biochemistry the chemistry of life
TRANSCRIPT
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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/nuclear_energy/fuel/atom.jpg
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Atomic Structure
• Hydrogen (H)
• Carbon (C)
• Nitrogen (N)
• Oxygen (O)
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Chemistry Video
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Chemistry• Chemical Bonds
– Covalent bonds share electrons– Ionic bonds borrow electrons– Hydrogen bonds form between
Hydrogen and O, F, or N
http://www.ider.herts.ac.uk/school/courseware/materials/images/covalent_bonding.gif
http://lc.brooklyn.cuny.edu/smarttutor/core3_21/images/nature/9.a.Ionicbond-nacl.gif
www.elmhurst.edu/.../images2/160hbondwater.gf
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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
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Chemistry
• pH scale – measure of H+ ions in a solution
Strong acid Neutral Strong base
0 7 14
H+ OH-
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Chemistry
• Buffers– Maintain a stable pH, even when acids or bases
are added
– Used to maintainhomeostasis
www.chemcollective.org/buffers/buffers3.php
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pH LabSolution Water Milk Soda Vinegar Ammonia
HypothesispH
Actual pH
Strong/Weak
Acid/Base/Neutral
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pH LabQuestions: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?
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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
1 + 1 = many + waterSmall + small = larger + water
http://img.tfd.com/wn/75/120881-wet.gif
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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
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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
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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
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Organic Compounds – Nucleic Acids
1. Nucleic Acids monomer polymer
Nucleotide nucleic acid
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Nucleic Acid Video
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A nucleotide is a ____ of DNA?
A) Monomer
B) Polymer
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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
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DNA Extraction
1. Chew your cheeks2. Spit cheek cells and saliva into cup3. Add 1 pipette full of extraction solution4. Swirl cup with liquids5. Pour into test tube6. Gently layer one pipette of cold alcohol on top of
liquid7. Draw up DNA with pipette8. To keep your DNA, add 1 pipette alcohol and
DNA into plastic container, close lid
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DNA Extraction 2
1. Mash fruit in plastic bag2. Add 1 pipette full of extraction solution2. Mash liquids together for 1 minute3. Strain with cheesecloth into test tube4. Gently layer one pipette of cold alcohol on top
of liquid5. Gather DNA with glass rod (twirl)6. To keep your DNA, add 1 pipette alcohol and
DNA into plastic container, close lid
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Organic Compounds2. Carbohydrates
– sugars, starches, fiber– End in “–OSE”
• Glucose, cellulose, sucrose
– Quick energy source: • 1 gram = 4 calories of food energy
http://www.retrotuckshopsweetsdirect.co.uk/images/sugar%20free%20bears.jpg
http://whatscookingamerica.net/Cookie/CookiePhotos/PowderedSugar2.jpg
http://www.treehugger.com/cellulose-jj-001.jpg
http://coppola.rsmart.com/files/u2/potato_2.gif
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Carbohydrates
• Monomer– Monosaccharide = glucose
mono = 1 saccharide = sugar
• Polymer– Disaccharide = sucrose (table sugar)
di = 2 sugars
– Polysaccharide = cellulose, starchpoly = many sugars
www.guineapigcages.com/images/BuddywithHay.jpg
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Carbohydrates
• Ex. Glucose C6H12O6 - made by plants during photosynthesis
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Carbohydrates Video
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Biochemistry Labs
Purpose: What macromolecules are necessary for life processes?
Hypotheses: (within data tables)• Carbohydrates• Lipids• Proteins
o Enzymes
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Biochemistry Lab - Carbohydrates
Sample Water Milk Bread Potato Juice
Hypothesis
Initial Color
Final Color
Result (+,-)
1. Place each food sample in a separate test tube2. Add pipette of Benedict’s solution3. Immerse in hot water bath for 1 – 3 minutes4. Note results:
+ = color change - = no change
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Biochemistry Lab - Carbohydrates
Sample Water Milk Bread Potato Juice
Hypothesis
Color
Result (+,-)
1. Place each food sample in a separate test tube2. Add pipette of Iodine solution3. Note results:
+ = blue/black - = brown/other
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Organic Polymers
3. Lipids– Fats, oils, waxes, cholesterol– Stored energy: 1 gram = 9 calories of food energy– Make up cell membranes
http://nymag.com/daily/intel/20061205donuts.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/4/45/NCI_butter.jpg/800px-NCI_butter.jpg
http://fitness102.blogspot.com/search/label/cholesterol
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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
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Lipids - Fats
Monomer
Fatty acid chain
Fatty acid chain
Fatty acid chain
Polymer
Lipid
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Lipids Video
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Biochemistry Lab - Lipids
Sample Water Potato chips Gelatin Oil Juice
Hypothesis
Color w/ Sudan III
Paper bag
Result (+,-)
Lipids Test – use Sudan III and brown paper bag
1. Place each sample in a separate test tube2. Add several drops of Sudan III solution3. 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
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Organic Molecules
4. Proteins– Structural foods– Used to build tissues– For transport of materials– Composed of C, H, O, N
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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
pro.corbis.com/images/CB108198.jpg?size=572...
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Proteins
Monomer• Amino acid (aa)
– 20 different aas
Polymer• Protein• aka = polypeptide
aa aaaa
aa aa aa
Peptide Bonds – between amino acids
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Proteins Video
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Biochemistry Lab - Proteins
Sample Water Milk Gelatin Bread Juice
Hypothesis
Initial Color
Final Color
Result (+,-)
Protein Test – use Biuret’s Solution
1. Place each food sample in a separate test tube2. Add pipette of Biuret’s solution3. Note results:
+ = dark purple/black color change - = no change
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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?
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Read a food label1. 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?
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Biochemistry Labs Liquid Lunch - YUM!
Purpose: Are there all of the necessary macromolecules in your lunch?
Your Lunch: Pizza and sodaHypothesis: ???Procedure:
1. Blend a pizza and soda in a blender2. Strain through a coffee filter3. Test for presence of macromolecules using indicators for each
substanceAnalysis:
List the organic substances found: Note which indicator was used for each organic substance.
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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
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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
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Proteins - EnzymesHow do enzymes work?Induced Fit Model – enzyme changes shape to fit
substrate, then returns to original shape
chsweb.lr.k12.nj.us/.../enzymesap/image136.gif
Enzyme Substrate
Active Site
Enzyme Substrate Complex
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Proteins - Enzymes
chsweb.lr.k12.nj.us/.../enzymesap/image136.gif
Lock and Key Model – enzyme fits with substrate like a key fits a lock, no change in enzyme shape
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Enzyme Video
http://videos.howstuffworks.com/hsw/10320-matter-and-energy-enzymes-video.htm
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Biochemistry Lab - EnzymesHydrogen peroxide is broken down by the
enzyme peroxidase (found in potatoes)H2O2 + peroxidase H2O + O2 (bubbles)
Sample Hypothesis(0 – 5)
Reaction (0 – 5)
Explanation
Empty Dish
Cooked Potato
Raw potato – sliced
Raw potato – mashed
Potato in NaOH (base)
Potato from refrigerator
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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?
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Enzyme Worksheet
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Toothpickase LabTime (sec.) Number Broken Total Broken
10 sec.
20 sec. (30 sec. total)
30 sec. (60 sec. total)
60 sec. (120 sec. total)
Table 1: Toothpickase Activity
Table 2: Rate of Toothpickase Enzyme Activity
Time Rate = Number / sec.
Initial (0 – 10 sec.)
60 – 120 sec.
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Toothpickase Lab - Analysis1. 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?