Chemistry of life UNIT 1 - CHAPTER 2

2.1 Atoms Atom - the basic unit of matter Subatomic particles Protons - positively charged particles (+) Neutrons – particles with a neutral charge (0) Electrons - negatively charged particle (−) Nucleus – center of the atom formed by a strong attraction between protons and neutrons

Atomic Structure

Elements Element - pure substance that consists entirely of one type of atom Ex. C – Carbon, He – Helium, O – Oxygen

Elements Atomic Number – the number of protons in an atom Atomic Mass – the number of protons + neutrons in an atom Atomic Charge – the difference between protons and electrons in an atom

elements

Isotopes Isotopes - atoms of the same element that differ in the number of neutrons The sum of the protons and neutrons in the nucleus of an atom is called its mass number (atomic mass). Isotopes are identified by their mass numbers. For example, carbon has three isotopes—carbon-12, carbon-13, and carbon-14. Each isotope has a different number of neutrons. Because they have the same number of electrons, all isotopes of an element have the same chemical properties.

Isotopes of Carbon 6 electrons 6 protons 6 neutrons 6 electrons

Radioactive Isotopes radioactive isotopes- have unstable nuclei that break down over time -radiation can be dangerous -can also be helpful to: *determine age of rocks *treat cancer *kill bacteria that cause food to spoil *trace substances through organisms

ions ion – a charged atom (+ or -) cation – a positively charged atom (+) an atom that loses one or more electrons anion – a negatively charged atom (-) an atom that gains one or more electrons

Using the Periodic Table Calculations: Atomic Number = number of protons Atomic Mass = protons + neutrons a.m. = p + n Atomic Charge = protons – electrons charge = p - e

Chemical Compounds chemical compound - a substance formed by the chemical combination of two or more elements in definite proportions. chemical formula- shows the kinds and number of each element in a compound ex- H2O CO2 H3PO4

Chemical bonds chemical bonds – a force that holds the atoms in compounds together The electrons that are available to form bonds are called valence electrons. Bond formation involves the electrons that surround each atomic nucleus. valence electrons e- in outermost energy level are involved in bonding

Ionic bonds ionic bond – bond formed when one or more electrons are transferred from one atom to another.

Ionic bond

Covalent Bonds covalent bond – bond formed when electrons are shared between atoms.

Covalent bonds molecule - the structure that results when atoms are joined together by covalent bonds

Covalent bonds

Covalent bonds When the atoms share two electrons, the bond is called a single bond. When atoms share four electrons it is called a double bond. When atoms share six electrons it is called a triple bond.

Van der waals forces Van der Waals forces- intermolecular force between molecules not a bond - weaker than ionic and covalent bonds ex: geckos on walls

2.2 Properties of Water

Polarity polarity – an unequal distribution of electrons between atoms of different elements All molecules are neutral (have a zero charge). Ex. H2O – Oxygen has 8 protons, Hydrogen has 1. Oxygen ‘s nucleus has a stronger attraction for electrons. Oxygen will have a partial negative charge, and Hydrogen a slight positive charge.

Polarity

Hydrogen bonds hydrogen bond – a weak bond formed by the difference in charge between polar molecules. A positive H atom will bond to a negative O, N, or F atom across polar molecules. Water can form 4 Hydrogen bonds allowing for special properties like cohesion and adhesion.

Hydrogen bonds

cohesion cohesion – attraction of molecules of the same substance Hydrogen Bonds - Water molecules come together forming hydrogen bonds causing cohesive properties. Water droplets – Cohesion of water molecules causes water to form droplets. Surface tension – Cohesion accounts for water’s surface tension which allows insects like water striders to walk on water.

cohesion

adhesion adhesion – an attraction between molecules of different substances Meniscus – Water in a cylinder dips in the center because adhesion to the sides is stronger than cohesion between water molecules. Capillary Action – The effect of water rising in a narrow tube against the force of gravity - due to water’s attraction to the sides of the tube. Ex. Plants drawing water from roots to leaves. Ex. Blood moving through capillaries.

adhesion

Solutions / suspensions mixture – a material composed of two or more elements or compounds – physically mixed but not chemically combined. Water can form two types of mixtures Solutions Suspensions

solutions solution – an aqueous mixture that is evenly distributed throughout (ex. salt water). solute – the substance that is dissolve in a liquid (ex. salt) solvent – the liquid substances in which the solute dissolves (ex. water) Water’s polarity makes it the universal solvent.

solutions

suspensions suspension – an aqueous mixture of water and non-dissolved material (ex. blood, Italian dressing)

Suspensions

Acids and bases Water is neutral because the number of positive hydrogen ions (H+) produced is equal to the number of negative hydroxide ions (OH-) produced. A water molecule can react to form hydrogen and hydroxide ions.

acids acid - any compound that forms H+ ions in solution. Acidic solutions contain higher concentrations of H+ ions than pure water and have pH values below 7. Strong acids tend to have pH values that range from 1 to 3. The hydrochloric acid produced by the stomach to help digest food is a strong acid.

acids

bases base - a compound that produces hydroxide ions (OH- ions) in solution Basic, or alkaline, solutions contain lower concentrations of H+ ions than pure water and have pH values above 7. Strong bases, such as lye, tend to have pH values ranging from 11 to 14.

bases

ph Scale pH scale - a measurement system designed to measure the concentration of H+ ions in solution. The pH scale ranges from 0 to 14.

Ph scale

ph

buffers buffers - are weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH. Controlling pH is important for maintaining homeostasis. One of the ways that the body controls pH is through dissolved compounds called buffers. Ex. Dissolved CO2 is a buffer.

2.3 Carbon Chemistry Carbon atoms have four valence electrons that can join with the electrons from other atoms to form strong covalent bonds. A carbon atom can bond to other carbon atoms, giving it the ability to form chains that are almost unlimited in length. Chains of carbon can even close upon themselves to form rings.

Carbon chemistry

macromolecules macromolecule – large biological molecules Made of smaller molecules Formed by polymerization – small units joined together to form a larger molecule monomer – one unit polymer – large molecule made of monomers

polymerization

polymerization

Organic compounds 4 Types of Organic Compounds Carbohydrates Lipids Proteins Nucleic Acids

carbohydrates Carbohydrates - compounds made up of carbon, hydrogen, and oxygen atoms, usually in a ratio of 1 : 2 : 1 (C, H, O) Function: Living things use carbohydrates as their main source of energy. Plants and some animals also use carbohydrates for structural purposes. Examples: Starches and sugars are examples of carbohydrates that are used by living things as a source of energy.

carbohydrates

Carbohydrates monosaccharides - single sugar molecules Monosaccharides include glucose, galactose (a component of milk), and fructose (found in many fruits). polysaccharides - the large macromolecules formed from monosaccharides Starches are examples of polysaccharides

lipids lipids – compounds made of mostly carbon and hydrogen in a 1:2 ratio (CHO). Oxygen is also present. Lipids are generally not soluble in water. Function: Lipids can be used to store energy. Some lipids are important parts of biological membranes and waterproof coverings. Examples: fats, oils, waxes, steroids

Lipids

lipids Many lipids are formed when a glycerol molecule combines with compounds called fatty acids. If each carbon atom in a lipid’s fatty acid chains is joined to another carbon atom by a single bond, the lipid is said to be saturated. The term saturated is used because the fatty acids contain the maximum possible number of hydrogen atoms.

lipids

Proteins Proteins - macromolecules that contain carbon, hydrogen, oxygen, and nitrogen (CHON). Proteins are polymers made of monomers called amino acids. Functions: control the rate of reactions regulate cell processes. form bones and muscles. transport substances into or out of cells help to fight disease Examples: keratin, collagen, elastin, etc.

proteins

proteins Proteins: levels of organization Primary: Amino acids have a specific protein chain. Secondary: The amino acids within a chain can be twisted or folded. Tertiary: The chain itself is folded. Quaternary: If a protein has more than one chain, each chain has a specific arrangement in space.

proteins

Nucleic acids Nucleic acids - macromolecules containing carbon, hydrogen, oxygen, nitrogen, and phosphorus (CHONP). Nucleic acids are polymers assembled from individual monomers known as nucleotides. Function: store and transmit hereditary, or genetic, information. Examples: DNA, RNA

Nucleic acids

Nucleic acids Nucleotides consist of three parts: a 5-carbon sugar a phosphate group a nitrogenous base Individual nucleotides can be joined by covalent bonds to form a polynucleotide, or nucleic acid.

Nucleic acids

2.4 chemical reactions/enzymes chemical reaction - a process that changes one set of chemicals into another set of chemicals. reactants - elements or compounds that enter into a chemical reaction. products - elements or compounds produced by a chemical reaction. Chemical reactions always involve changes in the chemical bonds that join atoms in compounds. Atoms and bonds are rearranged.

Chemical reactions

energy exothermic reaction – reaction that releases energy endothermic reaction – reaction that absorbs energy Chemical reactions that release energy often occur spontaneously. Chemical reactions that absorb energy will not occur without a source of energy.

energy When hydrogen gas reacts with oxygen to produce water vapor, it is an energy-releasing reaction in which energy is given off as heat. Reversing this reaction would require the addition of large amounts of energy.

energy

Activation energy In order to stay alive, organisms need to carry out reactions that require energy. Because matter and energy are conserved in chemical reactions, every organism must have a source of energy to carry out chemical reactions. Plants get their energy from the sun. Animals get their energy from eating plants or other animals.

Activation energy activation energy - energy needed to start a reaction. Activation energy is a factor in whether the overall chemical reaction releases energy or absorbs energy.

Activation energy

enzymes catalyst - substance that speeds up the rate of a chemical reaction. enzymes - proteins that act as biological catalysts. Enzymes speed up chemical reactions that take place in cells. Enzymes act by lowering the activation energy. Lowering the activation energy has a dramatic effect on how quickly the reaction is completed.

enzymes

enzymes Enzymes are very specific, generally catalyzing only one chemical reaction. For this reason, part of an enzyme’s name is usually derived from the reaction it catalyzes. Lactase – catalyzes lactose DNA Polymerase – catalyzes DNA polymers Helicase – unzips DNA helix

Enzyme-substrate complex enzyme-substrate complex – active site where reactants can be brought together to react, reducing the energy needed for reaction. substrates - reactants of enzyme-catalyzed reactions. The fit is so precise that the active site and substrates are often compared to a lock and key.

Enzyme-substrate complex

Enzyme regulation Enzymes can be affected by… pH temperature inhibitors - temporarily stop enzyme function by altering the active site (shape)

Enzyme function Enzymes… regulate chemical pathways. make material that cells need. release energy. transfer information.