THE CHEMISTRY OF LIFE

Biology Chapter 6

All matter is made up of atoms

• Atoms are the building blocks of matter

• All atoms have the same basic structure• They contain a nucleus

• Protons (+) and neutrons (0)• Electron clouds surround the nucleus

• Electrons (-)• In a neutral atom, the number of protons and electrons are equal

• Protons and electrons each have a charge of about 1.6x10-19 coulombs • The positive charge of the proton and the negative charge of the electron cancel out

• Neutrons have no charge

Elements

• Elements refer to atoms with a particular number of protons.• Every atom in the universe that has 6 protons is Carbon• The number of protons an element has is called its atomic number

• Elements cannot be broken down into simpler forms by chemical means• In chemical reactions, a molecule is broken down into elements

• Water can be broken down into 2 Hydrogen atoms and 1 Oxygen atom

• Elements can gain or lose electrons or neutrons and remain the same element• However, if the number of protons changes, the element changes

Elements in Human Body

• Life is primarily made up of 6 elements• Oxygen (O)-65%• Carbon (C)-18.5%• Hydrogen (H)-9.5%• Nitrogen (N)-3.3%• Carbon (Ca)-1.5%• Phosphorus (P)-1 %

• Mnemonic: Our Cooks Have No Cakes or Pies

• Other atoms, such as K, Na, Mg, Fe, etc. each make up less than 1% of the elements in the human body• However, all play important roles• Called trace elements

Electrons• Electrons are what determine the

chemical properties of substances• Electrons are located outside of the nucleus

in electron clouds

• The electron clouds have different energy levels• Only certain numbers of electrons can fit in

the difference energy levels• The first energy level can only ever hold 2

electrons• The second can only hold 8 electrons each

• If an energy level is not full, the atom is unstable • Noble gases (Ne, Ar, Kr, Xe, Rn) are very

stable (nonreactive) because they have full energy levels

• Li, Na, K, F, Cl, Br, and I are very reactive because they do not.

• They each have only 1 electron in their outer cloud, and really want to give it up

Ions

• Sodium, for example, has 11 protons, so it will have 11 electrons when it is neutral• The first energy level is full (2),• The second level is full (8)• Leaving 1 electron in the outermost level, which needs 8 to become

stable (Don’t worry about why…)• It is much easier to lose the 1 than gain 17…

• Sodium really wants to get rid of that 1, so will readily give up its electron

• In giving up its electron, sodium has more protons (11) than electrons (10).• 11+(-10)=+1

• It has a charge of +1, and has become a charged atom• This is called an ion

Ionic Bonds-Attraction between ions• Chlorine (atomic number 17)

• 2 electrons in the first level• 8 electrons in the second level • 7 electrons in the third level

• 1 short of being stable

• Chlorine will gladly take the electron from sodium• Chlorine will then have more electrons than protons (18 electrons, 17

protons), so becomes an ion: (-18)+17= -1

• Because chlorine then has a negative charge and sodium has a positive charge, they attract one another (like magnets)• The bond is rather weak

• Put into water, they will split easily.

• Everyone wins. Sodium has its levels full, chlorine has its levels full.• And we get NaCl (a.k.a. table salt)

Covalent Bonds-sharing electrons

• Oxygen (atomic number 8) has a similar problem• 1st energy level (2)• 2nd energy level (6)

• 2 short of stability

• Hydrogen (atomic number 1) also has a problem• 1st energy level (1)

• 1 short of stability

• Each need electrons, so decide to COoperate • 2 hydrogens work together with oxygen to share electrons

• This fills all energy levels

• This forms a water molecule

• The bonds are strong

Unequal Sharing-Polar Covalent Bonds• In a covalent bond, one atom generally controls the shared

electrons a little bit more than the other atoms• This creates areas of charge at the ends (POLES) of the molecule

• These molecules have small attractive forces and can bond easily to other atoms• Water

Chemical Equations

• ReactantsProducts

• Reactants are what react to produce the product

• Na + Cl NaCl• Must be balanced (same number of each element on each side of the

equation.)

• Hydrogen and oxygen each exist as molecules in nature: H2 and O2 respectively• Water formation:

•2H2 + O2 2 H2o•4H, 2O 4H 2O

Properties and Importance of Water• Water is the only raw material needed by every organism on earth.

• Water is needed for chemical reactions in the body to occur• The water dissolves the chemicals, and transports them

• Water’s polarity allows it to stick to itself (Cohesion) and to other charged atoms (ashesion)-Add purple words to notes• This leads to capillary action and surface tension• Also allows it to easily break apart ionic bonds

• Water has a high specific heat • Specific heat is the amount of energy needed to change the temperature of a

substance• It takes a lot of energy of raise or lower the temperature of water• This helps keep cells (which are mostly water) in homeostasis, as water acts a little as an

insulator

Cohesion and adhesion

Capillary Action

Surface Tension

pH Scale•Many chemical reactions in the body can occur only under specific conditions• One of these conditions is that the pH of a substance must be in a certain range•pH is the measure of how acidic or basic a solution is• pH of 7 is neutral (pure water)• pH above 7 is basic

• Blood, with a pH of 7.3-7.4, is slightly basic.

• Mucus lining the stomach is basic to prevent damage by stomach acid

• pH below 7 is acidic • Stomach acid is very acidic (1.5-3.5)

• Upset stomachs can be calmed with antacid (base with pH around 10)

Bases

• Bases are substances that form hydroxide ions (OH-) in water • Ammonia (NH3)

• Ammonia strips water molecules of a hydrogen ion, forming hydroxide ions• NH3 + H2O NH4

+ + OH¯

• Sodium Hydroxide (NaOH)-component in drain cleaners• Water breaks the weak ionic bond

• NaOH Na+ + OH-

Acids

• Acids are substances that form hydrogen ions (H+) in water• Hydrochloric acid (component of stomach acid) is a strong base

• HCl H+ + Cl-

Life Substances

• Life is based on Carbon (atomic number 6)• 1st energy level (2)• 2nd energy level (4)• Needs 4 to become stable

• Carbon can bond with other carbon atoms, or other atoms• Often forms long chains of atoms

• 4 main categories of biological macromolecules (large molecules)• Carbohydrates• Lipids• Proteins• Nucleic Acids

Structure of Biological Macromolecules

•All biological molecules are chains of molecules•Small molecules are bonded together to form one large molecule•Think cars on a train

• The small molecules (the cars) are called monomers (mono=1)• The large molecule (the train) is a collection of molecules called a polymer

(poly=many)• The monomers are bonded together by covalent bonds

Carbohydrates (a.k.a. Carbs and sugars)•Carbohydrates are made up of carbon, hydrogen, and oxygen

•They are often in a ratio around 1:2:1• Example: C6H12O6 , C12H22O11

•They are used by cells to provide energy•Sugars can be monosaccharides (monomer), disaccharides (polymer), or polysaccharides (polymer)

• Monosaccharides include:• Glucose (C6H12O6)• Fructose (C6H12O6)

• These are isomers, or molecules that have the same atoms, and the same number of each atom, but in different configurations

• When glucose and fructose are linked together, they form a polymer called a disaccharide • Sucrose: table sugar (C12H22O11)

• Polysaccharides are the largest carbohydrates• Starch

• Still a similar ratio, but can have several different numbers of atoms

Lipids• Large molecules made from carbon, hydrogen, and small amounts

of oxygen

• Fats, oils, waxes, steroids

• Used for energy storage

• Fatty acids and glycerol (monomers) form lipid chains (polymers)

• Saturated fats are lipids where each carbon is bonded to another carbon by a single bond• Saturated fats are solid at room temperature (butter, lard)

• Unsaturated fats have at least one carbon double bonded to another carbon• Unsaturated fats are liquid at room temperature (oils)

Proteins

• Large complex polymers composed of carbon, hydrogen, oxygen, nitrogen, and occasionally sulfur

• Extremely important to life• Build up biological structures• Play a role in immunity• Assist with chemical reactions

• Enzymes are proteins that help chemical reactions occur

• Monomers are amino acids. They join by special covalent bonds called peptide bonds

• Each protein has a specific 3-D shape that determines its job

Nucleic Acids

• Consist of Carbon, Hydrogen, Nitrogen, Oxygen, and Phosphorus atoms• Arranged in 3 groups

• A nitrogenous base• A phosphate group• A monosaccharide (ribose or deoxyribose)

• Most important molecule in an organism• Contains instructions for making all proteins

• Therefore, determines how an organism looks, acts, etc.• Hereditary material

• This is what is passed from parents to offspring

• Monomers are nucleotides