Microbiology: A Microbiology: A Systems Approach, 2Systems Approach, 2ndnd

ed.ed.Chapter 2: The Chemistry of Chapter 2: The Chemistry of

BiologyBiology

2.1 Atoms, Bonds, and Molecules: 2.1 Atoms, Bonds, and Molecules: Fundamental Building BlocksFundamental Building Blocks

MatterMatter: anything that occupies space and : anything that occupies space and has masshas mass

Can be liquid, solid, or gaseous stateCan be liquid, solid, or gaseous state Building blocks of matter- Building blocks of matter- atomsatoms

Subatomic particles of atoms- Subatomic particles of atoms- protonsprotons (p (p++), ), neutronsneutrons (n (n00), and ), and electronselectrons (e (e--))

Protons and neutrons make up the nucleus, Protons and neutrons make up the nucleus, electrons surround the nucleuselectrons surround the nucleus

Held together by the attraction of positive protons Held together by the attraction of positive protons to negative electronsto negative electrons

Figure 2.1

Different Types of Atoms: Elements Different Types of Atoms: Elements and Their Propertiesand Their Properties

Different numbers of protons, neutrons, Different numbers of protons, neutrons, and electrons in atoms create different and electrons in atoms create different elementselements

Each element has a characteristic atomic Each element has a characteristic atomic structure and predictable chemical structure and predictable chemical behaviorbehavior

Each assigned a distinctive name with an Each assigned a distinctive name with an abbreviated shorthand symbolabbreviated shorthand symbol

The Major Elements of Life and Their The Major Elements of Life and Their Primary CharacteristicsPrimary Characteristics

IsotopesIsotopes- variant forms of the same - variant forms of the same element that differ in the number of element that differ in the number of neutronsneutrons

Radioactive isotopes used in research and Radioactive isotopes used in research and medical applications and in dating fossils medical applications and in dating fossils and ancient materialsand ancient materials

Electron orbitals and shellsElectron orbitals and shells

Electron Orbitals and ShellsElectron Orbitals and Shells An atom can be envisioned as a central nucleus An atom can be envisioned as a central nucleus

surrounded by a “cloud” of electronssurrounded by a “cloud” of electrons Electrons rotate about the nucleus in pathways Electrons rotate about the nucleus in pathways

called called orbitalsorbitals- volumes of space in which an - volumes of space in which an electron is likely to be foundelectron is likely to be found

Electrons occupy energy shells, from lower-energy Electrons occupy energy shells, from lower-energy to higher-energy as they move away from the to higher-energy as they move away from the nucleusnucleus

Electrons fill the orbitals and shells in pairs starting Electrons fill the orbitals and shells in pairs starting with the shell nearest the nucleuswith the shell nearest the nucleus

Each element, then, has a unuiqe pattern of Each element, then, has a unuiqe pattern of orbitals and shellsorbitals and shells

Figure 2.2

Bonds and MoleculesBonds and Molecules

Most elements do not exist naturally in pure formMost elements do not exist naturally in pure form MoleculeMolecule- the smallest particle of matter that can have - the smallest particle of matter that can have

independent existence; a distinct chemical substance independent existence; a distinct chemical substance that results from one atom of a noble gas (Ne) or the that results from one atom of a noble gas (Ne) or the combination of two or more atoms (can be two atoms combination of two or more atoms (can be two atoms of the same element, such as Oof the same element, such as O22).).

CompoundsCompounds- are combinations of two or more - are combinations of two or more different elements joined by chemical bonds.different elements joined by chemical bonds.

Chemical BondsChemical Bonds- When two or more atoms share, - When two or more atoms share, donate, or accept electronsdonate, or accept electrons

Types of bonds formed and to which atoms and Types of bonds formed and to which atoms and element bonds are determined by the atom’s element bonds are determined by the atom’s valencevalence

Figure 2.3

Covalent Bonds and Polarity: Covalent Bonds and Polarity: Molecules with Shared ElectronsMolecules with Shared Electrons

Covalent bondsCovalent bonds- between atoms that - between atoms that share electrons (such as Hshare electrons (such as H22).).

The majority of molecules associated with The majority of molecules associated with living things are composed of single and living things are composed of single and double covalent bonds between C, H, O, double covalent bonds between C, H, O, N, S, and P.N, S, and P.

Figure 2.4

Polar vs. Nonpolar MoleculesPolar vs. Nonpolar Molecules

Some covalent bonds result in a Some covalent bonds result in a polarpolar molecule- an unequal distribution of molecule- an unequal distribution of charge (ex. Hcharge (ex. H22O).O). Polarity is a significant property of many large Polarity is a significant property of many large

molecules, influencing both reactivity and molecules, influencing both reactivity and structure.structure.

An electrically neutral molecule is An electrically neutral molecule is nonpolarnonpolar

Van der Waals forcesVan der Waals forces- weak attractions - weak attractions between molecules with low levels of between molecules with low levels of polaritypolarity

Figure 2.5

Ionic Bonds: Electron Transfer Among Ionic Bonds: Electron Transfer Among AtomsAtoms

• Electrons transferred completely from one atom Electrons transferred completely from one atom to another, without sharing, results in an to another, without sharing, results in an ionic ionic bond bond (ex. NaCl)(ex. NaCl)

Crystals with ionic bonds, when dissolved in a Crystals with ionic bonds, when dissolved in a solvent, can separate in to charged particles solvent, can separate in to charged particles called called ionsions in a process called in a process called ionizationionization

CationsCations- positively charged ions- positively charged ions AnionsAnions- negatively charged ions- negatively charged ions These ionic molecules that dissolve to form ions These ionic molecules that dissolve to form ions

are called are called electrolyteselectrolytes

Figure 2.6

Figure 2.7

Hydrogen BondingHydrogen Bonding

• Weak bond between Weak bond between a H covalently a H covalently bonded to one bonded to one molecule and an O or molecule and an O or N atom on the same N atom on the same or different molecule or different molecule (such as between (such as between water molecules)water molecules)

Figure 2.8

Chemical Shorthand: Formulas, Chemical Shorthand: Formulas, Models, and EquationsModels, and Equations

Molecular formula- gives atomic symbols Molecular formula- gives atomic symbols and the number of atoms of the elements and the number of atoms of the elements involved in subscript (Hinvolved in subscript (H22o, Co, C66HH1212OO66).).

Molecular formulas might not be unique Molecular formulas might not be unique (glucose, galactose, and fructose, for (glucose, galactose, and fructose, for example)example)

Structural formulas illustrate the Structural formulas illustrate the relationships of the atoms and the number relationships of the atoms and the number and types of bondsand types of bonds

Figure 2.9

Chemical EquationsChemical Equations

Equations are used to illustrate chemical Equations are used to illustrate chemical reactionsreactions Reactants- Reactants- Molecules entering the reactionMolecules entering the reaction ProductsProducts- the substances left by a reaction- the substances left by a reaction

Types of ReactionsTypes of Reactions

Synthesis: reactants bond together to form Synthesis: reactants bond together to form an entirely new moleculean entirely new molecule A + B A + B AB AB S + OS + O22 SO SO22 2H2H22 + O + O22 2H 2H22O (note that equations must be O (note that equations must be

balanced)balanced) Decomposition: bonds on a single reactant Decomposition: bonds on a single reactant

molecule are permanently broken to release molecule are permanently broken to release two or more product moleculestwo or more product molecules AB AB A + B A + B 2H2H22OO22 2H 2H22O + OO + O22

Types of Reactions:Types of Reactions: Exchange: The reactants trade places between Exchange: The reactants trade places between

each other and release products that are each other and release products that are combinations of the twocombinations of the two AB + XY AX + BY (reversible reaction)AB + XY AX + BY (reversible reaction)

CATALYSTSCATALYSTS

CatalystsCatalysts- increase the rate of the - increase the rate of the reactionreaction

Catalysts lower the energy required to get Catalysts lower the energy required to get reactions startedreactions started

Enzymes are biological catalystsEnzymes are biological catalysts Most enzymes are proteins, but other Most enzymes are proteins, but other

substances, e.g. RNA can occasionally substances, e.g. RNA can occasionally serve as enzymesserve as enzymes

Solutions: Homogeneous Mixtures of Solutions: Homogeneous Mixtures of MoleculesMolecules

SolutionSolution- a mixture of one or more - a mixture of one or more solutessolutes uniformly dispersed in a uniformly dispersed in a solventsolvent

The solute cannot be separated by filtration or The solute cannot be separated by filtration or settlingsettling

The rule of solubility- “like dissolves like”The rule of solubility- “like dissolves like” Water- the most common solvent in natural Water- the most common solvent in natural

systems because of its special characteristicssystems because of its special characteristics HydrophilicHydrophilic molecules- attract water to their surface molecules- attract water to their surface

(polar)(polar) HydrophobicHydrophobic molecules- repel water (nonpolar) molecules- repel water (nonpolar) Amphipathic Amphipathic molecules- have both hydrophilic and molecules- have both hydrophilic and

hydrophobic propertieshydrophobic properties

Concentration of SolutionsConcentration of Solutions

ConcentrationConcentration- the amount of solute - the amount of solute dissolved in a certain amount of solventdissolved in a certain amount of solvent In biological solutions, commonly expressed In biological solutions, commonly expressed

as molar concentration or molarity (M)as molar concentration or molarity (M)• One mole dissolved in 1 LOne mole dissolved in 1 L• One mole is the molecular weight of the compound One mole is the molecular weight of the compound

in gramsin grams

Figure 2.11

Acidity, Alkalinity, and the pH Acidity, Alkalinity, and the pH ScaleScale

AcidicAcidic solutions- when a component solutions- when a component dissolved in water (acid) releases excess dissolved in water (acid) releases excess hydrogen ions (Hhydrogen ions (H++) )

BasicBasic solutions- when a component releases solutions- when a component releases excess hydroxide ions (OHexcess hydroxide ions (OH--))

pH scalepH scale- measures the acid and base - measures the acid and base concentrations of solutionsconcentrations of solutions Ranges from 0 (most acidic) to 14 (most basic); 7 Ranges from 0 (most acidic) to 14 (most basic); 7

is neutralis neutral pH = -log[HpH = -log[H++]]

Figure 2.12

Neutralization ReactionsNeutralization Reactions

NeutralizationNeutralization reactions- occur in reactions- occur in aqueous solutions containing both acids aqueous solutions containing both acids and basesand bases

Give rise to water and other neutral by-Give rise to water and other neutral by-productsproducts

HCl + NaOH HCl + NaOH H H22O + NaClO + NaCl

The Chemistry of Carbon and Organic The Chemistry of Carbon and Organic CompoundsCompounds

Inorganic chemicalsInorganic chemicals- usually do not - usually do not contain both C and H (ex. NaCl, CaCOcontain both C and H (ex. NaCl, CaCO33))

Organic chemicalsOrganic chemicals- Carbon compounds - Carbon compounds with a basic framework of the element with a basic framework of the element carbon bonded to other atomscarbon bonded to other atoms Most of the chemical reactions and structures Most of the chemical reactions and structures

of living things involve organic chemicalsof living things involve organic chemicals

Carbon- the Fundamental Element of Carbon- the Fundamental Element of LifeLife

Valence makes it an ideal atomic building Valence makes it an ideal atomic building blockblock

Forms stable chains containing thousands Forms stable chains containing thousands of C atoms, with bonding sites available of C atoms, with bonding sites available

Can form linear, branched, or ringed Can form linear, branched, or ringed chains chains

Can form single, double, or triple bondsCan form single, double, or triple bonds Most often associates with H, O, N, S, and Most often associates with H, O, N, S, and

PP

Figure 2.13

Functional Groups of Organic Functional Groups of Organic CompoundsCompounds

Special molecular groups or accessory Special molecular groups or accessory molecules that bind to organic compounds- molecules that bind to organic compounds- functional groupsfunctional groups

Help define the chemical class of certain Help define the chemical class of certain groups of organic compoundsgroups of organic compounds

Give organic compounds unique reactive Give organic compounds unique reactive propertiesproperties Reactions of an organic compound can be Reactions of an organic compound can be

predicted by knowing the kind of functional group predicted by knowing the kind of functional group or groups it carriesor groups it carries

2.2 Macromolecules: Superstructures 2.2 Macromolecules: Superstructures of Lifeof Life

BiochemistryBiochemistry- study of the compounds of life- study of the compounds of life Biochemicals- organic compounds produced Biochemicals- organic compounds produced

by (or components of) living thingsby (or components of) living things Four main families- carbohydrates, lipids, Four main families- carbohydrates, lipids,

proteins, and nucleic acidsproteins, and nucleic acids Often very large, called Often very large, called macromoleculesmacromolecules All macromolecules except for lipids are formed All macromolecules except for lipids are formed

by polymerizationby polymerization• Repeating subunits (Repeating subunits (monomersmonomers) are bound in to ) are bound in to

chains of various lengths (chains of various lengths (polymerspolymers))

CarbohydratesCarbohydrates

CarbohydratesCarbohydrates: Sugars and : Sugars and PolysaccharidesPolysaccharides Most can be represented by the general Most can be represented by the general

formula (CHformula (CH22O)O)nn, where n = the number of , where n = the number of

units of this combination of atomsunits of this combination of atoms

Figure 2.14

CarbohydratesCarbohydrates Exist in a variety of configurationsExist in a variety of configurations

Sugar (Sugar (saccharidesaccharide)- a simple carbohydrate with a )- a simple carbohydrate with a sweet tastesweet taste

MonosaccharideMonosaccharide contains 3-7 carbons contains 3-7 carbons Disaccharide Disaccharide contains two monosaccharidescontains two monosaccharides PolysaccharidePolysaccharide contains five or more contains five or more

monosaccharidesmonosaccharides Monosaccharides and disaccharides are specified Monosaccharides and disaccharides are specified

by combining a prefix that describes a by combining a prefix that describes a characteristic of the sugar with the suffix –osecharacteristic of the sugar with the suffix –ose HexosesHexoses- six carbons- six carbons PentosesPentoses- five carbons- five carbons FructoseFructose- for fruit- for fruit

The Nature of Carbohydrate The Nature of Carbohydrate BondsBonds

Figure 2.15

The Functions of The Functions of PolysacharidesPolysacharides

Structural support and Structural support and protectionprotection

Serve as nutrient and Serve as nutrient and energy storesenergy stores

Cell walls in plants Cell walls in plants and many and many microscopic algae microscopic algae from from cellulosecellulose

Figure 2.16a

Other Important Other Important PolysaccharidesPolysaccharides

Include Include agaragar, , peptidoglycanpeptidoglycan, , chitinchitin, , lipopolysaccharidelipopolysaccharide, , glycocalyxglycocalyx, and , and glycogenglycogen

Figure 2.16b

Lipids: Fats, Phospholipids, and Lipids: Fats, Phospholipids, and WaxesWaxes

LipidsLipids- a variety of substances that are - a variety of substances that are not soluble in polar substancesnot soluble in polar substances

Will dissolve in nonpolar solventsWill dissolve in nonpolar solvents Main groups of lipidsMain groups of lipids

TriglyceridesTriglycerides-a single molecule of glycerol -a single molecule of glycerol bound to three fatty acidsbound to three fatty acids• Includes fats and oilsIncludes fats and oils

Figure 2.17

PhospholipidsPhospholipids PhospholipidsPhospholipids- -

Contain two fatty Contain two fatty acids attached to the acids attached to the glycerol with a glycerol with a phosphate group on phosphate group on the third glycerol the third glycerol binding sitebinding site Important membrane Important membrane

moleculesmolecules

Figure 2.18

Miscellaneous LipidsMiscellaneous Lipids

Steroids- complex ringed compounds Steroids- complex ringed compounds commonly found in cell membranes and commonly found in cell membranes and animal hormonesanimal hormones Best known- Best known- cholesterolcholesterol

• Waxes- esters formed between a long-Waxes- esters formed between a long-chain alcohol and a saturated fatty acidchain alcohol and a saturated fatty acid

Figure 2.19

Proteins: Shapers of LifeProteins: Shapers of Life

Predominant organic moleculesPredominant organic molecules Building blocks- Building blocks- amino acidsamino acids

20 different naturally occurring forms20 different naturally occurring forms Basic skeleton- a carbon (the α carbon) linked to Basic skeleton- a carbon (the α carbon) linked to

an amino group (NHan amino group (NH22), a carboxyl group ), a carboxyl group

(COOH), a hydrogen atom (H), and a variable R (COOH), a hydrogen atom (H), and a variable R groupgroup

Peptide bondPeptide bond forms between the amino group forms between the amino group on one amino acid and the carboxyl group on on one amino acid and the carboxyl group on another.another.

Figure 2.20

Protein Structure and DiversityProtein Structure and Diversity

Primary (1°) structurePrimary (1°) structure- the type, number, and - the type, number, and order of amino acids in the chainorder of amino acids in the chain

Secondary (2°) structureSecondary (2°) structure- when various - when various functional groups exposed on the outer surface of functional groups exposed on the outer surface of the molecule interact by forming hydrogen bondsthe molecule interact by forming hydrogen bonds Coiled configuration- α helixCoiled configuration- α helix Accordion pattern- β-pleated sheetAccordion pattern- β-pleated sheet

Tertiary (3°) structureTertiary (3°) structure- created by additional - created by additional bonds between functional groupsbonds between functional groups

Quarternary (4°) structureQuarternary (4°) structure- more than one - more than one polypeptide forms a large, multiunit proteinpolypeptide forms a large, multiunit protein

Figure 2.21

Protein ShapeProtein Shape

Each different type of protein develops a Each different type of protein develops a unique shape, so it can only react with unique shape, so it can only react with molecules that fit its particular surface molecules that fit its particular surface featuresfeatures Ex. Ex. enzymesenzymes and and antibodiesantibodies Native state- the functional three-dimensional Native state- the functional three-dimensional

form of a proteinform of a protein Denatured- when the protein’s native state Denatured- when the protein’s native state

has been disruptedhas been disrupted

The Nucleic Acids: A Cell Computer The Nucleic Acids: A Cell Computer and Its Programsand Its Programs

DNA- specially coded genetic programDNA- specially coded genetic program DNA transfers its program to RNADNA transfers its program to RNA Both are polymers of repeating units called Both are polymers of repeating units called nucleotidesnucleotides

Nucleotides- composed of three smaller units: a Nucleotides- composed of three smaller units: a nitrogen basenitrogen base, , a a pentosepentose sugar, and a phosphate. sugar, and a phosphate.

The nitrogen base can be one of two forms- a purine (two rings) The nitrogen base can be one of two forms- a purine (two rings) or a pyrimidine (one ring)or a pyrimidine (one ring)

• Two types of purines: Two types of purines: adenine (A)adenine (A) and and guanine (G)guanine (G)• Three types of pyrimidines: Three types of pyrimidines: thymine (T)thymine (T), , cytosine (C)cytosine (C), and , and uracil (U)uracil (U)• DNA contains all of the nitrogen bases except uracilDNA contains all of the nitrogen bases except uracil• RNA contains all of the nitrogen bases except thymineRNA contains all of the nitrogen bases except thymine

The nitrogen base is covalently bonded to ribose in RNA and The nitrogen base is covalently bonded to ribose in RNA and deoxyribose in DNAdeoxyribose in DNA

Phosphate (POPhosphate (PO443-3-) covalently bonds the sugars in series) covalently bonds the sugars in series

Figure 2.22

Figure 2.23

The Double Helix of DNAThe Double Helix of DNA

Formed by two long polynucleotide Formed by two long polynucleotide strandsstrands

Linked along their length by hydrogen Linked along their length by hydrogen bonds between complimentary pairs of bonds between complimentary pairs of nitrogen basesnitrogen bases Adenine pairs with thymineAdenine pairs with thymine Cytosine pairs with guanineCytosine pairs with guanine

Figure 2.24

RNA: Organizers of Protein SynthesisRNA: Organizers of Protein Synthesis

Also consists of a long chain of nucleotidesAlso consists of a long chain of nucleotides It is single stranded and contains ribose instead of It is single stranded and contains ribose instead of

deoxyribose anduracil instead of thyminedeoxyribose anduracil instead of thymine Several functional types of RNA formed using the Several functional types of RNA formed using the

DNA templateDNA template Messenger RNA (mRNA)- a copy of a gene that Messenger RNA (mRNA)- a copy of a gene that

provides the order and type of amino acids in a provides the order and type of amino acids in a proteinprotein

Transfer RNA (tRNA)- a carrier that delivers the Transfer RNA (tRNA)- a carrier that delivers the correct amino acids for protein assemblycorrect amino acids for protein assembly

Ribosomal RNA (rRNA)- a major component of Ribosomal RNA (rRNA)- a major component of ribosomesribosomes

ATP: The Energy Molecule of ATP: The Energy Molecule of CellsCells

Adenosine triphosphate (ATP)- Adenosine triphosphate (ATP)- a nucleotide a nucleotide containing adenine, ribose, and three phosphatescontaining adenine, ribose, and three phosphates

High-energy compound that gives off energy when High-energy compound that gives off energy when the bond is broken between the outermost the bond is broken between the outermost phosphatesphosphates

Releases and stores energy for cellular chemical Releases and stores energy for cellular chemical reactionsreactions

When the terminal phosphate bond is broken to When the terminal phosphate bond is broken to release energy, adenosine diphosphate (ADP) is release energy, adenosine diphosphate (ADP) is formedformed

ADP can be converted back to ATP when the third ADP can be converted back to ATP when the third phosphate is restored.phosphate is restored.

Figure 2.25

2.3 Cells: Where Chemicals Come to 2.3 Cells: Where Chemicals Come to LifeLife

The fundamental unit of life- The fundamental unit of life- cellcell Fundamental characteristics of cellsFundamental characteristics of cells

Tend to be spherical, polygonal, cubical, or Tend to be spherical, polygonal, cubical, or cylindricalcylindrical

Their protoplasm is encased in a cell or Their protoplasm is encased in a cell or cytoplasmic membranecytoplasmic membrane

Chromosomes containing DNAChromosomes containing DNA Ribosomes for protein synthesisRibosomes for protein synthesis

Eukaryotic and Prokaryotic Eukaryotic and Prokaryotic CellsCells

Eukaryotic cellsEukaryotic cells Found in animals, plants, fungi, and protistsFound in animals, plants, fungi, and protists Contain organelles that perform cell functions Contain organelles that perform cell functions

(such as the nucleus, Golgi apparatus, (such as the nucleus, Golgi apparatus, endoplasmic reticulum, vacuoles, and endoplasmic reticulum, vacuoles, and mitochondria)mitochondria)

Prokaryotic cellsProkaryotic cells Only found n bacteria and archaeOnly found n bacteria and archae No nucleus or other organellesNo nucleus or other organelles

Cell