CHAPTER 6

CHEMISTRY IN BIOLOGY

• CHAPTER 6.1 – ATOMS, ELEMENTS, & COMPOUNDS• MAIN IDEA – Matter is composed of tiny

particles called atoms.

• QUESTIONS: • What is the smallest unit of matter?• How are atoms and elements related?

•ATOMS•Chemistry is the study of

matter, its composition, and properties•Matter is anything that has

mass and takes up space.•Atoms are the building blocks

of matter

• THE STRUCTURE OF AN ATOM• Atoms are extremely small – millions can fit on the head of pin.• Composed of:– Protons• Positively charged• Located in nucleus (center of atom)

– Neutrons• No charge• Located in nucleus (center of atom)

– Electrons • Negatively charged• Located outside nucleus in energy levels• Constantly moving

• Electrons attracted to protons = atom no charge

• ELEMENTS• Element is a pure substance that

cannot be broken down into other substances by physical or chemical means.–Elements made of 1 type of atom.–# of protons = the atomic # of the

element–# of protons = # of electrons

• ISOTOPES• Isotopes have the same # of protons & the same #

of electrons, but the # of neutrons is different.• Isotope of the element has the same chemical

characteristics• Isotopes of an element are identified by adding the

number of protons and neutrons in the nucleus.– Ex: Carbon has 6 protons, carbon as element has

6 neutrons = 12 or C12

– EX: Carbon has 6 protons, carbon as isotope has 8 neutrons = 14 or C14

• FIGURE OUT WHAT THE MISSING NUMBERS ARE?

ELEMENT CHEMICAL SYMBOL

ATOMIC NUMBER

NUMBER OF PROTONS

NUMBER OF NEUTRONS

MASS NUMBER

Lithium 3 5 8Carbon C 6 12

P 15 16

• RADIOACTIVE ISOTOPES• Changing the # of neutrons DOES NOT change

the charge of the atom• When an isotope break down they give off

radiation• Use radioactive isotopes to determine the age

of objects–Scientists know how long it takes for the

radioactive material to break down completely.

• Use radioactive isotopes in medicine also.

RADIOACTIVE DECAY

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• COMPOUNDS• Compound is a pure substance formed when 2 or more different

elements combine.– EX: water = H2O salt = NaCl

• Compounds have unique characteristics– Always formed from a specific combination of elements in a

fixed ratio.• Ex: water is always 2 hydrogen & 1 oxygen• EX: salt is always one sodium & 1 chlorine

– Compounds are chemically and physically different from the elements that they are made from.

– Compounds cannot be broken down into simpler compounds or elements by physical means (tearing, crushing, etc.)• Can be broken down by chemical means into simpler

compounds or their original elements

• CHEMICAL BONDS• The force that holds compounds together is called a chemical

bond.• Electrons are involved directly in forming the chemical bonds.– Electrons located outside the nucleus in energy levels– Each energy level can only hold so many electrons• First energy level closest to nucleus can only hold 2

electrons• 2nd energy level can only hold 8 electrons• 3rd energy level can only hold 8 electrons

– Partially filled energy levels are not as stable as full energy levels• Atoms become more stable by either losing or gaining

electrons in the partially filled energy levels. They form bonds to do this

• 2 main types of chemical bonds:– Covalent bonds– Ionic bonds

• COVALENT BONDS

• Chemical bonds that form when electrons are shared are called covalent bonds.– Ex: water = H2O, pg. 152, fig. 9

• Most compounds in living organisms have covalent bonds holding them together. These substances are called molecules–Depending on the # of pairs of electrons that are

shared, covalent bonds can be single, double, or triple bonds• Pg. 153, fig. 10

• IONIC BONDS• Atoms are neutral (no charge because protons = electrons)• Some atoms will give away (donate) or gain (accept) electrons to fill

or empty the outer energy level to become more stable.• Ion is an atom that has gained or lost one or more electrons and now

carries an electrical charge.– EX: salt = NaCl• Sodium gives 1 electron away = + charge–Metals tend to donate electrons

• Chlorine gains/accepts the electron = - charge– Nonmetals tend to accept electrons

• Pg. 153 fig. 11• Ionic bond is an electrical attraction between two oppositely charged

atoms or groups of atoms called ions– Substances formed by ionic bonds are called ionic compounds– Most will dissolve in water

• Ions help to maintain homeostasis as they travel in & out of cells• Ions help transmit signals among cells that allow you to see, taste,

hear, feel & smell

Chemistry in BiologySection 1

• SECTION 6.2 – CHEMICAL REACTIONS• MAIN IDEA – Chemical reactions allow living

things to grow, develop, reproduce, and adapt.

I have 3 pieces of paper. One paper is burned, 1 piece is folded, one piece has a hole cut in the middle.

• Identify which piece of paper(s) have undergone chemical or physical changes.

• REACTANTS AND PRODUCTS• Chemical reaction is the process by which atoms or

groups of atoms in substances are reorganized into different substances.–Bonds are broken & formed during the chemical

reactions– Ex: rust–Clues to help know when chemical reactions have

taken place include the production of heat or light, formation of a new gas, liquid, or solid

• Physical change alters a substance’s appearance, but not its composition.

• CHEMICAL EQUATIONS• In written chemical equations, chemical

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

• Reactants are the substances that you started with and will be on the left side of the arrow

• Products are the substances that are formed during the reaction and will be on the right side of the arrow–Ex: reactants products

• ENERGY OF REACTIONS• Most compounds in living things cannot

undergo chemical reactions without energy.• ACTIVATION ENERGY• Activation energy is the minimum

amount of energy (can be in the form of heat) needed for reactants to form products in a chemical reaction.–Some reactions rarely happen because

they have a very high activation energy

• ENZYMES• All living things carry out chemical reactions.–Proceed very slowly because activation

energy is high• Catalyst is a substance that lowers the

activation energy needed to start a chemical reaction.–Job of catalyst – speed up chemical

reactions•Does not increase amount of product•Does not get used up in the reaction

• ENZYMES CONTINUED• Enzymes are special proteins whose job is to be a biological

catalysts– Essential for life– Enzymes not use up in the reaction– Has an “ase” ending• Ex: amylase, used in the breakdown of amylose (starch)

– Enzymes are specific for one reaction– Substrates are reactants that bind to the enzyme at a

specific location called the active site.• Have complementary shapes–Ex: puzzle pieces fit exactly into one another

– Decrease the activation energy necessary to initiate the chemical changes

• ENZYMES CONTINUED–Enzyme-substrate complex = substrate

bound to active site on the enzyme•Helps chemical bonds in the reactants to

be broken and new bonds to form creating the products

–Factors such as pH, temperature, & other substances affect enzyme activity.•Human enzymes are most active at the

optimal temperature close to 37°C

• ENZYME-SUBSTRATE COMPLEX

• SECTION 6.3 – WATER AND SOLUTIONS• MAIN IDEA – The properties of water make it

well suited to help maintain homeostasis in an organism.

• QUESTIONS: What is the chemical equation for liquid water?

• What is the chemical equation for ice? Water Vapor?

• WATER’S POLARITY– With the water molecule the electrons spend

more time around the oxygen than the hydrogen. – Creates a slightly negative charge around the oxygen

and a slight positive charge around the hydrogen.– Molecules that have an unequal distribution of charges

are called polar molecules.• MIXTURES WITH WATER• Mixture is a combination of two or more substances in

which each substance retains its individual characteristics and properties

• HOMOGENEOUS MIXTURES• If the mixture has a uniform composition throughout it is called

homogeneous.– Ex: Kool-aid & water

• Solution is another name for a homogeneous mixture.• Solutions are made up of 2 components:– Solvent is a substance in which another substance is

dissolved• EX: water

– Solute is the substance that is dissolved in the solvent.• EX: Kool-aid

• HETEROGENEOUS MIXTURES• In the heterogeneous mixture you can see the individual

substances.– EX: salt & pepper, sand & water

• ACIDS AND BASES• Acids release a hydrogen ion (H+)– The more hydrogen ions = more acidic solutions

• Bases release a hydroxide ions (OH-)– The more hydroxide ions = more basic solutions

• Ph AND BUFFERS

• pH is the measure of concentration of H+ (hydrogen ions) in the solution–Neutral is 7 on the pH scale–Acidic solutions have a high concentration of H+

and are lower than 7 on the pH scale–Basic solutions have more OH- than H+ and are

higher than 7 on the pH scale• Most biological processes carried out by cells occur

between the range of 6.5 & 7.5 on the pH scale.• Buffers are mixtures than can react with acids or

bases to keep the pH within a particular range.• Blood has buffers to keep the pH about 7.4

• pH SCALE

• SECTION 6.4 – THE BUILDING BLOCKS OF LIFE• MAIN IDEA – Organisms are made up

of carbon-based molecules.

• QUESTION: How many bonds can carbon form with other atoms?

• ORGANIC CHEMISTRY• Life is considered carbon based because

carbon is in almost all biological molecules.• Carbon has 4 electrons in its outer most

energy level leaving space for 4 more electrons.–Carbon likes to covalently bond with 4

other atoms creating compounds in the shape of straight chains, branched chains, and rings

• MACROMOLECULES• Macromolecules are large molecules that

are formed by joining smaller organic molecules together.–Also called polymers (poly means

many)• Polymers are molecules made from

repeating units of identical or nearly identical compounds called monomers held together by covalent bonds.–EX: resembles a chain

• CARBOHYDRATES• Carbohydrates are compounds composed of

carbon, hydrogen and oxygen in a ratio of 1 oxygen and 2 hydrogen atoms for each carbon atom.

• Monomer for carbohydrates are called monosaccharides– Ex: glucose

• Disaccharide are two monosaccharides joined together.– Ex: sucrose & lactose

• Polysaccharides are many monosaccharides joined together– Ex: glycogen, cellulose

• CARBOHYDRATES – CONTINUED• Carbohydrates function is to provide

short term energy and structural support–Glucose and glycogen are used as an

energy source•EX: sugars, starches (bread, noodles, potatoes)

–Cellulose are tough fibers that provide structural support for plants

• LIPIDS• Lipids are molecules made mostly of

carbon and hydrogen• Lipids make up the group of fats, oils

and waxes• Function of lipids is to store long

term energy and provide barriers

• SATURATED AND UNSATURATED FATS• Basic structure of a lipid includes a fatty acid tail• Tails with all single carbon bonds are called

saturated fats – Ex: solid at room temperature = Butter

• Tails with at least one double bond in the tail are called unsaturated fats.– Ex: liquid at room temperature = olive oil

• Tails with more than one double bond in the tail are called polyunsaturated fats– Ex: liquid at room temperature

• PHOSPHOLIPIDS• Phospholipids are responsible for the structure and

function of the cell membrane• Lipids are hydrophobic (means it does not dissolve

in water)– Serves as a barrier for biological membranes

• STEROIDS• Steroids include substances such as cholesterol and

hormones–Cholesterol provides the starting point for other

necessary lipids such as vitamin D and the hormones estrogen & testosterone

• PROTEINS• Protein is a compound made of amino acids

(monomer)• Amino acids are small compounds that are made of

carbon, nitrogen, oxygen, hydrogen, and sometimes sulfur.–All amino acids share the same general structure

• AMINO ACID STRUCTURE• There are 20 different amino acids• Proteins are made from combining different amino

acids together by covalent bonds called peptide bonds

• 3 DIMENSIONAL PROTEIN STRUCTURE• After the amino acids are joined the amino acid chain will

fold into a unique 3 dimensional shape• Some proteins will combine with other proteins• PROTEIN FUNCTION• Proteins make up about 15% of your total body mass and

are involved in nearly every function of your body• Cells contain almost 10,000 different proteins that:– provide structural support– transport substances inside the cell and between cells– communicate signals within a cell and between cells– speeds up chemical reactions– control cell growth

• NUCLEIC ACIDS• Nucleic acids are complex macromolecules that store and transmit

genetic information.• Nucleic acids are made up of smaller repeating subunits called

nucleotides, which contain carbon, nitrogen, oxygen, phosphorus, and hydrogen atoms– Nucleotide is the monomer– Each nucleotide has a nitrogenous base, a sugar and phosphate

• There are 2 types of nucleic acids:– DNA – deoxyribonucleic acid• Contains the sugar deoxyribose

– RNA – ribonucleic acid • Contains the sugar ribose

• When nucleotides join together the sugar molecule will bond to the phosphate of the next nucleotide

• Nitrogen bases will form hydrogen bonds between them in DNA

• NUCLEIC ACIDS – CONTINUED• A nucleotide that is made up of 3 phosphates, sugar

& nitrogen base is called ATP (adenosine triphosphate)

• ATP is a storehouse of chemical energy that can be used by cells in a variety of reactions.–ATP will release energy when you break the bond

between the 2nd and 3rd phosphate group– Less energy is released when the bond between

the 1st & 2nd phosphate group is broken