The Chemistry of Life2.1 The Nature of Matter

2.2 Properties of Water

2.3 Carbon Compounds

2.4 Chemical reactions and enzymes

What is an atom?

•Building blocks of life - the basic unit of matter

•Name comes from greek term – atomos – unable to be cut

•Very very small – 100million = 1cm

•Made of three subatomic particles – protons, neutrons and electrons

What is a subatomic particle?• Protons and Neutrons - the

same mass• Protons have a positive charge• Neutrons carry no charge at all

• Strong forces bind protons and neutrons to form a nucleus

• Electrons – negatively charged particles

• 1/1840 mass of a proton

• Equal number of protons and electrons = neutral charge

What is an element? How are they arranged on the periodic table?

Elements• Pure substance – consists of only one type

of atom

•More than 100, but less than 20 are common

• Number of protons –atomic number

• Atomic number of carbon – 6

• Each carbon atom has 6 protons and therefore 6 electrons

• Numbers of neutrons in an element can vary

What is an isotope?

•All carbon isotopes have 6 protons

•Number of neutrons can vary• 6, 7, 8

•There are different isotopes of carbon

•Total number of protons and neutrons = mass number

•Mass number is used to identify different isotopes

•Atomic mass - weighted average of different isotopes

Calculating weighted average

•Weighed average atomic mass = • sum of (atomic mass X modal abundance) for each isotope of carbon

•Because all isotopes have the same number of electrons, all isotopes have the same chemical properties

Mass number exact weight (amu) percent abundance

12 12.000000 98.90

13 13.003355 1.10

Answer =(12 x 0.9890) + (13.003355 x 0.011) = 12.011 amu

What is a radioactive isotope? Why are they useful? •When the nuclei of an isotopes is

unstable, it is radioactive• This means the nuclei will “break

down” at a constant rate over time• Radiation can be dangerous, but also

very useful• Can be used to date the age of rock• Can be used to treat cancer• Kill bacteria in food• Use a tracer to follow movements

of substances in organisms

What is a chemical compound?

•Most elements are found combined with other elements

• Chemical compound - combination of two or more elements in definite proportions

•We write a chemical formula in a kind of shorthand• Eg. H

2O

•Water contains one hydrogen and two oxygen atoms

What is a chemical bond? Are there different types? •Electrons in the outer shell dictate what kind of chemical bonds

atoms can form• These electrons are called valence electrons

Ionic bonds

•Where one or more electrons are transferred from one atom to another

•This distorts the neutral charge of atoms• Positive and negative ions generated• Positive and negative ions are attracted to each other• A strong bond is formed

•Common with extreme ends of the periodic table

Salt formation

Covalent bonds

• Sometime electrons can be shared• Moving electrons travel around the nuclei of

both atoms

• The basis for a covalent bond• Possibility for single, double or triple bonds

•Resultant structure called a molecule

Van der Waals forces

• Sharing can sometimes be a bit one sided• Some elements have a stronger ability to attract

electrons than others

•Even when equal, the rapid movement of electrons can can create regions that have positive and negative charges• Results in a slight attraction between these

areas

•Not as powerful as ionic bonds! • But can hold molecules together

The Chemistry of Life2.2 Properties of water

Why is water essential to life on Earth?

• It makes up 60% of the human body

• Is known as the universal solvent

•Presence of liquid water means that life might be present somewhere

•Why is water so special?

The Water molecule

• Found in a liquid state over most of the Earth’s surface

•Neutral charge – 10 Protons and 10 electrons

•Polarity of water molecule

•A polar molecule is one where the charges are unevenly distributed

Hydrogen bonding•Polar molecules can attract to each other

•Attraction between partial +ve charge of H atom and partial –ve charge of another molecule is a hydrogen bond• Oxygen, nitrogen and fluorine are common partial negative charged particles

•Hydrogen bonds are not strong• But they give water a number of unique characteristics

• Explain why water expands upon freezing

• Explains why water can dissolve so many substances

Cohesion

•Cohesion is an attraction between molecules of the same substance

• Water is very cohesive• One water molecule can have 4 hydrogen

bonds at the same time

• Results in water being molecules being drawn together• Explains why drops of water form beads on a

smooth surface

• Provides surface tension – allowing for some insects to walk on the a ponds surface

Adhesion

•The attraction between molecules of different substances• Water will stick to the side of glass tubes, or

graduated cylinders• Results in a meniscus

• Adhesion between water and glass is stronger than cohesion between water molecules

• Water can also rise in narrow tubes against the force of gravity – capillary action. • One of the forces that draws water out of roots and into

stems and leaves in plants• But, cohesion holds the column of water itself together as it

rises

Heat Capacity

•Heat Capacity – the amount of heat energy required to rise the temperature

•The multiple hydrogen bonds means that it takes a large amount of heat energy to cause the molecules to move faster, raising the temperature of the water

•Water has a relatively high heat capacity

• Large bodies of water can absorb a lot of heat with only small changes in temperature• Protects organisms in the water

•Water can also aid in the regulation of cell temperature

What is a mixture?

•Mixture – material composed of 2 or more elements or compounds• Physically mixed together• Not chemically combined

•Water can form 2 types of mixtures• Solutions and Suspensions

How does water’s polarity influence it’s properties of a solvent?• In an ionically bonded compound,

ions are attracted to polar water molecule • Ions break away• Become dispersed• Form a solution

• Solutions are evenly distributed throughout the solution

• In Salt water solution

• Table salt – solute

•Water - solvent

The universal solvent

•Water is a very versatile solvent

• It can break dissolve:• Salts• Sugars• Minerals• Gasses• Other solvents…

•All because of it’s polarity

•When no more solute can be dissolved the solution is saturated.

Besides tasting the water, how could you test to show that the salt is there, even though you can’t see it?

•Weigh it

•Measure changes in volume….

Suspension

•When something in water separates into pieces so small that they do not settle out• Movement of water molecules keeps them suspended • Mixture known as a suspension

•Blood is a great example of a solution and suspension• Blood – mostly water• Many dissolved compounds• Cells can’t dissolve, and are held in suspension

Complete the table

Substance Definition Examples

Physical combination of to or more substances

Cinnamon sugar

Solute

Water in saltwater

Mixture of water and non dissolved substance

blood

Solution

Complete the table

Substance Definition Examples

Mixture Physical combination of to or more substances

Cinnamon sugar

Solute Substance that is dissolved Salt in saltwater

Solvent Substance in which Solute is dissolved

Water in saltwater

Suspension Mixture of water and non dissolved substance

blood

Solution Mixture in which all substances are evenly distributed

Saltwater

Acids, bases and pH

•Water molecules can split into H+ ions and OH- ions

• In pure water only 1 in 550 million molecules split• Number of Positive and Negative ions are equal• pH is neutral - 7

The pH Scale

• Indicates the concentration of H+ ions in solution

•Ranges from 0 to 14• Below 7 is acidic• Above 7 is basic

•The lower pH the greater the acidity

•pH scale is logarithmic • Each step on the pH scale represents a factor of 10 increase from the

previous step

Acids and bases

•Both can be very corrosive

Acid

•Any compound that forms H+ ions in solution

•Have higher H+ concentrations than pure water

•Therefore have a pH of less than 7

•1 – 3 is a strong acid

•Example is hydrochloric acid in your stomach

Base

•A base is a compound that produces OH- ions (hydroxide)• Lower concentrations of H+ ions than pure water• pH > 7• Strong bases such as NaOH (used in soap making) have pH’s ranging from 11

– 14

Buffer

•A weak acid and/or a base that can react with a strong acid or base to prevent a sharp, sudden change

• Important in the human body• Where pH must be kept between 6.5 and 7.5• If pH is lower or higher than can affect chemical reactions that take place

within cells

•Controlling pH is one form of homeostasis

•Blood must be kept at pH 7.4• Changes are controlled by bicarbonate and phosphate ions

Buffers cont…•Buffers do not keep a solution neutral

•There are many different buffers in the world – each is designed for a fixed pH range• One may work from 2 – 6• Another from 10 – 12

•All contain a weak acid and a weak base component• Acid component will release H+ ions if base is added• Base component will absorb H+ ions if acid is added• The solution does not become as acidic or basic as it would have without the

buffer

Writing exercise

• Suppose you are a writer for a natural history magazine for children. This month’s issue will feature insects. Write a paragraph explaining why some bugs, such as the water strider, can walk on water

Carbon CompoundsSection 2.3

Carbon properties•Due to carbon’s 4 valence electrons, carbon can bond with MANY

other elements

•Most common are• Hydrogen• Oxygen• Phosphorous• Sulphur• Nitrogen

•This is the basis for the molecules of life, the basis of all living organisms

What compounds contain carbon?• Carbon dioxide• Carbon monoxide• Chalk• Carbon• Sugar• Protein• Crude oil• Alcohol• Fats• Nucleic acids

Chains of carbon

•Carbon can also bond with itself

•Can give rise to chains of nearly unlimited length• Single, double, or triple covalent bonds• Can also form rings

•Millions of possibilities for large and complex structures

•Carbon is the most versatile element on earth

Acetylene

Methane

Macromolecules• Giant molecules

• Made of thousands, or hundreds of thousands of giant molecules• Most formed via polymerization

• Large compound built by joining smaller ones together• Smaller unit – monomer

• Can be identical or different • Larger unit – polymer

• 4 major groups of macro molecules• Carbohydrates• Lipids• Nucleic acids• Proteins

Polymerization

•Two types of polymerization• Addition

• Monomers join together with no change in their molecule

• Condensation• A small molecule is released when two monomers are joined together

• Often water

+ =

Hydrolysis

•Both condensation reactions and hydrolysis are extremely common biochemical processes

+=

H2O

Carbohydrates• Carbon, hydrogen and Oxygen

• Ratio – 1:2:1

•Main source of energy in all living things• Also sometimes used for structural

purposes

• Breakdown of sugars provides energy

• Excess sugars stored in complex carbohydrates – starches

• In starch glucose is the monomer

Simple sugars (monosaccharides)•Glucose most common

• Other examples galactose (in milk), fructose (in fruit),

•Basic building block of carbohydrates

• Sucrose (ordinary sugar) is a disaccharide• Made from combining glucose and

fructose – two simple sugars

Complex Carbohydrates – polysaccharides • Formed from many monosaccharides• Plants store sugar in a polysaccharide called starch

• Stores excess sugar

• Cellulose – another examples of a polysaccharide• Also provides strength and rigidity to a plant

• Glycogen – example of polysaccharide in humans• How animals store excess sugar - “animal starch”

•When we have low blood sugar levels, the body breaks down glycogen to glucose• Glycogen in muscles supplies energy for muscle contraction and movement

Lipids•Mostly made of carbon and

hydrogen

•Not soluble in water

•A large and varied group• Common categories are fats, oils

and waxes

• Formed from glycerol combing with a fatty acid

•Two types of fatty acids• Saturated• Unsaturated

Fatty acids• Saturation is related to the number of hydrogen atoms

• If it contains the maximum possible number it is saturated• Otherwise it is unsaturated

• If the fatty acid contains one C to C double bond it is unsaturated

• If it contains more than one C to C double bond it is polyunsaturated • Unsaturated fatty acids tend to be liquid at room temperature

• E.g. Olive oil

• Can also help to lower blood cholesterol levels

Data exercise Page 48

Nucleic acids

•Hydrogen, oxygen, nitrogen, carbon and phosphorous

•Made from nucleotides

•Nucleic acids store and transmit hereditary or genetic information• Ribonucleic acid (RNA)• Deoxyribonucleic acid (DNA)

Protein•Contain nitrogen alongside carbon,

hydrogen and oxygen

•Polymers of molecules called amino acids

•Amino acids have• Amino group – NH2• Carboxyl group – COOH

•Covalent bonds called peptide bonds link amino acids together via a condensation reaction

Peptide bond formation

Protein

• Functional molecule built from one or more polypeptides

•Proteins can: • control the rate of a reaction• regulate cell processes• form important structures • transport substances in or out of cells• help fight disease

Structure and Function

•More than 20 amino acids are found in nature

•All have carboxyl and amino groups

•Any amino acid can be joined to another through covalent bonds

• Side chain group (R group) provides differences• Gives rise to a large number of different properties and functions

• Acidic, basic, polar, non polar….

• Information on how amino acids should be assembled is stored In DNA

Levels of organization•The shape of a protein

is determined by a number of forces• Ionic bonds• Covalent bonds• Hydrogen bonds• Van der waals forces

• Shape can be very important for a proteins function• enzyme

The Chemistry of Life2.4 Enzyme activity

What happens to chemical bonds during chemical reactions?•Chemical reaction – process that changes one group of chemicals to

another• Mass and energy are conserved• Can happen slowly or quickly

•Reactants – elements or compounds that enter into a chemical reaction

•Products – Elements or compounds produced by a chemical reaction

•Chemical reactions involve changes in the chemical bonds that join atoms together in compounds

Energy in reactions• Energy is released or absorbed whenever

a bond is formed or broken

• Chemical reactions always involve changes in energy

• Chemical reactions that release energy often occur independently

• Chemical reactions that require energy will not occur without an energy source

• Example of energy releasing reaction – hydrogen reacting with oxygen• Energy released as heat, light and sound• To generate H

2 from H

2O you need to put in

a lot of energy

What are common sources of energy?

• In order to stay alive organisms need energy

•Every organism must have a source of energy to carry out chemical reactions• Energy is conserved in chemical reactions

•Plants get energy from light

•Animals get energy from food

•Energy released during day to day processes

What is activation energy?•Reaction that release energy do not always occur spontaneously

•How do you burn paper?• You light it with a match…• Then the cellulose in paper releases both heat and light energy

•Activation energy is the energy required to get a reaction started

What is the difference between an endothermic and an exothermic reaction?

What is a catalyst?• Some reactions have very high activation energies, or occur too slowly to

be of any use• A catalyst speeds up the rate of a reaction• Lower a reaction’s activation energy• Catalysts are not used up during a reaction

Enzymes

•What role do enzymes play in living things, and what affects their function?

• Enzymes are proteins that acts as nature’s catalyst

• They speed up chemical reactions that take place in cells

• Like all catalysts they lower the activation energy

• This Formula explains how carbon dioxide is removed from the body

• In nature this is a very slow reaction• In the presence of carbonic anhydrase it occurs 10million times faster

• Essentially Instantaneous!

Example - carbonic anhydrase

Enzyme – substrate complex• Chemical reactions depend on reactants colliding

• With enough energy to ensure that the reaction takes place• Existing bonds need to break, new bonds need to form• If insufficient bonds remain unchanged after collision

• Enzymes provide a site where reactants can be bought together to react• Reduces required amount of energy for a reaction• Reactants in an enzyme catalyzed reaction are called a substrate

• Substrates bind to active site of an enzyme• Complementary shapes• Like a lock and key

Regulation of enzyme activity• Enzymes can be affected by any variable

that affects the rate of a reaction• Temperature• pH• Regulatory molecules

• Temperature is key•Most enzymes in human body work best

at 37 °C.• Enzymes work best at specific pH

conditions •When conditions aren’t ideal enzymes

can become denatured• Enzymes can be switched off by chemical

signals when they are not needed