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

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Atomic Structure

• Hydrogen (H)

• Carbon (C)

• Nitrogen (N)

• Oxygen (O)

Chemistry Video

Chemistry• Chemical Bonds

– Covalent bonds share electrons– Ionic bonds borrow electrons– Hydrogen bonds form between

Hydrogen and O, F, or N

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http://lc.brooklyn.cuny.edu/smarttutor/core3_21/images/nature/9.a.Ionicbond-nacl.gif

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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)

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Chemistry

• pH scale – measure of H+ ions in a solution

Strong acid Neutral Strong base

0 7 14

H+ OH-

Chemistry

• Buffers– Maintain a stable pH, even when acids or bases

are added

– Used to maintainhomeostasis

www.chemcollective.org/buffers/buffers3.php

pH LabSolution Water Milk Soda Vinegar Ammonia

HypothesispH

Actual pH

Strong/Weak

Acid/Base/Neutral

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?

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

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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

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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

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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

Organic Compounds – Nucleic Acids

1. Nucleic Acids monomer polymer

Nucleotide 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. 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

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

Organic Compounds2. Carbohydrates

– sugars, starches, fiber– End in “–OSE”

• Glucose, cellulose, sucrose

– Quick energy source: • 1 gram = 4 calories of food energy

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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

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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

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

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

Organic Polymers

3. Lipids– Fats, oils, waxes, cholesterol– Stored energy: 1 gram = 9 calories of food energy– Make up cell membranes

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http://fitness102.blogspot.com/search/label/cholesterol

Lipids - Fats• Insoluble in water

– doesn’t mix in water• Hydrophobic

– hydro = water phobic = fearing• Soluble in alcohol

– will mix with alcohol

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Lipids - Fats

Monomer

Fatty acid chain

Fatty acid chain

Fatty acid chain

Polymer

Lipid

Lipids Video

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

Organic Molecules

4. Proteins– Structural foods– Used to build tissues– For transport of materials– Composed of C, H, O, N

Proteins

• 1 gram = 4 calories of food energy• Ex. meats, nuts, eggs

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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

Proteins Video

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

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 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?

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.

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

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Proteins - EnzymesHow do enzymes work?Induced Fit Model – enzyme changes shape to fit

substrate, then returns to original shape

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Enzyme Substrate

Active Site

Enzyme Substrate Complex

Proteins - Enzymes

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Lock and Key Model – enzyme fits with substrate like a key fits a lock, no change in enzyme shape

Enzyme Video

http://videos.howstuffworks.com/hsw/10320-matter-and-energy-enzymes-video.htm

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

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 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.

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?