Chapter 6 Chemistry in Chapter 6 Chemistry in BiologyBiology

6.1 Atoms, Elements & 6.1 Atoms, Elements & CompoundsCompounds

6.2 Chemical Reactions6.2 Chemical Reactions

6.3 Water and Solutions6.3 Water and Solutions

6.4 The Building Blocks of Life6.4 The Building Blocks of Life

6.1 Atoms, Elements, and 6.1 Atoms, Elements, and CompoundsCompounds

Main idea: Matter is composed of tiny Main idea: Matter is composed of tiny particles called atomsparticles called atoms

Objectives:Objectives: Identify the particles that make up atomsIdentify the particles that make up atoms Diagram the particles that make up an atomDiagram the particles that make up an atom Compare covalent bonds and ionic bondsCompare covalent bonds and ionic bonds Describe van der Waals forcesDescribe van der Waals forces

Review VocabularyReview Vocabulary Substance: a form of matter that has a uniform Substance: a form of matter that has a uniform

and unchanging compositionand unchanging composition

AtomsAtoms

Chemistry is the study of matter. Atoms are the building blocks of matter. Neutrons and protons are located at the

center of the atom called the nucleus. Protons are positively charged particles (p+). Neutrons are particles that have no charge

(n0). Electrons are negatively charged particles

that are located outside the nucleus (e-).

AtomsAtoms

ElementsElements

An element is a pure substance that cannot be broken down into other substances by physical or chemical means.

There are over 100 known elements, 92 of which occur naturally.

Each element has a unique name and symbol.

All of this data, and more, are collected in an organized table called the periodic table of elements.

The Periodic Table of Elements Horizontal rows are called periods. Vertical columns are called groups.

IsotopesIsotopes

Atoms of the same element that have the same number of protons and electrons but have a different number of neutrons

Radioactive IsotopesRadioactive Isotopes

When a nucleus breaks apart, it gives off radiation that can be detected and used for many applications.

Examples include Carbon dating and Examples include Carbon dating and radiation therapy to treat cancer.radiation therapy to treat cancer.

CompoundsCompounds A pure substance formed when two or more

different elements combine Each compound has a chemical formula made up

of the chemical symbols from the periodic table. Water – H2 O Sodium Chloride – NaCl – Table Salt Hydrocarbons composed of Carbon and Hydrogen:

Methane – CH4

Compounds are always formed from a specific combination of elements in a fixed ratio.

Compounds are chemically and physically different than the elements that comprise them.

Compounds cannot be broken down into simpler compounds or elements by physical means.

However, compounds can be broken down into However, compounds can be broken down into simpler compounds or elements by chemical simpler compounds or elements by chemical means.means.

Chemical BondsChemical Bonds Compounds such as water, salt, and methane are Compounds such as water, salt, and methane are

formed when two or more substances combine.formed when two or more substances combine. The force that holds the substances together is The force that holds the substances together is

called a chemical bond.called a chemical bond. The nucleus determines the chemical identity of The nucleus determines the chemical identity of

the atom.the atom. The electrons are involved directly in forming the The electrons are involved directly in forming the

chemical bonds.chemical bonds. Electrons travel around the nucleus of an atom in Electrons travel around the nucleus of an atom in

areas called energy level.areas called energy level. Each energy level has a specific number of Each energy level has a specific number of

electrons that it can hold at any time.electrons that it can hold at any time. The first energy level, which is the level closest to The first energy level, which is the level closest to

the nucleus, can hold up to two electrons. the nucleus, can hold up to two electrons. The second can hold up to eight.The second can hold up to eight.

Chemical Bonds Chemical Bonds A partially-filled energy level is not as stable as A partially-filled energy level is not as stable as

an energy level that is empty or completely filled.an energy level that is empty or completely filled. Atoms become more stable by losing electrons or Atoms become more stable by losing electrons or

attracting electrons from other atoms.attracting electrons from other atoms. This results in the formation of chemical bonds This results in the formation of chemical bonds

between atoms.between atoms. It is the forming of chemical bonds that stores It is the forming of chemical bonds that stores

energy and the breaking of chemical bonds that energy and the breaking of chemical bonds that provides energy for processes of growth, provides energy for processes of growth, development, adaptation, and reproduction in development, adaptation, and reproduction in living things.living things.

Two main types of chemical bonds – Two main types of chemical bonds – Covalent bondsCovalent bonds Ionic bondsIonic bonds

Covalent BondsCovalent Bonds Chemical bond that forms

when electrons are shared.

Most compounds in living organisms have covalent bonds holding them together.

A molecule is a compound in which the atoms are held together by covalent bonds.

Depending on the number of pairs of electrons that are shared, covalent bonds can be single (H2), double (O2), or triple (N2).

Ionic BondsIonic Bonds Recall that for an atom to be most stable, Recall that for an atom to be most stable,

the outermost energy level should be either the outermost energy level should be either empty of completely filled.empty of completely filled.

Some atoms tend to give up (donate) or Some atoms tend to give up (donate) or obtain (accept) electrons to empty or fill the obtain (accept) electrons to empty or fill the outer energy level in order to be stable.outer energy level in order to be stable.

An atom that has lost or gained one or more An atom that has lost or gained one or more electrons becomes an ion and carries an electrons becomes an ion and carries an electric charge.electric charge.

An ionic bond is an electrical attraction An ionic bond is an electrical attraction between two oppositely charged atoms or between two oppositely charged atoms or groups of atoms called ions.groups of atoms called ions.

Ionic BondsIonic Bonds Ions in living things include sodium, potassium, Ions in living things include sodium, potassium,

calcium, chloride, and carbonate ions.calcium, chloride, and carbonate ions. They help maintain homeostasis as they travel in They help maintain homeostasis as they travel in

and out of cells.and out of cells. In addition, ions help transmit signals among cells In addition, ions help transmit signals among cells

that allow you to see, taste, hear, feel, and smell.that allow you to see, taste, hear, feel, and smell.

Ionic BondsIonic Bonds

Some atoms tend to donate or accept Some atoms tend to donate or accept electrons more easily than other atoms.electrons more easily than other atoms.

Metals tend to donate electronsMetals tend to donate electrons Nonmetals tend to accept electronsNonmetals tend to accept electrons Ionic compounds have unique Ionic compounds have unique

characteristics:characteristics: Most dissolve in water; when dissolved in Most dissolve in water; when dissolved in

solution they can carry an electric currentsolution they can carry an electric current Most are crystalline at room temperatureMost are crystalline at room temperature Generally have higher melting points than Generally have higher melting points than

compounds formed by covalent bondscompounds formed by covalent bonds

Van der Waals ForcesVan der Waals Forces Due to the movement of electrons in a molecule around

the nuclei, temporary areas of slightly positive and negative charges occur around the molecule.

When molecules come close together, 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.

Van der Waals Forces are not as strong as covalent and Van der Waals Forces are not as strong as covalent and ionic bonds, but they play a role in biological forces.ionic bonds, but they play a role in biological forces.

Van der Waals forces in water hold the water molecules Van der Waals forces in water hold the water molecules together, forming droplets and a surface of watertogether, forming droplets and a surface of water

Ven der Waals forces are the attractive forces between Ven der Waals forces are the attractive forces between the water molecules, not the forces between the atoms the water molecules, not the forces between the atoms that make up water.that make up water.

6.2 Chemical Reactions6.2 Chemical Reactions

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

Objectives:Objectives: Identify the parts of a chemical reactionIdentify the parts of a chemical reaction Relate energy changes to chemical reactionsRelate energy changes to chemical reactions Summarize the importance of enzymes in living Summarize the importance of enzymes in living

organismsorganisms Review VocabularyReview Vocabulary

Process: a series of steps or actions that produce Process: a series of steps or actions that produce an end productan end product

Reactants and ProductsReactants and Products

A chemical reaction is the process by which atoms or groups of atoms in substances are reorganized into different substances.

Chemical bonds are broken and/or formed during chemical reactions.

Clues that a chemical reaction has taken place include the production of heat or light, and formation of a gas, liquid, or solid.

Chemical EquationsChemical 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.

The arrow can be read as “yields” or “react to form”.

Chemical EquationsChemical Equations

Glucose and oxygen react to form carbon dioxide and water.

Balanced Equations Balanced 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.

Multiply the coefficient by the subscript for each element. You can see in this example that there are six carbon atoms, twelve hydrogen atoms, and eighteen oxygen atoms on each side of the arrow.

The equation confirms that the number of atoms on each The equation confirms that the number of atoms on each side is equal, and therefore the equation is balanced.side is equal, and therefore the equation is balanced.

Energy of ReactionsEnergy of Reactions

Most compounds in Most compounds in living things cannot living things cannot undergo chemical undergo chemical reactions without reactions without energy.energy.

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

ExothermicExothermic

This reaction is exothermic and released heat energy.

The energy of the product is lower than the energy of the reactants.

EndothermicEndothermic

This reaction is endothermic and absorbed heat energy.

The energy of the products is higher than the energy of the reactants.

EnzymesEnzymes

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 it does not get used up in the reaction.

Special proteins called enzymes are biological catalysts that speed up the rate of chemical reactions in biological processes.

Enzymes usually end in “ase” and are specific to one reaction.

Example: Amylase is found in saliva and aids in the digestion of food in the mouth.

How Enzymes WorkHow Enzymes Work

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. Once the substrates bind to the active site, the active site

changes shape and forms the enzyme-substrate complex. The enzyme-substrate complex 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.

Enzyme ActivityEnzyme Activity

Factors that affect enzyme activity:Factors that affect enzyme activity: pHpH TemperatureTemperature Other substancesOther substances

Enzymes affect many biological Enzymes affect many biological processes and are the chemical processes and are the chemical workers in a cell.workers in a cell.

6.3 Water and Solutions6.3 Water and Solutions Main idea: The properties of water make it Main idea: The properties of water make it

well-suited to help maintain homeostasis in well-suited to help maintain homeostasis in an organism.an organism.

Objectives:Objectives: Evaluate how the structure of water makes it a Evaluate how the structure of water makes it a

good solvent.good solvent. Compare and contrast solutions and suspensions.Compare and contrast solutions and suspensions. Describe the difference between acids and bases.Describe the difference between acids and bases.

Review Vocabulary:Review Vocabulary: Physical property: characteristic of matter, such Physical property: characteristic of matter, such

as color or melting point, that can be observed or as color or melting point, that can be observed or measured without changing the composition of measured without changing the composition of the substance.the substance.

Water’s PolarityWater’s Polarity Water molecules are formed by covalent Water molecules are formed by covalent

bonds that link two Hydrogen (H) atoms to bonds that link two Hydrogen (H) atoms to one oxygen (O) atom.one oxygen (O) atom.

Because electrons are more strongly Because electrons are more strongly attracted to oxygen’s nucleus, the attracted to oxygen’s nucleus, the electrons in the covalent bond with electrons in the covalent bond with hydrogen are not shared equally.hydrogen are not shared equally.

In water, the electrons spend more time In water, the electrons spend more time near the oxygen nucleus than they do near the oxygen nucleus than they do near the hydrogen nuclei.near the hydrogen nuclei.

This, along with the bent shape of water, This, along with the bent shape of water, results in the oxygen end of the molecule results in the oxygen end of the molecule having a slightly negative charge and the having a slightly negative charge and the hydrogen ends of the molecule a slightly hydrogen ends of the molecule a slightly positive charge.positive charge.

Water’s PolarityWater’s Polarity

Molecules that have an unequal distribution of charges are called polar molecules.

Polarity is the property of having two opposite poles.

A hydrogen bond is a weak electrostatic attraction or interaction involving a hydrogen atom and a fluorine, oxygen, or nitrogen atom.

Hydrogen bonding is a strong type of Van der Waals interaction.

Water’s PolarityWater’s Polarity

Properties of WaterProperties of Water

Water is vital to life on Earth, its Water is vital to life on Earth, its properties allow it to provide properties allow it to provide environments suitable for life and to environments suitable for life and to help organisms maintain homeostasis.help organisms maintain homeostasis.

Humans can survive many days without Humans can survive many days without food, but can survive only a few days food, but can survive only a few days without water.without water.

Water is called the universal solvent Water is called the universal solvent because many substances dissolve in it.because many substances dissolve in it.

Properties of WaterProperties of Water

Liquid water becomes more dense as Liquid water becomes more dense as it cools to 4°C.it cools to 4°C.

Yet ice is less dense than liquid water.Yet ice is less dense than liquid water. As a result, nutrients in bodies of As a result, nutrients in bodies of

water mix due to changes in water water mix due to changes in water density during spring and fall.density during spring and fall.

Also, fish can survive winter because Also, fish can survive winter because ice floats-they continue to live and ice floats-they continue to live and function in the water beneath the ice.function in the water beneath the ice.

Water is Adhesive & CohesiveWater is Adhesive & Cohesive Adhesive – it forms hydrogen bonds with Adhesive – it forms hydrogen bonds with

molecules on other surfaces.molecules on other surfaces. Capillary action is the result of adhesion -Capillary action is the result of adhesion -

water travels up the stem of a plant, and water travels up the stem of a plant, and seeds swell and germinate. seeds swell and germinate.

Cohesive – the molecules are attracted to Cohesive – the molecules are attracted to each other due to hydrogen bonds.each other due to hydrogen bonds.

This attraction creates surface tension, This attraction creates surface tension, which causes water to form droplets and which causes water to form droplets and allows insects and leaves to rest on the allows insects and leaves to rest on the surface of a body of water.surface of a body of water.

Mixtures with WaterMixtures with Water A mixture is a combination of A mixture is a combination of

two or more substances in two or more substances in which each substance retains which each substance retains its individual characteristics its individual characteristics and properties.and properties.

A mixture that has a uniform composition throughout is a homogenous mixture and is also known as a solution.

A solvent is a substance in which another substance is dissolved.

A solute is the substance that is dissolved in the solvent.

Mixtures with WaterMixtures with Water

The components remain distinct in heterogenous mixtures.

Suspension - particles settle out - sand and water.

Colloid - particles do not settle out – fog, smoke, butter, mayonnaise, milk, paint, ink, and blood.

Acids and BasesAcids and Bases

Substances that release hydrogen ions (H+) when dissolved in water are called acids.

Substances that release hydroxide ions (OH–) when dissolved in water are called bases.

pH and BufferspH and Buffers

The measure of concentration of H+ in a solution is called pH.

Acidic solutions have an abundance of H+ ions and pH values lower than 7.

Basic solutions have an abundance of OH- ions and pH values higher than 7.

Buffers are mixtures that can react with acids or bases to keep pH within a particular range.

6.4 The Building Blocks of Life6.4 The Building Blocks of Life

Main idea: Organisms are made up of Main idea: Organisms are made up of carbon-based molecules.carbon-based molecules.

Objectives:Objectives: Describe the role of carbon in living organisms.Describe the role of carbon in living organisms. Summarize the four major families of biological Summarize the four major families of biological

macromolecules.macromolecules. Compare the functions of each group of Compare the functions of each group of

biological macromolecules.biological macromolecules. Review Vocabulary:Review Vocabulary:

Organic compound: carbon-based substance Organic compound: carbon-based substance that is the basis of living matter.that is the basis of living matter.

Organic ChemistryOrganic Chemistry The element carbon

is a component of almost all biological molecules.

Carbon has four electrons in its outermost energy level.

One carbon atom can form four covalent bonds with other atoms.

Carbon CompoundsCarbon Compounds Carbon compounds can be in the shape of

straight chains, branched chains, and rings. Together carbon compounds lead to the diversity

of life on Earth.

MacromoleculesMacromolecules

Carbon atoms can be joined to form carbon molecules.

Large molecules that are formed by Large molecules that are formed by joining smaller organic molecules joining smaller organic molecules together are called macromolecules.together are called macromolecules.

Polymers are molecules made from repeating units of identical or nearly identical compounds linked together by a series of covalent bonds.

Biological MacromoleculesBiological MacromoleculesGroupGroup ExamplesExamples FunctionFunction

CarbohydratCarbohydrateses

Pasta, breads & Pasta, breads & grainsgrains

Stores energyStores energy Provides structural supportProvides structural support

LipidsLipids Beeswax, fat & oilsBeeswax, fat & oils Stores energyStores energy Provides steroidsProvides steroids Waterproofs coatingsWaterproofs coatings

ProteinsProteins HemoglobinHemoglobin

and Amylaseand Amylase

Transport substancesTransport substances Speeds reactionsSpeeds reactions Provides structural supportProvides structural support Provides hormonesProvides hormones

Nucleic AcidsNucleic Acids DNA stores genetic DNA stores genetic info in the cell’s info in the cell’s nucleusnucleus

Stores and communicates Stores and communicates genetic informationgenetic information

CarbohydratesCarbohydrates Compounds composed of carbon, hydrogen, and oxygen in a ratio of

one oxygen and two hydrogen atoms for each carbon atom—(CH2O)n The subscript n indicates the number of (CH2O) units in a chain. Values of n ranging from 3 to 7 are called simple sugars or

monosaccharides (glucose). Two monosaccharides joined together form a dissaccharide (sucrose –

table sugar & lactose – component of milk). Longer carbohydrate molecules are called polysaccharides

(glycogen). Energy sources, cellulose-structural support in cell walls of plants, Energy sources, cellulose-structural support in cell walls of plants,

and chitin-outer shells of shrimp, lobster & small insects, as well as and chitin-outer shells of shrimp, lobster & small insects, as well as the cell wall of some fungi.the cell wall of some fungi.

LipidsLipids Molecules made mostly of carbon and

hydrogen that make up the fats, oils and waxes.

Lipids are composed of fatty acids, glycerol, and other components.

The primary function is to store energy. A triglyceride is a fat if it is solid at room

temperature and an oil if it is liquid at room temperature (stored in fat cells of the body).

Plant leaves are coated with lipids called Plant leaves are coated with lipids called waxes to prevent water loss, and the waxes to prevent water loss, and the honeycomb in a beehive is made of honeycomb in a beehive is made of beeswax.beeswax.

Saturated and Unsaturated FatsSaturated and Unsaturated Fats

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.

Phospholipids & SteroidsPhospholipids & Steroids

The structure and function of the cell The structure and function of the cell membrane is due to phospholipids.membrane is due to phospholipids.

Phosphate head is polar or hydrophilicPhosphate head is polar or hydrophilic Fatty acid tail is non-polar or hydrophobicFatty acid tail is non-polar or hydrophobic Lipids overall are hydrophobic, which Lipids overall are hydrophobic, which

means they do not dissolve in water.means they do not dissolve in water. This characteristic is important because it This characteristic is important because it

allows lipids to serve as barriers in allows lipids to serve as barriers in biological membranes.biological membranes.

Steroids include substances such as Steroids include substances such as cholesterol and hormones.cholesterol and hormones.

ProteinsProteins

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.

Amino AcidsAmino Acids

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).

Amino AcidsAmino Acids

The variable group makes each amino acid The variable group makes each amino acid different.different.

There are 20 different variable groups, and There are 20 different variable groups, and proteins are made of different combinations proteins are made of different combinations of all 20 different amino acids.of all 20 different amino acids.

Several covalent bonds called peptide bonds Several covalent bonds called peptide bonds join amino acids together to form proteins.join amino acids together to form proteins.

A peptide forms between the amino group of A peptide forms between the amino group of one amino acid and the carboxyl group of one amino acid and the carboxyl group of another.another.

Three-dimensional Protein Three-dimensional Protein StructureStructure

The number and the order in which the amino acids are joined define the protein’s primary structure.

After an amino acid chain is formed, it folds into a unique three-dimensional shape, which is the protein’s secondary structure, such as a helix or a pleat.

Protein FunctionProtein Function

Proteins make up about 15% of your total Proteins make up about 15% of your total body mass and are involved in nearly body mass and are involved in nearly every function of your body.every function of your body.

Muscle, skin and hair all are made of Muscle, skin and hair all are made of protein.protein.

Your cells contain about 10,000 different Your cells contain about 10,000 different proteins that provide structural support, proteins that provide structural support, transport substances inside the cell and transport substances inside the cell and between cells, speed up chemical between cells, speed up chemical reactions, and control cell growth.reactions, and control cell growth.

Nucleic AcidsNucleic Acids

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.

Six major nucleotides, all of which have three units – a phosphate, a nitrogenous base and a sugar.

Nucleic AcidsNucleic Acids

Nucleic AcidsNucleic Acids Two types of nucleic acids (Two different sugars).Two types of nucleic acids (Two different sugars).

Deoxyribonucleic acid (DNA)Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)Ribonucleic acid (RNA)

In nucleic acids, the sugar of one nucleotide In nucleic acids, the sugar of one nucleotide bonds with the phosphate of another nucleotide.bonds with the phosphate of another nucleotide.

The nitrogenous base that sticks out from the The nitrogenous base that sticks out from the chain is available for hydrogen bonding with other chain is available for hydrogen bonding with other bases in other nucleic acids.bases in other nucleic acids.

DNA often is called the “genetic code” because DNA often is called the “genetic code” because DNA stores all the instructions for organisms to DNA stores all the instructions for organisms to grow, reproduce, and adapt.grow, reproduce, and adapt.

The primary function of RNA is to use the The primary function of RNA is to use the information stored in DNA to make proteins.information stored in DNA to make proteins.