the chemistry of life organic chemistry – the study of all compounds that contain bonds between...

THE CHEMISTRY OF LIFETHE CHEMISTRY OF LIFE

Organic chemistry – the study Organic chemistry – the study of all compounds that contain of all compounds that contain bonds between carbon atomsbonds between carbon atoms

ELEMENTSELEMENTS

o An An elementelement is a is a substance that substance that cannot be broken cannot be broken down into simpler down into simpler chemical chemical substancessubstances

• The main components of a The main components of a living cell are carbon, living cell are carbon, hydrogen, nitrogen, hydrogen, nitrogen, oxygen, phosporus, and oxygen, phosporus, and sulfursulfur

• CHNOPSCHNOPS

ATOMATOM

• An An atomatom is the smallest particle of is the smallest particle of an element that has the an element that has the characteristics of that elementcharacteristics of that element

• Structure:Structure:– Nucleus – composed of Nucleus – composed of protonsprotons (+) (+)

and and neutronsneutrons (0) (0)– Electron cloud – Electron cloud – electronselectrons (-) (-)

ATOMATOM• Atomic number = # protons = # Atomic number = # protons = #

electronselectrons

• Atomic mass = # protons + # neutronsAtomic mass = # protons + # neutrons

• To calculate # neutrons, subtract the # To calculate # neutrons, subtract the # of protons from the mass number.of protons from the mass number.

Example:Carbon has atomic number 6, so it has 6 protons and 6 electrons.It has a mass number of 12 (round to the nearest whole number) so it has 12 – 6 = 6 neutrons.

ISOTOPESISOTOPES

• IsotopesIsotopes are atoms of the same are atoms of the same element with different numbers of element with different numbers of neutrons.neutrons.

Example: carbon 12 and carbon 14Example: carbon 12 and carbon 14

Carbon 12 has 6 neutrons while carbon Carbon 12 has 6 neutrons while carbon 14 has 8 neutrons.14 has 8 neutrons.

COMPOUNDCOMPOUND

• A A compoundcompound is a is a substance that is substance that is composed of atoms composed of atoms of 2 or more of 2 or more different elements different elements chemically chemically combined. combined.

CHEMICAL BONDSCHEMICAL BONDS

• Covalent bonds – atoms Covalent bonds – atoms share share electronselectrons to form a to form a molecule. molecule. Ex: HEx: H22OO

• Ionic bonds – atoms form ions by Ionic bonds – atoms form ions by gaininggaining or losing electronsor losing electrons; ionic ; ionic compoundscompounds are formed when ions of are formed when ions of opposite charge bond together. Ex: opposite charge bond together. Ex: NaClNaCl

CHEMICAL REACTIONS IN AN CHEMICAL REACTIONS IN AN ORGANISMORGANISM

• MetabolismMetabolism – all the chemical reactions – all the chemical reactions that occur within an organismthat occur within an organism

• AnabolismAnabolism – the reactions that build – the reactions that build complex molecules from simpler onescomplex molecules from simpler ones

• CatabolismCatabolism – the reactions that break – the reactions that break down complex molecules into simpler down complex molecules into simpler onesones

MIXTURESMIXTURES• A A mixturemixture is a combination of is a combination of

substances in which the individual substances in which the individual components retain their own components retain their own properties (physically combined, not properties (physically combined, not chemically).chemically).

• A A solutionsolution is a mixture in which one or is a mixture in which one or more substances (solutes) are more substances (solutes) are distributed evenly in another distributed evenly in another substance (solvent).substance (solvent).

• A A suspensionsuspension is a mixture of is a mixture of nondissolved materials in water.nondissolved materials in water.

pHpH• pH is a measure of how acidic or pH is a measure of how acidic or

basic a substance is.basic a substance is.

• The pH scale goes from 0 to 14.The pH scale goes from 0 to 14.

• The pH of pure water is 7 or neutral.The pH of pure water is 7 or neutral.

• Substances added to water can lower Substances added to water can lower or raise the pH.or raise the pH.

• A pH below 7 is acidic.A pH below 7 is acidic.

• A pH above 7 is basic.A pH above 7 is basic.

DEFINITIONS:DEFINITIONS:

• AcidAcid – any – any substance that substance that form hydrogen ions form hydrogen ions (H(H++) in water) in water

• BaseBase – any – any substance that substance that form hydroxide form hydroxide ions (OHions (OH--) in water) in water

WATERWATER

• Water makes up 70 Water makes up 70 to 95% of most to 95% of most organisms, organisms, therefore it is the therefore it is the most common most common compound found in compound found in most cells.most cells.

The water molecule is a polar The water molecule is a polar molecule.molecule.

• A A polar moleculepolar molecule has an has an uneven distribution of uneven distribution of charge; it has a positive end charge; it has a positive end and a negative end.and a negative end.

• Polar molecules form a weak Polar molecules form a weak bond when the positive end bond when the positive end of one molecule is attracted of one molecule is attracted to the negative end of to the negative end of another.another.

• This weak bond is called a This weak bond is called a hydrogen bondhydrogen bond..

Properties of water due to it Properties of water due to it polarity:polarity:

• Water molecules are cohesive (stick Water molecules are cohesive (stick together) and adhesive (stick to other together) and adhesive (stick to other substances) due to the hydrogen substances) due to the hydrogen bonding.bonding.

• Water is able to absorb large amounts of Water is able to absorb large amounts of heat. As a result, lakes and oceans heat. As a result, lakes and oceans stabilize air and land temperatures.stabilize air and land temperatures.

• Water absorbs heat when it evaporates, Water absorbs heat when it evaporates, allowing organisms to release excess allowing organisms to release excess heat.heat.

Properties cont:Properties cont:

• Because water expands when it Because water expands when it freezes, ice floats. This prevents freezes, ice floats. This prevents lakes and oceans from freezing solid. lakes and oceans from freezing solid.

• Water is able to dissolve many Water is able to dissolve many substances, so the water inside and substances, so the water inside and outside of cells is able to carry outside of cells is able to carry nutrients into and around cells, and nutrients into and around cells, and wastes away from cells.wastes away from cells.

ORGANIC CHEMISTRYORGANIC CHEMISTRY

• This is the study This is the study of organic of organic compounds, compounds, those those compounds compounds containing containing carbon and carbon and made by living made by living organisms.organisms.

CARBONCARBON• Has 4 electrons to share in Has 4 electrons to share in

its outer shellits outer shell• Can bond with up to 4 Can bond with up to 4

other atoms or compoundsother atoms or compounds• Can bond to other carbon Can bond to other carbon

atoms in chains and rings atoms in chains and rings to form large complex to form large complex moleculesmolecules

• Can form single, double, or Can form single, double, or triple bonds (single bond – triple bonds (single bond – shares 1 electron, double – shares 1 electron, double – shares 2 electrons, etc.)shares 2 electrons, etc.)

CARBONCARBON

• Can form Can form isomersisomers – – compounds with compounds with the same simple the same simple formula but formula but different 3-D different 3-D structuresstructures

• PolymerPolymer – a large molecule formed – a large molecule formed when many smaller molecules bond when many smaller molecules bond together. The smaller molecules are together. The smaller molecules are called called monomersmonomers..

• PolymerizationPolymerization – process of building – process of building polymerspolymers

• Condensation reactionCondensation reaction – reaction by – reaction by which polymers are formed; also which polymers are formed; also called called dehydration synthesisdehydration synthesis

• HydrolysisHydrolysis – reaction by which – reaction by which polymers are broken apartpolymers are broken apart

The Macromolecules of lifeThe Macromolecules of life

• Cells can make a variety of Cells can make a variety of macromoleculesmacromolecules (large polymers) from (large polymers) from a relatively small set of a relatively small set of monomersmonomers (building blocks).(building blocks).

CARBOHYDRATESCARBOHYDRATES• Used by cells to store and release Used by cells to store and release

energyenergy

• Composed of C, H, and O with a ratio of Composed of C, H, and O with a ratio of 2H:1O2H:1O

• Monomer (building block) is a Monomer (building block) is a monosaccharidemonosaccharide, or simple sugar: , or simple sugar: examples are glucose and fructoseexamples are glucose and fructose

• A A disaccharidedisaccharide is formed when two is formed when two monosaccharides bond together; monosaccharides bond together; example sucrose = fructose + glucoseexample sucrose = fructose + glucose

Carbs cont.Carbs cont.• The largest carbohydrates are the The largest carbohydrates are the

polysaccharidespolysaccharides starch, glycogen, starch, glycogen, cellulose, and chitincellulose, and chitin– StarchStarch – how plants store food they make – how plants store food they make– GlycogenGlycogen – how animals store food – how animals store food

reserves in the liverreserves in the liver– CelluloseCellulose – structural material in plant cell – structural material in plant cell

walls; the fiber in the food you eatwalls; the fiber in the food you eat– ChitinChitin – structural material in fungal cell – structural material in fungal cell

walls; in the exoskeletons of arthropodswalls; in the exoskeletons of arthropods

LipidsLipids• Commonly called Commonly called fats andfats and

oilsoils• Are insoluble in water Are insoluble in water

because the molecules are because the molecules are nonpolarnonpolar

• Used for energy storage, Used for energy storage, insulation, and protective insulation, and protective coverings; they are a major coverings; they are a major component in cell component in cell membranesmembranes

• Contain numerous C-H Contain numerous C-H chains called fatty acidschains called fatty acids

Lipids cont.Lipids cont.

• Saturated fatsSaturated fats contain only contain only singlesingle bonds bonds in the C-H chains; are solid at room in the C-H chains; are solid at room temperaturetemperature

• Unsaturated fatsUnsaturated fats contain some contain some doubledouble bonds in the C-H chains; are liquid at bonds in the C-H chains; are liquid at room temperatureroom temperature

ProteinsProteins

• Monomers are Monomers are amino acidsamino acids

• There are 20 amino acids composed of C, H, O, N, and There are 20 amino acids composed of C, H, O, N, and SS

• Proteins are formed by the bonding of amino acids; the Proteins are formed by the bonding of amino acids; the bond is called a bond is called a peptide bondpeptide bond

Functions of proteins:Functions of proteins:

• Structural – hair, nailsStructural – hair, nails• Transport – Transport –

hemoglobinhemoglobin• Movement – muscle Movement – muscle

fibers and fibers and cytoskeletal elementscytoskeletal elements

• Defense – antibodiesDefense – antibodies• Regulation of cell Regulation of cell

functions – hormones functions – hormones and enzymesand enzymes

• A protein’s function depends on its A protein’s function depends on its specific specific conformationconformation (3-D (3-D structure); the sequence of amino structure); the sequence of amino acids and the shape of the chain are acids and the shape of the chain are a consequence of attractions a consequence of attractions between the chain’s parts.between the chain’s parts.

EnzymesEnzymes• Important Important proteinsproteins• An enzyme is a An enzyme is a biological catalystbiological catalyst• It speeds up reactions by lowering It speeds up reactions by lowering

activation energyactivation energy needed to start the needed to start the reactionreaction

• The enzyme causes a chemical reaction The enzyme causes a chemical reaction to occur without being changed itselfto occur without being changed itself

• Each enzyme has a definite 3-D shape Each enzyme has a definite 3-D shape that allows it to recognize and bind with that allows it to recognize and bind with its its substratesubstrate (substrate = reactant) (substrate = reactant)

• The The active siteactive site is the is the place where the place where the substrate binds and the substrate binds and the action occursaction occurs

• Most cells function best Most cells function best within a narrow range of within a narrow range of temperature and pH; at temperature and pH; at very high temperature or very high temperature or extremes of pH, the 3-D extremes of pH, the 3-D structure of the protein structure of the protein changes and its function changes and its function is alteredis altered

Nucleic AcidsNucleic Acids• DNADNA and and RNARNA• Function – control cell activities by Function – control cell activities by

directing protein synthesisdirecting protein synthesis• Monomers are Monomers are nucleotides nucleotides which are made which are made

up of a nitrogenous base, a sugar, and a up of a nitrogenous base, a sugar, and a phosphate groupphosphate group

• DNA – DNA – deoxyribonucleic aciddeoxyribonucleic acid is the master is the master genetic codegenetic code

• RNA – RNA – ribonucleic acidribonucleic acid functions to make functions to make copies of DNAcopies of DNA

DNA replicating, or the making of a new copy