to 120,000) Based on the DNA from six individuals; Thus, provides little information regarding genetic diversity within the population Estimated that 95% of our DNA content is not important; Represents evolutionary “baggage” Highlights the need for continued sequencing of genomes from other organisms to identify essential genes and their functions Biochemistry pre-dated the human genome project HGP has influenced a lot of disciplines and areas of research 4 Major Classes of Biomolecules Proteins – Needed for the synthesis of enzymes, hormones, cells, and tissues with the building blocks known as amino acids Nucleic Acids – Contains all instructions needed in making a complete organism as well as the functions of each cell 2 types of Nucleic Acids: Deoxyribonucleic Acid Ribonucleic Acid Carbohydrates – Most abundant class of bioorganic molecules Provides the body with energy Lipids (Fats) – Provides a major way of strong chemical energy and carbon Biochemistry Clinical Biochemistry – Helps to diagnose and manage diseases through analysis of fluids and substances Physiological Chemistry Normal processes in the body Pathological Chemistry Abnormal processes in the body Is both a life science and a chemical science It explores the chemistry of living organisms and the molecular basis for the changes occurring in living cells Has become the foundation for understanding all biological processes It has provided explanations for the causes of many diseases in humans, animals, and plants Major Causes of Disease Physical Agents – Mechanical trauma, temperature extremes, radiation (includes radiation emitted by x-rays), and electric shock Chemical Agents – Toxic compounds, drugs Biologic Agents – Viruses, bacteria, fungi, parasites, and biochemistry professors Genetic Disease Oxygen Lack – Loss of blood (can be acute or chronic), decreased oxygen-carrying capacity of blood, and mitochondrial poisoning Immunologic Reactions – Anaphylaxis, autoimmune disorders Anaphylaxis – Hypersensitivity to foreign proteins or drugs; Results from sensitization following prior contact with causative agent Nutritional Imbalances – Deficiencies, excesses Endocrine Imbalances – Hormonal deficiencies/excesses REVIEW OF BIOMOLECULES 20% 80% Contain a delocalized bonding that involves 6-membered carbon rings Contain a benzene ring or a derivative of the benzene ring Unsaturated – 1 or more carboncarbon bonds are present May contain double or triple bonds or both Chemically more reactive than saturated hydrocarbons – Due to presence of multiple bonds 3 classes based on the type of multiple bonds: Alkenes, Alkynes, and Aromatics Take note of functional groups Functional groups - Portions of a molecule where most chemical reactions take place In a saturated hydrocarbon – Functional groups = carboncarbon multiple bond Hydrocar bons Aliphatic Saturated Contain single C-H bond Alkanes Contain only single bond (Ethane) Inorganic Compounds (Approx. 1.7 million) Organic Compounds (Approx. 10 million) Unsaturated Contain 2 or more C-H bond Alkenes Contain at least one double bond (Ethene) Alkynes Contain at least one triple bond (Ethyne) Aromatic General molecular formula for Alkanes – CnH2n+2 Single carbon-carbon bond Carbon atom arrangement – Acyclic (no rings) N – number of carbon atoms present # of hydrogen atoms present is always twice the number of carbon atoms + 2 3 simplest alkanes: Methane Ethane Propane Organic Compounds – Obtained from living organisms Inorganic Compounds – Obtained from mineral constituents of the earth Organic Compounds – Chemical basis of life 2 General Classifications HYDROCARBONS Contain only carbon and hydrogen ALIPATHIC HYDROCARBONS Linear chains of carbon atoms No benzene rings or a derivative of the benzene ring ALKANES, ALKENES, AND ALKYNES Alkenes – Contain 1 or more carbon-carbon double bond Alkynes – Contain 1 or more carbon-carbon triple bond Saturated – Includes simplest types of hydrocarbons Named as such because there is no more room for something else (additional atoms) AROMATIC HYDROCARBONS Close rings of carbon atoms Aside from the carbon at each point, there are also hydrogens connected Two Categories of Saturated Hydrocarbons Acyclic There are 3 different methods for showing 3D structures of Alkanes Dash-wedge-line structures Ball-and-stick models Space-filling models Structural Formula Structure of Alkanes and other types of organic compounds are generally presented in 2 dimensions (2D) 3D is difficult to draw Makes no attempt to perfectly portray the angles of bonds and geometry of molecules that should be present in each of the compounds Two-dimensional structural representation that shows how the various atoms in a molecule are bonded to each other Two types: Expanded and condensed Expanded – Shows all atoms and all bonds Condensed – Uses groupings of atoms in which central atoms and the atoms connected are written as a group Cyclic Alkenes Ending –ene – Double bond is present Alkenes are acyclic containing one or more double bonds General molecular formula: CnH2n Functional group: Carbon-carbon double bond Simplest type of alkene contains only one double bond Cycloalkenes – Cyclic unsaturated hydrocarbon that contains 1 or more carbon-carbon double bonds within the ring system Example of naturally occurring alkene = Pheromones – Compound used by insects and some animals to transmit messages to other members of the same species Alkynes 1st carbon is bonded to 3 hydrogen atoms, 4th is bonded to the middle carbon atom, middle carbon atom is bonded to 2 hydrogen atoms and to the last carbon atom, last carbon atom is bonded to the middle and has bonds to 3 hydrogen atoms Condensed structural formula could also be abbreviated: Both mean the same Structural Formula (Continuation) Line-angle structural formula Line – Represents a carbon-carbon bond Carbon atom is understood to be present at every point where 2 lines meet and at the ends of the line General molecular formula: CnH2n-2 Acyclic unsaturated hydrocarbons that contain 1 or more carboncarbon triple bonds Alkyne functional group: Carbon-carbon triple bond Simplest alkyne: Ethyne (Acetylene) – A gas that burns with a very hot flame; Used to melt and connect pieces of metal Aromatic Hydrocarbons It is an unsaturated cyclic hydrocarbon that does not readily undergo addition reactions E.g., Benzene Contains a delocalized bonding Delocalized – Covalent bond in which electrons are shared among more than 2 atoms Circle – Electrons associated with double bonds that move around the ring Also represents an aromatic ring system Functional group present in aromatic compounds General classifications Substituted Hydrocarbons – Hydrocarbon derivatives Which one or more hydrogen atoms is replaced by another atom or group of atoms Functional group Is an atom or group of atoms arranged in a particular way that is primarily responsible for the chemical and physical properties of the molecule in which it is found Alcohol is the first type of hydrocarbon derivative containing a single oxygen atom Functional group for alcohol: Hydroxyl group (-OH) General formula: R-OH Hydroxyl group is bonded to a saturated carbon atom Ether are good solvents for other organic compounds Organic compound in which an oxygen atom is bonded to 2 carbon atoms using a single bond Haloalkanes – Halogeno alkanes or alkyl halides Derived from alkanes containing one or more halogens Examples of Halogens: Fluorine Chlorine Bromine Iodine Amines are an organic derivative of ammonia Functional group contains nitrogen Functional group: Amino group Represented by –NH2 Neurotransmitters – Biochemically important amines E.g. Acetylcholine Next 3 functional groups contains Carbonyl Carbonyl functional group – Carbon bonded to oxygen using a double bond Differ on what atom the carbonyl carbon atom is bonded to Aldehyde – Functional group is bonded to hydrogen atoms Ketones – Functional group is bonded to carbon atoms Carboxylic Acid Carboxylic – Organic compound whose functional group is carboxyl group Carbonyl group is bonded to a hydroxyl group Ester Carbonyl carbon atom must be bonded to an oxygen These 4 contains: Carbon, hydrogen, and oxygen Amides contain nitrogen A carboxylic acid derivative Amino group replaces the hydroxyl group of carboxylic acid Functional group: Carbonyl group bonded to NH Carbon-Oxygen Groups 2nd – Aldehyde 4th – Carboxylic Acid Carbon-Sulfur Groups 1st – Sulfur-containing carbonyl group Addition of sulfur to carbonyl group – Results to different classes of compounds Depends on whether the sulfur atom replaces oxygen or carbon If oxygen is replaced by sulfur – Results to thiocarbonyl compounds (E.g. Thioaldehydes – Thiols; Thioketones – Thions) If carbon is replaced by sulfur – Results to sulfoxides Functional group: Carbon or oxygen bonded to sulfur by a double bond Carbon-Nitrogen Groups Esters and Amines Hydrophobicity vs. Hydrophilicity Hydrophobic Refers to the physical property of a molecule that is repelled from a mass of water Alkanes, oils, and fats Hydrophilic Refers to a physical property of a molecule that can transiently bond with water (H2O) through hydrogen bonding Chemical Bonds – Attractive force holding 2 atoms together. It results from interactions between electrons Chemical compounds – Divided into 2 broad classes Ionic compounds Have high melting points Good conductors of electricity when in molten or liquid state or in a solution Molecular compounds Have lower melting points Does not conduct electricity in molten state Both also differ in their chemical bonds 2 Principal Classes Ionic Bonding Involves a transfer of one or more electrons from one atom (or group of atoms) to another, leading to the formation of an ionic bond Present in ionic compounds Covalent Bonding Involves a sharing pairs of electrons between atoms Present in molecular compounds Non-polar covalent bond – There is equal sharing of electrons Polar covalent bond – There is unequal sharing of electrons Hydrogen Bonding Hydrogen atom is bonded to a small, highly electronegative atom Used by water to self-associate Can associate with functional groups and enables water to dissolve organic molecules Properties of Water Composed of two hydrogen atoms linked by covalent bonds to a single atom of oxygen Water molecule is irregular – Slightly skewed tetrahedron Contains oxygen covalently bonded to 2 hydrogen atoms Hydrogen bonding in water. Hydrogen bonds (Shown as dashed green lines) are formed between water molecules to produce a highly ordered and open structure Interactions with Water – Involves more dispersed variations of electromagnetic interactions between or within molecules Non-Covalent Bonds Ionic Bond or Electrostatic Interactions This occurs between oppositely charged groups within or between biomolecules Involves salt bridges Salt bridges – Possess a strength that is comparable to hydrogen bonds; Has the ability to act over a larger distance Hence, electrostatic interactions are involved in binding of molecules and ions in proteins and nucleic acids Hydrogen Bond Hydrogen bonds between 2 molecules will be disrupted by water Water forms hydrogen bonds with the molecules Conversely, hydrogen bonding between 2 molecules is stronger in the absence of water Van der Waals Interactions/Forces Results from attractions generated by the rapid movement of electrons of all neutral; atoms Biomolecules which are neither polar nor charged interact with each other using this interaction Van der Waals forces is weaker than hydrogen bonds and they act over very short distances However, it is extremely numerous
