The Chemical Basis of Life PDF

**The Chemical Basis of Life** **Matter, Mass, and Weight** - **Matter** **-** Anything that occupies space and has mass (solid, liquid, or gas) - **Mass** **-** Amount of matter in an object - **Weight** **-** Gravitational force acting on an object of a given mass **Elements and Atom...

**The Chemical Basis of Life** **Matter, Mass, and Weight** - **Matter** **-** Anything that occupies space and has mass (solid, liquid, or gas) - **Mass** **-** Amount of matter in an object - **Weight** **-** Gravitational force acting on an object of a given mass **Elements and Atoms** - **Element** **-** simplest type of matter having unique chemical properties \- Ex. C, H, O, N, Ca, K, Na, Cl - **Atom** **-** smallest particle of an element that has the chemical characteristics of that element **Atomic Structure** 1\. Atoms consist of neutrons, positively charged protons, and negatively charged electrons. 2\. An atom is electrically neutral because the number of protons equals the number of electrons. 3\. Protons and neutrons are in the nucleus, and electrons can be represented by an electron cloud around the nucleus. - **Atomic Number** **-** number of protons in each atom of an element **-** also the number of electrons (since the number of electrons and number of protons are equal) - **Mass Number** **-** number of protons and neutrons in each atom \- e.g. Mass number of carbon (12) consisting of 6 protons and 6 neutrons **Chemical Bonds** - **What is it?** **-** occurs when outermost electrons are transferred or shared between atoms - **Types** - Ionic binding - Covalent bonding **Ionic Bonding** - **Ions** **-** are electrically charged particles formed when atoms lose or gain electrons **-** Ex. Na^+^ - **Ionic bonding** **-** results when electrons are transferred between atoms, creating oppositely charged ions \- attraction between two oppositely charged ions \- e.g. Na^+^ and Cl^-^ are held together to form sodium chloride (NaCl), or table salt **Covalent Bonding** - Formed when atoms share one or more pairs of electrons - Resulting combination of atoms is called **molecule** - e.g. covalent bond between 2 Hydrogen atoms to form a Hydrogen molecule - **Single covalent bond** - Sharing of one pair of electrons by two atoms - Indicated by a single line between the symbols of the atoms (H-H) - **Double covalent bond** - Sharing of two pairs of electrons by two atoms - e.g. carbon atom combines with two oxygen atoms to form carbon dioxide - Indicated by a double line between the atoms (O═C═O) - **Polar covalent bond** - Unequal, asymmetrical sharing of electrons between two atoms - Molecules with asymmetrical electrical charge are called **polar molecules** - e.g. two hydrogen atoms can share their electrons with an oxygen atom (H~2~O) - **Nonpolar covalent bond** - Equal sharing of electrons between two atoms - Molecules with a symmetrical electrical charge are called **nonpolar molecules** **Hydrogen Bonds** - Polar molecules have a positive end and a negative end - Hydrogen bond forms when positive end of one polar molecule is weakly attracted to negative end of another polar molecule - The attraction between molecules is much weaker than in ionic or covalent bonds - ***Dissociation*** \- the separation of ions in an ionic compound by polar water molecules. \- when ionic compounds dissolve in water, their ions **dissociate**, or separate, from each other because the positively charged ions are attracted to the negative ends of the water molecules, and the negatively charged ions are attracted to the positive ends of the water molecules. \- these dissociated ions are sometimes called ***electrolytes*** Sodium chloride (table salt) dissociates in water. The positively charged Na+ are attracted to the negatively charged oxygen (*red)* end of the water molecule, and the negatively charged Cl− are attracted to the positively charged hydrogen (*blue)* end of the water molecule. **Chemical Reactions** - **What are they?** \- the change of a substance into a new one that has a different *chemical* identity. - **Reactants** **-** substances that are altered or incorporated into another substance in a chemical reaction - **Products** **-** substances resulting from the chemical reaction **A + B → C + D** Reactants Product **Classification of Chemical Reactions** - **Synthesis reactions** **-** two or more reactants combine to form a larger, more complex product \- **e.g. A + B → AB** **ADP + P → ATP** - **Decomposition reactions** **-** reactants are broken down into smaller, less complex products **- e.g. AB → A + B** **ATP → ADP + P** - **Exchange reactions** \- combination of a decomposition reaction and a synthesis reaction **-** in decomposition, reactants are broken down. \- in synthesis, the products of the decomposition reaction are combined **- e.g. AB + CD → AC + BD** **HCl + NaOH → NaCl + H~2~O** - **Reversible reactions** \- a chemical reaction that can proceed from reactants to products and from products to reactants \- when the rate of product formation is equal to the rate of reactant formation, the reaction is said to be at **equilibrium** \- at **equilibrium**, the amount of the reactants relative to the amount of products remains constant. \- indicated by two arrows pointing in opposite directions **- e.g. CO~2~ + H~2~O H^+^ + HCO~3~^-^** **Energy** - **What is it?** \- the capacity to do work - **Subdivided into:** **Potential energy --** stored energy that could do work but is not doing so **Kinetic energy** -- does work by causing the movement of an object - **Chemical energy** \- a form of potential energy stored in the bonds of chemical compounds (atoms and molecules). It is released in a chemical reaction, often producing heat as a by-product (exothermic reaction). Batteries, biomass, petroleum, natural gas, and coal are examples of stored chemical energy. **-** e.g. breakdown of ATP **ATP** - **What does it stand for?** adenosine triphosphate - **What is it?** often called the energy currency of cells because it is capable of both storing and providing energy - When ATP is broken down (ATP → ADP + P) energy is released. **Rate of Chemical Reactions** - The rate of a chemical reaction increases when 1. the concentration of the reactants increases 2. the temperature increases 3. catalyst is present - A catalyst (enzyme) increases the rate of a chemical reaction without being altered permanently **Acids and Bases** - **Acid** \- a proton (hydrogen ion) donor \- any substance that releases hydrogen ions (H^+^) in water \- e.g. HCl (hydrochloric acid) in the stomach forms H^+^ and chloride ions (Cl^-^) - **Base** \- a proton acceptor \- Ex. NaOH (sodium hydroxide) forms sodium ions (Na^+^) and hydroxide ions (OH^-^). The hydroxide ion is a proton acceptor that binds with a H^+^ to form water. **pH Scale** - **Neutral solution** \- has equal number of H^+^ and OH^-^ \- pH of 7 - **Acidic solution** \- has a greater concentration of H^+^ than of OH^-^ \- pH less than 7 - **Basic solution** \- has fewer H^+^ than OH^-^ \- pH greater than 7.0 - **7.35 to 7.45** \- the normal pH range for human blood - **Acidosis** \- blood pH drops below 7.35 \- nervous system is depressed, the individual becomes disoriented and possibly comatose - **Alkalosis** \- blood pH rises above 7.45 \- nervous system becomes overexcitable, individual can be extremely nervous, or have convulsions - **Salts** **-** forms when an acid reacts with a base \- e.g. HCl + NaOH →NaCl + H~2~O - **Buffers** \- chemicals that resist changes in pH when acids or bases are added **Inorganic vs. Organic Molecules** - **Inorganic molecules** \- those that do not contain carbon but include such carbon-containing substances as carbon dioxide (CO~2~) and carbon monoxide (CO). **- e.g.** O2, CO~2~ and water - **Organic molecules** **-** contain carbon atoms bound together by covalent bonds **Inorganic Molecules** - **Oxygen (O~2~)** \- small, nonpolar, inorganic molecule consisting of 2 oxygen atoms bound together by a double covalent bond. - **Carbon dioxide (CO~2~)** **-** consists of one carbon atom bound to 2 oxygen atoms \- each oxygen atom is bound to the carbon atom by a double covalent bond - **Oxygen (O~2~)** \- small, nonpolar, inorganic molecule consisting of 2 oxygen atoms bound together by a double covalent bond. - **Carbon dioxide (CO~2~)** **-** consists of one carbon atom bound to 2 oxygen atoms \- each oxygen atom is bound to the carbon atom by a double covalent bond - **Carbon dioxide (CO~2~)** **-** produced when food molecules, such as glucose, are metabolized within the cells of the body \- once **CO~2~** is produced, it is eliminated from the cell as a metabolic by-product, transferred to the lungs by the blood, and exhaled during respiration. \- If **CO~2~** is allowed to accumulate within cells, it becomes toxic. - **Water (H~2~O)** **-** an inorganic molecule that consists of one atom of oxygen joined by polar covalent bonds to two atoms of hydrogen. Roles: \- Stabilizing body temperature \- Providing protection \- Facilitating chemical reactions \- Transporting substances **Organic Molecules** **1. CARBOHYDRATES** - Provide the body with energy - Contain C, H, O atoms - For each carbon atom, there are 2 hydrogen atoms and 1 oxygen atom \- Ex. C~6~H~12~O~6~ - **Monosaccharides** are the building blocks of carbohydrates that form more complex carbohydrates, such as disaccharides and polysaccharides - **Disaccharides** **-** 2 monosaccharides joined by a covalent bond \- e.g. Glucose + fructose = sucrose \- e.g. Glucose + galactose = lactose - **Polysaccharides** \- many monosaccharides bound in long chains \- Ex. Starch, grain, vegetables, glycogen, etc. **Functions of Carbohydrates** - Short-term energy storage - Converted to glucose quickly - Glucose is used to make ATP (energy) - Brain cells require glucose **2. LIPIDS** - Substances that dissolve in nonpolar solvents, such as alcohol or acetone, but not in polar solvents, such as water. - composed mainly of carbon, hydrogen, and oxygen, but other elements, such as phosphorus and nitrogen, are minor components of some lipids. - contain a lower proportion of oxygen to carbon than do carbohydrates. - e.g. Fats, phospholipids, eicosanoids, and steroids **A. Fats** - important energy-storage molecules; they also pad and insulate the body. - The building blocks of fats are **glycerol** and **fatty acids.** - Glycerol is a 3-carbon molecule with a **hydroxyl group (---OH)** attached to each carbon atom, and fatty acids consist of a carbon chain with a **carboxyl group** attached at one end. - **Triglycerides** are the most common type of fat molecules. These have three fatty acids bound to a glycerol molecule. **Fatty Acids** - **Saturated if it contains only single covalent bonds between the carbon atoms. Sources of saturated fats include beef, pork, whole milk, cheese, butter, eggs, coconut oil, and palm oil.** - **Unsaturated if it has one or more double covalent bonds. They are the best type of fats in the diet because, unlike saturated fats, they do not contribute to the development of cardiovascular disease.** a. Palmitic acid is a saturated fatty acid; it contains no double bonds between the carbons. (b) Linolenic acid is an unsaturated fatty acid; note the three double bonds between the carbons, which cause the molecule to have a bent shape. **- Monounsaturated fats,** such as olive and peanut oils, have one double covalent bond between carbon atoms. \- **Polyunsaturated fats,** such as safflower, sunflower, corn, and fish oils, have two or more double covalent bonds between carbon atoms. **- Trans fats** are unsaturated fats that have been chemically altered by the addition of H atoms. The process makes the fats more saturated and hence more solid and stable (longer shelf-life). However, the change in structure of these chemicals makes the consumption of *trans fats an even greater factor than saturated fats in the risk for cardiovascular disease.* **B. Phospholipids** - similar to triglycerides, except that one of the fatty acids bound to the glycerol is replaced by a molecule containing phosphorus. - A phospholipid is polar at the end of the molecule to which the phosphate is bound and nonpolar at the other end. - The polar end of the molecule is attracted to water and is said to be **hydrophilic (water-loving).** The nonpolar end is repelled by water and is said to be **hydrophobic (water-fearing).** **C. Eicosanoids** - a group of important chemicals derived from fatty acids. - Eicosanoids are made in most cells and are important regulatory molecules. Among their numerous effects is their role in the response of tissues to injuries. - **e.g. prostaglandins** which have been implicated in regulating the secretion of some hormones, blood clotting, some reproductive functions, and many other processes. **D. Steroids** - composed of carbon atoms bound together into four ring like structures. e.g. Cholesterol is an important steroid because other steroid molecules are synthesized from it. Bile salts, which increase fat absorption in the intestines, are derived from cholesterol, as are the reproductive hormones estrogen, progesterone, and testosterone. In addition, cholesterol is an important component of cell membranes. Steroids are four-ringed molecules that differ from one another according to the groups attached to the rings. Cholesterol, the most common steroid, can be modified to produce other steroids **Functions of Lipids** - Long term energy storage - Insulates against heat loss - Protective cushion for organs - Cholesterol is part of the cell membrane structure **3. PROTEINS** - All **proteins contain carbon, hydrogen, oxygen, and nitrogen, and** most have some sulfur. - The building blocks of proteins are **amino acids,** which are organic acids containing an **amine** **group (--NH2)** and a **carboxyl group.** - There are 20 basic types of amino acids. Humans can synthesize 12 of them from simple organic molecules, but the remaining 8 so-called essential amino acids must be obtained in the diet. Denaturation - the alteration of a protein shape through some form of external stress (e.g, abnormally high temperatures, changes in pH), in such a way that it will no longer be able to carry out its cellular function. **Functions of Proteins** - Used to make skin, hair, nails, muscles - For transport (e.g. Hemoglobin transports oxygen in the blood) - Act as enzymes - Immune system functions - Muscle contractions (actin and myosin) - Part of cell membrane Enzymes - Biological molecules (proteins) that accelerate, or catalyze chemical reactions. - A protein catalyst that increases the rate of a chemical reaction without being altered permanently **4. Nucleic Acids** - Composed of C, H, O, N, P - **Nucleotides are the building blocks** - Each nucleotide is composed of a monosaccharide with an attached phosphate and a nitrogenous organic base. - DNA nucleotides contain the monosaccharide deoxyribose and the organic bases adenine, thymine, guanine, and cytosine. DNA occurs as a double strand of joined nucleotides and is the genetic material of cells. RNA nucleotides are composed of the monosaccharide ribose. The organic bases are the same as for DNA, except that thymine is replaced with uracil. RNA play important roles in gene expression or protein synthesis