L2 BIO 101 Chemistry of Life PDF

Chemistry of Life Course: BIO 101: Introduction to Biology Chapter: 2 Matter: Anything physical that takes up space is matter. The amount of matter is its mass. Matter is composed of elements and compounds.  Elements An element is a substance that cannot be broken down into any other sub...

Chemistry of Life Course: BIO 101: Introduction to Biology Chapter: 2 Matter: Anything physical that takes up space is matter. The amount of matter is its mass. Matter is composed of elements and compounds.  Elements An element is a substance that cannot be broken down into any other substance. Every element is made up of its own type of atom. This is why the chemical elements are all very different from each other. Fundamental forms of matter. The periodic table lists all the known elements, grouping together those with similar properties. Most elements are metals, which are shiny and conduct electricity well. Metals include gold, aluminium and iron which are all solid at room temperature. Mercury is the only metal that is liquid at room temperature. Some elements are non-metals. Most nonmetals are gases at room temperature and do not conduct electricity. Non-metal elements with these properties include oxygen, hydrogen and chlorine. A few non-metals, such as carbon and sulphur, are in a solid state at room temperature. What Are Atoms? Smallest particles that retain properties of an element Made up of subatomic particles: Protons (+) Electrons (-) Neutrons (no charge) 4  Hydrogen and Helium Atoms electron proton neutron HYDROGEN HELIUM 5 Atomic Number Number of protons All atoms of an element have the same atomic number Atomic number of hydrogen = 1 Atomic number of carbon = 6 Atomic number of sodium= 11 6 Mass Number Number of protons + Number of neutrons Isotopes vary in mass number Isotopes vary in mass number 7 Isotopes Atoms of an element with different numbers of neutrons (different mass numbers) Hydrogen 1 or Protium has 1 proton, 0 neutron Hydrogen 2 or Deuterium has 1 proton, 1 neutron Hydrogen 3 or Tritium has 1 proton, 2 neutrons 8 Electrons Carry a negative charge (-) Repel one another Are attracted to protons in the nucleus Move in orbitals 9 Electron Orbitals Orbitals are volumes of space that surround the nucleus Orbitals can hold up to two electrons Atoms differ in the number of occupied orbitals Orbitals closest to nucleus are lower energy and are filled first 10 Shell Model Shell is something that is made up of orbitals First shell Lowest energy Holds 1 orbital with up to 2 electrons Second shell CALCIUM 20p+ , 20e- 4 orbitals hold up to 8 electrons 11 Chemical Bonds Bond is union between electron structures of atoms Atoms bond to form molecules Molecules may contain atoms of only one element - O2 Molecules of compounds contain more than one element - H2O 12 Chemical Bonds 13 Important Bonds in Biological Molecules Ionic Bonds Covalent Bonds Hydrogen Bonds 14 1. Ionic Bonding In ionic bond one atom loses electrons, becomes positively charged ion and another atom gains these electrons, becomes negatively charged ion Charge difference attracts the two ions to each other 15 Ion Formation Atom has equal number of electrons and protons - no net charge Atom loses electron(s), becomes positively charged ion Atom gains electron(s), becomes negatively charged ion 16  Formation of NaCl: example of ionic bond formation Sodium atom (Na) Outer shell has one electron Chlorine atom (Cl) Outer shell has seven electrons Na transfers electron to Cl forming Na+ and Cl- Ions remain together as NaCl 17 2. Hydrogen Bonding Hydrogen bonds are bonds created between hydrogen and highly electronegative molecules. Molecules held together by polar covalent bonds has no NET charge However, atoms of the molecule carry different charges Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule 18 Water containing Hydrogen bond is a Polar Molecule Molecule has no net charge O Oxygen end has a slight negative charge Hydrogen end has a slight positive charge H H 19 Hydrophilic & Hydrophobic Substances Hydrophilic substances Polar Hydrogen bond with water Example: sugar Hydrophobic substances Nonpolar Repelled by water Example: oil 20 Why Ice Floats In ice, hydrogen bonds lock molecules in a lattice Water molecules in lattice are spaced farther apart than those in liquid water Ice is less dense than water 21  Liquid Water Water is both weak base and weak acid The acidity/Basicity of a solution is measured by pH. A figure expressing the acidity or alkalinity of a solution on a logarithmic scale on which 7 is neutral, H+ lower values are more acidic and higher values more + _ O H+ H alkaline. The values span from 0 to 14. The pH is + _ O + H + equal to −log₁₀c, where c is the hydrogen ion concentration in moles per litre. 22 The pH Scale Measures H+ concentration of fluid Change of 1 on scale means 10X change in H+ concentration Highest H+ Lowest H+ 0---------------------7-------------------14 Acidic Neutral Basic 23 Examples of pH Pure water is neutral with pH of 7.0 Acidic Stomach acid: pH 1.0 - 3.0 Lemon juice: pH 2.3 Basic Seawater: pH 7.8 - 8.3 Baking soda: pH 9.0 24 Acids & Bases Acids Donate H+ when dissolved in water Acidic solutions have pH < 7 Example: HCl Bases Accept H+ when dissolved in water Basic solutions have pH > 7 Example: NH3 25 Weak and Strong Acids Weak acids Reluctant H+ donors Can also accept H after giving it up Carbonic acid (H2CO3) is example Strong acids Completely give up H+ when dissolved Hydrochloric acid (HCl) is example 26  Buffer System or Buffer Solution A buffer solution is an aqueous solution Many life forms thrive only in a of a weak acid and its conjugate base, relatively small pH range, so they or a weak base and its conjugate acid. utilize a buffer solution to maintain Its pH changes very little when a small a constant pH. amount of strong acid or base is added One example of a buffer solution to it. found in nature is blood. The Buffer solutions are used as a means of body’s acid–base balance is keeping pH at a nearly constant value normally tightly regulated, keeping in a wide variety of chemical the arterial blood pH between 7.38 applications. and 7.42. 27 Types of Buffer Solutions Buffers are broadly divided into two types: acidic and alkaline buffer solutions. Acidic buffers are solutions that have a pH below 7 and contain a weak acid and one of its salts. For example, a mixture of acetic acid and sodium acetate acts as a buffer solution with a pH of about 4.75. Alkaline buffers, on the other hand, have a pH above 7 and contain a weak base and one of its salts. For example, a mixture of ammonium chloride and ammonium hydroxide acts as a buffer solution with a pH of about 9.25. 28 3. Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell Single covalent bond, H2 Double covalent bond, H2O Triple covalent bond, NH3 29 Covalent Bonding Depending on the polarity that is creation of positive and negative poles, covalent bonds can be of two types. 1. Non-polar covalent bond 2. Polar covalent bond 30 Nonpolar Covalent Bonds Atoms share electrons equally Nuclei of atoms have same number of protons Example: Hydrogen gas (H-H) 31 Polar Covalent Bonds Number of protons in nuclei of participating atoms is NOT equal Electrons spend more time near nucleus with most protons Water - Electrons more attracted to O nucleus than to H nuclei 32 Polar Covalent Bonds 33  Carbon Bonding Behavior The carbon atom is unique among elements in its tendency to form extensive networks of covalent bonds not only with other elements but also with itself. Carbon has four valence electrons, so it can achieve a full outer energy level by forming four covalent bonds. Carbon can form single, double, or triple covalent bonds with other carbon atoms. 34  35 Fig- Carbon bonds on different compounds  Functional Groups A functional group is defined as an atom or group of atoms within a molecule that has similar chemical properties whenever it appears in various compounds. They give organic compounds their different properties. Example- carboxyl (-COOH) present in carboxylic acids 36 37  Structure 1- Allylamine Structure 2- Ethane-1,2-diamine Structure 3- Propane-1,3-diamine Structure 38 4- 1-Heptanamine Fig- The same functional group in different compounds Polyatomic Compounds There are two types of compounds: 1. Inorganic Compounds: matter which is not derived from living organisms and contains no organically produced carbon. 2. Organic Compounds: large source of carbon-based compounds found within natural and engineered, terrestrial, and aquatic environments. What are Biomolecules? Biomolecule are molecules and ions present in organisms that are essential to one or more biological processes. Most biomolecules are organic compounds containing four major elements e.g. carbon, hydrogen, oxygen, and nitrogen. 40  Carbohydrates A carbohydrate is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms. Carbohydrates perform numerous roles in living organisms. They can storage energy(e.g. starch and glycogen), act as structural components 41 (e.g. cellulose in plants) and even form the backbone of the genetic molecule known as RNA.  42 Fig- Classification of carbohydrates  Glycosidic Bond A glycosidic bond is a covalent bond formed between a carbohydrate molecule and another molecule. In this reaction, the hydroxyl group (OH) of the carbohydrate combines with the hydrogen of another organic molecule, releasing a molecule of water and forming a covalent bond. 43 Fig: Sucrose is formed when a monomer of glucose and a monomer of fructose are joined in a dehydration reaction  Lipids Lipids are molecules that contain hydrocarbons and make up the basic building blocks of biological membranes. They have various function in living cells. Lipids are not soluble in water as they are non-polar, but are soluble in non-polar solvents such as chloroform. Examples of lipids include fats, oils, waxes, certain vitamins (such as A, D, E and K), hormones etc. The functions of lipids include storing energy, signaling, and acting as structural components of cell membranes. 44  Ester Bond Glycerol is a small organic molecule with three hydroxyl (OH) groups, while a fatty acid consists of a long hydrocarbon chain attached to a carboxyl group. The basic unit of lipids are triglycerides. A triglyceride is formed when 1 glycerol molecule links with 3 fatty acid molecules by means of ester bond (covalent 45 bond). Fig: The glycerol molecule (having three OH− groups) links with three fatty acids via an ester bond  3 Major Types of Lipids Glycolipids are a class of lipids containing carbohydrate residues. Their role is to maintain the stability of the cell membrane and to facilitate cellular recognition. A phospholipid is a type of lipid molecule that is the main component of the cell membrane. Sterols are unique among lipids in that they have a multiple-ring structure. They contain a planar (flat) steroid ring, for example- cholesterol. 46  Fig- Glycolipid 47 Fig- Sterol Saturated and Unsaturated Fats 48  Proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins within a cell have many functions, including building cellular structures and serving as enzyme catalysts for cellular chemical reactions that give cells their specific characteristics. They help in metabolism by providing 49 structural support and by acting as enzymes, carriers and hormones.  Peptide Bond Within a protein, multiple amino acids are linked together by peptide bonds, thereby forming a long chain. A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts 50 with the amino group of the other molecule, releasing a molecule of water (H2O). Fig- Formation of a peptide bond 51  52 Figure 7: Protein structure has four levels of organization  Protein Shapes Fibrous proteins Globular proteins are are typically generally compact, elongated and soluble, and insoluble. spherical in shape. Examples - Examples - collagen, found in Myoglobin, which is the bones, found in muscle muscles, skin tissues. 53 Fig: Fibrous and globular proteins  Nucleic Acids Nucleic acids are essential for all forms of life, and it is found in all cells. The functions of nucleic acids have to do with the storage and expression of genetic information. The building blocks of nucleic acids are nucleotides. 54  Deoxyribonucleotides Nucleotides that compose of DNA are called deoxyribonucleotides. The three components of a deoxyribonucleotide are a five-carbon sugar called deoxyribose, a phosphate group and a nitrogenous base. DNA stores the information needed to build and control the cell. 55 Fig: (a) deoxyribonucleotide. (b) The five carbons within deoxyribose  Nitrogenous Bases The nitrogenous bases adenine (A) and guanine (G) are the purines; they have a double-ring structure with a six-carbon ring fused to a five-carbon ring. The pyrimidines, cytosine (C) and thymine (T), are smaller nitrogenous bases that have only a six-carbon ring structure. Thymine is unique to DNA 56 Fig- Structure of purines and pyrimidines  Complementary Base Pairs In DNA, adenine (A) and thymine (T) are complementary base pairs, and cytosine (C) and guanine (G) are also complementary base pairs. The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds between them, whereas cytosine 57 and guanine form three hydrogen bonds between them.  Ribonucleotides Nucleotides that compose of RNA are called ribonucleotides. The three components of a ribonucleotide are a pentose sugar called ribose, a phosphate group and a nitrogenous bases (Adenine, Uracil, Guanine and Cytosine). The RNA-specific pyrimidine uracil forms a complementary base pair with adenine and is used instead of the thymine used in DNA. The primary role of RNA is to convert the information stored in DNA into proteins. 58 Fig -(a) Ribonucleotides contain the pentose sugar ribose instead of the deoxyribose found in deoxyribonucleotides. (b) RNA contains the pyrimidine uracil in place59 of thymine found in DNA. 60