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Matter: anything that has mass &
occupies space
Atoms: The basic unit of matter
Protons (+) and neutrons (0) in nucleus
Electrons (-) in orbits around nucleus
Atomic number = number of protons
Atomic mass = mass of protons +
neutrons
Charge:
Neutral atoms: electron # = proton #
Ions: # of electrons & protons differ
Periodic Table
Atomic number is shown for
each element.
Arrangement of the electrons:
First shell: Can hold 2
electrons
Every other shell can hold up
to 8 electrons.
Chemical Bonds : How elements “hook up” with eachother
a. Covalent bond: two atoms share one or more pairs of
valence electrons Example: diatomic hydrogen
These atoms are sharing!
b. Ionic bond: atoms donate or receive electrons from other
atoms Example: sodium chloride
Sodium needs to lose an electron, and chlorine needs to gain one these two atoms are a very compatible pair!
There is no sharing of electrons, sodium gives away one electron to
chlorine.
However, this introduces something new. Sodium now has 11 protons,
but only 10 electrons (because it has given one away). Chlorine has
17 protons, but now has 18 electrons (as it has taken an extra one
from Sodium). The effect of this is easy to calculate - it leaves the
atoms with a charge - they are no longer neutral.
The Na+ (Sodium) with one more positive proton than negative
electrons is positively charged, and the Cl- (Chlorine) with one extra
negative electron is negatively charged. However as a pair, they are
still neutral (the sodium is "+1" and the chlorine is "-1").
Any atom that carries a charge is called an ION and ions can be positive
or negative. The ions in this example would be written as Na+ and Cl-..
They are bonded by ionic attraction. This type of bonding, where atoms
give away or accept electrons to form a pair of charged ions, is called
IONIC bonding.
http://chemistry.about.com/library/weekly/blatomquiz.htm
http://chemistry.about.com/library/weekly/blatomquiz.htm
Elements
Cannot be decomposed into simpler substances (by any
chemical reaction).
Are made up of only one kind of atom (i.e. atoms
having the same atomic number).
Compounds
Can be decomposed into its elements by chemical
means only.
Are made up of two or more elements
EX. H2O
Vocabulary
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Organic compounds
Acids
Carbohydrates
Lipids
Proteins
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Nucleic Acids
Monosaccaride
Polysaccharide
Glycogen
Dehydration
Synthesis
ACID: A solution that has an excess of H+ ions. It
comes from the Latin word "acidus" which means
"sharp".
BASE: A solution that has an excess of OH- ions.
Another word for base is ALKALI.
NEUTRAL: A solution which has a pH of 7. It is
neither acidic nor basic.
That pH scale we talked about is actually a measure of the number
of H+ ions in a solution. If there are a lot of H+ ions, the pH is very
low. If there are a lot of OH- ions, that means the number of H+
ions is very low, so the pH is high.
pH Scale:
Acids have pH values
under 7
Bases have pH values
over 7
What is the pH of
normal rain?
Normal rain has a pH of
about 5.6. It is slightly
acidic because naturally
present carbon dioxide
from the Earth's
atmosphere dissolves in
the rain drops to form
carbonic acid.
pH Testing: Use pH paper to test the following substances.
Predict which household products (ammonia, vinegar, lemon juice,
tap water, snapple,) would fall on the pH scale.
Procedure:
1. Pipette a 5 mL of the flavin extract from the red cabbage in
each test tube
2. Take a dropper of each sample to be tested and place it in the
test tubes ONE AT A TIME.
3. Record your color change and indicate the pH number
associated with it.
4. Take the pH paper and dip it into each sample to test.
5. Observe the color. Match it with the scale provided on the
tube.
iNOrganiC
• Substances can
contain either
carbon or
hydrogen, but NOT
TOGETHER
• Examples: H2O,
CO2, vitamins,
minerals
There are 6 elements critical in the
survival of living organisms:
1.
2.
3.
4.
5.
6.
CARBON (C)
HYDROGEN (H)
OXYGEN (O)
NITROGEN (N)
PHOSPHOROUS (P)
SULFUR (S)
These elements combine to form key organic compounds critical
to living organisms.
Organic compounds: Carbon based and contain Hydrogen at
the same time.
4 groups of organic compounds which are critical:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
What is the biological importance of organic
compounds?
Carbohydrates
• Organic compounds,Contain C, H, O arranged
in a ring. Ex: sugars and starches
• Primary source of energy
• Can be single units of C6H12O6- called
monosaccharides or chains of these units called
Polysaccharides.
• Anything ending in “ose” is a sugar
• Ex: fructose, sucrose, glucose, galacatose
• Cellulose- common starch made by plants
• Glycogen- common starch made by animals
Structural
Formula of
Glucose:
C6H12O6
CH OH
H
C
C
H
OH
H
C
C
C
H
H
OH
HO
O OH
Starch is many repeating units of monosaccharides.
Sources of Carbs
• Sugars are found in honey, fruit (both fresh and
dried) soft drinks, milk and sugar.
• Starches are found in cereals, pasta, flour, bread,
potatoes, root and pulse vegetables.
• Cellulose or Dietary Fiber is found in whole
cereals, whole meal bread, outer skins of fruit
and vegetables, brown rice and oatmeal
How do these units “get together” when there isn’t any
“space” for a bond to be formed?
Construct a glucose molecule and examine its bonds.
See if you can devise a way to connect 2
monosaccharides.
Do you have anything left over?
Dehydration Synthesis:
Loss of
water
Act of
creating
By releasing one water molecule, 2
sugars can be added together for form
a larger molecule.
Hydrolysis: The insertion of a water molecule to
split apart a molecule.
The Pros and Cons of
Lipids:
•Extremely large molecules
•Release lots of energy
when broken down
•Used for long term food
storage
•Used as an insulator
•Used to cushion vital
organs
•Waterproof covering of
fruits and leaves
•Incorporated into
structures like the cell
membrane
Structure of lipid(fats, oils, waxes)
3 fatty acids
Consist of
long chains of
carbons
1 glycerol molecule acts as a
backbone
Lipids in Cell Membrane
Saturated versus Unsaturated fats
A saturated fat is a fat or fatty
acid in which there are no double
bonds between the carbon atoms
of the fatty acid chain. Saturated
fats tend to be solid at room
temperature
•Diets high in saturated fat
correlate in some studies with an
increased incidence of
atherosclerosis and coronary heart
disease
•Saturated fat is found in dairy
products, especially cream and
cheese and in meat as well as in
many prepared foods.
Clogged Artery
Unsaturated Fats: They are called unsaturated because they
could hold more hydrogen atoms than they do.
Unsaturated Fats
• Come mainly from
plant and fish
sources such as peas,
beans, and lentils,
whole cereals, nuts,
cooking oils,
margarine, and oily
fish
• These fats are better
for you
Protein: Structure and function
•Contain C,H,O,N
•Most abundant organic compound
•Made from different assortments of amino
acids
•Below is a single amino acid
H
H
N
C
O
C
OH
H
R
R is a radical group that changes with every different
amino acid.
Function of Proteins:
•Transporters in the cell membrane
•Major component of muscle cells
•Hormones : control growth and development
•Antibodies: function in immunity
•Enzymes: Control reactions
Proteins in Cell Membrane
Sources of Proteins
• High Biological Value
Proteins come mainly from
animal foods such as
meat, fish, eggs, cheese
and milk. However some
plant foods provide this
type of protein e.g. soy
bean.
• Low Biological Value
Proteins come mainly from
plant foods such as peas,
beans and lentils (pulse
vegetables), whole cereals
and nuts. These foods also
contain fiber and are low in
fat.
Levels of Protein Structure
“Structural features of proteins are usually described at four
levels of complexity:
Primary Structure: the linear arrangEment of amino acids in a
protein and the location of covalent bonds between amino acids.
Secondary Structure: areas of folding or coiling within a
protein; helix or a sheet.
Tertiary Structure: the final three-dimensional structure of a
protein, which results from a large number of non-covalent
interactions between amino acids
A PROTEIN’S
FUNCTION IS
DETERMINED
BY ITS SHAPE!!
Nucleic Acids
• Organic compounds
• Ex: DNA, RNA
• Deoxyribose Nucleic
Acid
• Found in EVERY
living cell
• Function: Store
hereditary
information
What are
Nucleotides?
• DNA is a long chain
made up of
nucleotides
• Nucleotides consist
of:
1. Deoxyribose (a
sugar)
2. Phosphoric Acid
3. Nitrogen (organic)
Base
What are the
Nitrogen Bases?
• There are 2 types of
Nitrogen Bases:
1. Purines - Large
• Adenine (A)
• Guanine (G)
2. Pyrimidines - small
• Thymine (T) (DNA)
• Cytosine (C) (DNA)
• Uracil (U) (RNA)
Base Pairing
• In a DNA double helix, one
strand is made up of a purine
(either A or G)
• The other strand is made up
of a pyrimidine (T or C)
• When the 2 separate strands
are bonded together, A bonds
with T
• And G bonds with C
• Think: AT Garden City
• RNA is different (instead of A
bonding with T, it bonds with
U)
DNA Double Strand
• Notice that the sugar
and the phosphate are
on the outside of the
helix and the base pairs
are parallel to each
other and on the inside
of the helix
• The 2 strands are held
together by hydrogen
bonds
Enzymes: Enzymes are the organizers and orchestrators of
all chemical reactions.
Their presence determines how fast a reaction will occur and
under what conditions a reaction will occur.
Characteristics of an enzyme:
1. They are proteins which have a definite shape which
determines who they will link up with.
2. Enzymes link up with specific
molecules called substrate. (the
material acted upon by enzymes)
The substrate molecules are smaller than
the enzyme & fit into specific places on
the surface called active
sites.
Enzyme-substrate complex
Enzymes lock in to an enzyme substrate complex and “unlock”
when the reaction is over.
3. Enzymes are
affected by
temperature.
Most do not
function above
60o C.
4. Enzymes
work best under
certain pH
conditions.
5. Enzymes are needed in
very small quantities. A
single enzyme molecule
may be used over and over
because it is not used up.
6. Enzymes are specific
Saturation levels:
Lock and Key Model-Why is this a good choice of a model?
Which is the
enzyme?
Which is the active
site?
Which is the
substrate?
Enzymes
denature at high
temperatures.
Their shape
changes and they
no longer fit.
Enzymatic Reactions
CO2 + H2O
X
H2CO3
Carbon dioxide combines with water to form carbonic acid
which is then transported to the lings and disassociated to
form carbon dioxide and water which is exhaled.
The “X” represents the enzyme which controls the reaction.
Catalase reactions
The body produces H2O2 (hydrogen peroxide) which is toxic
in large amounts. The body cells have an enzyme to break it
down called catalase.
This enzyme is present in liver.
+
Liver
H2O4
This reaction produces water and oxygen.
Design an experiment to investigate how a variable
will affect the rate of reaction of the enzyme catalase.
Independent variable: Temperature, pH, Amount of enzyme,
amount of substrate.
Dependent variable: the way you measure the rate of reaction. Can
be:
1. The time it takes for the disk to rise in the beaker
2. The amount of time the disk continues to bubble.
How are you going to conduct the experiment?
Procedure: The exact steps you will take.
Includes:
1. The number of trials
2. The experimental group and the control group
3. The data table you will use
Results:
Average the data obtained over several trials
Organize it into the data table and come up with a general trend or
observation.
Note any additional comments (sources of error)
Graph your results
Analyze and Conclude
Does you data support you hypotheses? Why or why not?
What did you learn about enzyme reactions when doing this
experiment?
X
2H2O2 ----> 2H2O + O2
1. In the above reaction, what does the “X” represent?
2. In your experiment, how did you show that enzymes are
reusable?
3. What was the gas that was causing the bubbles?
4. What did you predict would happen to the reaction when
the liver was heated? Why?