Century High School

Unit 3

Biochemistry

Biology

Century High School

Name ______

Hour ______

Teacher ______

Assignments – Unit 1

AssignmentDate DueScore______

It’s in the Bag______

Periodic Table Work______

Penny Lab______

Ice Cream______

pH Lab - Cabbage______

Carbohydrates______

Fats______

7. Proteins______

8. Enzymes______

TOTAL HOMEWORK SCORE______

Quizzes______

______

Unit Test______

Notes – Unit 3 –Biology

Structure of Atoms

Building blocks of all matter

Central Core =

Protons

Mass =

Charge =

Neutrons

Mass =

Charge =

Nucleus has an overall charge of ______

Electrons

Mass =

Charge =

Atom overall charge = ______

The Periodic Table

Mass Number

Atomic Number

Isotopes

Compounds and Molecules

Two or more elements combined chemically is a Molecule
Many molecules together form a Compound

The smallest particle of a compound with independent existence is:

one molecule of that compound example: H2O

Electrons and Energy Levels

Electrons spin around the nucleus in specific regions called ______

The farther out – the more energy available.

# of electrons

1st level

2nd level

3rd level

Atoms may have over 6 energy levels. In biology we rarely go past 3 in basic biochemistry. Always fill the levels from the inside (closest to the nucleus) out.

Examples:

Look at the Nobel Gasses – What is special about them????

Important Bonds

Covalent Bonds

molecules

H2O

Ionic Bonds

An atom that has gained or lost an electron is called an ______.

NaCl

HCl

Properties of Matter

Physical Properties

Chemical Properties

States of Matter

______

______

______

Physical Properties:

______

______

______

______

Chemical Properties:

______

______

______

______

Chemical Properties and Chemical Change

“When a substance undergoes a chemical change, it is changed into one or more different substances.

Properties of Chemical Change

______

______

______

______

CONSERVATION OF MASS (atoms cannot disappear or come out of nothing)

Balancing of equations (simple example)

Energy and Chemical Change

Any process of change involves the conversion of one form of energy into another

Energy an object has because of position is called ______

The energy of motion = ______

ENZYMES (to be continued after we learn a little biochem)

Activation Energy –

A chemical that speeds up a reaction is called a ______

Proteins that do this are called ______.

Substrate –

Active Site –

EXAMPLE:

Properties of Water

Polarity of the water Molecule

Hydrogen Bonding

Temperature and Stabilizing effects

Cohesion

Mixtures – Combine, but not chemically

Solutions (homogeneous mixture) – sugar water

Substance that dissolves others is called ______

Solvent Properties of water -

Substance that is dissolved ______

Examples:

Heterogeneous mixtures

Suspensions

Look cloudy – particles are larger than molecules

Examples:

Colloids

Smaller than suspension, but larger than solute

Molecules form a ______

Examples:

Acids, Bases and Buffers

Acids

Bases

Salts

Buffers

The pH scale

1 (acid)

7 (neutral

14 (base)

Organic Chemistry

Carbon Compounds in Cells

The molecules of life are called ______

Organisms consist mostly of which elements/atoms?

______

______

______

______

______

______

The Chemistry of Carbon

Carbon bonds to ______other molecules

Carbon can form ______, ______, ______

Functional Groups of Carbon

A chain of carbon and hydrogen is called a ______

Examples:

(There is ENERGY in these bonds!!!) (Do you recognize the molecules?)

Other important carbon based groups:

Hydroxyl Group

Carboxyl Group

Amino Group

Phosphate Group

Monomer

Dimer

Polymer

Macromolecules – Carbohydrates, Lipids, Proteins, Nucleic Acids

IMPORTANT CONSTRUCTION TERMS

Monomer

Dimer

Polymer

Dehydration

Hydrolysis

CARBOHYDRATES

These contain ______

Examples: ______

The monomers that make them up are called ______

They are used in living things for? ______

These monomers usually form a ring structure, especially in water.

Examples: Glucose and Fructose

Glucose:

Fructose:

They have the same number of atoms but different arrangement. They are therefore called ______.

The condensation of two monosaccharides is called ______

Example: Sucrose

The largest carbohydrates are ______

The reaction that breaks down complex molecules – reverse of condensations is called ______. (We have an enzyme to do this which is called ______.

Starch verses cellulose

Test for Carbohydrates (The BS Test)

TEST / Monosaccharide / Disaccharide / Polysaccharide
Iodine
Benedicts Solution

LIPIDS

Lipids contain ______

Examples: ______

They are used in living things for ______

Basic Structure = ______and ______

Drawing:

(Triglyceride)

GlycerolFatty Acids

Saturated Fats –

Unsaturated Fats –

All are insoluble in water – A good test? ______

Phospholipids (found in ______):

GlycerolFatty Acids (2) Phosphate (1)

Test for FATS

Test / FAT / NOT A FAT
Brown Paper
Water Solution
Lighter Fluid

Proteins

Proteins are made of ______

Examples are ______

Basic Monomers are ______

The Amino Acid

Each one contains four distinct groups:

______

______

______

______

There are ______different amino acids

Protein Structure

Through a series of ______reactions, amino acids are joined into a chain to form a ______.

This is a special bond called a ______

Two amino acids = ______

Three or more amino acids = ______

These are used by living things for ______

Three dimensional structure of Proteins (it’s all about SHAPE)

Level I

Level II

Level III

Level IV

DENATURATION:

Different types of proteins

______

______

Other molecules can be attached to proteins.

Examples: Glycoproteins and Lipoproteins

Test for Proteins? ______

Test / Protein / Not a Protein
Nitric Acid

NUCLEIC ACIDS (Just the basics – more will come in later units)

All instructions for cellular activity are in the ______

There are two kinds of nucleic acids

______

For :

Where is it found?

______

For:

Where is it found?

Both are made of complex monomers called:______.

The bond between the nucleotides is called a ______.

It is formed by ______.

Basic drawing of nucleotide

Practice with the Periodic Table

Fill in the blanks on this table using the periodic table found above and the abbreviations needed.

Number / Element / Symbol / Atomic Mass / Atomic Number / Protons / Neutrons / Electrons
1 / Carbon / C / 12.011 / 6 / 6 / 6 / 6
2 / Oxygen
3 / 7
4 / 26.98
5 / P
6 / Magnesium
7 / Mn
8 / 35.45
9 / 11
10 / 30
11 / 126.9
12 / Fe
13 / Sulfur
14 / 20
15 / 19

Diagramming Atoms

Add the correct number of protons and neutrons in the nucleus

Then put the correct number of electrons in each energy level around the nucleus.

Example: Boron (B) Atomic Number = 5, Atomic Mass = 11

Oxygen (O) / Nitrogen (N) / Carbon (C )
Calcium (Ca) / Chlorine (Cl) / Sodium (Na)

Chemical Changes

It is important that you learn to improve your power of observation in order to detect chemical changes. Chemical changes constantly go on all around you, but they often go unnoticed. The burning of gas inside an automobile engine, the cooking of food, and the life processes within your body are all complicated chemical changes that you may not notice. The burning of wood and the explosion of a firecracker are examples of chemical change that are more obvious. Chemical change occurs when one substance becomes a new substance with a totally different set of chemical and physical properties. We will consider four signs that let us know when a chemical change has occurred.

When mixing chemicals, a chemical change usually has taken place when:

1. There is a color change

2. There is a change in temperature

3. There is formation of a gas (bubbles etc.)

4. There is formation of a precipitate (a solid forms)

Materials:10 grams of calcium chloride

10 grams of sodium bicarbonate

10 ml of bromthymol blue solution

1 Ziploc bag

Observations: Describe the physical properties of each of the materials you are using today:

Material / Physical Properties
Calcium Chloride
Sodium Bicarbonate
Bromthymol Blue Solution
Plastic Bag

B. Assemble: Place all materials in a Ziploc bag, keeping all chemicals separate from each other. Force out all the air and seal the bag completely. DO NOT ALLOW THE CHEMICALS TO MIX!!!

C. Now Mix the contents: As you mix the chemicals observe closely what takes place in the bag and try to decide if a chemical change and/or physical change has occurred. Look with your eyes, feel with your hands, and listen with your ears for the signs of a chemical change. Record your observations here:

Sign of Change (1 of the 4) / How did you notice it

D. REPEAT: In a clean Ziploc bag, mix the materials again as you did before but instead of the 10 ml of bromthymol blue, use only water (10 ml).

Sign of Change (1 of the 4) / How did you notice it

E. Conclusion:

1. What makes you think you created a chemical change in the bag?

2. Did you create a chemical change the second time when you substituted water for the bromthymol blue solution?

3. When do you think we might want to add bromthymol blue to a chemical reaction? What do you think it indicates (guesses are welcome)?

Important Abbreviations (You will probably use most of these in biology)

Hydrogen (H)Magnesium (Mg)Nickel (Ni)

Helium (He)Aluminum (Al)Copper (Cu)

Lithium (Li)Silicon (Si)Zinc (Zn)

Beryllium (BePhosphorus (P)Silver (Ag)

Boron (B)Sulfur (S)Iodine (I)

Carbon ( C)Argon (Ar)Barium (Ba)

Nitrogen (N)Potassium (K)Gold (Au)

Oxygen (O)Calcium (Ca)Mercury (Hg)

Fluorine (F)Manganese (Mn)Chlorine (Cl)

Neon (Ne)Iron (Fe)

Sodium (Na)Cobalt (Co)

Penny Lab

Do three trials to see how many drops you can fit on a penny. The dropper cannot touch the penny or the water on the penny.

Trial 1______Trial 2______Trial 3______

Draw what your penny looks like with the water on it.

1 drop15 dropsfull

Why does the water bubble on the penny?

Now dry off the penny and rub a drop of detergent onto the penny. Do you think it will hold more drops of less drops?

Trial 1______Trial 2______

What do you think the soap did to the hydrogen bonds on the penny?

Oil and grease is hydrophobic. What does hydro mean? What does phobia mean?

What charges do you think are around a grease molecule?

Soap is amphipathic. Hypothesize what you think soap does to hydrophobic molecules and water.

What would happen to a water strider if you added soap to the water it was walking on? If you added oil?

Bottom of Form

A Study of the Freezing Point of Water

Materials:1 cup milk (whole milk, low fat or skim)

1 tablespoon of sugar

Flavors as needed

Large Ziploc freezer bag

Small Ziploc freezer bag

Salt

Mittens

Cups and spoons for eating

Procedure:

Pour 1 cup of milk into a small Ziploc bag. Add 1 tablespoon of sugar and then seal the bag tightly. Put about 2 inches of ice into a large Ziploc bag. Add about 1/3 cup of salt to the large bag with the ice. Insert the small Ziploc bag into the large bag and then seal the large bag tightly. Now put on your mittens and gently shake the bag and roll it in your hands. Share this duty with your partner so that you don’t get too tired or too cold. When the ice cream thickens to your liking, insert your thermometer into the large bag and measure the temperature of the ice in the bag. Now insert the temperature into the ice bucket without salt and record its temperature. Remove your ice-cream and enjoy.

Temperature of pure ice = ______

Temperature of ice with salt = ______

Analysis

What is the freezing point of water?

Why do you think that the ice lowered the freezing point? (How do you know that it lowered the freezing point of the water?

Draw the crystal structure of pure ice.

Draw the crystal structure of ice with salt in it.

Do you think it is easier for a crystal to form in pure solution or with salt? Why?

When a scuba diver goes ice-diving in Minnesota, the water is always the same temperature regardless of the temperature outside. How do we know that?

When the Titanic sunk it was in the salty North Atlantic. Was the water at 0 degrees centigrade (32 degrees F)? Why do you think that?

What other uses can you think of (other than making ice-cream) for this property of salt water?

Cabbage Rainbows

Introduction: The pH of a solution helps to identify the level of acidity or alkalinity. The pH is a number related to the concentration of hydrogen ions in solution.

Some common foods, such as red cabbage and radishes, contain colored pigments that change color depending on what pH the substance is at. Red cabbage juice turns red in acids and blue in bases.

Purpose: In this activity you will check the pH of come common household products. You will first check the product using the red cabbage and then you will check using pH paper.

Materials: 50 ml red cabbage juice, eye droppers, commercial pH paper strips,, various household solutions to be tested, colored pencils, microtiter plates, white paper.

Procedure:

Place 5 drops of red cabbage juice in each of 10 wells for the microtiter plate. Place one drop of the 10 unknown substances into each well of the plate.
Set up a second microtiter plate with the unknown substances only and check the pH of these with the pH paper.
Record both the pH and the cabbage color of your unknown substance.

______

Conclusions

What color is the red cabbage juice alone?

Which household products were acidic?

Which household products were basic?

Was the cabbage juice equally effective in finding the pH as compared to the paper.

Can you think of any other foods that may act as acid/base indicators?

Do we use these indicators in harvesting food?

Make an approximation chart of the color of cabbage associated with each pH

pH CHART - CABBAGE

2 3 4 5 6 7

8 9 10 11 12 13 14

The pH Scale Applied to Biology

pH 14Lye and Bleach

pH 13

pH 12

Increasingly

basicpH 11

pH 10Desert Pool

pH 9

______

pH 8Sea Water

Human BloodLife

NeutralpH 7Saliva / Soil / Waterexists

Milk In this

pH 6Rain WaterRange

pH 5

pH 4Acid Water / Peat Bogs

IncreasinglyOrange Juice______

acidpH 3Cola Drinks

pH 2Stomach Contents

pH 1Hydrochloric Acid

Carbohydrates: Chemistry and Identification

Today, scientists use a combination of biology and chemistry for their understanding of life and life processes. Thus, an understanding of some chemistry of living things is necessary. Carbohydrates make up a large group of chemical compounds found in cells. Carbohydrates are an energy source or are used I making cell structures.

Procedure:

Examine the chemical formula for water, H2O.

What elements make up water?

How many molecules of water are represented by the formula H2O?

What do the lines between O and H in the structural formula of water represent?

Carbohydrate Models

There are three different groups of carbohydrates. They are called monosaccharides, disaccharides and polysaccharides. “Saccharide” means sugar.

GLUCOSE

A single molecule sugar is called a monosachcharide. The prefix “mono-“means one. However, the one molecule can have different shapes due to a different arrangement of atoms. Three monosaccharides are glucose, fructose, and galactose.

Examine the structural formulas of glucose, fructose and galactose.

What three chemical elements are present in the three monosaccharides shown? (NOTE: The letter “C” stands for carbon, “H’ stands for hydrogen and “O” stands for oxygen.)

How many atoms of carbon are present in a molecule of

Glucose? ______
Fructose? ______

Add subscripts to the following to indicate the proper simple formula. Fill in the blanks by counting the tota. Number of carbon, hydrogen, and oxygen atoms in each molecule.

Glucose C ____ H ____ O ____

FructoseC ____ H ____ O ____

Compare the structural formula of glucose to the structural formula of fructose.

a. Are they exactly the same in shape?

Are they both monosaccharides?

Group 2 Disaccharides (double molecule sugars)

Two monosaccharide sugar molecules can join chemically to form a larger carbohydrate molecule called a double sugar, or disaccharide. The prefix “di-“ means two. By chemically joining a glucose molecule with a fructose molecule, a double sugar called sucrose is produced.

In order to join the two molecules, an OH from one molecule and an H from another must be removed.

8.The H and OH ends that were removed can also fit together with each other to form a molecule. This new molecule has a simple formula of ______and is called ______.

Different disaccharide molecules can be made by joining other monosaccharides in different combinations. By chemically joining a glucose molecule with another glucose molecule, a double sugar called maltose is formed.

How many monosaccharide molecules are needed to form one sucrose molecule? ______

How many monosaccharide molecules are needed to form one maltose molecule? ______.

Group 3. Polysaccharides (many molecule sugars)

Just as double sugars were formed from two single sugar molecules, polysaccharides are formed when many single sugars are joined chemically. The prefix “poly-“ means many. Starch, glycogen, and cellulose are the three most common polysaccharides in biology. They consist of long chains of glucose molecules joined.

What must be removed from the glucose molecules in order to have them easily fit together? ______

The simple formula for a polysaccharide is written as (C6H10O5)n. The n equals the number of times the C6H10O5 group is repeated.

Identification of Carbohydrates

Benedicts Test

Fill a 500 ml beaker half full of water. Bring the water to a boil on a hot plate. The boiling water is called a hot water bath.
Number three clean test tubes one to three.

Tube 1 – 30 drops of monosaccharide solution
Tube 2 – 30 drops of disaccharide solution
Tube 3 – 30 drops of polysaccharide solution

Add 30 drops of Benedict’s solution (BS) to each tube.
Place the test tubes into the hot water bath for five minutes.
Use a test tube holder to remove the tubes from the hot water bath.
Observe any color changes in the solutions. NOTE: A color change may or may not occur when BS is added to a carbohydrate and then heated. A change from blue to green, yellow, orange, or red occurs if a monosaccharide is present. The original blue color will remain after heating if a disaccharide or polysaccharide is present.
Record in Table 1 the color of the solutions in the tubes in the column marked “Benedict’s Color After Heating.”

TABLE 1: Results of Tests With Known Carbohydrates

Tube Number / Carbohydrate Type / Change in Color After Heating with Benedict’s / Change in Color After Adding Iodine
1 / Monosaccharide
2 / Disaccharide
3 / Polysaccharide

Iodine Test

Number three clean test tubes one to three.

Tube 1 – 30 drops of monosaccharide solution
Tube 2 – 30 drops of disaccharide solution
Tube 3 – 30 drops of polysaccharide solution

Add 4 drops of iodine solution to each tube.
Mix the contents of each tube by gently swirling.
Record in Table 1 the color of the solutions in the three tubes in the column marked “Iodine Color”. NOTE: A color change may or may not occur when iodine solution is added to a carbohydrate. A change from its original rust color to deep blue-black occurs if a polysaccharide is present. The original color of the carbohydrate remains if a disaccharide or monosaccharide sugar is present.

Chemical Tests on Unknown Carbohydrates