Chemistry in Biology

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Chemistry in Biology
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The Big Idea

• Atoms are the foundation of biological chemistry
  and the building blocks of all living things.

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Section 6.1 Main Idea

• Matter is composed of tiny particles called atoms.

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• I. Chemistry is the study of matter.
• A. Matter is anything that takes up space
  and has mass.
• -Everything in the universe has matter.
• -Matter is composed of atoms.
• B. Mass is the amount of matter that an
  object has.
• -Mass and weight are not the same thing.
• C. Weight is the pull of gravity on an object

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• Composition of Matter
• A. Elementspure substances that cannot be
  broken down into simpler kinds of matter
• Made of one type of atom
• More than 100 elements (92 naturally occurring)
• 90 of the mass of an organism is composed of 4
  elements (oxygen, carbon, hydrogen, and nitrogen)
• Each element has a unique chemical symbol
• -consists of 1-2 letter
• -first letter is always capitalized
• -Ex O, C, F, Al, Ag, Mg

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• B. Atomsthe simplest particle of an element
  that still has all the properties of that
  element
• Atoms are so small that their true structure
  cannot be observed. Our understanding of the
  structure of atoms is based on scientific models.

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• C. Parts of an atom
• The nucleus of an atom contains two types of
  particles
• 1. Protonpositively charge
• 2. Neutronhas no charge, neutral
• The nucleus contains most of the mass of the
  atoms
• All atoms of a given element have the same number
  of protons

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• The third particle of the atom is the electron
  which is located outside the nucleus in energy
  levels (electron clouds).
• -first energy level holds 2 electrons
• -second holds 8 electrons
• Electrons have a negative charge.
• Number of protons is balanced by an equal number
  of electrons therefore there is no charge of the
  atom.
• All atoms have this same basic structure.

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Structure of an Atom
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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• D. Neutrons
• The number of neutrons varies slightly among
  atoms for the same element.
• Atoms of the same element that have different
  numbers of neutrons are referred to as isotopes
  of that element

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• Changing the number of neutrons does not change
  the overall charge of the atom but can affect the
  stability of the nucleus causing it to decay or
  break apart. Such isotopes give off radiation
  and referred to as radioactive isotopes.

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• E. Atomic Mass and Atomic Number
• Protons and neutrons each have a mass of 1 amu
  (atomic mass unit) or Dalton.
• The atomic mass of an element is equal to the
  number of protons plus the number of neutrons in
  the nucleus of the atom.
• The atomic number of an element is equal to the
  number of protons.

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The Periodic Table
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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• F. Periodic Table
• The elements are arranged by their atomic number
  on the Periodic Table.
• The horizontal rows are called periods and tell
  the number of energy levels.
• The vertical groups are called families and tell
  the outermost number of electrons.

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• G. Compounds
• Compounds are pure substances formed when two or
  more different elements combine.
• -Ex H20, CO2, and C6H12O6
• Compounds are always formed from a specific
  combination of elements in a fixed ratio.
• Compounds cannot be broken down into simpler
  compounds or elements by physical means.
• -can be broken down by chemical means into
  simpler compounds or into their original
  elements
• -H2O can be broken down into hydrogen gas and
  oxygen gas

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• Elements can undergo chemical reactions to
  combine with other elements in order to become
  stable.
• Stable elements have their outer energy level
  filled-meaning they have 8 electrons

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• Chemical Formulas
• Subscript after a symbol tell the number of atoms
  of each element
• H20 has 2 atoms of hydrogen 1 atom of oxygen
• Coefficients before a formula tell the number of
  molecules
• 3O2 represents 3 molecules of oxygen or (3x2) 6
  atoms of oxygen

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• CHEMICAL BONDS
• The force that holds atoms together is known as a
  chemical bond.
• Electrons are directly involved in the formation
  of chemical bonds.
• -They travel around the nucleus of an atom in
  areas called energy levels.
• -Each energy levels has a specific number of
  electrons that it can hold at any time
• -The first energy level which is closest to the
  nucleus can hold up to 2 electrons.
• -The second energy level can hold 8 electrons.

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• Types of Chemical Bonds
• 1. Covalent bondforms when atoms share one
  or more pairs of electrons
• A molecule is a compound in which the atoms are
  held together by covalent bonds.
• Can be a single, double, or triple bond depending
  on number of pairs of electrons shared.

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Covalent Bond
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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• 2. Ionic Bondforms when atom gives up
  electrons and another receives electrons in order
  to become stable
• Electrical attraction between two oppositely
  charged atoms or groups of atoms called ions.
• Most ionic compounds are crystalline at room
  temperature and have higher melting points than
  molecular compounds formed by covalent bonds.

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• Sodium and Chlorine
• -both atoms are unstable
• -to become stable, sodium gives away 1 electron
  and becomes positive, chlorine receives 1
  electron and becomes negative

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6.1 ATOMS, ELEMENTS, and COMPOUNDS
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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• Some atoms tend to donate or accept electrons
  more easily than other atoms.
• The elements identified as metals tend to donate
  electrons.
• The elements identified as nonmetals tend to
  accept electrons.

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6.1 ATOMS, ELEMENTS, and COMPOUNDS

• 3. van der Waals Forces
• Defined as the attraction between molecules
• This occurs when molecules come close together,
  and the attractive forces between slightly
  positive and negative regions pull on the
  molecules and hold them together.
• The strength of the attraction depends on the
  size of the molecule, its shape, and its ability
  to attract electrons
• Important in biological processes.

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Section 6.2 Main Idea

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

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6.2 Chemical Reactions

• Reactants and Products
• A. Chemical Reactions
• A chemical reaction is the process by which atoms
  or groups of atoms in substances are reorganized
  into different substances.
• Clues that a chemical reaction has taken place
  include the production of heat or light, and
  formation of a gas, liquid, or solid.
• Chemical bonds are broken and formed during
  chemical reactions

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6.2 Chemical Reactions

• Chemical Equations
• Chemical formulas describe the substances in the
  reaction and arrows indicate the process of
  change.
• Reactants are the starting substances, on the
  left side of the arrow.
• Products are the substances formed during the
  reaction, on the right side of the arrow.
• Reactants Products

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6.2 Chemical Reactions

• Glucose and oxygen react to form carbon dioxide
  and water.
• Is this equation written correctly?

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6.2 Chemical Reactions

• C. Balancing Equations
• The law of conservation of mass states matter
  cannot be created or destroyed.
• The number of atoms of each element on the
  reactant side must equal the number of atoms of
  the same element on the product side.

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Balancing EquationsPractice

1. Fe Cl2 ? FeCl3
2. H2 O2 ? H2O
3. C2H6 O2 ? CO2 H2O
4. CO2 H2 ? CH4 H2O
5. Al O2 ? Al2O3

1. 2Fe 3Cl2 ? 2FeCl3
2. 2H2 O2 ? 2H2O
3. 2C2H6 7O2 ?4CO2 6H2O
4. CO2 4H2 ? CH4 2 H2O
5. 4Al 3O2 ? 2Al2O3

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Bell-Ringer

1. QUIETLY find your seat.
2. Sit down and prepare for the quiz.
3. Clear your desk of everything except a writing
   utensil.
4. Failure to do so will result in a 10pt deduction
   on your quiz.

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Quiz

• A ____________is the process by which atoms or
  groups of atoms in substances are reorganized
  into different substances.
• _____________ is/are the attraction between
  molecules.
• _____________ states matter cannot be created nor
  destroyed.
• Subscripts tell the number of _____________ per
  element.
• Coefficients tell the number of ______________.

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6.2 Chemical Reactions

• ENERGY
• Energy is defined as the ability to do work or
  cause a change.
• States of Matter
• Solidparticles are packed tightly and move
  slowly
• Liquidparticles move freely and take the shape
  of the container
• Gasparticles move rapidly and have no definite
  shape

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6.2 Chemical Reactions

• C. Energy of Reactions
• The activation energy is the minimum amount of
  energy needed for reactants to form products in a
  chemical reaction.

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6.2 Chemical Reactions

• Exothermic Reaction

• Endothermic Reaction

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6.2 Chemical Reactions

• D. Energy Changes in Chemical Reactions
• This reaction is exothermic and released heat
  energy.
• The energy of the product is lower than the
  energy of the reactants.

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6.2 Chemical Reactions

• This reaction is endothermic and absorbed heat
  energy.
• The energy of the products is higher than the
  energy of the reactants.

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6.2 Chemical Reactions

• ENZYMES
• A. An enzyme is a biochemical catalyst.
• A catalyst is a substance that lowers the
  activation
  energy needed to start a chemical reaction.
• It does not increase how much product is made and
  is not used up in the reaction.

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6.2 Chemical Reactions

• The reactants that bind to the enzyme are called
  substrates.
• The specific location where a substrate binds on
  an enzyme is called the active site.
• The active site changes shape and forms the
  enzyme-substrate complex, which helps chemical
  bonds in the reactants to be broken and new bonds
  to form.

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6.2 Chemical Reactions

• B. Enzyme Action
• Enzyme and substrate link together.
• Chemical reaction occurs
• Substrate becomes something new and the enzyme is
  let go.
• The enzyme can be reused.

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Enzyme Action
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6.2 Chemical Reactions

• Factors such as pH, temperature, and other
  chemicals affect enzyme activity.
• When enzymes are exposed to one of these factors,
  they may become denatured.
• -Denaturing causes the enzyme to not be as
  effective or possibly quit working altogether.

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Examples of Biological Enzymes

• http//www.woisd.net/moodle/mod/resource/view.php?
  id43

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Section 6.3 Main Idea

• The properties of water make it well suited to
  help maintain homeostasis in an organism.

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6.3 Water and Solutions

• Waters Polarity
• Molecules that have an unequal distribution of
  charges are called polar molecules.
• Polar molecules have one side that has a postive
  charge and the other has a negative charge.
• Water is a polar molecule.
• B. Water molecules are held together by weak
  hydrogen bonds.
• A hydrogen bond is a weak interaction involving a
  
  hydrogen atom and a fluorine, oxygen, or nitrogen
  atom.
• Hydrogen bonds are important in biological
  processes.

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6.3 Water and Solutions
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6.3 Water and Solutions

• Properties of Water
• 1. Cohesion is the attractive force between
  particles of the same kind. This property allows
  water to bulge from the top of a filled glass
  without spilling over.
• 2. Adhesion is the attractive force between
  unlike substances.
• Together these properties make it possible for
  water to move upwards against the force of
  gravity in a narrow tube.
• This phenomenon is called capillarity.

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6.3 Water and Solutions

• Mixtures with Water
• Mixture--a combination of two or more substances
  in which each substance retains its
  individual characteristics
• Homogenous mixture--one that has a uniform
  composition throughout a solution
• Solvent--a substance in which another substance
  is dissolved (Ex tea)
• Solute--the substance that is dissolved in the
  solvent (Ex sugar)

Food coloring dissolved in water forms a
homogenous mixture.
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6.3 Water and Solutions

• E. In a heterogeneous mixture, the components
  remain distinct.
• In a suspension, the components will eventually
  settle to the bottom.
• In a colloid, the particles will not settle over
  time. Examples include fog, smoke, butter,
  mayonnaise, milk, paint, and ink.

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6.3 Water and Solutions

1. Concentrationthe measure of how much of a
   substance is dissolved
2. Saturated solutionone in which nothing else can
   dissolve
3. Aqueous solutionwater is the solvent

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6.3 Water and Solutions

• IV. Acids and Bases
• A. Substances that release hydrogen ions (H)
  when dissolved in water are called acids.
• B. Substances that release hydroxide ions (OH)
  when dissolved in water are called bases.

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6.3 Water and Solutions
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6.3 Water and Solutions

• C. The pH Scale
• The measure of concentration of H in a solution
  is called pH.
• -Ranges from 0-14 with 7 being neutral
• Acidic solutions have pH values lower than 7.
• -have a sour taste
• Basic solutions have pH values higher than 7.
• -have a bitter taste
• Buffers are mixtures that can react with acids or
  bases to keep the pH within a particular range.
• -help neutralize a bodys pH level

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6.3 Water and Solutions
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Section 6.4 Main Idea

• Organisms are made up of carbon-based molecules.

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6.4 The Building Blocks of Life

• Organic Chemistry
• The element carbon is a component of almost all
  biological molecules.

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6.4 The Building Blocks of Life

• Carbon has four electrons in its outermost energy
  level.
• One carbon atom can form four covalent bonds
  with other atoms.
• Carbon compounds can be in the shape of straight
  chains, branched chains, and rings.

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6.4 The Building Blocks of Life
Macromolecules

• Carbon atoms can be joined to form carbon
  molecules.
• Macromolecules are large molecules formed by
  joining smaller organic molecules together.
• Polymers are molecules made from repeating units
  of identical or nearly identical compounds linked
  together by a series of covalent bonds.

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6.4 The Building Blocks of Life
Carbohydrates

• Compounds composed of carbon, hydrogen, and
  oxygen in a ratio of one oxygen and two hydrogen
  atoms for each carbon atom(CH2O)n

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6.4 The Building Blocks of Life

• Values of n ranging from three to seven are
  called simple sugars, or monosaccharides.
• Two monosaccharides joined together form a
  disaccharide.
• Longer carbohydrate molecules are called
  polysaccharides.

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6.4 The Building Blocks of Life
Lipids

• Molecules made mostly of carbon and hydrogen
• A triglyceride is a fat if it is solid at room
  temperature and an oil if it is liquid at room
  temperature.

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6.4 The Building Blocks of Life

• Lipids that have tail chains with only single
  bonds between the carbon atoms are called
  saturated fats.
• Lipids that have at least one double bond between
  carbon atoms in the tail chain are called
  unsaturated fats.
• Fats with more than one double bond in the tail
  are called polyunsaturated fats.

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6.4 The Building Blocks of Life
Proteins

• A compound made of small carbon compounds called
  amino acids
• Amino acids are small compounds that are made of
  carbon, nitrogen, oxygen, hydrogen, and sometimes
  sulfur.

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6.4 The Building Blocks of Life

• Amino acids have a central carbon atom.
• One of the four carbon bonds is with hydrogen.
• The other three bonds are with an amino group
  (NH2), a carboxyl group (COOH), and a
  variable group (R).

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6.4 The Building Blocks of Life

• The number and the order in which the amino acids
  are joined define the proteins primary
  structure.
• After an amino acid chain is formed, it folds
  into a unique three-dimensional shape, which is
  the proteins secondary structure, such as a
  helix or a pleat.

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6.4 The Building Blocks of Life

• Nucleic acids are complex macromolecules that
  store and transmit genetic information.
• Nucleic acids are made of smaller repeating
  subunits called nucleotides, composed of carbon,
  nitrogen, oxygen, phosphorus, and hydrogen atoms

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6.4 The Building Blocks of Life