The Chemistry of Life:Biochemistry

Gallagher, Biology 392

Put the following terms in size order:

• Atom

• Cell

• Proton

• Protein

• Carbohydrate

• Muscle

• Electron

The Nature of Matter

• Matter is defined as anything that takes up space

• Is there anything that is not matter?• All living things take up space and are

made of matter.• Non-living things that take up space are

also made of matter• YOU are made of the same material as

your desk!

What distinguishes living from non-living?

ProtonsNeutronsElectrons

Non-living matter

LIFE!

Organic

Molecules orCompounds

Inorganic

Cells

AtomsElements: Shown in

Periodic TableNot bonded

bonded

ATOMS• Basic unit of matter• Structure of an atom

– Nucleus- protons and neutrons held together by the “strong force”

• Protons (+)• Neutrons (o)

– Surrounding the nucleus - Electron Cloud (orbitals)• Electrons (-) only contains about 1/200th mass of

proton or neutron• Constantly moving within orbital- attracted to the

nucleus by the “weak force”• Size: 1,000,000 (million) side by side = 1 cm • Atoms like to be neutral- no charge

– Equal number of protons and electrons

Electron orbitals

1st orbital can only hold 2 electrons (too close to nucleus- not much space)

2nd orbital can hold up to 8

3rd orbital can hold up to 8

Elements

• Pure substances• A grouping of the same type of atoms• More than 100 elements exist (shown in the periodic

table)• Carbon Elements:

The Periodic Table of Elements

• Shows all the elements that exist naturally or are synthetic

• Each element is represented by a single capital letter or a capital letter followed by a lowercase letter

• What other information does the periodic table provide for each element?

Atomic Number# of protons

(and also # of electrons)

Chemical symbol

Name of Element

Atomic MassThe weight Of carbon

atom oraverage

weight of all isotopes

6

CCarbon

12.011

Learning Checkpoint• Draw a representation of a lithium atom.

• Draw a representation of a Sodium atom.

• What are the three subatomic particles and their charges?

• What is the only actual difference between gold and mercury?

• What is the atomic mass of lead?

Isotopes

• Atoms of the same element that differ in the number of neutrons they contain

• Isotopes are named by their mass number.– Mass number- protons + neutrons– Example: Carbon isotopes- Carbon 12, Carbon 13,

Carbon 14– Remember: # of protons does not change– All isotopes of an atom have the same chemical

properties.

Radioactive Isotopes

• Have unstable nuclei that break down at a constant rate over time.

• As it breaks down radiation is released• Good things: used to date fossils, cancer

treatment, “tracer” to follow a substance in an organism, kill bacteria

• Bad things: radiation is dangerous and can cause cancer

Compounds and Molecules

• Atoms need to bond together to make molecules or compounds– Molecule- 2 or more of the same atom

bonded together: H2, O2, O3

– Compound- two or more of different atoms bonded together in a specific ratio: C6H12O6

• Molecules and compounds are written out in a chemical formula:

Bonding

• Covalent Bond- atoms share a pair of electrons (sometimes share 2 (double bond) or 3 (triple bond) pairs)

Ionic Bond- One atom (very unstable) gives 1, 2 or 3 electrons away to another atom. The atom that loses electrons becomes positively charged. The atom that gains the electrons becomes negatively charged. The opposite charges cause the atoms to “bond” together (opposites attract).

Example of a Covalent BondExample of Covalent Bonding- Water

Na (sodium) is very unstable because it only has one e- in its outer orbital. Cl’s (chlorine) outer orbital is

almost filled. Na gives its lonely e- to Cl.

Na become Na+ Cl becomes Cl-

Their opposite charges cause them to be attracted to one another- This is an ionic bond.

Example of Ionic Bonding-NaCl

Learning Checkpoint• What is an isotope?

• What are some positive uses of isotopes?

• What is the difference between molecules and compounds?

• Why is it important that atoms bond?

• What causes atoms to bond?

• Explain the difference between an ionic bond and a covalent bond.

2-2 WATER!

• 75% of the Earth is covered with water• 60-70% of your body is water• Water can be found in almost everything we eat

and drink• Without any water at all you would die in 3 days

Properties of Water

• Less dense when frozen (ice floats)

• Polarity

• Hydrogen bonds– Adhesion– Cohesion

• Making Mixtures

• Making Acids and Bases

Water Density

• Ice is less dense than liquid water

• When water freezes air is trapped within the frozen ice making the cube larger and less dense

• Benefits:– Fish and plant life can survive in liquid layers

of water under ice

Polarity

• Water molecules are polar

• Although the molecule is neutral overall there is a shift of charge within the molecule The much larger molecule, Oxygen,

pulls more on the shared e-This end of the molecule becomes slightly

more negative.

Hydrogen ends become slightly

positive

Hydrogen Bonding• Due to polarity, water molecules attract to

one another

• Slightly negative oxygen attracts slightly positive hydrogen from another molecule

• This attraction between molecules is COHESION.

• Water molecules are also attracted to other materials. This is ADHESION.

COHESION

Water molecules attractTo glass molecules

And form a meniscus

Water molecules attract To one another-

causes water to “bead”

ADHESION

Mixtures

• Two or more elements physically mixed together but not chemically combined

1. Solutions- a solute (salt) is dissolved into a solvent (water

– Distributes evenly*Due to water’s polarity it can dissolve ionic compounds

and other polar molecules making it THE GREATEST SOLVENT ON EARTH!

2. Suspensions- added substance does not dissolve but breaks into small enough pieces that it remains suspended in the water and does not settle out.

Making Acids and Bases

• Water molecules can react to form individual ions: H2O H+ + OH-

• In pure water this occurs naturally but the amount of H+ is always = to the amount of OH- so water remains neutral

• Some solutions made with water become acidic or basic. This is determined by the amount of H+ (hydrogen ions) in the solution

• This is measured on the pH scale

Acids

• Any compound that forms H+ ions in solution

• H+ ions > OH- ions

• Range from just below 7 to 0 on the pH scale

• The closer to 0 the more acidic the solution

• Examples: stomach acid, lemon juice

Bases (Alkaline)

• Any compound that forms 0H- ions in solution

• OH- ions > H+ ions

• Range from just above 7 to 14 on the pH scale

• The closer to 14 the more basic the solution

• Examples: lye, bleach, oven cleaner

Buffers

• Weak acids or bases that can react weith strong acids or bases

• Used to regulate pH and prevent sharp sudden changes in pH

• There are natural buffers in your blood that keep the pH at 6.5 to7.5

Learning Checkpoint

• Why is ice less dense than water?

• What does it mean to say water molecules are polar?

• What is the difference between adhesion and cohesion?

• What makes a solution acidic or basic?

• How is acidity measured?

2-3 Carbon Compounds

• Why Carbon?– Carbon can from 4 covalent bonds (can create many

different compounds)– Carbons can bond to one another forming large

chains or rings• Linking of carbons can form very large

molecules called Macromolecules• Each individual unit is called a monomer. When

they are linked together they are called a polymer.

• 4 macromolecules necessary for life: carbohydrates, lipids, protein, nucleic acids

Nucleic Acid

• Contain hydrogen, oxygen, nitrogen, carbon and phosphorus

• Monomer- nucleotide• Polymer- DNA or RNA• Store or transmit genetic information

*Nucleic Acids will be studied in greater detail when we study genetics

Carbohydrates

• Made of carbon, hydrogen and oxygen (ratio of 1:2:1)

• Monomer- monosaccharides (simple sugars): glucose, galactose and fructose– Disaccharides- 2 sugars linked together: sucrose,

maltose, lactose

• Polymer- polysaccharides: glycogen (animals), starch and cellulose (plants)

• Main source of energy

Lipids

• Made mostly of carbon and hydrogen and some oxygen

• Not soluble in water: fats, oils and waxes

• Monomer: all lipids have an end called glycerol in which fatty acid chains attach

• Polymer- lipid

• Used to store energy, also for membrane structure

Saturated vs. unsaturated fats

Saturated- no double bondsbetween carbons, all possible hydrogens

Unsaturated- at least one double bond,

less hydrogen, can bend

Protein

• Contain nitrogen, carbon, hydrogen and oxygen (amino group and carboxyl group)

• Monomer- amino acid

• Polymer- polypeptide or protein

• Control reactions, regulate cell processes, form bones and muscles, transport and help fight disease

Identify the Macromolecule

Chemical reactions

• Process that changes one set of chemicals (reactants) into another set of chemicals (products

• Activation energy

-“The starting push” of chemical reactions

-The minimal amount of energy required to get a chemical reaction started

Enzymes

• proteins that lower the activation energy required and allow reactions to happen at the normal temperature of cells.

• Each enzyme is specific (only works on one particular reaction)

• Can be used over and over again for that reaction• The reactant that the enzyme helps is called the

substrate. The enzyme is usually named after the substrate with the ending –ase added to it.

• Coenzymes are non-protein helper molecules that sometimes assist enzymes with their job.

Learning Checkpoint

• What are the 4 carbon compounds necessary for life?

• What is the main function of carbohydrates?

• What are some of the functions of protein in the body?

• What is the easiest way to distinguish a lipid from a carbohydrate?

• What is a monomer and a polymer?