the chemistry of life

THE CHEMISTRY THE CHEMISTRY OF LIFEOF LIFE

CHAPTER 2CHAPTER 2

Honors NotesHonors Notes

SECTION 2-1: THE SECTION 2-1: THE NATURE OF MATTERNATURE OF MATTER

REMEMBER…REMEMBER… Atoms are made up of electrons (-), Atoms are made up of electrons (-),

neutrons (neutral), and protons (+)neutrons (neutral), and protons (+) Proton number = atomic number = Proton number = atomic number =

type of elementtype of element IsotopeIsotope – atoms of same element, – atoms of same element,

but with a different number of but with a different number of neutronsneutrons

BondsBonds

Ionic bondIonic bond – when – when electrons are transferred electrons are transferred from one atom to anotherfrom one atom to anotherExample NaClExample NaCl

Covalent bondCovalent bond – electrons – electrons are shared between atomsare shared between atomsExample HExample H22OO

COVALENT BOND #’SCOVALENT BOND #’S

Atoms want to fill their Atoms want to fill their electron shells. An atom electron shells. An atom wants to make just enough wants to make just enough bonds to fill its shells.bonds to fill its shells.

H makes one bondH makes one bondO makes two bondsO makes two bondsC makes four bondsC makes four bonds

Protons +11Electrons -11Charge 0

Protons +17Electrons -17Charge 0

Protons +11Electrons -10Charge +1

Protons +17Electrons -18Charge -1

Sodium atom (Na)

Chlorine atom (Cl)

Chloride ion (Cl-)

Sodium ion (Na+)

SECTION 2-2: PROPERTIES SECTION 2-2: PROPERTIES OF WATEROF WATER PolarityPolarity – uneven distribution of – uneven distribution of

electrons between the hydrogen and electrons between the hydrogen and oxygen atoms oxygen atoms Oxygen is bigger and attracts the Oxygen is bigger and attracts the

electrons more than hydrogenelectrons more than hydrogen Hydrogen bondsHydrogen bonds – slightly positive, – slightly positive,

polar H atoms are attracted to polar polar H atoms are attracted to polar negative atoms like Onegative atoms like O

CohesionCohesion – attraction between – attraction between molecules of same substancemolecules of same substanceWater has high surface tension Water has high surface tension

(allows some bugs to walk on (allows some bugs to walk on water)water)

AdhesionAdhesion - attraction between - attraction between molecules of different substancesmolecules of different substancesCapillary action (water moves up a Capillary action (water moves up a

straw along the sides)straw along the sides)

Acids, Bases, and pHAcids, Bases, and pH

HH22O HO H++ + OH + OH--

Water Water Proton Proton ++ hydroxide hydroxide ionion

pH scalepH scale – indicates the – indicates the concentration of Hconcentration of H+ +

pH = 7 = neutral (HpH = 7 = neutral (H++ = OH = OH--)) BaseBase = pH above 7 (lower H = pH above 7 (lower H+ + than than

pure water)pure water) AcidAcid = pH below 7 (higher H = pH below 7 (higher H+ + than than

pure water)pure water) BufferBuffer – weak acids or bases that – weak acids or bases that

can prevent sharp, sudden changes can prevent sharp, sudden changes in pHin pHExample: bicarbonateExample: bicarbonate

http://www.epa.gov/acidrain/education/site_students/phscale.html

SECTION 2-3: CARBON SECTION 2-3: CARBON COMPOUNDSCOMPOUNDS

Organic compoundsOrganic compounds- those - those compounds that contain carbon compounds that contain carbon

Chemical FormulasChemical Formulas - show how many - show how many and which atoms are in a compound and which atoms are in a compound

Structural FormulasStructural Formulas - show the - show the arrangement of the atoms in a arrangement of the atoms in a compoundcompound

LIFE’S BACKBONELIFE’S BACKBONE

Most of the compounds that make Most of the compounds that make up living things contain carbon. In up living things contain carbon. In fact, carbon makes up the basic fact, carbon makes up the basic structure, or “backbone,” of these structure, or “backbone,” of these compounds. Each atom of carbon compounds. Each atom of carbon has four electrons in its outer has four electrons in its outer energy level, which makes it energy level, which makes it possible for each carbon atom to possible for each carbon atom to form four covalent bonds with form four covalent bonds with other atoms. other atoms.

Carbon’s tetrahedral Carbon’s tetrahedral shapeshape

http://www.chem.uic.edu/web1/OCOL-II/WIN/STRUCT/SB/14.HTM

Carbon-Carbon bonds can be single, Carbon-Carbon bonds can be single, double, or even triple. This bonding double, or even triple. This bonding characteristic allows for a virtually limitless characteristic allows for a virtually limitless number of different carbon compounds. number of different carbon compounds. Each carbon compound has a different Each carbon compound has a different structure. For example, carbon atoms can structure. For example, carbon atoms can bond together to form chains that can be bond together to form chains that can be straight or branching. They can bond to straight or branching. They can bond to form single or multiple ring structures. form single or multiple ring structures. They can even bond to form crystalline or They can even bond to form crystalline or hollow polyhedrons—multi-sided 3 hollow polyhedrons—multi-sided 3 dimentional molecules. dimentional molecules.

DiamondDiamond

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C-60 “Buckey Ball”C-60 “Buckey Ball”

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Other PolyhedronsOther Polyhedrons

A*

C

D*

G*

H*

E

F

B*

Organic molecules are named using Organic molecules are named using an internationally recognized an internationally recognized (IUPAC) system of naming Also, (IUPAC) system of naming Also, other kinds of atoms can be attached other kinds of atoms can be attached to the carbon chain. to the carbon chain.

IsomersIsomers - compounds with the - compounds with the same chemical formula, but same chemical formula, but different structure (ex. different structure (ex. propanol and isopropanol)propanol and isopropanol)

Functional GroupsFunctional Groups

Functional groups are like power Functional groups are like power attachments that change the job attachments that change the job (chemical and physical properties) that a (chemical and physical properties) that a molecule does.molecule does.

We’ve already looked at the hydroxyl –We’ve already looked at the hydroxyl –OH group. Now let’s look at some others:OH group. Now let’s look at some others:

Chemical Compound Formula Name of Compound Chemical Compound Formula Name of Compound ExampleExample

Esters Esters Esters EstersMethyl salicylate

Biology text reference

MACROMOLECULESMACROMOLECULES

Monomers (smaller units) Monomers (smaller units) join to make polymers or join to make polymers or macromoleculesmacromoleculesCarbohydrates Carbohydrates LLipidsipidsProteins Proteins Nucleic acidsNucleic acids

CARBOHYDRATESCARBOHYDRATES

Organic Organic compounds composed compounds composed of carbon, hydrogen and oxygen of carbon, hydrogen and oxygen with a ratio of two hydrogen with a ratio of two hydrogen atoms to every one oxygen atomatoms to every one oxygen atom

Made up of sugars Made up of sugars

USE OF CARBOHYDRATESUSE OF CARBOHYDRATES

Source of energy for many Source of energy for many living things living things

Examples: sugar and starch Examples: sugar and starch

TYPES OF TYPES OF CARBOHYDRATESCARBOHYDRATES

MonosaccharidesMonosaccharidesDisaccharidesDisaccharidesPolysaccharidesPolysaccharides

MONOSACCHARIDESMONOSACCHARIDES

Only one sugar moleculeOnly one sugar moleculeExamples -Examples -glucoseglucose, fructose, , fructose,

andand galactose galactose All three are All three are CC66HH1212OO66, but they , but they

are isomersare isomersDraw GlucoseDraw Glucose

DISACCHARIDESDISACCHARIDES

Double sugars (two Double sugars (two monosaccharides combined) monosaccharides combined)

Examples: sucrose, lactose, and Examples: sucrose, lactose, and maltose maltose

All are isomers with the chemical All are isomers with the chemical formula formula CC1212HH2222OO1111

POLYSACCHARIDESPOLYSACCHARIDES

Long chains of monosaccharides Long chains of monosaccharides joined together joined together

Examples: Examples: starchstarch, , glycogenglycogen, , and and cellulosecellulose

PlantsPlants store excess sugar as store excess sugar as starchstarch, and break it down for , and break it down for energyenergy

Representation of a Polysaccharide

HumansHumans store excess sugar store excess sugar as as glycogenglycogen, & break it , & break it down for energy down for energy

CelluloseCellulose used by used by plants plants for for structural purposes.structural purposes.

DEHYDRATION SYNTHESISDEHYDRATION SYNTHESIS

Two molecules join together Two molecules join together by losing a molecule of water by losing a molecule of water

HYDROLYSIS REACTIONHYDROLYSIS REACTION

Larger molecules broken down Larger molecules broken down into smaller molecules by the into smaller molecules by the addition of water addition of water

LIPIDSLIPIDS

Include Include fatsfats, , oilsoils, , steroidssteroids & & waxeswaxes

Composed of carbon, hydrogen Composed of carbon, hydrogen and oxygen, but the # of H atoms and oxygen, but the # of H atoms per molecule is much greater per molecule is much greater then the # of O atoms then the # of O atoms

An example, An example, CC5757HH110110OO66

USES OF LIPIDSUSES OF LIPIDS

Stored for energy Stored for energy Form basic structure of cell Form basic structure of cell

membranesmembranesProtection Protection Insulation Insulation Waterproof coveringsWaterproof coverings

THE STRUCTURE OF SOME FATSTHE STRUCTURE OF SOME FATS

Built from 2 basic molecules: Built from 2 basic molecules: GlycerolGlycerol - an alcohol - an alcohol Fatty AcidsFatty Acids - a long - a long

carbon chain with a -COOH carbon chain with a -COOH (carboxyl group) at one end(carboxyl group) at one end

Triglyceride StructureTriglyceride Structure

http://library.tedankara.k12.tr/chemistry/vol5/Proteins%20peptides%20fats%20structure%20heme%20proteins/z245.htm

Phospholipid StructurePhospholipid Structure

http://library.tedankara.k12.tr/chemistry/vol5/polarity%20and%20activity/z247.htm

Different types of fatty acids: Different types of fatty acids: SaturatedSaturated - all single, covalent - all single, covalent

bonds in between carbons in bonds in between carbons in chain chain

UnsaturatedUnsaturated - one double bond - one double bond between carbons in chainbetween carbons in chain

PolyunsaturatedPolyunsaturated - many - many double bonds between double bonds between carbons in chaincarbons in chain

CholesterolCholesterol - another lipid, - another lipid, made by animals, both helpful made by animals, both helpful & harmful & harmful

PROTEINPROTEIN

Made up of amino acids Made up of amino acids linked togetherlinked together

Composed of C, H, & O as Composed of C, H, & O as well as nitrogen, N, and well as nitrogen, N, and possibly sulfurpossibly sulfur

USES OF PROTEINSUSES OF PROTEINS

build living materials like musclebuild living materials like muscle act as enzymes to help carry out act as enzymes to help carry out

chemical reactionschemical reactions fight diseasefight disease transport particles into or out of transport particles into or out of

cellscells act as markers on cells act as markers on cells

Alanine Serine

General structure

Each has same basic structure Each has same basic structure with the only difference being with the only difference being the “R” group the “R” group

Amino acids are linked by Amino acids are linked by peptide bonds (formed by peptide bonds (formed by dehydration synthesis) dehydration synthesis)

Essential Amino Acids

There are 20 main amino acids

Peptide bondPeptide bond is between two is between two amino acids amino acids

PolypeptidePolypeptide – (a protein) – (a protein) many amino acids joined many amino acids joined

Aminoacids

Nucleic AcidsNucleic Acids

Nucleic Acids are molecules that are Nucleic Acids are molecules that are used for the storage of energy or used for the storage of energy or information.information.

Some examples of Nucleic Acids are Some examples of Nucleic Acids are DNA (deoxyribonucleic acid), RNA DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and ATP (ribonucleic acid), and ATP (adenosine triphosphate)(adenosine triphosphate)

Nucleic Acids are made of Nucleic Acids are made of monomers called NUCLEOTIDES.monomers called NUCLEOTIDES.

NucleotidesNucleotides

http://dnatesting.biz/nucleotides.png

DNA 3DDNA 3D

MATTER AND ENERGYMATTER AND ENERGY Have you ever sat around a campfire or Have you ever sat around a campfire or

watched flames flicker in a fireplace? The watched flames flicker in a fireplace? The burning of wood is a chemical reaction—a burning of wood is a chemical reaction—a process that changes one set of chemicals process that changes one set of chemicals into another set of chemicals. A chemical into another set of chemicals. A chemical reaction always involves changes in chemical reaction always involves changes in chemical bonds that join atoms in compounds. The bonds that join atoms in compounds. The elements or compounds that enter into a elements or compounds that enter into a chemical reaction are called reactants. The chemical reaction are called reactants. The elements or compounds produced by a elements or compounds produced by a chemical reaction are called products. As chemical reaction are called products. As wood burns, molecules of cellulose are wood burns, molecules of cellulose are broken down and combine with oxygen to broken down and combine with oxygen to form carbon dioxide and water vapor, and form carbon dioxide and water vapor, and energy is released.energy is released.

QUESTIONSQUESTIONS

1.1. What are the reactants when wood What are the reactants when wood burns?burns?

2.2. What are the products when wood What are the products when wood burns?burns?

3.3. What kinds of energy are given off What kinds of energy are given off when wood burns?when wood burns?

4.4. Wood doesn’t burn all by itself. Wood doesn’t burn all by itself. What must you do to start a fire? What must you do to start a fire? What does this mean in terms of What does this mean in terms of energy?energy?

5.5. Once the fire gets started, it keeps Once the fire gets started, it keeps burning. Why don’t you need to burning. Why don’t you need to keep restarting the fire?keep restarting the fire?

SECTION 2-4: CHEMICAL SECTION 2-4: CHEMICAL REACTIONSREACTIONS

Chemical reactions always involve Chemical reactions always involve breaking bonds in reactants and breaking bonds in reactants and making bonds in productsmaking bonds in products

Some reactions release energy and Some reactions release energy and therefore usually occur therefore usually occur spontaneouslyspontaneously

Other reactions need energy to Other reactions need energy to happenhappen

Activation energyActivation energy – the – the minimum amount of energy minimum amount of energy needed to start a reactionneeded to start a reaction

Enzymes Enzymes are catalysts which are catalysts which speed up chemical reactionsspeed up chemical reactions

EnzymesEnzymes are are proteinsproteins that that lowerlower activation energyactivation energy and and allow reactions to occur at allow reactions to occur at normal temperatures normal temperatures

Reaction pathwaywith enzyme

Reaction pathwaywithout enzyme

Activation energywithout enzyme

Activation energywith enzyme

Each enzyme is specific and Each enzyme is specific and has a specific shape has a specific shape

Enzymes are not permanently Enzymes are not permanently changed and are not used up changed and are not used up in the reactionin the reaction

They are continuously They are continuously recycled! recycled!

Most enzymes end in Most enzymes end in --asease Reactants are called Reactants are called

substratessubstrates

EnzymesEnzymes

The area where the enzyme The area where the enzyme interacts is called the interacts is called the active siteactive site

Think of the substrate as a Think of the substrate as a flexible key that must fit into the flexible key that must fit into the active siteactive site

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Example LysozymeExample Lysozyme

Q: What is it?Q: What is it? A:A: Q: How does it work?Q: How does it work? A:A: TutorialTutorial Animation without tutorialAnimation without tutorial

Enzyme

Substrates

Active site

Products

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