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Chapter 6: Chemistry in Biology

Chapter Worksheet | Element Foldable | Chem4kids

Ch. 6.1 Atoms, Elements, and Compounds

The study of the building blocks of life is the science of Chemistry

Atoms

Chemistry is the study of matter, its composition, and properties. Matter is anything that has mass and takes up space.

Atoms- the building blocks of matter

Greek philosophers proposed that all matter is made of tiny, indivisible particles.

The structure of an atom

Atoms are made up of protons, neutrons, and electrons.

Nucleus- the center of the atom; Protons- positively charged particles; Neutrons- particles that have no charge; Electrons- negatively charged particles that are located outside the nucleus.

Electrons constantly move around an atom's nucleus in energy levels. Overall charge of atom is zero.

Elements

Element- a pure substance that cannot be broken down into other substances by physical or chemical means.

Elements are made of only one type of atom. Over 100 known elements, 92 occur naturally. Each has element has a unique name and symbol. Periodic table organizes elements.

The Periodic Table of the Elements

Has horizontal rows (periods), and vertical columns (groups). Elements of same group have similar chemical and physical properties.

Isotopes

Atoms of the same element have same number of protons. Isotopes- atoms of same element with different numbers of neutrons. Example: Carbon-12 & Carbon- 14

Isotopes have the same chemical characteristics.

Radioactive Isotopes

Changing the number of neutrons does not change the overall charge of the atom but can change the stability of the nucleus. In some the nucleus decays giving off radiation that can be detected.

Carbon-14 exists in all living things. Half-life, the amount of time for half of atom to decay, can be used to calculate age of object by how much Carbon-14 remains. Other radioactive isotopes used in medicine.

Compounds

Elements can combine into more complex substances. Compound- a pure substance formed when two or more different elements combine. Each compound has a chemical formula made of chemical symbols: NaCl, H2O

Formed from specific combination of elements in a fixed ratio. Have different chemical and physical properties from the elements that form them. Can't be broken down by physical means, but can by chemical.

Chemical Bonds

Compounds are formed when two or more substances combine. Electrons involved directly with in forming chemical bonds. Electrons travel in energy levels outside the nucleus. Each level holds a specific number of electrons; inner most two, next level holds eight.

Partially filled energy levels are less stable than full or empty levels. Atoms become more stable by attracting or losing electrons.

Formation of bonds stores energy while breaking bonds releases energy. This energy fuels processes for life. There are two main types of chemical bonds- covalent and ionic

Covalent Bonds

Covalent bond- when electrons are shared between atoms. With water, two hydrogens share their outer electron with oxygen to fill oxygen's outer shell.

Most compounds in living organisms have covalent bonds. Molecules- a compound in which the atoms are held together by covalent bonds. Can be single, double, or triple bonds.

Ionic Bonds

Ion- an atom that has lost or gained one or more electrons and carries an electric charge.

Ionic bond- an electrical attraction between two oppositely charged atoms or groups of atoms called ions. Substances formed by ionic bonds are called ionic compounds.

Ions in living things help maintain homeostasis as they travel in and out of cells. Ions also transmit signals among cells.

van der Waals Forces

Elements in a covalent bond do not always attract electrons equally. An unequal distribution of electrons create a temporary area of slightly positive and negative charges.

The attractive forces between the positive and negative regions pull on the molecules and hold them together; called van der Waals forces. Not as strong as covalent and ionic bonds. Geckos use these to climb walls.

van der Waals forces in water

Areas of slight positive and negative charges around the water molecule are attracted to opposite charge of other nearby water molecules. These forces hold water molecules together. Forms droplets, water surface.

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Ch. 6.2 Chemical Reactions

Chemical reactions allow living things to grow, develop, reproduce, and adapt.

Reactants and Products

Rust (iron oxide) is a result of a chemical reaction . Chemical reaction- the process by which atoms or groups of atoms in substances are reorganized into different substances. Chemical bonds are broken and formed during reactions.

Physical changes are not chemical reactions. Water to ice for example.

Chemical Equations

Chemical formulas describe the substances in the reaction with arrows indicating the process of change.

Reactants and Products

Reactants- the starting substances, on the left side of the arrow. Products- the substances formed by the reaction, on the right side of the arrow

Balanced Equations

In chemical reactions matter is not created or destroyed (Law of conservation of mass). The number of atoms on reactant side equals the number of atoms on the product side. Coefficients and subscripts indicate the quantities of each atom.

Energy of Reactions

Activation Energy- the minimum amount of energy needed for a reaction to occur. Some reactions rarely happen because they have a very high activation energy.

Energy change in chemical reactions

Endothermic: heat energy is absorbed; the energy of the products is higher than the energy of the reactants. Exothermic: heat energy is released. In all reactions there is a change in energy from making and breaking chemical bonds. Exothermic reactions maintain internal body temperature (37º).

Enzymes

Organisms have many chemical reactions that occur; these reactions occur very slowly due to high activation energy. Another chemical must be present to lower the activation energy and speed up the reaction.

Catalyst- a substance that lowers the activation energy needed to start a chemical reaction.

Does not get used up, does not change quantity of product.

Enzymes- special proteins that speed up the rate of chemical reactions in biological processes.

Enzyme names describe what it does; amylase in saliva breaks down amylose a components of starch. most enzymes are specific to one reaction.

Substrates- the reactants that bind to the enzyme. Active site- specific location where a substrate binds to an enzyme.

Active site and substrate have complementary shapes like puzzle pieces. Once the substrates bind to the active site, the active site changes shape and forms the enzyme-substrate complex. The complex helps helps chemical bonds in the reactants to be broken and new bonds to form. The substrates react to form products. The enzyme then releases the products.

Factors such as pH, temperature, and other substance affect enzyme activity.

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Ch. 6.3 Water and Solutions

Water's Polarity

Water formed by covalent bonds; electrons of hydrogen atoms spend more time near oxygen nucleus due to larger positive attraction. Result: Oxygen end is slightly negative, and hydrogen end slightly positive.

Polar molecules- molecules that have an unequal distribution of charges so they have a oppositely charged regions. When the oppositely charged ends come close together a weak electrostatic attraction results.

Hydrogen bond- a weak interaction involving a hydrogen atom and a flourine, oxygen, or nitrogen atom. These are strong type of van der Waals force.

Mixtures with Water

Mixture- a combination of two or more substance in which each substance retains it's individual characteristics and properties.

Homogeneous mixtures

When a mixture has a uniform composition throughout. Solution- another name for homogeneous mixture.

Two components: Solvent- a substance in which another substance is dissolved. Solute- the substance that is dissolved in the solvent.

Examples: saliva- water, proteins, and salts; air- solution of gases

Heterogeneous mixtures

Mixture in which the components remain distinct.

Suspension; a heterogeneous mixture in which particles settle to the bottom. Colloid- a heterogeneous mixture in which particles do not settle out. Example: milk, blood

Acids and bases

Acids- substances that release hydrogen ions (H+) when dissolved in water. The more ions, the more acidic.

Bases- substances that release hydroxide ions (OH-) when dissolved in water. The more hydroxide ions released, the more basic.

pH and buffers

pH- the measure of concentration of H+ in a solution.

Pure water is neutral with pH of 7. Acids have more H+ and pH lower than 7, bases have more OH- than H+ and pH higher than 7.

Majority of biological processes occur between pH 6.5 and 7.5. Buffers- mixtures that can react with acids or bases to keep the pH within a particular range.

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Ch. 6.4 The Building Blocks of Life

Organisms are made up of carbon-based molecules.

Organic Chemistry

Carbon is a component of almost all biological molecules. Organic chemistry is a branch of chemistry dedicated to study of organic compounds.

Carbon has four electrons in its outer shell. It can form four covalent bonds with other atoms. Carbon can bond to each other to form straight chains, branched chains, and rings.

Macromolecules

Most cells store small carbon compounds that serve as building blocks for large molecules.

Macromolecules- large molecules that are formed by joining smaller organic molecules together. Also called polymers. Polymers- molecules made from repeating units of identical or nearly identical compounds called monomer linked together by a series of covalent bonds.

Four major categories: carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

Compounds composed of carbon, hydrogen, and oxygen in a ratio of one oxygen and two hydrogen atoms for each carbon atom. General formula of (CH2O)n. Monosaccharides (simple sugars) n is 3 to 7. Example: glucose for energy

Disaccharide formed when two monosaccharides join. Also for energy: sucrose, lactose

Polysaccharide are larger carbohydrates. Glycogen used for energy between meals when broken down into glucose.

Carbohydrates have other roles than energy. Cellulose used by plants for support in cell walls. Chitin is a polysaccharide that contains nitrogen used for: shells of crustaceans, cell walls of fungi.

Lipids

Lipids- molecules made mostly of carbon and hydrogen that makeup the fats, oils, and waxes. Composed of fatty acids, glycerol, and other components. Mainly used to store energy.

Saturated and Unsaturated Fats

Basic structure has a fatty acid tail. Tail is chain of carbon atoms bonded with hydrogen and other carbon atoms by single or double bonds. Saturated fats: tail with only single bonds, Unsaturated fats: have at least one double bond, Polyunsaturated fats: fats with more than one double bond in the tail.

Phospholipids

Make up the structure and function of the cell membrane. Lipids are hydrophobic: not dissolved in water. Makes barriers

Steroids

Includes cholesterol and hormones. Starting point for some necessary lipids such as vitamin D, estrogen, and testosterone.

Proteins

Building blocks of living things. Protein- compound made of small carbon compounds called amino acids. Amino Acids- small compounds made of carbon, nitrogen, oxygen, hydrogen, and sometimes sulfur. All share the same general structure.

Amino Acid Structure

Amino Acids have a central carbon with four covalent bonds: one with hydrogen, one with amino group (-NH2), one with carboxyl group (-COOH), and one to a variable group (-R)

Variable group makes each amino acid different. 20 different variable groups. Proteins made up of the different amino acids. Peptide bonds join the amino acids together. Peptide bond formed between amino group of one amino acid and the carboxyl group of another.

Three-dimensional Protein Structure

The number of amino acids, and the order they are joined determines the proteins primary structure. Once assembled, the protein folds into its secondary structure. Tertiary structure can be globular, some form a fourth level by combining with other proteins.

Protein Function

Proteins make up about 15% of body mass and involved in nearly every function of our body. Example: muscles, skin, hair. In cells: provide support, transport materials, communicate, and more.

Nucleic Acids

Nucleic Acids- store and transmit genetic information. Nucleotides- building blocks of nucleic acids; carbon, nitrogen, oxygen, phosphorus, hydrogen. Five nucleotides, all have same three units: phosphate, nitrogenous base, and a ribose sugar.

Two types of nuclei acids: DNA (deoxyribonucleic acid) and RNA (ribose nucleic acid). Sugar of one nucleotide bonds to phosphate of another; nitrogenous base forms hydrogen bond with other bases in opposite nucleic acid.

ATP (adenosine triphosphate) is a nucleotide with three phosphate groups. Used for storing chemical energy.

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