2. Chemical Basis for Life

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Chemical Basis for Life Chemical Basis for Life


Learning ObjectivesLearning Objectives List the characteristics of each of the subatomic particles.List the characteristics of each of the subatomic particles. Differentiate between a molecule and a compound.Differentiate between a molecule and a compound. List and describe the types of chemical bonds that may form List and describe the types of chemical bonds that may form

between elements.between elements. Give the general equations for synthesis, decomposition, and Give the general equations for synthesis, decomposition, and

exchange reactions.exchange reactions. Differentiate between organic and inorganic compounds; Differentiate between organic and inorganic compounds;

hydrophobic and hydrophilic molecules; acids and bases.hydrophobic and hydrophilic molecules; acids and bases. List the unique properties of the water molecule.List the unique properties of the water molecule. Describe the actions of a buffer system.Describe the actions of a buffer system. List the components of carbohydrates, lipids, proteins, and nucleic List the components of carbohydrates, lipids, proteins, and nucleic

acids.acids. List the functions of body proteins.List the functions of body proteins. Describe the actions of enzymes.Describe the actions of enzymes.


MatterMatter

Anything that occupies space and has Anything that occupies space and has mass mass

Matter can exist as a gas, liquid, or solid.Matter can exist as a gas, liquid, or solid. Matter is composed of elements.Matter is composed of elements.


ElementsElements

Nitrogen, oxygen, hydrogen, and carbon Nitrogen, oxygen, hydrogen, and carbon make up 96% of all matter found in living make up 96% of all matter found in living organisms.organisms.


AtomsAtoms

The smallest unit of The smallest unit of an element which an element which retains the unique retains the unique properties of the properties of the element element

Composed of smaller Composed of smaller subatomic particles subatomic particles ProtonsProtons NeutronsNeutrons ElectronsElectrons


AtomsAtoms

Ion: an atom that Ion: an atom that has lost or gained has lost or gained an electron, giving an electron, giving it a positive or it a positive or negative charge. negative charge.

Isotopes: atoms that Isotopes: atoms that contain a different contain a different number of neutrons.number of neutrons.


Electron ShellElectron Shell

The area around the nucleus where The area around the nucleus where electrons have their most likely position.electrons have their most likely position.

Electrons of lower energy exist in the first Electrons of lower energy exist in the first electron shell closest to the nucleus; electron shell closest to the nucleus; electrons of higher energy are in the electrons of higher energy are in the second electron shell. second electron shell.


Electron ShellElectron Shell


Molecules and CompoundsMolecules and Compounds

If two or more atoms of different elements If two or more atoms of different elements are joined, the result is a are joined, the result is a moleculemolecule..

A molecule is the smallest unit of a A molecule is the smallest unit of a compoundcompound that retains the properties of that retains the properties of that compound.that compound.


Covalent BondsCovalent Bonds

A A covalent bondcovalent bond is formed when atoms is formed when atoms share electrons.share electrons. single covalent bondsingle covalent bond —— one electron is shared one electron is shared double covalent bond double covalent bond —— two electrons are two electrons are

shared shared triple covalent bondtriple covalent bond —— three electrons are three electrons are

shared shared


Polar Water MoleculePolar Water Molecule

The shared electrons in a covalently The shared electrons in a covalently bonded molecule may spend more time bonded molecule may spend more time near one atom than the other. near one atom than the other.

The shared electrons in a water molecule The shared electrons in a water molecule spend more time near the oxygen than the spend more time near the oxygen than the hydrogen atoms. hydrogen atoms.


Polar Water MoleculePolar Water Molecule

This distribution of electrons gives the This distribution of electrons gives the molecule a slight positive charge on the molecule a slight positive charge on the hydrogen side of the molecule and a slight hydrogen side of the molecule and a slight negative charge on the oxygen side of the negative charge on the oxygen side of the molecule.molecule.


Ionic BondIonic Bond

An ionic bond is formed An ionic bond is formed when when electrons are transferred from electrons are transferred from one atom to another.one atom to another.

Ionic bonds are most Ionic bonds are most

often formed between atoms often formed between atoms

that have fewer than two that have fewer than two

electrons in their outer electron electrons in their outer electron shell and those that have shell and those that have almost full outer electron shells.almost full outer electron shells.


Hydrogen BondHydrogen Bond A A bond between hydrogen bond between hydrogen

atoms already covalently atoms already covalently bonded in a molecule to bonded in a molecule to oppositely charged oppositely charged particlesparticles

Hydrogen bonds are Hydrogen bonds are weaker than ionic or weaker than ionic or covalent bonds. covalent bonds. They are formed mostly They are formed mostly

betweenbetween molecules.molecules. They can also form They can also form between between

parts of the same moleculeparts of the same molecule..


Chemical ReactionsChemical Reactions

The formation and breaking of chemical The formation and breaking of chemical bondsbonds

They require energy input or release They require energy input or release energy.energy.

Three types of chemical reactions:Three types of chemical reactions:1.1. SynthesisSynthesis

2.2. DecompositionDecomposition

3.3. Exchange reactionsExchange reactions


Chemical ReactionsChemical Reactions

Factors that influence reaction ratesFactors that influence reaction rates Concentration of reactantsConcentration of reactants Temperature of the environmentTemperature of the environment Activation energyActivation energy Some reactions require the presence of a Some reactions require the presence of a

catalyst or enzyme.catalyst or enzyme.• Reaction speed is increased when there are more Reaction speed is increased when there are more

catalyst proteins present.catalyst proteins present.


Inorganic CompoundsInorganic Compounds

Inorganic molecules Inorganic molecules Do not contain hydrocarbon groups Do not contain hydrocarbon groups Often have ionic bonding Often have ionic bonding Examples: water, salts, acids, and bases.Examples: water, salts, acids, and bases.


Role of WaterRole of Water

Water is the universal solvent. Water is the universal solvent. Water is an ideal transport medium.Water is an ideal transport medium. Water has a high heat capacity and a Water has a high heat capacity and a

high heat of vaporization.high heat of vaporization. Water is used for lubrication.Water is used for lubrication.


SaltsSalts Salts are mineral Salts are mineral

compounds that have compounds that have ionic bonds.ionic bonds.

Salts are the principle Salts are the principle form of minerals that form of minerals that enter and are stored in enter and are stored in the body. the body.


SaltsSalts When salts are added to When salts are added to

water they immediately water they immediately ionizeionize Salts in their ionic form are Salts in their ionic form are

known as electrolytes.known as electrolytes. Electrolytes are Electrolytes are

substances that have the substances that have the ability to transmit an ability to transmit an electrical charge.electrical charge.


Acids and BasesAcids and Bases Acids:Acids:

Ionically bonded substances that release hydrogen ions Ionically bonded substances that release hydrogen ions (H(H++) in water) in water

Example: hydrochloric acid (HCl) dissociates into HExample: hydrochloric acid (HCl) dissociates into H++ and and ClCl−− ions ions

Bases:Bases: Ionically bonded substances that release a hydroxyl ion Ionically bonded substances that release a hydroxyl ion

(OH(OH−−) in water) in water Example: sodium hydroxide (NaOH) dissociates into NaExample: sodium hydroxide (NaOH) dissociates into Na++

and OHand OH−− ions ions Acids and bases are also electrolytes Acids and bases are also electrolytes —— when when

they ionize in water, they can transmit electricity.they ionize in water, they can transmit electricity.


pH ScalepH Scale

Acidity and alkalinity are Acidity and alkalinity are measured on a pH scale. measured on a pH scale.

The scale ranges from 1 (the The scale ranges from 1 (the most acidity) to 14 (the most most acidity) to 14 (the most alkaline, alkaline, or basic). or basic).

A pH of 7 in the middle of the A pH of 7 in the middle of the scale is neutral.scale is neutral.


BuffersBuffers

Buffers are weak acids and bases that do Buffers are weak acids and bases that do not completely ionize in water. not completely ionize in water.

By not allowing excessive hydrogen or By not allowing excessive hydrogen or hydroxyl ions to accumulate, buffers help hydroxyl ions to accumulate, buffers help the cell maintain a neutral pH. the cell maintain a neutral pH.

Buffer system example: carbonic acid and Buffer system example: carbonic acid and bicarbonate. Hbicarbonate. H22COCO33 H H++ + HCO + HCO33

− − 2H 2H++

+ CO+ CO33−2−2


Organic and Inorganic CompoundsOrganic and Inorganic Compounds

Organic compounds Organic compounds Contain hydrocarbon groups and often contain Contain hydrocarbon groups and often contain

a functional group a functional group Usually are covalently bonded Usually are covalently bonded Examples: carbohydrates, lipids, proteins, and Examples: carbohydrates, lipids, proteins, and

nucleic acidsnucleic acids Many of the organic molecules used in the Many of the organic molecules used in the

body are body are macromoleculesmacromolecules..


CarbohydratesCarbohydrates Functions: used for energy, storage of energy, and Functions: used for energy, storage of energy, and

cellular structurescellular structures


CarbohydratesCarbohydrates Functions: used for energy, storage of energy, and Functions: used for energy, storage of energy, and

cellular structurescellular structures Monosaccharides: contain three to seven carbon Monosaccharides: contain three to seven carbon

atoms in a chain or ring.atoms in a chain or ring. Example: glucose, chemical formula CExample: glucose, chemical formula C66HH1212OO66

Disaccharides: two monosaccharides joined Disaccharides: two monosaccharides joined togethertogether Example: glucose + fructose = sucrose.Example: glucose + fructose = sucrose.

Polysaccharides: combinations of many Polysaccharides: combinations of many monosaccharidesmonosaccharides Examples: glycogen, starch, and cellulose Examples: glycogen, starch, and cellulose


Dehydration Synthesis and HydrolysisDehydration Synthesis and Hydrolysis

Dehydration synthesis: Dehydration synthesis: Water is created Water is created during the reaction that forms during the reaction that forms disaccharides.disaccharides.

Hydrolysis: Hydrolysis: When a disaccharide is When a disaccharide is decomposed into its monosaccharide decomposed into its monosaccharide components, water is used in the reaction.components, water is used in the reaction.


LipidsLipids

Functions: used in the body for energy and Functions: used in the body for energy and stored in fat for future energy needsstored in fat for future energy needs

Four classes of lipids: Four classes of lipids: neutral fatsneutral fats phospholipidsphospholipids steroids steroids eicosanoidseicosanoids


Neutral FatsNeutral Fats Neutral fatsNeutral fats are also are also

called called triglyceridestriglycerides. . Contain three fatty acids Contain three fatty acids

and a glycerol molecule and a glycerol molecule A A glycerolglycerol molecule is a molecule is a

modified three-carbon modified three-carbon simple sugar.simple sugar.

A fA fatty acidatty acid is a chain of is a chain of carbon atoms with one or carbon atoms with one or two hydrogen atoms two hydrogen atoms attached to each carbon attached to each carbon by single or double by single or double bonds. bonds.


Saturated vs. Unsaturated FatsSaturated vs. Unsaturated Fats

A fatty acid is called A fatty acid is called saturatedsaturated when all when all the bonds in the hydrocarbon chain are the bonds in the hydrocarbon chain are single bonds and as many hydrogen single bonds and as many hydrogen atoms as possible are attached to carbon. atoms as possible are attached to carbon.

A fatty acid is called A fatty acid is called unsaturatedunsaturated when when there are some double bonds between the there are some double bonds between the carbon and hydrogen atoms. carbon and hydrogen atoms.


PhospholipidsPhospholipids Contain two fatty Contain two fatty

acids attached to acids attached to glycerol extending in glycerol extending in one direction one direction

Phosphate group Phosphate group (PO(PO44) attached to a ) attached to a

nitrogen-containing nitrogen-containing compound extending compound extending in the other directionin the other direction


PhospholipidsPhospholipids

The phosphate The phosphate group side is group side is hydrophilic and hydrophilic and polar.polar.

The fatty acid side The fatty acid side is hydrophobic and is hydrophobic and nonpolar.nonpolar.


SteroidsSteroids Lipids that take theLipids that take the

form of four interlocking form of four interlocking hydrocarbon rings hydrocarbon rings

Hydrophobic and Hydrophobic and nonpolar nonpolar

Different types of Different types of steroids are formed by steroids are formed by attaching attaching

unique functional groups unique functional groups to the four-ring structure to the four-ring structure

of the molecule.of the molecule.


EicosanoidsEicosanoids

Lipids formed from a 20-Lipids formed from a 20-carbon fatty acid and a carbon fatty acid and a ring structure ring structure PProstaglandins: rostaglandins:

mediate inflammationmediate inflammation Thromboxane: Thromboxane: mediates mediates

platelet function platelet function Leukotrienes:Leukotrienes: mediate mediate

bronchoconstriction and bronchoconstriction and increased mucus increased mucus production production


ProteinsProteins

ProteinsProteins are the most abundant organic are the most abundant organic molecules in the body. molecules in the body.

Composed primarily of C, O, H, and NComposed primarily of C, O, H, and N Made of amino acidsMade of amino acids Functions: used for cell structures and Functions: used for cell structures and

structural body tissues, for controlling structural body tissues, for controlling chemical reactions, for regulating growth, chemical reactions, for regulating growth, for transporting molecules, for defending for transporting molecules, for defending the body against invaders, for catalyzing the body against invaders, for catalyzing all reactions occurring in the bodyall reactions occurring in the body


Amino AcidsAmino Acids 20 different amino acids 20 different amino acids

used by the body used by the body Contains a central carbon Contains a central carbon

atom attached to a atom attached to a hydrogen atom, an hydrogen atom, an amino amino groupgroup (NH (NH22), a ), a carboxyl carboxyl

groupgroup (COOH) and a side (COOH) and a side chain (designated by the chain (designated by the letter “R”)letter “R”)

The R group defines each The R group defines each amino acid. amino acid.


Amino AcidsAmino Acids

The specific combination of amino acids is The specific combination of amino acids is determined by the cell’s DNA. determined by the cell’s DNA.

Two amino acids are linked together by Two amino acids are linked together by dehydration synthesis. dehydration synthesis. The carboxyl group of one amino acid links The carboxyl group of one amino acid links

with the amino group of another amino acid via with the amino group of another amino acid via a a peptide bondpeptide bond..

AA polypeptide polypeptide is a chain of ten or more is a chain of ten or more amino acids linked together. amino acids linked together.


Structure of ProteinsStructure of Proteins

Primary structure: the Primary structure: the sequence and number of sequence and number of amino acids that link amino acids that link together to form the peptide together to form the peptide chainchain



Secondary structure: the Secondary structure: the

natural bend of parts of natural bend of parts of

the peptide chain as it the peptide chain as it

is formed in three is formed in three

dimensionsdimensions The most common shapes The most common shapes

that chains of amino acids that chains of amino acids

assume are the alpha helix assume are the alpha helix and the beta-pleated sheet.and the beta-pleated sheet.



Tertiary structure: the Tertiary structure: the overall shape of a overall shape of a single protein moleculesingle protein molecule



Quaternary structure: Quaternary structure: two or more protein two or more protein chains join to form a chains join to form a complex complex macromolecule. macromolecule.


Types of ProteinsTypes of Proteins

Structural proteinsStructural proteins are stable, rigid, are stable, rigid, water-insoluble proteins that are used for water-insoluble proteins that are used for adding strength to tissues or cells.adding strength to tissues or cells. Examples: collagen, fibrin, and keratinExamples: collagen, fibrin, and keratin

Functional proteinsFunctional proteins are generally water- are generally water-soluble and have a flexible, three-soluble and have a flexible, three-dimensional shape that can change under dimensional shape that can change under different circumstances.different circumstances. Examples: hemoglobin, antibodies, enzymes, Examples: hemoglobin, antibodies, enzymes,

and protein-based hormonesand protein-based hormones


EnzymesEnzymes

Enzymes are proteins that act as catalysts Enzymes are proteins that act as catalysts to speed up a chemical reaction without to speed up a chemical reaction without themselves being altered or destroyed. themselves being altered or destroyed.

Enzymes are specific to the reaction they Enzymes are specific to the reaction they catalyze.catalyze.

SubstratesSubstrates are the substances enzymes are the substances enzymes act upon.act upon.


EnzymesEnzymes

An enzyme fits its substrate exactly and is An enzyme fits its substrate exactly and is itself unaltered at the end of the reaction.itself unaltered at the end of the reaction.

Enzymatic reactions often take place in a Enzymatic reactions often take place in a series of reactions, with the products of series of reactions, with the products of one reaction acting as the substrate for the one reaction acting as the substrate for the next reaction.next reaction.


Nucleic AcidsNucleic Acids

Nucleic acidsNucleic acids are the largest molecules in are the largest molecules in the body the body

Composed of C, O, H, N, and P Composed of C, O, H, N, and P Two classes of nucleic acids: Two classes of nucleic acids:

DNA (deoxyribonucleic acid) DNA (deoxyribonucleic acid) — — exists mainly exists mainly in the nucleus (but also in mitochondria) and is in the nucleus (but also in mitochondria) and is the molecule that contains all the instructions the molecule that contains all the instructions needed by the cell to build protein needed by the cell to build protein

RNA (ribonucleic acid)RNA (ribonucleic acid) — — transfers transfers instructions out of the nucleus and into the instructions out of the nucleus and into the cytoplasm of the cell; builds proteins cytoplasm of the cell; builds proteins


NucleotidesNucleotides Molecular building blocks of nucleic acids Molecular building blocks of nucleic acids Consist of a nitrogenous base plus a 5-Consist of a nitrogenous base plus a 5-

carbon (pentose) sugar plus a phosphate carbon (pentose) sugar plus a phosphate group group

The sugar in DNA is deoyxribose and in The sugar in DNA is deoyxribose and in RNA, ribose.RNA, ribose.


NucleotidesNucleotides The five nucleotides are The five nucleotides are

named for their named for their itrogenous base: itrogenous base: Adenine (A), guanineAdenine (A), guanine

(G), and (G), and cytosine (C) cytosine (C)

occur in both DNA an occur in both DNA an RNA RNA

Uracil (U) occurs only Uracil (U) occurs only in RNA in RNA

Thymine (T) occurs Thymine (T) occurs only in DNA only in DNA


NucleotidesNucleotides The nucleic acid is formed by the sugar The nucleic acid is formed by the sugar

and phosphate groups joined in a long and phosphate groups joined in a long chain with the nitrogenous base.chain with the nitrogenous base.

The information needed to produce The information needed to produce proteins is determined by the order of the proteins is determined by the order of the nucleotides.nucleotides.


NucleotidesNucleotides A grouping of three A grouping of three

nucleotides is the code nucleotides is the code for a specific amino acid. for a specific amino acid.

A gene is a sequence of A gene is a sequence of

nucleotides that carries nucleotides that carries

the information to make the information to make

one peptide chain. one peptide chain.


DNADNA DNA is constructed of DNA is constructed of

two parallel strands two parallel strands of the nucleotides A, of the nucleotides A, G, C, and T. G, C, and T.

The strands are The strands are connected by connected by hydrogen hydrogen

bonds between the bonds between the nitrogenous bases. nitrogenous bases.


DNADNA Adenine can bond Adenine can bond

only with thymine, only with thymine, and guanine can and guanine can bond only with bond only with cytosine. cytosine.

The two strands of The two strands of bonded nucleic acid bonded nucleic acid twist around each twist around each other in a spiral other in a spiral called a called a double helixdouble helix..


RNARNA

RNA consists of a single strand of the RNA consists of a single strand of the nucleotides nucleotides

A, G, C, and U. A, G, C, and U. Three types of RNA: Three types of RNA:

TransferTransfer MessengerMessenger Ribosomal RNA Ribosomal RNA


ATPATP The energy needed by the body is stored The energy needed by the body is stored

in the phosphate bonds of in the phosphate bonds of the ATP the ATP molecule.molecule.

ATP is an RNA nucleotide containing ATP is an RNA nucleotide containing

adenine with two additional phosphate adenine with two additional phosphate

groups attached. groups attached.

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2. Chemical Basis for Life