Download - Chemistry of Life
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Chemistry of Chemistry of LifeLife
Green = IMPORTANT NOTES
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How much do How much do you already you already
know?know?
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Let’s start smallLet’s start small• Matter: any physical
substance that has mass and takes up space
• Atom: the basic unit of matter o From the Greek word atomos
– unable to be cut
• Protons (+) and Neutrons (n) are found in the nucleus in equal amounts
• Electrons (-) are in constant motion in the space around the nucleus
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Element: a pure substance that Element: a pure substance that
consists of entirely one type of consists of entirely one type of
atom atom
Atomic Number: # of protons
Element symbol
Atomic Mass: # of protons + # of neutrons
Element name
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Periodic Table of ElementsPeriodic Table of Elements
Arranged from left to right by increasing atomic numberColors indicate similar atomic properties
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Elements Elements Important Important
to Lifeto Life
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IsotopesIsotopes• An isotope is a variation of
chemical element due to a different number of neutrons.
• Identify isotopes by the atomic mass
• Since the number of electrons remains the same the chemical properties remain the same
• Radioactive isotopes have an unstable nuclei and will eventually break down
• Used to date fossils, trace atoms through metabolism, diagnosis cancer, etc…
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Electron Energy Electron Energy LevelsLevels
• Valence Electrons are the outer electrons that can participate in chemical bonding
Energy Level
# of electrons
1 2
2 8
3 8
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Octet RuleOctet Rule• Atoms tend to gain,
lose, or share one or more of their valence electrons to achieve a filled outer electron shell
• Trying to achieve stability like the Noble Gases
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CompoundsCompounds• A compound is composed of 2 or more elements
o Physical and chemical properties are usually very different from the original individual elements
• This is achieved by chemical bonds1. Ionic Bonds2. Covalent Bonds3. Van der Waals Forces 4. Hydrogen Bonds (We will get to this later with Water)
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Ionic BondsIonic Bonds• 1 or more electrons
transferred from 1 atom to another
• Ions: an atom or molecule that has gained or lost one or more of its valence electrons. o Gain electron = NEGATIVEo Lose electron = POSITIVE
• Resulting ions have a strong attraction for one another
7 valence electrons
1 valence electrons
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Covalent BondsCovalent Bonds• Electrons are shared
by 2 atoms. o The electron travels
between the 2 nuclei
1 valence electrons
1 valence electrons
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Lewis Dot ModelLewis Dot Model
Ionic Bonds Covalent Bonds
Valence Electrons are represented by dots around the symbol
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Van Der Waals ForcesVan Der Waals Forces• Intermolecular forces
that are not ionic or covalent
• Weak attraction between atoms, molecules, and surfaces
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MetabolismMetabolism• Metabolism: the sum of all chemical reactions
within a living organism • Anabolism: chemical reaction in which simple
substances are combined to form a more complex substance o Need energy = Endergonic
• Catabolism: chemical reaction in which complex substances are broken down into more simple substances o Release energy = Exergonic
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Chemical ReactionsChemical ReactionsExample of Anabolism: •Dehydration Synthesis: monomers of organic compounds bind together through a chemical reaction to form a polymer (with water as a product of the reaction)
Monomer + Monomer Polymer +Water
Example of Catabolism: •Hydrolysis: The reverse of the dehydration reaction
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Chemical ReactionsChemical Reactions• A chemical reaction is a process that changes or
transforms a set of chemicals into another
CH3COOH + NaHCO3 CO2 + H20 + CH3COONaAcetic Acid + Sodium Bicarbonate Carbon dioxide + water + sodium
acetate
Reactants Products
• Chemical reactions involve changes in chemical bonds that join atoms and compounds
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Energy Energy TransformationsTransformations
• Energy is released or absorbed whenever a chemical bond is broken or formed
• Exergonic: releases energy – typically spontaneous
• Endergonic: absorbs energy – requires a source of Eo Living organisms obtain their energy from raw materials such
as the sun or other living organisms
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Higher Energy
Lower Energy
Even though this is an energy releasing reaction, a small amount of activation energy is still needed to get this reaction started
Activation Energy: Energy required to get a reaction started
Exergonic
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Lower Energy
Higher Energy
A larger amount of activation energy is needed in this reaction in order to achieve a higher energy state of the products
Endergonic
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EnzymesEnzymes• Chemical reactions that are too slow or have a
high activation energy need a helping hand
• Catalysts: substances that speed up the rate of a chemical reaction
• Enzymes are proteins that act as biological catalystso They speed up reactions that take place inside cells
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EnzymesEnzymes• How do they do this?
• Catalysts lower the activation energy of a reaction allowing the reaction to occur quicker and with less energy
• Enzymes are very specific and generally only catalyze one reaction
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Regular Reaction
Reaction with Catalyst
The activation energy for the reaction with the catalyst is much smaller than the original activation energy
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Enzyme-Substrate Enzyme-Substrate ComplexComplex
• In order for a reaction to occur, reactants must collide together with enough energy to break and form bonds
• Enzymes provide a site where the reactants can be brought together.
• The reactants of an enzyme-catalyzed reaction are known as Substrates.
• The site in which the substrate binds on the enzyme is called the Active Site.
• The enzyme remains UNCHANGED after a reaction. This allows one enzyme to catalyze many reactions.
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Enzyme-Substrate Enzyme-Substrate ComplexComplex
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Enzyme-Substrate Enzyme-Substrate ComplexComplex
Substrate
Active Site
Active Site
Substrate
Lock and Key Analogy
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Organic CompoundsOrganic Compounds• Organic compounds all contain carbon • Carbon has 4 valence electrons which allows it to bond
with 4 other elements including itself• Compounds that make up Organic compounds: C, H,
O, N, P, S o Or NHCOPS
• There are 4 types of organic compounds: 1. Carbohydrates2. Lipids3. Proteins 4. Nucleic Acids
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Macromolecules Macromolecules • Macromolecules “giant molecules” are made out
of many small molecules
• Polymerization: large compounds are built by joining smaller units together
• Monomers “single”• Polymers “many parts”
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Chemical ReactionsChemical Reactions• Dehydration Synthesis: monomers of organic
compounds bind together through a chemical reaction to form a polymer (with water as a product of the reaction)
Monomer + Monomer Polymer +Water
• The reverse of this reaction is called Hydrolysis
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Carbohydrates Carbohydrates • Compounds made of C, H, O • Usually a 1:2:1 ratio • 4 calories/gram• Living things use carbohydrates as a main source of
energy and sometimes for structural purposes • Monomer: Monosaccharide “simple sugars”
o Glucose: supplies immediate energy for cellso Fructoseo Galactose
• Polymer: Polysaccharide “complex sugars”o Glycogen: Animal storage o Starch: Plant storageo Cellulose: Plant structures
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CarbohydratesCarbohydratesGlucose Glycogen
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LipidsLipids• Compounds made of C,H, O• Not water soluble• Fats, oils, waxes, steroids• 9 calories/gram• Living things use lipids for stored energy sources,
insulation, membrane structure, vitamin and mineral storage.
• Composed of one glycerol molecule (alcohol) and 3 fatty acids
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LipidsLipidsTriglyceride Molecule: 1 glycerol + 3 Fatty
Acids
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Phospholipid BilayerPhospholipid Bilayer• Makes up almost all
living organisms cell membranes
• Barrier that prevents water soluble molecules from diffusing across
• Composed of 2 layers of phospholipids
• Phospholipids have a hydrophilic head and 2 hydrophobic tails
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LipidsLipids• Cholesterol: is a
steroid produced by the liver
• It is both fat soluble and water soluble
• It is an essential component of the cell membrane
• Also important in the manufacturing of other steroids, bile acids, and vitamin D
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Lipids Lipids • Saturated fats: all single bonds with maximum
number of Hydrogen o Solid at room temperature
• Monounsaturated fats: 1 double bond • Polyunsaturated fats: more than one double bond
o Both mono and polyunsaturated fats are liquid at room temperature
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Fat gets a bad rap Fat gets a bad rap • In the 1950s biochemist Ancel Keys conducted
“The Seven Countries Study” • This study demonstrated a strong positive
correlation between amount of fat consumed and heart diseaseo Although these results were published, the results are actually
inconclusive since Ancel Keys left a number of countries out of his study.
• From Ancel Key’s Study, the Low Fat Diet/Heart Healthy Diet was born
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Saturated FatsSaturated Fats• Examples:
o Lauric Acid: coconuts, breast milk o Palmitic Acid: animal productso Stearic Acid: meat and eggs
• Benefits: improve memory, increase levels of “good cholesterol”
• High levels of saturated fats in combination with a poor diet is not recommended, however you do not need to avoid saturated fats like the plague
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Unsaturated FatsUnsaturated Fats• Examples of Monounsaturated Fats:
o Oleic Acid: olive oil, avocados, nuts
• Benefits of Monounsaturated Fats: antioxidants, decrease “bad cholesterol”
• Examples of Polyunsaturated Fats: o The most common types are Omega-3 and Omega-6 fatty acidso Essential fats: cannot make these in our body o A 1:1 ratio of Omega-3:Omega-6 is ideal - however, most of
standard American diets do not have this ratio
• Benefits of Polyunsaturated Fats: anti-inflammatory
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Trans-fats Trans-fats • Trans fats are created when a polyunsaturated fat
is transformed into a saturated fat o Hydrogen atoms are added to the molecule until it becomes a
saturated fat. This process is called hydrogenation. o Examples: Margarine
• Trans fats can lead to heart disease by increasing blood lipids
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Proteins Proteins • Compounds made of C, H, O, N• 4 calories/gram• Living things use proteins for growth and repair,
controls rates of chemical reactions (enzymes), cell membrane, transport, NOT an energy source
• Monomers: Amino Acidso 20 different amino acids
• Polymers: Polypeptideso Different structures of polypeptide chains o Sequence of amino acids is dictated by DNA
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Amino AcidAmino Acid
• Amine Group• Carboxyl Group• R group
o Accounts for variability and diversity
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Primary Structure: •Sequence of amino acids
Secondary Structure: •Alpha-helices •Beta-sheets •Held together by H-bonds
Tertiary Structure: •Secondary structure folded onto itself
Quaternary Structure: •2 or more tertiary structures combined together.
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Nucleic AcidsNucleic Acids• Compounds made up of C, H, O, N, P
o NHCOPS
• Nucleic Acids store and transmit heredity or genetic information (DNA and RNA)
• Monomers: Nucleotides o Nucleotides composed of: a sugar, triphosphate, and a
nitrogenous baseo 5 nitrogenous bases: Adenine, Guanine, Thymine, Cytosine,
Uracil
• Polymers: DNA & RNAo DNA: deoxyribonucleic acido RNA: ribonucleic acid
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Nucleic AcidsNucleic AcidsNucleotide DNA
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WaterWater
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Properties of Water Properties of Water 1. Water is a POLAR
MOLECULE!!!!• In a covalent bond,
electrons are not equally shared among atoms
• This unequal sharing of electrons causes a slight positive and slight negative charge on the molecule
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Properties of WaterProperties of Water2. Water is able to form many Hydrogen Bonds•Polar molecules can attract one another via the slight charges on the molecule. These are very weak bonds. •This gives water unique properties
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Properties of Water Properties of Water 3. Water can be found in
all 3 phases of matter: solid, liquid, gas
3. Water molecules expand when frozen causing it to be less dense than in the liquid state.
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Properties of Water Properties of Water 5. Water is cohesive. • Cohesion is the
attraction between molecules of the same substance
• “Like attracts Like” • Water molecules
“stick” to one another • This also creates
surface tension
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Properties of Water Properties of Water 6. Water is adhesive. • Adhesion is an
attraction between molecules of different substance
• Water can adhere to the walls of vessels causing it to move up the vessel. This is called Capillary Action.
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Properties of Water Properties of Water 7. Water has a high heat capacity•Specific Heat: amount of heat required to raise the temperature by 1 degree Celsius
o The specific heat of water is higher than the specific heat of land
o This also allows water to hold heat well.
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Properties of WaterProperties of Water8. Water is a universal solvent. •It is able to to dissolve more substances than any other liquid•This property allows water to carry with it nutrients, chemical, and minerals•Water’s polarity allows it dissolve ionic and polar compounds
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Solutions & Solutions & SuspensionsSuspensions
• Solvent: Dissolving substance
• Solute: Substance being dissolved
• Solution: type of mixture where all the components are evenly distributed
• Suspension: when materials in a solvent don’t dissolve but break into pieces
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Acids and BasesAcids and Bases• Water molecules split apart to form ions:
H20 H+ + OH-
• H+: hydrogen ion • OH-: hydroxide ion • The number of positive and negative charges
evens out. Pure water is neutral (pH 7)• pH: measures the concentration of hydrogen ions
(H+)
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Acids, Bases, & Acids, Bases, & BuffersBuffers
• Acids are any compounds that form H+ ions in a solution
• Bases are any compounds that produce OH- ions in a solution
• Buffers: are weak acids or bases that react with strong acids or bases to prevent sharp sudden changes in pHo pH of most cells is 6.5-7.5o In order to maintain this balance we use buffers
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pH ScalepH Scale
Acids: H+ > OH-
Bases: H+ < OH-
Each step is a
factor of 10. •A pH of 4 has 10x more
H+ than a pH of 5