Download BASIC CHEMISTRY

BASIC CHEMISTRY
AND
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 ATOM
particle
proton
electron
neutron
charge
(+)
(-)
()
mass
1 amu
0
1 amu
location
in nucleus
in orbitals
in nucleus
A “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 1
2 electrons
orbit
Level 2
8 electrons
orbit
Level 3
8 electrons
orbit
Remember: A “Happy Atom” has all its orbital places filled.
CHEMICAL BONDING
Chemical bond = force of attraction that holds atoms
together
There are two kinds of bonds
between atoms
1. 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
HYDROGEN ATOM
HYDROGEN ATOM
OXYGEN ATOM
Covalent Bond = chemical bond
that is formed by the sharing of
electrons (covalent bonds form
molecules)
Remember: A “Happy Atom” has all its orbital places filled.
IONIC BOND
Ionic 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 BOND
Sodium and Chlorine ions are formed –
What is an ion?
Ion = atom with an excess charge by the loss or gain of
electrons
Sodium 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
Na
Cl
Na
The (+) charge of
Na is attracted to
the (-) of the Cl and
this attraction forms
an ionic bond!
Cl
CHEMICAL FORMULAS
Each element (symbol)
All elements are listed in the periodic table
and its proportions (subscripts)
are represented information
For example C6H12O6 means:



6 atoms of Carbon (C)
12 atoms of hydrogen (H)
6 atoms of oxygen (O)
CHEMICAL FORMULAS
Examples are:
H 2O
CO2
C6H12O6
CH4
STRUCTURAL FORMULAS
A Structural formula shows the kinds and
number of atoms as well as the chemical
bonds
glucose
H
O
H
water
benzene
H
C
C
H
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
BIOCHEMISTRY
The 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
compounds
 May 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 water
2. SALTS
• Help maintain water balance in the cells
• Provide ions for many biological processes
3) 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
electrons
It has 4 vacancies in
the outer energy
level
2.
1.
6+
3.
4.
CHEMICAL COMPOUNDS OF LIFE
Living 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. CARBOHYDRATES
II. LIPIDS
III. 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 !
CARBOHYDRATES
DISACCHARIDE = two simple sugars joined
POLYSACCHARIDE = several simple sugars joined
POLYMERS = long chains of repeating molecules
(many) (molecules)
CARBOHYDRATES
Sugars 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!
CARBOHYDRATES
BUILDING 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 organism
2 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 FATS
Fats 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.DNA
2.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 DNA
DNA
• 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 acid
RNA 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.
2.
3.
4.
5.
One central carbon atom (C)
One carboxyl group (COOH)
One amino group (NH3)
One hydrogen atom (H)
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 VOCABULARY
Dipeptide = two amino acids bonded together
The peptide bond = the bond between amino acids
Polypeptide = a long chain
of amino acids
ORGANIC
COMPOUND
CARBOHYDRATES
ATOMS
CHO
H:O is 2:1
ex: C6H12O6
glucose
BUILDING
BLOCKS
EXAMPLES
•Monosaccharides
(simple sugars)
•Disaccharides
(2 sugars)
•Polysaccharides
(many sugars)
•glucose, fructose,
galactose
•maltose, sucrose,
lactose
•starch, cellulose,
glycogen, chitin
USES
Quick energy
“ose” ending
carbon ring shape
ORGANIC
COMPOUND
CARBOHYDRATES
BUILDING
BLOCKS
EXAMPLES
CHO
H:O is 2:1
ex: C6H12O6
glucose
•Monosaccharides
(simple sugars)
•Disaccharides
(2 sugars)
•Polysaccharides
(many sugars)
•glucose, fructose,
galactose
•maltose, sucrose,
lactose
•starch, cellulose,
glycogen, chitin
CHO
H:O is › 2:1
ex: C20H24O3
1 glycerol
3 fatty acids
(hydrocarbon
chain)
ATOMS
LIPIDS
fats, oils, waxes
USES
Quick energy
“ose” ending
carbon ring shape
Stored energy
makes up cell
membrane
ORGANIC
COMPOUND
CARBOHYDRATES
LIPIDS
BUILDING
BLOCKS
EXAMPLES
CHO
H:O is 2:1
ex: C6H12O6
glucose
•Monosaccharides
(simple sugars)
•Disaccharides
(2 sugars)
•Polysaccharides
(many sugars)
•glucose, fructose,
galactose
•maltose, sucrose,
lactose
•starch, cellulose,
glycogen, chitin
CHO
H:O is › 2:1
ex: C20H24O3
1 glycerol
3 fatty acids
(hydrocarbon
chain)
CHON
20 amino acids
dipeptide (2)
polypeptide
(many)
ATOMS
PROTEINS
USES
Quick energy
“ose” ending
carbon ring shape
fats, oils, waxes
Stored energy
makes up cell
membrane
glycine, alanine
Build and repair
insulin,
hemoglobin
ie: muscles
hormones
enzymes
ORGANIC
COMPOUND
CARBOHYDRATES
LIPIDS
BUILDING
BLOCKS
EXAMPLES
CHO
H:O is 2:1
ex: C6H12O6
glucose
•Monosaccharides
(simple sugars)
•Disaccharides
(2 sugars)
•Polysaccharides
(many sugars)
•glucose, fructose,
galactose
•maltose, sucrose,
lactose
•starch, cellulose,
glycogen, chitin
CHO
H:O is › 2:1
ex: C20H24O3
1 glycerol
3 fatty acids
(hydrocarbon
chain)
CHON
20 amino acids
dipeptide (2)
polypeptide
(many)
ATOMS
PROTEINS
NUCLEIC ACIDS
CHOPN
Nucleotides
(sugar, phosphate
nitrogenous base)
USES
Quick energy
“ose” ending
carbon ring shape
fats, oils, waxes
Stored energy
makes up cell
membrane
glycine, alanine
Build and repair
insulin,
hemoglobin
ie: muscles
hormones
enzymes
DNA =
deoxyribonucleic
acid
RNA = ribonucleic
acid
hereditary
material
protein synthesis
Complete page 15
in your packet
DEHYDRATION SYNTHESIS
DEHYDRATION = to remove water
SYNTHESIS = 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
HYDROLYSIS
To 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 =
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)
3. dehydration synthesis =
4. hydrolysis =
Combining molecules by the
removal of water
Breaking down molecules by the addition
of water
Complete pages
18, 19, and 20 in
your packet
ENZYMES
The 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
ENZYMES
A 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 SPECIFICITY
How 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.
(enzyme)
substrate -------------> product
Each enzyme is specific for one
and ONLY one substrate
(one lock - one key)
active site: part of the enzyme
that fits with the substrate
Note that the active site has a
specific fit for this particular
substrate and no other.
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
maltose
down ________
Lipases (lip/ases) = enzymes that break
lipids
down ______
Proteases (prote/ases) = enzymes that
break down ________
proteins
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+ + OHNeutral 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 scale
pH 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
Indicators
Indicator: 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)