chemistry of life

Chemistry of Chemistry of LifeLife

Green = IMPORTANT NOTES

How much do How much do you already you already

know?know?

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

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

Periodic Table of ElementsPeriodic Table of Elements

Arranged from left to right by increasing atomic numberColors indicate similar atomic properties

Elements Elements Important Important

to Lifeto Life

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…

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

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

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)

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

Covalent BondsCovalent Bonds• Electrons are shared

by 2 atoms. o The electron travels

between the 2 nuclei

1 valence electrons

1 valence electrons

Lewis Dot ModelLewis Dot Model

Ionic Bonds Covalent Bonds

Valence Electrons are represented by dots around the symbol

Van Der Waals ForcesVan Der Waals Forces• Intermolecular forces

that are not ionic or covalent

• Weak attraction between atoms, molecules, and surfaces

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

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

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

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

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

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

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

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

Regular Reaction

Reaction with Catalyst

The activation energy for the reaction with the catalyst is much smaller than the original activation energy

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.

Enzyme-Substrate Enzyme-Substrate ComplexComplex

Enzyme-Substrate Enzyme-Substrate ComplexComplex

Substrate

Active Site

Active Site

Substrate

Lock and Key Analogy

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

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”

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

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

CarbohydratesCarbohydratesGlucose Glycogen

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

LipidsLipidsTriglyceride Molecule: 1 glycerol + 3 Fatty

Acids

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

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

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

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

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

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

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

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

Amino AcidAmino Acid

• Amine Group• Carboxyl Group• R group

o Accounts for variability and diversity

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.

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

Nucleic AcidsNucleic AcidsNucleotide DNA

WaterWater

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

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

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.

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

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.

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.

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

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

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+)

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

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