Biochemistry
The Chemistry of Life
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Chemistry
• Atomic structure
– Atoms –
• smallest unit of matter
• everything is made of atoms
• atoms contain: protons, neutrons, electrons
– Elements important in life
• Make up organic molecules
– Hydrogen, carbon, nitrogen, oxygen
– CHON
http://www.eskom.co.za/nucl
ear_energy/fuel/atom.jpg
Atomic Structure
• Hydrogen (H)
• Carbon (C)
• Nitrogen (N)
• Oxygen (O)
Chemistry Video
Chemistry
http://www.ider.herts.ac.uk/sc
hool/courseware/materials/ima
ges/covalent_bonding.gif
• Chemical Bonds
– Covalent bonds share electrons
– Ionic bonds borrow electrons
– Hydrogen bonds form between
Hydrogen and O, F, or N
http://lc.brooklyn.cuny.edu/smarttutor/core3_21/images/nature/9.a.Ionicbond-nacl.gif
www.elmhurst.edu/.../images2/160hbondwater.gf
Chemistry
• pH – scale used to
measure “power of
Hydrogen”
• If a solution is
acidic (0 – 6),
neutral (7), or
basic (8 – 14)
ghs.gresham.k12.or.us/.../notes/chpt2/water.gif
Chemistry
• pH scale – measure of H+ ions in a solution
0
7
14
Strong acid
H+
Neutral
Strong base
OH-
Chemistry
• Buffers
– Maintain a stable pH, even when acids or bases
are added
– Used to maintain
homeostasis
www.chemcollective.org/buffers/buffers3.php
pH Lab
Solution
Hypothesis
pH
Actual
pH
Strong/Weak
Acid/Base/
Neutral
Water
Milk
Soda
Vinegar
Ammonia
pH Lab
Questions:
1. Which substances appeared to have a pH below
7? Which substances appeared to have a pH
above 7?
2. Which solutions were neutral?
3. Which solutions donated H+ ions?
4. What term describes the body’s balancing of
acidic and basic conditions?
5. Which part of this lab contained the dependent
variable?
Organic molecules are
macromolecules
• How are they made?
• Dehydration Synthesis
– Aka: Condensation
– to make larger by removing water
– Ex. building proteins, sugars, and fats
– Monomer + monomer = polymer + H2O
http://img.tfd.com/wn/75/120881-wet.gif
1
Small
+
1
+ small
= many
= larger
+ water
+ water
Organic Molecules
• How are they broken down?
• Hydrolysis – breaking down into smaller
pieces with water
– Ex. digestion
– Polymer + H2O = monomer + monomer
– Large
+ water = smaller + smaller
– Many
+ water = 1
+ 1
www.dkimages.com/discover/previews/742/68543.JPG
Organic Compounds or Molecules
• Must contain carbon and hydrogen (C & H)
• Four groups
– Nucleic Acids – DNA , RNA
– Carbohydrates – Sugar, starch, fiber
– Lipids – fats, oils, waxes
– Proteins – enzymes, meat, nuts
http://newtraditions.chem.wisc.edu/FPTS/fbform/1styrenf.gif
Organic Compounds
1. Nucleic Acids
• DNA (deoxyribonucleic acid)
– carries genetic or hereditary code in nucleus of
cell
– Controls protein production
in cells
• RNA (ribonucleic acid)
– Actually makes the protein at ribosomes
Organic Compounds – Nucleic Acids
1. Nucleic Acids
monomer
Nucleotide
polymer
nucleic
acid
Nucleic Acid Video
A nucleotide is a ____ of DNA?
A) Monomer
B) Polymer
Where can nucleic acids be found
in the cell?
A) In the nucleus
B) In the cytoplasm
C) In the ribosome
D) All the above
DNA Extraction
1.
2.
3.
4.
5.
6.
Chew your cheeks
Spit cheek cells and saliva into cup
Add 1 pipette full of extraction solution
Swirl cup with liquids
Pour into test tube
Gently layer one pipette of cold alcohol on top
of liquid
7. Draw up DNA with pipette
8. To keep your DNA, add 1 pipette alcohol and
DNA into plastic container, close lid
DNA Extraction 2
1.
2.
2.
3.
4.
Mash fruit in plastic bag
Add 1 pipette full of extraction solution
Mash liquids together for 1 minute
Strain with cheesecloth into test tube
Gently layer one pipette of cold alcohol on top
of liquid
5. Gather DNA with glass rod (twirl)
6. To keep your DNA, add 1 pipette alcohol and
DNA into plastic container, close lid
Organic Compounds
2. Carbohydrates
http://www.retrotuckshopsweetsdirect.co.uk/images/sugar%20free%20bears.jpg
– sugars, starches, fiber
– End in “–OSE”
• Glucose, cellulose, sucrose
– Quick energy source:
• 1 gram = 4 calories of food energy
http://whatscookingamerica.net/Cookie/CookiePhotos/PowderedSugar2.jpg
http://coppola.rsmart.com/files/u2/potato_2.gif
http://www.treehugger.com/cellulose
-jj-001.jpg
Carbohydrates
• Monomer
– Monosaccharide = glucose
mono = 1
saccharide = sugar
• Polymer
– Disaccharide = sucrose (table sugar)
di = 2 sugars
– Polysaccharide = cellulose, starch
poly = many
sugars
www.guineapigcages.com/images/BuddywithHay.jpg
Carbohydrates
• Ex. Glucose C6H12O6 - made by plants during
photosynthesis
Carbohydrates Video
Biochemistry Labs
Purpose: What macromolecules are necessary
for life processes?
Hypotheses: (within data tables)
•
Carbohydrates
•
Lipids
•
Proteins
o Enzymes
Biochemistry Lab - Carbohydrates
Carbohydrate (Sugar) Test – use Benedict’s Solution
Tests for monosaccharides
Sample
Water
Milk
Bread
Potato
Hypothesis
Initial Color
Final Color
Result (+,-)
1.
2.
3.
4.
Place each food sample in a separate test tube
Add pipette of Benedict’s solution
Immerse in hot water bath for 1 – 3 minutes
Note results:
+ = color change - = no change
Juice
Biochemistry Lab - Carbohydrates
Carbohydrate (Starch) Test – use Iodine
Tests for polysaccharides
Sample
Water
Milk
Bread
Potato
Hypothesis
Color
Result (+,-)
1. Place each food sample in a separate test tube
2. Add pipette of Iodine solution
3. Note results:
+ = blue/black
- = brown/other
Juice
Organic Polymers
3. Lipids
– Fats, oils, waxes, cholesterol
– Stored energy: 1 gram = 9 calories of food energy
– Make up cell membranes
http://upload.wikimedia.org/wikipedia/commons/thumb/4/45/NCI_b
utter.jpg/800px-NCI_butter.jpg
http://fitness102.blogspot.com/search/label/cholesterol
http://nymag.com/daily/intel/20061205donuts.jpg
Lipids - Fats
• Insoluble in water
– doesn’t mix in water
• Hydrophobic
– hydro = water phobic = fearing
• Soluble in alcohol
– will mix with alcohol
http://www.huntsman.com/advanced_materials/Images/8171/INMR.jpg
http://i153.photobucket.com/albums/s222/thepeacemaker_2007/__Hydrophobia___by_Shukaku_chan.jpg
Lipids - Fats
Monomer
G
L Fatty acid chain
Y
C Fatty acid chain
E
R
O Fatty acid chain
L
Polymer
Lipid
Lipids Video
Biochemistry Lab - Lipids
Lipids Test – use Sudan III and brown paper bag
Sample
Water
Potato chips
Gelatin
Oil
Juice
Hypothesis
Color w/
Sudan III
Paper bag
Result (+,-)
1. Place each sample in a separate test tube
2. Add several drops of Sudan III solution
3. Note results:
+ = deep dark red
- = diluted red or pink
4. Place small amount of each sample on paper bag
+ = oily spots on paper bag
- = wet spot dries up
Organic Molecules
4. Proteins
– Structural foods
– Used to build tissues
– For transport of materials
– Composed of C, H, O, N
pro.corbis.com/images/CB108198.jpg?size=572.
Proteins
• 1 gram = 4 calories of food energy
• Ex. meats, nuts, eggs
www.vegparadise.com/images/protein2.jpg
http://www.theroadhousegrill.net/assets/images/steak.jpg
..
Proteins
Monomer
• Amino acid (aa)
Polymer
• Protein
• aka = polypeptide
– 20 different aas
aa
aa
aa
Peptide Bonds –
between amino acids
aa
aa
aa
Proteins Video
Biochemistry Lab - Proteins
Protein Test – use Biuret’s Solution
Sample
Water
Milk
Gelatin
Bread
Juice
Hypothesis
Initial Color
Final Color
Result (+,-)
1. Place each food sample in a separate test tube
2. Add pipette of Biuret’s solution
3. Note results:
+ = dark purple/black color change
- = no change
Biochemistry Labs - Conclusion
1. List the various substances tested and the
organic molecules found in each one.
2. Of the substances tested, which one(s) would
have the highest calorie count? Give
evidence.
3. What was the control in each experiment?
Why?
Read a food label
1. Calculate total calories:
use total fat, total carbohydrates,
and total proteins
2. From the total carbohydrates, how
many calories come from sugars
alone?
3. How many servings are there in a
container, and what is the serving
size?
4. What other nutrients are available
from this food?
Biochemistry Labs
Liquid Lunch - YUM!
Purpose: Are there all of the necessary macromolecules in
your lunch?
Your Lunch: Pizza and soda
Hypothesis: ???
Procedure:
1. Blend a pizza and soda in a blender
2. Strain through a coffee filter
3. Test for presence of macromolecules using indicators for each
substance
Analysis:
List the organic substances found:
Note which indicator was used for each organic substance.
Organic Polymers
4. Proteins
– Enzymes – specific type of
protein
•
•
•
•
Used to speed up reactions
End in –ASE: lactase, sucrase
Work on specific substrates
Are reusable, not used up in
reaction
• Can be destroyed (denatured)
by heat, pH
Proteins - Enzymes
Act as a catalyst to
speed up reactions
by lowering
activation (starting)
energy
– Activation energy –
energy (temperature)
needed to start a
reaction, lowered by
enzymes
– Optimal energy – energy
(temperature) needed for
reaction to work best
www.columbia.edu/.../purves6/figure06-14.jpg
Proteins - Enzymes
How do enzymes work?
Induced Fit Model – enzyme changes shape to fit
Enzyme
substrate, then returns to original shape
Enzyme
Substrate
Active Site
Substrate
Complex
chsweb.lr.k12.nj.us/.../enzymesap/image136.gif
Proteins - Enzymes
Lock and Key Model – enzyme fits with substrate like a
key fits a lock, no change in enzyme shape
chsweb.lr.k12.nj.us/.../enzymesap/image136.gif
Enzyme Video
http://videos.howstuffworks.com/hsw/10320matter-and-energy-enzymes-video.htm
Biochemistry Lab - Enzymes
Hydrogen peroxide is broken down by the
enzyme peroxidase (found in potatoes)
H2O2 + peroxidase  H2O + O2 (bubbles)
Sample
Empty Dish
Cooked Potato
Raw potato –
sliced
Raw potato –
mashed
Potato in NaOH
(base)
Potato from
refrigerator
Hypothesis Reaction
(0 – 5)
(0 – 5)
Explanation
ENZYMES
•Define enzyme:
•Define catalyst:
•Define substrate:
•Enzyme names usually end in -_________.
•What is the function of the active site in an enzyme?
•Explain lock and key model of enzyme activity.
•How is the lock and key model different from the induced fit explanation?
•How does temperature affect enzyme activity?
•Why are only small amounts of enzymes needed in substrate reactions?
•What is denaturation? Why is a high fever dangerous?
•What is meant by enzyme specificity?
•List four factors that affect the rate of an enzyme-substrate reaction.
•After an enzyme-substrate reaction takes place, what happens to the structure of the enzyme?
Enzyme
Worksheet
Toothpickase Lab
Table 1: Toothpickase Activity
Time (sec.)
Number Broken Total Broken
10 sec.
20 sec. (30 sec. total)
30 sec. (60 sec. total)
60 sec. (120 sec. total)
Table 2: Rate of Toothpickase Enzyme Activity
Time
Initial (0 – 10 sec.)
60 – 120 sec.
Rate = Number / sec.
Toothpickase Lab - Analysis
1. Calculate initial rate of enzyme activity by dividing the
number of toothpicks broken by the change in time
(10 sec.). Record the initial rate (no naked numbers!).
formula: ∆Y = change in amount
∆X change in time
2. Calculate the rate of enzyme activity between 60 – 120
seconds.
3. What happens to the reaction rate as the supply of
unbroken toothpicks runs out?
4. How does the “active site” of toothpickase fit the
concept of induced fit?