Honors Biology Chapter 2

The Nature of Matter

2-1 The Nature of Matter

• Objective: You will be able to explain an

atom, element, and compound, describe the

types of bonds, explain why bonding is

important, and describe isotopes and their

functions.

Atoms

• Smallest basic unit of matter

• Subatomic particles:

• Protons- positive (+1)

• Neutrons- neutral

• Electrons- negative (-1)

• Nucleus in the middle=protons+ neutrons

Molecules/Compounds

• Substance composed of 2 or more elements

chemically combined.

• H2O= 2 hydrogens, 1 oxygen

Bonding• Bonds hold elements together to make

compounds

• Bonds store energy

• Types:

– Covalent- elements share electrons

– Ionic- electrons are added or taken away from

other elements

– Hydrogen bond- Weak chemical attraction

between a slightly positive hydrogen atom and a

slightly negative atom usually N or O.

Ionic Bonds

• Bond between 2 ions of

opposite charge

• Form ionic compounds

• Ions=charged particle

(gained or lost

electron)

• Metal gives electron to

nonmetal

Covalent Bond• 2 atoms sharing

electrons

– polar=unequal sharing

– Nonpolar=equal sharing

• Form molecules

• Nonmetal + nonmetal

• More than 2 electrons

can be shared (multiple

bonds)

Check for Understanding

• 1. What are the 2 main types of bonds?

• 2. Which bond is found in molecules?

• 3. What type of compound is found between

ions of opposite charge?

• 4. Which bond shares electrons?

• 5. What is created when molecules don’t

share the electrons equally?

• 6. How are positive ions formed? Negative

ions?

Properties of Water

• Objectives:

• List the properties of water

• Explain why water has so many properties

• Discuss how the properties of water affect

living things.

Properties of Water

• Water is the most abundant compound in

living organisms 2/3 of body is water.

• Composed of 2 atoms of hydrogen linked by

covalent bonds to 1 atom of oxygen

• Polar molecule: oxygen is not sharing

electrons nicely/equally with hydrogens

• Oxygen becomes slightly negative, hydrogens

become slightly positive.

Hydrogen Bonding

• Water’s polarity allows

it to form hydrogen

bonds with other

water molecules

• The hydrogen of one

water molecule is

attracted to the

oxygen of another

water molecule.

Properties of Water due to Polarity

and Hydrogen Bonding:• Cohesion- attraction of water molecules to

each other

• Helps create surface tension, beading of water

and animals walking on water.

• 2. Adhesion- attraction

of water to other

charged molecules

• Important for capillary

action- transporting

water from the roots of

plants to their leaves.

• 3. High Specific Heat- water resists a change in

temperature

• All the heat absorbed or released by water

goes 1st to break and for hydrogen bonds

instead of increasing or decreasing

temperature

• Example- water in ocean/lakes stays fairly

stable allowing life to continue

• 4. Universal Solvent- can

dissolve or break apart

many substances

• Will only dissolve polar and

ionic compounds

(hydrophilic)

• Nonpolar does not have any

+ or – ends that the water

would be attracted to in

order to pull them apart

(hydrophobic)

Solutions and Suspensions

–Solutions

–All the components of a solution are evenly

distributed throughout the solution.

–In a salt–water solution, table salt is the solute—

the substance that is dissolved.

–Water is the solvent—the substance in which

the solute dissolves.

Acids, Bases, and pH

•Acids, Bases, and pH• A water molecule can react to form hydrogen and

hydroxide ions.

• Water is neutral because the number of positive

hydrogen ions (H+) produced is equal to the number of

negative hydroxide ions (OH-) produced.

pH

• Measure of H+ ions in a solution

• Scale of 1-14

• More H+=more acidic, Lower pH#

• Less H+= more basic, Higher pH#

• The concentration of H+ and OH- in pure

water is equal= pH7

Acids, Bases, and pH•At a pH of 7, the

concentration of H+

ions and OH- ions is

equal.

•Pure water has a pH

of 7.

Solutions with a pH

below 7 are called acidic

because they have more

H+ ions than OH- ions.

The lower the pH, the

greater the acidity. Acid rain

Tomato juice

Lemon juice

Stomach acids

The pH Scale

Solutions with a pH

above 7 are called basic

because they have more

OH- ions than H+ ions.

The higher the pH, the

more basic the solution.

The pH Scale

Soap

Bleach

Oven cleaner

Ammonia solution

Acids and Bases

• Acids

– Proton Donors

– Release H+ ions in solution

– Ex-HCL

• Bases

– Proton acceptors

– Release hydroxyl ions (OH-)

– Ex-NaOH

Acids, Bases, and pH

–Buffers

•The pH of the fluids within most cells in the human body must generally be kept between 6.5 and 7.5.

• If the pH is lower or higher, it will affect the chemical reactions that take place within the cells.

Acids, Bases, and pH

–*Controlling pH is important for

maintaining homeostasis.

–One of the ways that the body controls

pH is through dissolved compounds called

buffers.

–*Buffers are weak acids or bases that

can react with strong acids or bases to

prevent sharp, sudden changes in pH.

• pH in most organisms needs to be kept within

a very narrow range.

• A small change in pH can disrupt cell

processes

• Buffers within an organism are used to

regulate pH so that pH homeostasis can be

maintained.

– Helps because it can bind to H+ ion when the H+

conc. Is high or release H+ ions when the H+

conc. Is low.

Check for Understanding

• 1. Why is water a polar molecule?

• 2. explain a hydrogen bond.

• 3. Explain the difference between adhesion

and cohesion.

• 4. What causes water to have such a high

specific heat?

• 5. What substances will not dissolve in water?

• 6. Explain why hydrophilic substances will

dissolve in water.

• 7. Explain the differences between the pH of

acids and bases.

• 8. If a cell’s pH increases, what would a buffer

do?

Carbon

• Objectives:

• Discuss carbon and its importance in

biological compounds.

Carbon

• The basic element of organic compounds

– Inorganic compounds=no carbon

• Has 4 valence electrons available for bonding

• Likes to share electrons which causes covalent

bonds.

• Most common bonding partners: hydrogen,

oxygen, nitrogen, or another carbon atom.

• Carbon is important for 2 reasons

1.Carbon has 4 valence electrons that can form

strong covalent bonds.

2.Carbon can bond with itself.

Check for Understanding

Questions• 1. What is an organic molecule?

• 2. How many bonds can a carbon atom make?

• 3. What other atoms does carbon typically

bond with?

Polymerization

• Objectives:

• Describe a polymer

• explain how polymers are formed and broken

down.

Macromolecules•Macromolecules

•Macromolecules are

formed by a process

known as

polymerization.

•The smaller units,

or monomers, join

together to form

polymers.

Dehydration Synthesis

• Joining monomers together by taking the

hydroxyl group of one monomer and

hydrogen of another to form water.

Hydrolysis

• Breaking polymers into monomers by the

addition of water molecules

• -OH and H are restored on monomers

Nucleic Acids

• Objectives:

• Identify the chemical structure of a nucleic

acid.

• Discuss the uses nucleic acids in living things.

Nucleic Acids

•Nucleic Acids-C, H, O, N, P• Nucleic acids are macromolecules containing

hydrogen, oxygen, nitrogen, carbon, and phosphorus.

• *Nucleic acids are polymers assembled from individual

monomers known as nucleotides.

• Monomer=nucleotides

• Made of a 5-carbon sugar, a phosphate group, and a

nitrogen containing molecule/base

• Holds the cell’s genetic information (information for

making and building proteins)

• 2 types of nucleic acids:

• 1. DNA (deoxyribonucleic acid)- stores the

information for making proteins contains

deoxyribose sugar

• 2. RNA(ribonucleic acid)- helps build protein

contains ribose sugar.

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.

Check for Understanding

• 1. What are the monomers for nucleic acids?

• 2. What are the 2 types of nucleic acids?

• 3. What are the functions of each type of

nucleic acid?

Carbohydrates

• Objectives:

• Identify the chemical structure of a

carbohydrate.

• Discuss the uses of carbohydrates in living

things.

Carbohydrates•Carbohydrates- CHO (carbon, hydrogen,

oxygen) in a 1:2:1 ratio

•Monomer=monosaccharide

•Store and release energy

•Body’s main energy source

•Typically end in –ose

•Glucose, fructose, galactose

•Ex. Sugar, rice, bread, pasta

Carbohydrates can be linear

Carbohydrates can be cyclic

• Typically cyclic in aqueous solution

Carbohydrate functions- Living things use carbohydrates as their main

source of energy.

– structure in plants (cellulose)

–used as fiber for animals.

–The carbon, hydrogen, and oxygen are used for

amino acids and fatty acids.

Carbohydrates

– The breakdown of sugars, such as glucose,

supplies immediate energy for all cell activities.

–Living things store extra sugar as complex

carbohydrates known as starches.

Types of Carbohydrates

• 1. Monosaccharides-simple sugars

• Glucose- most common source of sugar to

make energy

• Fructose- fruit sugar

• Deoxyribose- major component of DNA

• Ribose- major component of RNA

• 2. Disaccharides- two simple sugars joined by

dehydration synthesis

• Lactose(glucose/galactose)- found in mammals

milk

• Sucrose (glucose/fructose)- table sugar; found

in honey, fruits, and vegetables

• 3. Polysaccharides- long chains of simple sugars

joined by dehydration synthesis

• Starch-found in plants (roots), many glucoses joined

together in a long straight chain

• Glycogen- found in animals (liver or muscles)

• Many glucoses joined with branching

• When energy is needed by animals, a glucose is

hydrolyzed

• Cellulose- found in plant cell walls

• Very strong, long chain of glucoses joined together

• Can’t be digested by animal, but important because

stimulates the digestive tract to make mucus for

passage of waste.

Caloric value of Carbohydrates

• The caloric value is dependent on the number

of carbon-hydrogen bonds.

• If you have more carbohydrates than needed

they are converted to fats and stored.

• Lipids have the most caloric value

• Carbohydrates and Proteins have the same

amount.

Check for Understanding Question

• 1. How is a polymer made?

• 2. How is a polymer broken down?

• 3. What is the monomer for carbohydrates?

• 4. What is the function of carbohydrates?

• 5. What elements are found in carbohydrates?

• 6. Which polysaccharides are found in plants?

Animals?

Lipids

• Objectives:

• Identify the chemical structure of a lipid.

• Discuss the uses of lipids in living things.

Lipids

• Fats, oils, waxes, or sterols

• Made of C, H, O

• Nonpolar molecules (hydrophobic) not

soluble in water

• Monomer= glycerol bonded to fatty acids

• Provide insulation, protection, and store

energy long term

• Not the body’s 1st energy source (carbs are)

• Per gram, a lipid has more energy than a

carbohydrate because it has more carbon-

hydrogen bonds; however, it will always use

carbohydrates 1st as its energy source

• Ex- lard, butter, olive oil, peanut oil

• They contain two component molecules

(glycerols and fatty acids).

Lipids

– *Uses of Lipids

1. store energy, protects, insulates

2. important parts of biological membranes

3. waterproof coverings.

4. Production of some vitamins and hormones.

Characteristics of Lipids• 1. Saturated

• All single bonded carbons in fatty acid chain

• Solids at room temperature (fats)

• Ex. Lard, butter, bacon grease

• 2. Unsaturated

• At least one double or triple bonded carbon

• Liquid at room temperature (oils)

• Double/triple bond creates “kinks” or bends in chain which

gives more spacing between fatty acids allowing them to slide

past each other more easily

• Ex. Oilve oil, vegetable oil,

3. Fused rings- ex cholesterol, estrogen, testosterone

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.

lards, solid at room temperature, no double

bonded carbon

Lipids

–*If there is at least one carbon-carbon double

bond in a fatty acid, it is unsaturated.

–*Lipids whose fatty acids contain more than one

double bond are polyunsaturated.

–Lipids that contain unsaturated fatty acids tend

to be liquid at room temperature.

Carbohydrates can be linear

Types of Lipids

• Triglycerides- glycerol

molecule bonded to 3

fatty acids

• Fats and oils

• Long term energy

storage molecule

• 2. Phospholipids-

glycerol bonded to

2 fatty acids and a

phosphate

containing group

• Found in cell

membranes

• 3. Steroids- four fused/interlocking rings with

other functional or hydrocarbon groups

attached.

• Ex. Cholesterol (most abundant steroid- found

in cell membranes, brain), sex hormones

(estrogen, progesterone, testosterone), bile

salts, vitamin D

Caloric Value of Lipids

• Fats have a greater caloric value because fats

contain more energy (ATP) per gram than

carbohydrates or proteins.

Check for Understanding

Questions• 1. What are the functions of lipids?

• 2. What elements make up lipids? Why is this

different than carbs?

• 3. What are the types of lipids?

• 4. Which has more hydrogen, a saturated or

unsaturated lipid?

• 5. A ring shape is characteristic of what type of

lipid?

Proteins

• Objectives:

• Identify the chemical structure of a protein

• Discuss the uses of proteins in living things.

• List the things that affect the

structure/function of a protein

Proteins

•Made of C,H, O, and N

•Monomer= amino acids

•Diverse group with many different functions:

–1. structural-support and maintainance of cell shape

(as connective tissue and keratin in hair and nails).

–2. Contractile- mechanical work (muscles)

–3. Storage- keep essential substances readily

available

• 4. Defensive- provide protection against

foreign matter (antibodies)

• 5. Transport- carry substances through blook

to rest of body (hemoglobin)

• 6. Hormonal- regulate body functions by

sending messengers (insulin)

• 7. Enzymatic- catalyzed/speed up chemical

reactions without being changed itself (ATP

synthase)

Amino Acids• 20 Amino acids

• 12 made by the body, others must be

consumed (meat, nuts, beans)

• All amino acids have a central carbon with 4

different partners

– 1. Carboxyl group 2. Amino group

– 3. Hydrogen 4. R group or side chain varies

Structure

• Amino acids joined

together by dehydration

synthesis to form a

covalent bond called a

peptide bond (-OH from

carboxyl group of one

amino acid and the H

from the amino group of

another amino acid)

• 2 amino acids=dipeptide

• 3 or more=polypeptide

Function of Proteins

–*Some proteins control the rate of reactions and

regulate cell processes.

–*Some proteins are used to form bones and

muscles.

–*Other proteins transport substances into or out

of cells or help to fight disease.

Protein Levels of Structure

• 1. Primary Structure-

linear sequence of

amino acids

• Specific order

determines structure

and specific gene made

• 2. Secondary

Structure- regular

and repeated coiling

and folding.

• Gives the ability to

hydrogen bond

between functional

groups of the amino

acids.

• 3. Tertiary Structure-

folding in on itself due

to interactions between

side chain/R groups

• Held together in 3-D

shape by hydrogen

bonds, disulfide bridges,

ionic bonds, etc.

between side chains

• Globular and soluble

• 4. Quaternary Structure- interaction among

several polypeptide complexes

• Can be the same subunits or different

• Ex- hemoglobin, enzymes

Shape Determines Function• Denaturation- unraveling of protein shape

making them lose their function and becomin

inactive

• pH and temperature- changes in these cause

hydrogen bonds and other bonds between

side chains to be broken.

Caloric Value of Proteins

• Proteins have the same caloric value per gram

as carbohydrates.

Check for Understanding

• 1. What are the monomers for proteins?

• 2. What makes amino acids different from one

another?

• 3. What do proteins do?

• 4. How many peptide bonds would you find in

a polypeptide 10 amino acids long?

• 5. What type of protein structure only

involves hydrogen bonding between different

functional groups of amino acids?

• 6. What type of protein structure involves

interactions between amino acid R groups?

• 7. What type of protein structure allows them

to become more soluble?

• 8. What happens when a protein denatures?

2–4 Chemical Reactions and Enzymes

Copyright Pearson Prentice Hall

•Everything that happens in an organism, growth,

interactions with the environment, reproduction,

and movement Is based on chemical reactions.

•A chemical reaction is a process that changes

one set of chemicals into another set of

chemicals.

Example

• Cells constantly produce chemical

reactions as normal part of their activity.

• CO2 is carried by your blood to your lungs.

• CO2 is not very soluble in H20. Your

blood stream could not dissolve enough

to carry it away from your tissues.

•A chemical reaction takes place.

• CO2+ H2O H2CO3

• Carbonic

acid

•In the lungs the reaction is reversed

•H2CO3 CO2+H2O

•*When chemical bonds are formed or broken energy

is released or absorbed.

Energy in Reactions

•*Activation energy – energy needed to get a reaction

started.

Enzymes

•Some chemical reactions that make life possible are

too slow or have activation energies that are too high

to make them practical for living tissue.

1. Enzymes speed up chemical reactions and lower

activation energy.

2. Enzymes are proteins

3. Enzyme ends in ase.

4. Substrates-molecules that change into new

products

–What happens to chemical bonds during

chemical reactions?

–Chemical reactions always involve changes in the

chemical bonds that join atoms in compounds.

–How do energy changes affect whether a

chemical reaction will occur?

–Energy Changes

Chemical reactions that release energy often occur

spontaneously. Chemical reactions that absorb energy will

not occur without a source of energy.

Example

•Remember the reaction in your lungs:

• CO2+H2O H2CO3

•This reaction is so slow that it would build up in your body and be toxic.

•The enzyme carbonic anhydrase speeds up the reaction by a factor of 10 million.

•Every organism must have a source of energy to carry out chemical reactions.

• Plants- from sunlight

• Animals- from eating

•The energy that is needed to get a reaction started is called activation energy.

Enzymes

•*A catalyst is a substance that speeds up the

rate of a chemical reaction.

•*Catalysts work by lowering a reaction's

activation energy.

•*Catalysts are not altered in this process and

can be used over and over again.

•Enzymes are proteins that are used as catalysts.

– Why are enzymes important to living things?

–*Enzymes are proteins that act as biological

catalysts.

–*Enzymes speed up chemical reactions that take

place in cells.

–*Enzymes act by lowering the activation energy.

Enzymes

•*Lowering the activation energy has a dramatic

effect on how quickly the reaction is completed.

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.

•Enzyme Action• For a chemical reaction to take place, the reactants must

collide with enough energy so that existing bonds will be

broken and new bonds will be formed.

• If reactants do not have enough energy, no reaction will

take place.

–The Enzyme-Substrate Complex

• *Enzymes provide a site where reactants can be

brought together to react, reducing the energy needed

for reaction.

• *The reactants of enzyme-catalyzed reactions are

known as substrates.

–The substrates glucose and ATP bind to the

active site on the enzyme, hexokinase, forming an

enzyme-substrate complex.

–*The fit is so precise that the active site and

substrates are often compared to a lock and key.

–The enzyme and substrates remain bound

together until the reaction is done and the

substrates are converted to products.

–The products of the reaction are released and

the enzyme is free to start the process again.

–Active site- location on enzyme where substrate

fits.

Enzyme Action

•An Enzyme-Catalyzed Reaction

How is enzyme activity like a lock

and key?• 1. An active site on the enzyme is like the lock

and the substrate is like the key.

• 2. The substrate comes into the enzyme and

fits perfectly on the active site.

• 3. The enzyme then contributes energy to get

the reaction started.

4. Once the reaction is finished, the reactants

leave the active site.

5. The enzyme is free and ready to take on

another substrate.

–Regulation of Enzyme Activity

• Enzymes can be affected by any variable that influences

a chemical reaction.

• Enzymes work best at certain pH values.

• Many enzymes are affected by changes in temperature.

• Buffers within an organism are used to regulate pH so

that pH homeostasis can be maintained. A small

change in pH can disrupt cell processes.

Reaction Types

• Endergonic or

Endothermic – takes in

energy or heat –

reaction vessel will feel

cool to the touch.

• Exergonic or

Exothermic – gives off

energy or heat –

Reaction vessel will feel

warm to the touch, or

light will be seen.

Checking for Understanding

1. How are and enzyme and a catalyst similar?

2. What role does an enzyme have in a

biochemical reaction?

3. Any enzyme (can/cannot) work in any

chemical reaction?

4. What kind of macromolecule is an enzyme?

5. What is the name given to a reaction that

releases chemical energy?