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