basic chemistry and biochemistry

BASIC CHEMISTRYAND

BIOCHEMISTRY

BASIC CHEMISTRY

MEET THE ELEMENTS

http://www.youtube.com/watch?v=d0zION8xjbM

ATOMIC THEORY OF MATTER(vocabulary)

1.Atoms = building blocks of matter that cannot be divided any further by ordinary chemical means

2.Molecule = two or more atoms combined that act as a single particle, the smallest particle that retains the properties

3.Elements = substances made of only one kind of atom

ATOMIC THEORY OF MATTER(vocabulary)

4. Compounds = two or more kinds of atoms in a substance in definite proportions

5. Isotopes = varieties in the normal number of neutrons on the nucleus(The atomic number stays the same, the mass number changes)

6. Radioactivity = a nuclear process in which an atom is undergoing changes by emitting charged particles

STRUCTURE OF THE ATOMparticle charge mass locationproton (+) 1 amu in nucleuselectron (-) 0 in orbitalsneutron ( ) 1 amu in nucleusA “Happy Atom” has

all its orbital places filled.

7. Atomic number = # of protons (also the number of electrons in a neutral atom)

8. Atomic mass or mass number = number of protons plus the number of neutrons in the nucleus.

ATOMIC ORBITALS(energy levels)

nucleus

Level 12 electrons orbit

Level 28 electrons orbit

Level 38 electrons orbit

Remember: A “Happy Atom” has all its orbital places filled.

CHEMICAL BONDINGChemical bond = force of attraction that holds atoms

together

There are two kinds of bonds between atoms1. Covalent Bonds = chemical

bond that is formed by the sharing of electrons

2. Ionic Bonds = chemical bond that is formed by transfer of electrons

COVALENT BOND

Covalent Bond = chemical bond that is formed by the sharing of electrons (covalent bonds form molecules)

HYDROGEN ATOM HYDROGEN ATOM

OXYGEN ATOM

Remember: A “Happy Atom” has all its orbital places filled.

IONIC BONDIonic bond = chemical bond that is formed by transfer

of electrons

Remember: A “Happy Atom” has all its orbital places filled

Sodium (Na) has 1 electron in its outer energy level – is it happy?

Chlorine (Cl) has 7 electron in its outer energy level – is it happy?

IONIC BONDSodium and Chlorine ions are formed –

What is an ion?Ion = atom with an excess charge by the loss or gain of

electronsSodium has lost one electron (one less (–) charge) so it now has a net charge of +1

Chlorine has gained one electron (one more (–) charge) so it now has a net charge of -1

The (+) charge of Na is attracted to the (-) of the Cl and this attraction forms an ionic bond!

Na Cl

Na Cl

CHEMICAL FORMULASEach element (symbol)

and its proportions (subscripts)

are represented information

All elements are listed in the periodic table

6 atoms of Carbon (C)12 atoms of hydrogen (H)6 atoms of oxygen (O)

For example C6H12O6 means:

CHEMICAL FORMULASExamples are:

H2O

CO2

C6H12O6

CH4

STRUCTURAL FORMULASA Structural formula shows the kinds and

number of atoms as well as the chemical bonds

H

HO

H HCC

benzene

water

glucose

acetylene

CHEMICAL EQUATIONS

Reactants = the original substances before a chemical reaction (left of the arrow)

Products = new substances formed after a chemical reaction (right of the arrow)

Law of Conservation of Mass = mass can neither be created or destroyed (chemical reaction formulas must

balance)

+

2 molecules of hydrogen(2H2)

+ 1 molecule of oxygen (O2)

2 molecules of water(2H2O)

Complete pages 6 and 7 in your packet

BIOCHEMISTRYThe Chemical Compounds of Life

BIOLOGICALLY IMPORTANT COMPOUNDS

ORGANIC COMPOUNDS:Species that naturally contain carbon and

hydrogen (living organisms and their products)Most also contain O (oxygen) and N (nitrogen)Only a few elements are found in organic

compoundsMay also have P (phosphorous), S (sulfur), Fe

(iron), Ca (calcium), Na (sodium), Cl (chlorine), Mg (magnesium), K (potassium)

BIOLOGICALLY IMPORTANT COMPOUNDS

INORGANIC COMPOUNDS:

DO NOT CONTAIN CARBON (with hydrogen)May have carbonate compounds (CO2, CaCO,

etc.) but not carbon with hydrogen.Living organisms do contain inorganic

compounds

IMPORTANT INORGANIC COMPOUNDS

1. WATER• The most important inorganic compound in living

organisms• 65% of the body• Many biological processes require water2. SALTS• Help maintain water balance in the cells• Provide ions for many biological processes3) ACIDS and BASES• Help maintain homeostasis

The Structure of Organic Compounds• Organic compounds are large and complex because of the

carbon atom• Four vacancies for electrons allow 4 covalent bonds

Carbon has an atomic # of 6 which means it has 6 protons and 6 electronsIt has 4 vacancies in the outer energy level

2.1.

4.

3.

6 +

CHEMICAL COMPOUNDS OF LIFELiving organisms depend upon a variety of molecules for their

survival. Some are used to build complex parts of an organism; some supply energy; while others provide instructions for the operation of the organism.

There are many organic compounds found in organisms, but they can be classified into 4 main types:

I. CARBOHYDRATESII. LIPIDSIII. NUCLEIC ACIDS IV. PROTEINS

CARBOHYDRATES • Carbohydrates are compounds of C (carbon),

H (hydrogen), and O (oxygen)• They have the same ratio H:O as in water

(H2O) = 2:1 (twice as many H as O)* Monosaccharides = simple sugars = C6H12O6

• ALWAYS END IN “OSE”EX: MALTOSE, FRUCTOSE, GLUCOSE

• RELEASE ENERGY WHEN BREAKING DOWN GLUCOSE INTO CO2 AND H2O

• C6H12O2 CO2 + H2O

• MOST ORGANISMS USE GLUCOSE AS A SOURCE OF ENERGY

CARBOHYDRATES

THIS IS A MONOSACCHARIDE MOLECULE!THIS IS A SIMPLE SUGAR!THIS IS GLUCOSE!THIS IS C6H12O6 !

CARBOHYDRATESDISACCHARIDE = two simple sugars joined

POLYSACCHARIDE = several simple sugars joined

POLYMERS = long chains of repeating molecules(many) (molecules)

CARBOHYDRATESSugars stored in plants are called STARCH

Sugars stored in the liver of animals are called GLYCOGEN

Glycogen will be changed into glucose when the body needs it for energy!

CARBOHYDRATESBUILDING BLOCKS OF CARBOHYDRATES ARE SIMPLE SUGARS OR MONOSACCHARIDES

LIPIDS(fats, oils, and waxes)

• Made of carbon, oxygen, and hydrogen(there less oxygen in lipids than in carbohydrates)

• Reserve energy supply in an organism2 times as much energy as carbohydrates

»Plants store oils in seeds»Mammals store fats under the skin

• Waxes are formed from fatty acids and substances similar to glycerol

• Fats and oils are formed from fatty acids and glycerol

LIPIDS(fats, oils, and waxes)

BUILDING BLOCKS of LIPIDS (fats and oils) ARE 1 GLYCEROL + 3 FATTY ACIDS

The Structure of a Fatty Acid

Lipid molecule

The Fatty Acid has 2 parts:1.Chain of carbon atoms with hydrogen atoms bonded

(hydrocarbon chain)2.Carboxyl group

SATURATED vs UNSATURATED FATTY ACIDS

SATURATED FATTY ACIDS:Fats that have all single carbon-to-carbon bonds•Tend to be solids at room temperature (ie. butter)•Tend to increase the amount of cholesterol in the body•Cause deposits that lead to hardening and narrowing of arteries

SATURATED vs UNSATURATED FATTY ACIDS

UNSATURATED FATSFats that have a double or triple carbon-to-carbon bond•Tend to be oils at room temperature•Tend to decrease blood cholesterol

Polyunsaturated fats = a chain that has more than one double or triple bond

Complete the crossword puzzle on page 11 in your

packet

NUCLEIC ACIDS

• Compounds that contain phosphorus (P) and nitrogen (N)

• Also carbon, hydrogen, and oxygen

Two types of Nucleic Acids:

1.DNA2.RNA

NUCLEIC ACIDS(DNA)

DNA = deoxyribonucleic acid

• Found in the nucleus of the cell

• Directs and controls heredity information and the development and activities of the cell

THE STRUCTURE OF DNA

DNA is made of:Repeated chains of nucleotides

Nucleotides are made of:• 5 carbon sugar

(deoxyribose)• Phosphate group (PO4)

• Nitrogenous base (A,T,C,G)

THE STRUCTURE OF DNADNA• The DNA molecule is made of repeating

chains of nucleotides• The sugar and phosphate groups are the

sides of the ladder• Nitrogenous base pairs are the rungs of

the ladder• The bases are adenine (A), thymine (T),

cytosine (C), and guanine (G)• adenine (A) always pairs with thymine (T)• cytosine (C) always pairs with Guanine

(G)

RNA RNA = ribonucleic acidRNA structure:• A single strand or chain of

bases• The sugar is ribose• The base thymine is replaced

with uracil• RNA is involved with protein

synthesis

PROTEINS• Compounds that contain nitrogen, carbon,

hydrogen, and oxygen• Many contain sulfur and phosphorus• Great range of properties that give live

complexity• 20 different amino acids found in proteins

AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS

STRUCTURE OF AN AMINO ACID

1. One central carbon atom (C)2. One carboxyl group (COOH)3. One amino group (NH3)4. One hydrogen atom (H)5. One side chain (R)

GLYCINE is the simplest amino acid – the side chain is only one H atom

Examples of the

different amino acids

PROTEIN VOCABULARYDipeptide = two amino acids bonded together

The peptide bond = the bond between amino acids

Polypeptide = a long chain of amino acids

ORGANIC COMPOUND ATOMS BUILDING

BLOCKS EXAMPLES USES

CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6

glucose

•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)

•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin

Quick energy

“ose” ending

carbon ring shape

ORGANIC COMPOUND ATOMS BUILDING

BLOCKS EXAMPLES USES

CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6

glucose

•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)

•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin

Quick energy

“ose” ending

carbon ring shape

LIPIDSC H O H:O is › 2:1ex: C20H24O3

1 glycerol3 fatty acids(hydrocarbon chain)

fats, oils, waxes

Stored energymakes up cell membrane

ORGANIC COMPOUND ATOMS BUILDING

BLOCKS EXAMPLES USES

CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6

glucose

•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)

•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin

Quick energy

“ose” ending

carbon ring shape

LIPIDSC H O H:O is › 2:1ex: C20H24O3

1 glycerol3 fatty acids(hydrocarbon chain)

fats, oils, waxes

Stored energymakes up cell membrane

PROTEINS

C H O N

20 amino acidsdipeptide (2)polypeptide (many)

glycine, alanine

insulin, hemoglobin

Build and repair

ie: muscles hormonesenzymes

ORGANIC COMPOUND ATOMS BUILDING

BLOCKS EXAMPLES USES

CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6

glucose

•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)

•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin

Quick energy

“ose” ending

carbon ring shape

LIPIDSC H O H:O is › 2:1ex: C20H24O3

1 glycerol3 fatty acids(hydrocarbon chain)

fats, oils, waxes

Stored energymakes up cell membrane

PROTEINS

C H O N

20 amino acidsdipeptide (2)polypeptide (many)

glycine, alanine

insulin, hemoglobin

Build and repair

ie: muscles hormonesenzymes

NUCLEIC ACIDS

C H O P NNucleotides (sugar, phosphate nitrogenous base)

DNA = deoxyribonucleic acidRNA = ribonucleic acid

hereditary material

protein synthesis

Complete page 15 in your packet

DEHYDRATION SYNTHESISDEHYDRATION = to remove waterSYNTHESIS = to make more complex

H and OH are removed from the glucose molecules (to make water), this is the dehydration part

Then the two glucose molecules have open bonding sites so they can join together to make more complex, this is the synthesis part.

Dehydration synthesis = to make more complex by removing water

HYDROLYSISTo break down by adding water

Turn to page 17 in your packet

Dehydration Synthesis of a Carbohydrate

In carbohydrates, two monosaccharides form a bond to create a disaccharide

Dehydration Synthesis of a Protein

In proteins, two amino acids form a peptide bond to create a dipeptide molecule

Dehydration Synthesis of a Fatty Acid

In lipids, we remove 3 molecules of water!Then the glycerol molecule bonds with the 3 fatty acids

Vocabulary Review

1. monomer =

2. polymer =

3. dehydration synthesis =

4. hydrolysis =

A small molecule that will combine with other small molecules to form a chain

A large molecule (chain) formed from combined repeated smaller units (monomers)

Combining molecules by the removal of water

Breaking down molecules by the addition of water

Complete pages 18, 19, and 20 in your

packet

ENZYMESThe importance of enzymes:• Enzymes are proteins• Enzymes enter the chemical reaction

temporarily and are not changed• Enzymes are used over and over again• Enzymes are organic catalysts

ENZYMESA catalyst is a substance that brings about

a chemical reaction without being changed itself

The substrate is the substance the enzyme acts upon

HOW ENZYMES WORK• The active site matches up with the substrate• Forms enzyme-substrate complex• Enzyme will either break down or bond

molecules• Enzymes are very specific – one specific

enzyme matches one specific substrate

http://www.kscience.co.uk/animations/anim_2.htm

ENZYME SPECIFICITYHow do enzymes work?

substrate: molecules upon which an enzyme acts. The enzyme is shaped so that it can only lock up with a specific substrate molecule.

Each enzyme is specific for one and ONLY one substrate

(one lock - one key)

active site: part of the enzyme that fits with the substrateNote that the active site has a specific fit for this particular substrate and no other.

(enzyme)substrate -------------> product

REMEMBER:Each enzyme is specific for

one and ONLY one substrate

If the substrate and enzyme are not a match – the reaction will not proceed

TWO ENZYME THEORIES

1. LOCK AND KEY THEORY

2. INDUCED FIT THEORY

Naming the Enzyme• The prefix comes from the substrate (the

material acted upon)• Enzymes end in “ase” (the suffix)For example:

Maltase (malt/ase) = an enzyme that breaks down ________

Lipases (lip/ases) = enzymes that break down ______

Proteases (prote/ases) = enzymes that break down ________

lipids

proteins

maltose

FACTORS AFFECTING ENZYME FUNCTION:

• REMEMBER…• Enzymes are powerful• one enzyme molecule can catalyze thousands

of substrate reactions each second• enzymes speed up the reaction without

raising the temperature of the environment • BUT…

ENZYME REACTION vs TEMPERATURE• Enzymes work the best at certain temperatures,

usually the temperature of the natural environment

Enzymes become denatured at high temperatures (the high temp will change the shape of the active site so the enzyme no longer fits)

ENZYME REACTION vs pH

• Enzymes work the best at a certain pH, usually the pH of the natural environment

ENZYME REACTION vs CONCENTRATIONS

• The rate of an enzyme controlled reaction depends upon the concentrations of enzymes and substrates

COENZYMES

SOME ENZYMES NEED SUBSTANCES CALLED COENZYMES IN ORDER TO FUNCTION

• Coenzymes are organic substances• Coenzymes are not proteins• Most coenzymes are vitamins

A COENZYME ALLOWS AN ENZYME TO PERFORM ITS CATALYTIC FUNCTION

Acids, Bases, and Salts

TERMS

• Acids = any compound that produces hydrogen ions (H+) in solution

HCl = H+ + Cl-

• Base = any compound that produces hydroxide ion (OH-) in solution

NaOH = Na+ + OH-

TERMS

• Neutralization = when quantities of acids and bases are mixed together and no extra H+ or OH- remain

HCl + NaOH NaCl + H2O (acid) + (base) (salt) + (water)

TERMS

• Salts = the ionic compound obtained from the neutralization reaction between and acid and a base

HCl + NaOH --- Na+ + Cl- + H2O Solid NaCl (salt) found if water is

evaporated

The pH scale

H2O --- H+ + OH-

Neutral pure water, no excess of H+ or OH-

(not an acid or a base)

• If the H+ concentration increases, it becomes acidic

• If the OH- concentration increases, it becomes basic

The pH scalepH measures the concentration

of H+ Scale runs 0 - 14

• if the [H+] > [H2O] = acid

• if the [H+] < [H2O] = base

The Scale• high [H+] = acids = low pH

values = 0 - 6• neutral = 7• low [H+] = bases = high pH

values = 8 – 14

IndicatorsIndicator: substance that changes color

when pH goes above or below a certain value

• Litmus: Red = acid / Blue = base• Methyl orange: red to yellow indicates

base• Phenolphthalein: colorless to red

indicates base(compare to indicator paper to read

actual pH)