the chemistry of life. atoms the study of chemistry begins with this basic unit of matter comes...

CHAPTER 2The Chemistry of Life

Atoms

The study of chemistry begins with this basic unit of matter

Comes from the Greek atomos = “unable to cut”

Protons

Same mass as a neutron Positively charged particles Found in nucleus (center of atom) The # of protons determine the element

Neutrons

Same mass as a proton Neutral charge Found in nucleus The # of neutrons determine the isotope

Electron

Negatively charged particle 1/1840 the mass of a proton Constantly in motion in shells

surrounding the nucleus Attracted to positive protons, but stay

outside of the nucleus due to their energy

The # of electrons determine the charge

Element

A pure substance that consists entirely of one type of atom

Represented by one or two letter symbols

Atomic Number – the number of protons; unique to each element

Isotopes

Isotopes – atoms of the same element that have different numbers of neutrons (ex: Carbon-12; Carbon-13; Carbon-14 pg. 36)

Radioactive Isotopes – isotopes whose nuclei are unstable and break down at a constant rate over time

Element

Mass number – the sum of protons and neutrons (daltons)

Atomic Mass – the “weighted” avg. of the masses of an element’s isotopes; units are Atomic Mass Unit (amu)

Compounds A substance formed by the chemical

combination of two or more elements in definite proportionsShorthand through the chemical formula; H2O,

NaClThe chemical and physical properties of

compounds are usually very diff than the individual elements’ properties

Chemical bond

What holds compounds and molecules together

Covalent Bond; Ionic Bond; Hydrogen Bond

Van der Waals Forces

Covalent Bond Forms when electrons are shared between

atoms The moving electrons are located in a region

bt the atoms where the orbitals of the atoms overlap

Sharing of two electrons – single covalent bond

Sharing of four electrons – double covalent bond

Sharing of six electrons – triple covalent bond Molecule – structure that results when atoms

are joined together by covalent bonds; smallest unit of most compounds ex: water

Ionic Bond

Forms when one or more electrons are transferred from one atom to another

An atom that loses electrons → becomes positively charged

An atom that gains electrons → becomes neg. charged

IONS – atoms that gain or lose electrons The attraction bt Ions is strong and it is

called an ionic bond ex: NaCl

Hydrogen Bond

Not as strong as covalent or ionic bonds The strongest of the bond that can for

between molecules Due to polarity Most common in water molecules

Van der Waals Forces

Intermolecular forces of attraction bt molecules due to unequal sharing of electrons

Due to the difference in the attraction of electrons

They can hold molecules together, especially when the molecules are large

Properties of Water

Water“blue planet” → water covers ¾ of the

earth’s surfaceSingle most abundant compound in

most living thingsOne of the few compounds that is a

liquid at temps found on earthWater expands as it freezesIce is less dense than liquid water, so it

floats

Water Molecule

Neutral (pos charge on its 10protons balance out 10 electrons)

Polarity O2 pulls Hydrogen’s electrons toward itselfO2 has a slight neg charge; Hydrogens

have a slight pos chargePolar molecule – a molecule in which the

charges are unevenly distributed (molecule is like a magnet with the poles)

Water Molecule

Hydrogen BondsBetween nearby molecules due to polarityCOHESION – an attraction bt molecules of

same substanceADHESION – an attraction bt molecules of

diff substances

Solutions and Suspensions Water isn’t always pure; usually a

mixture Mixture – a material composed to two or

more elements or compounds that are physically mixed together but not chemically combined (salt and pepper; sugar and sand)

Mixture

Solutions – components are equally distributed throughout the sln 1) Solute – sub that is dissolved

2) Solvent – sub in which the solute dissolves (Ex: salt and water)

Mixture

Suspension – mixtures of water and non-dissolved material (Ex: sugar and water; blood)

Acids and Bases

Water molecules can react to form ions Use double arrows to show can happen

either direction

H2O H+ + OH –Water hydrogen ion + hydroxide ion

Acids and Bases

pH scale = measurement system that indicates the concentration of H+ ions in a solution Scale ranges from 0 to 14At 7, concentration of H+ and OH- are equal

creating a neutral solutionBelow a pH of 7, solutions are considered

acidic (more H+ ions)Above a pH of 7, solution are considered

basic (less H+ ions, more OH-)

Acids and Bases

Acids Any compound that forms H+ ions in

solution; donates H+ increases concentrations of H+

Below 7 on scaleStrong acids, like those produced by your

stomach are 1-3 on pH scale

Acids and Bases

Bases A compound that

produces OH- ions in sln OR takes H+ out of sln

Also known as alkaline solutions

Above 7 on the pH scaleStrong bases are 11-14

on the pH scale

Acids and Bases

BuffersWeak acids or bases that can react with

strong acids or bases to prevent sharp, sudden changes in pH

Impt in maintaining homeostasis in body (ex: blood pH)

Carbon Compounds

Organic Chemistry The study of all compounds that contain

bonds between carbon atomsOriginally thought to be only compounds

produced by living organismsFriedrich Wӧhler (1828) synthesized urea

from ammonium cyanate

Properties of Carbon

Four valence electrons – 4 single strong covalent bonds

Ability to form large, complex molecules Single, double or triple covalent bonds Different shapes: linear, branch, rings

(pg 44)

Macromolecules

“giant molecule” Formed by Polymerization – large

compounds are built by joining smaller ones together

Monomers join to form Polymers Four types of organic compounds found

in living things: Carbohydrates, Lipids, Nucleic Acids, and Proteins

Carbohydrates

Compounds made up of carbon, hydrogen and oxygen atoms usually in a ration of 1:2:1

Living things use carbs as their main source of energy

Starch; Glucose

Carbohydrates

Monomers are simple sugars or monosaccharides; in milk, fructose

Main source of energySugars = immediate energy for all cell activityStarches = stored extra sugar as complex carbs

Monosaccharides = single sugar molecules Disaccharides = 2 monosaccharide molecules

joined by a covalent bond Polysaccharides = large maacromolecules

formed from many monosacc. Joined by covalent bonds

Lipids

A large and varied group of biological molecules made mostly from carbon and hydrogen atoms

Monomoers are fatty acid + glycerol (generally)

Lipids

Hydrophobic hydrocarbons Fats, oils and waxes Saturated Fatty Acids = fatty acid with all

single bonded Cs Unsaturated Fatty Acids = fatty acid with

1+ double bond Polyunsaturated Fatty Acids = fatty acid

with 2+ double bonds

Nucleic Acids

Contain hydrogen, Oxygen, Nitrogen, Carbon and Phosphorous

Monomers are Nucleotides = consists of three partsA 5-Carbon SugarA phosphate groupA nitrogenous base

Store and transmit hereditary or genetic infoRibonucleic Acids (RNA) – contains sugar riboseDeoxyribonucleic Acids (DNA) – contains the sugar

deoxyribose

Proteins

Contain nitrogen as well as carbon, hydrogen and oxygen

Monomers are Amino Acids = compounds with an amino group (-NH2) on one and a carboxyl group (-COOH) on the other end

More than 20 diff amino acids are found in nature

Amino acids differ in their R group (may be acidic, basic, polar, nonpolar, etc)

Proteins

Each protein has a specific roleControl the rate of rxRegulate cell processesForm bones and muscleTransport substances into or out of cellsHelp fight disease

Proteins

Up to four levels of organizationPrimary = sequence of amino acids in the protein

chainSecondary = amino acids within the chain can be

coiled or folded(alpha helix and beta pleats) Tertiary = interactions bt AAQuaternary = multiple chain interact

Protein structure

Chemical Rx

Process that changes or transforms one set of chemicals into another

Mass and energy are conserved Some occur slow Some occur fast ALWAYS involve changes in the

chemical bonds that join atoms in compounds

Reactants Products

Chemical Reactions

When you exhale, you release CO2. It goes into your bloodstream, where it dissolves in water to be transported to your lungs

CO2 + H2O H2CO3

carbon dioxide + water carbonic acid

Energy in Reactions

Always an exchange in energy during a chemical rx

Energy released may come in several forms including heat, light, sound

Energy is neither created nor destroyed, but rather stored in the chemical bonds

Energy in Rxns

Spontaneous chemical rxns – takes little energy to release a lot

Nonspontaneous chem rxns – takes a lot of energy to release very little

The energy that is put into the chem rxn is the Activation Energy

Some chem rxns require so much energy they would not occur w/o a Catalyst – sub that speeds up the rate of a chem rxn by lowering the activation energy

Enzyme Action

Enzymes – proteins that act a biological catalysts; they speed up chem rxns that take place in cells

For Chem rxns to occur must need several things to occurActivation energyReactants must collide(at right angle)Chem bonds must be brokenChem bonds must be formed

Energy-Absorbing Rxns

Enzyme-Substrate Complex Enzymes provide the site where

reactants can be brought together to react; those reactants are known as Substrates – reactants of enzyme-catalyzed rxns

Enzyme-Substrate Complex Substrates bind to the ACTIVE SITE of the

enzyme The active site and substrates have

complementary shapes = lock and key Enzyme and substrates are held together by

intermolecular forces Binding forms the enzyme-substrate complex Complex must be maintained during the chemical

rxn Upon completion of rxn, the products are

released and the enzyme is ready for another rxn

Enzyme-Substrate Complex

Regulation of Enzyme Activity1) pH

2) Temperature

3) Can be turned “off” by cells when not needed

4) Chemicals that destroy the protein’s bonds

5) Change in solvent