Biology 12

…IS LIFE

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MOUNT BAKER SECONDARY SCHOOL

TEACHER: Mr. G. Duchscherer Room 201 MATERIALS REQUIRED: An ORGANIZED Three-ring binder with a constant supply of loose leaf paper, ruler, pencil, a good eraser and a curious nature. GENERAL RESPONSIBILITIES: Show up on time at the start of class and after break Be prepared and be ‘with it”. (do readings, bringing a pencil, etc.) Respect the needs and learning rights of others Check your assignments and labs as you go to clear up problems right away. ATTENDANCE : Attendance is critical for your success in this course. When you are late or absent, class still goes on―it is up to you to keep up with the course material. Instruction begins at the bell so it is imperative that you are ready to start at this time. ASSIGNMENTS, LABS AND EXAMS: All labs and assignments must be completed on time as the information will be carried forward for next period’s concepts. Answers can be checked at the front desk in front of the teacher. This gives me a chance to address any difficulties you might encounter as you learn the material. You are always allowed to “check” an answer once you have demonstrated a sufficient attempt at answering it. Students are not allowed to “get” answers from the front desk without at least trying to figure it out. Personal holidays taken during instructional time will be the sole responsibility of the student to catch up independently on the information missed.

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ASSESSMENT AND GRADING: Course mark breakdown: Students are ready to write the unit exams once all labs and assignments are complete. 5 Unit Exams each worth 20% of the course mark totaling 100% The above gets reduced to a mark out of 75% and the In-Class Final Exam is worth the remaining 25% of the school mark. I have read and understood this outline Student Signature ___________________________________

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BIOLOGY 12

ORDER OF TOPICS AND TESTS

1. Experimental Design (1, 10-14)

2. Biochemistry (2, 19-30)

3. Cellular Compounds (2, 31-44)

4. Enzymes (6, 101-114)

5. Cytology • cell parts (3, 45-66) • movement of materials (4, 67-80)

TEST 1

6. Nucleic Acids (25, 501-511) • replication • transcription • translation • mutations (24, 490-495, 516)

7. Cancer (25, 518-522)

8. Human Organization • tissues (11, 193-201) • feedback loops (11, 206-208)

9. The Digestive System (12, 213-238)

TEST 2

10. The Fetal Pig • anatomy dissection guide

TEST 3

11. The Nervous System (17, 317-342) 12. The Endocrine System (20, 391-411) 13. The Circulatory System (13, 239-260) 14. Blood (13, 249-253) (14, 276)

TEST 4

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15. The Respiratory System (15, 281-300) 16. The Excretory System (16, 301-315) 17. The Reproductive System (21, 413-428)

TEST 5

FINAL EXAM PART A (covers units 4 and 5) FINAL EXAM PART B (covers units 1 and 2)

*** Your readings are crucial to your success in this course. Other readings from various sources will be provided that must be read so you can obtain a more complete

understanding of the biology concepts. ***

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Handing in Labs, and Group Assignments in Biology 12

1. Every student is required to make their own individual copy of the lab or group assignment. Your name goes on the top right hand corner along with your block.

2. You may discuss answers, questions, and conclusions with your lab partners. This is why you have a lab group. Your group must come to consensus on all answers, or conclusions for your lab/assignment.

3. On the due date for your lab/assignment, you will be given time to look over

each other’s work before I collect all of your labs/assignments. If your own copy is not included, you will not receive a mark.

4. You are allowed to select one lab/assignment that goes on top of the rest of the

labs/assignments. As long as all the other labs/assignments beneath this one are complete, I will base your group’s mark on the top lab/assignment. If a lab/assignment attached below is not complete, that person will get a separate mark from the rest of the group.

5. If you want to hand in your own work, You must work on all questions and

conclusions by yourself, and you cannot have the benefit of asking your lab partners for answers. Although you performed the lab procedures with other people, you will do all the questions and conclusions by yourself in a different location. Do not share/discuss or get answers from the lab group that you performed the lab with.

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OBJECTIVE SHEET SCIENTIFIC METHOD 1. Discriminate between a hypothesis and a theory in science. 2. Write a formal hypothesis. Include dependent and independent variables. 3. Explain the role of control in an experiment. 4. Identify pseudo-scientific claims. OBJECTIVE SHEET BIO CHEMISTRY 1. Describe the structure of a carbon atom. 2. Define the following terms: compound, isotope, ion, ionic bond, covalent bond, oxidation, reduction, octet rule, polar molecule, dissociation, hydrogen bond, acid, base, pH scale, buffer, structural formula, inorganic compound. 3. Explain how atoms react with one another to form ionic and covalent compounds. 4. Describe how the polarity of water molecules results in hydrogen bonding. 5. Describe the role of water as a solvent, and temperature regulator. 6. Indicate the importance of pH to biological systems.

The Three Isotopes of Carbon

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Inductive and Deductive Reasoning Both forms of reasoning are important in contributing to the scientific process. Deduction takes established Theories and allows scientists to make predictions about new situations. A scientist could also re-word a hypothesis and then make specific tests about new data. Induction is also called generalizing. It is the opposite of deduction. Induction allows scientists to take specific observations and develop an explanation of the observations called a theory.

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The Nature of Science and the Scientific Method Although scientists and their particular science may differ in their focuses, scientists- biologists, chemists, physicists, geologists, and so forth, study the natural world and share scientific methods that usually include all of the following key features: observation, hypothesis, and testing a hypothesis using a controlled experiment. A hypothesis is a testable statement or tentative explanation for an observation made by a scientist. They test their hypotheses in a variety of ways, producing results that are open to verification by other experts. If other scientists repeatedly verify the results over a long period of time, a theory may be developed. Any experiment performed that tests a proper hypothesis has to have several characteristics that confirm the validity of the methods used to verify the results. Experiments must test only one variable to a set of controlled conditions. A theory comes from a well-supported and well-tested hypothesis. Unfortunately, many people misuse the meaning of the word theory. To the average Canadian, the word theory just means “I have an idea”, when in science, a theory is developed only after extensive testing confirms an idea (for now) over many years. Because a hallmark of science is the testable hypothesis, science does not try to explain philosophical, religious, or teleological questions such as “What is the meaning of life?” or “Does life exist after death?” within the framework of the scientific inquiry. This is not to say that these questions are not important; it is to say that they cannot be tested using scientific methods. Mistakes occur in science all the time. History is full of old theories that have been proven wrong or erroneous in many ways. This suggests that scientific theories are “falsifiable.” Within this ability to prove methods and theories as false lies sciences’ greatest strength – self-correction. If a mistake is made honestly or dishonestly, in time it will be “flushed out” of the system by the lack of verification by other experts. Science as a way of knowing allows us to avoid dogmatism, which is when a person bases a conclusion on authority rather than logic and evidence. Scientific progress is the cumulative growth of a system of knowledge over time, in which useful features are retained and non-useful features are abandoned, based on the rejection or confirmation of testable knowledge. Technology Allows us to apply the knowledge of science to everyday life so that we may be more productive.

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Experimental Design: The Formal Hypothesis A hypothesis is a tentative, testable statement that proposes a possible explanation to some natural phenomena or event. It often contains a prediction as to the outcome. Parts of a Hypothesis The test of the hypothesis is the experiment. It is a test of how two variables might be related. The first is the dependent variable and it is the one that the experimenter observes and/or measures from the results that occur. The second variable is called the independent variable. This is the one that the experimenter controls. Formalized hypotheses are always written showing a relationship between these two kinds of variables using an “if-then” statement. Scientists devise a controlled experiment to test a given hypothesis. Formal hypotheses are always written in this fashion:

*If (dependent variable) is related to (independent variable), then (prediction)* Use the statements below to re-write the dependent and independent variable.

1. Candy causes tooth decay. 2. Cholesterol causes heart disease. 3. Ultraviolet light may cause skin cancer. 4. Cell phones cause brain tumors. 5. Temperature may cause leaves to change colour.

Dependent variables Independent variables

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Re-write each of the previous 5 statements as a formal hypothesis.

1. _________________________________________________________ ___________________________________________________________ 2. _________________________________________________________ ___________________________________________________________ 3. _________________________________________________________ ___________________________________________________________ 4. _________________________________________________________ ___________________________________________________________ 5. _________________________________________________________ ___________________________________________________________

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Using the Scientific Method In order to observe factors that affect the rate of cellular respiration, the following experiment was performed: Procedure 1. Equal amounts of muscle tissue was placed into five numbered test tubes and

heated to 37 Celsius.

2. Oxygen, ADP, and glucose were added to each test tube. The amount of CO2 generated each second was recorded.

3. The results for test tube 1 are shown in the graph below. 4. The following steps were done 1400 sec. after the start of the experiment.

Test tube 2 Glucose is removed from the test tube

Test tube 3 Oxygen is removed from the test tube

Test tube 4 The temperature was raised to 60C and oxygen was removed

Test tube 5 A hormone called thyroxin was added to the test tube

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Questions 1. What are the constant factors in all of the test tubes? ___________________________________________________________ 2. List the independent variables. ___________________________________________________________ 3. Which test tube is the control? Give a reason for your choice. Why is the control

necessary? ___________________________________________________________ ___________________________________________________________ ___________________________________________________________ 4. Which test tube is prepared incorrectly if it is to be part of a controlled experiment.

Give a reason for your choice. ___________________________________________________________ ___________________________________________________________ 5. What product would be produced in the test tube 3? Name the process. (hint: it

hurts your muscles) ___________________________________________________________ 6. Write a formal hypothesis for any one of the properly prepared test tubes. Include

the dependent and independent variable. ___________________________________________________________ ___________________________________________________________

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Elements and Atoms text reference 20-25 Which six elements are most commonly associated with life? Provide their symbol. Notice the isotope symbol for a carbon atom on page 21. Write isotope symbols and draw Bohr diagrams for the other two carbon isotopes. Ionic and Covalent Bonds Both types of bonding occur in atoms so that they can “fill the octet rule”. Atoms will share or transfer electrons to fill their valence energy level. This creates a more stable electron configuration in the atom. In ionic bonds, the atom that loses an electron gets “oxidized” while the atom that receives the electron is said to be “reduced”. An easy way to remember redox reactions is by using the saying:

LEO the lion says GER

LEO – loss of electrons is oxidation GER – gaining electrons is reduction Metals on the periodic table tend to become oxidized while Nonmetals tend to become reduced in ionic bonds.

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Water is a polar molecule with partial charges on the hydrogens and the oxygen. A polar molecule is neutral overall but has regions of charge. Because water is polar, it causes hydrogen bonding to occur with other water molecules. A hydrogen bond occurs when a slightly positive H+ atom from one molecule of water is attracted to a slightly negative O- atom from a different molecule. This attraction does not destroy molecules of water but rather gives water its properties as a substance. In your notebook, write down 5 properties of water due to hydrogen bonding.

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Dissociation of Water A B C Beaker A Water has a neutral pH. It has a pH of 7. Water will naturally dissociate into equal numbers of H+ and OH- and then reform back into water molecules repeatedly. By definition, a neutral pH is defined as any substance with equal numbers of H+ and OH- Beaker B Adding some hydrochloric acid to the neutral water changes the ratio of H+ and OH- in this beaker. Water will split the HCl into H+ and Cl-. This causes a greater number of H+ than OH- in the beaker. By definition, an acid can be defined as any substance with a greater amount of H+ than OH-. Beaker C Adding some sodium hydroxide to the neutral water changes the ratio of H+ and OH- in this beaker. Water will split the NaOH into Na+ and OH-. This causes a greater number of OH- than H+ in the beaker. By definition, a base can be defined as any substance with a greater amount of OH- than H .

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OBJECTIVE SHEET ORGANIC MOLECULES

1. Recognize the structure of an amino acid, carbohydrate, a saturated and unsaturated fatty acid, glycerol, nucleotides, ADP and ATP.

2. Use dehydration (condensation) synthesis to monomers to form polymers, and use hydrolysis to split them back into monomers.

3. Distinguish among carbohydrates, lipids, proteins, and nucleic acids with

respect to chemical structure.

4. Differentiate among monosaccharides disaccharides and polysaccharides.

5. Compare and contrast saturated and unsaturated fats in terms of their molecular structure.

6. Describe the location and explain the importance of the following in the human

body: neutral fats, steroids, phospholipids.

7. Draw a generalized amino-acid and identify the amine, the acid (carboxyl group) and the R-groups.

8. Differentiate among the primary, secondary, tertiary, and quaternary structure

of proteins.

9. List the main functions of carbohydrates, lipids, and proteins.

10. Relate the structure of the ATP molecule to its role as the “energy currency” of the cell.

11. Define the following terms: macromolecule, denaturation, hydrophobic,

hydrophilic, HDL, LDL.

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CHEMICAL COMPOUNDS OF LIFE Organic compounds contain carbon. Carbon has the ability to form covalent bonds with other kinds of atoms or with carbon atoms. As a result, carbon atoms may be bonded into longer chains, or rings. Four different kinds of organic molecules are found in large quantities in organisms.

Proteins Proteins are made of amino acids, from fifty to as many as a hundred thousand. Proteins contain the elements C, H, O, N and sometimes S. They are the most abundant substance of life, making up about 50% of the dry weight of living things (except plants). Their energy yield is 3.1 calories per gram. Below is a list of some types of proteins.

Structural proteins -collagen, silk, virus coats, microtubules Regulatory proteins -hormones, (insulin, glucagon) Contractile proteins -actin, myosin (found in muscle cells) Transport proteins -hemoglobin, myoglobin Storage proteins -egg white (albumin) Protective proteins -antibodies Membrane proteins -antigens, membrane-transport protein Enzymes -sucrase, pepsin

Amino Acids Amino acids are the building blocks of protein. There are 20 different kinds, each with the same “backbone” but with a different side chain. They join through a process called dehydration synthesis producing peptide bonds between the amino acids and forming polypeptide chains. (see diagram)

The Levels of Protein Structure ASSIGNMENT Make a short note in your binder on the types of protein structure. (pgs. 37-39) What type of bonds are responsible for each type of structure? Define denaturation, what effect does this have on the function of a protein?

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Carbohydrates These are the sugars (hydrates of carbon). They contain the atoms C, H, and O with a 2:1 ratio of H to O. They are characterized by the functional group “OH” the hydroxyl group that makes them highly soluble in water. They provide short-term energy storage in molecules of the body. Carbohydrates yield 3.8 calories per gram. They also form a variety of structural components in cells. There are three main kinds of carbohydrates:

monosaccharides - the simple sugars, containing 3 to 7 carbons

disaccharides -double sugars formed when two monosaccharides join by a process called dehydration synthesis.

-disaccharides break apart by hydrolysis to make monsaccharides.

polysaccharides –means “many sugars” formed through dehydration synthesis. These are polymers of simple sugars.

READING ASSIGNMENT Read pages 32 to 33. In your notebook under the title “Carbohydrates”, define isomer and polymer. List the components of maltose, sucrose, lactose, cellulose, glycogen, and amylose (starch). List three types of polysaccharides and explain the difference between each type. State the function of each type of polysaccharide.

Lipids These are made up of the neutral fats, phospholipids, steroids, waxes and oils. Lipids are composed of C, H, and O, while in addition, the phospholipids contain a phosphate.

Lipids are made up of fatty acids, which are hydrocarbon chains, and an alcohol. Neutral fats and oils have the 3-carbon alcohol called glycerol. Lipids are insoluble in water. They are components of cell membranes, they function as long-term energy storage molecules and they yield 9.3 calories per gram. Lipids also form chemical messengers (the sex hormones), act as insulation and padding, and forms protective coatings on leaves, fruits, and exoskeletons of insects. Phospholipids have a double polar head which is hydrophilic (water loving) and non-polar tails which are hydrophobic (water hating). This forms the structure of the cell membrane of all living organisms.

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Fatty Acids These can be saturated which means that there are only single bonds between the carbon atoms. Unsaturated means that the carbon atoms have at least one double bond between the carbon atoms. If many double bonds are present, they are said to be polyunsaturated. Unsaturated fats tend to be oily liquids and are more common in plants. Examples include olive, peanut and corn oils. Animal fats such as butter and lard contain saturated fatty acids and are usually solid at room temperature. Saturated fats have been linked with heart disease since they play a role in the build up of deposits that harden and narrow arteries. Cholesterol is an example of a saturated fat. READING ASSIGNMENT Read pages 34 and 35. Under the heading “Soaps are Emulsifiers”, explain the action of bile and soaps. Nucleic Acids (DNA and RNA) DNA is the hereditary molecule. RNA, working together with DNA directs and controls the activities of the cell. Nucleic acids are made of nucleotides which consist of three subunits: a 5 carbon sugar (ribose or deoxyribose), a phosphate group, and one of four nitrogenous bases. The four bases are categorized into two different types of bases Purines and Pyrimidines. We will study these molecules in more detail later in the course. ASSIGNMENT Read pages 40-41. Look closely at the diagrams.

**ALWAYS READ THE CHAPTER SUMMARIES**

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Aspartame: A Popular Synthetic Sweetener (for interest only) North Americans have developed quite a sweet tooth! Our annual per capita consumption of sugar has increased from less than 2 kg per person in 1860 to more than 70 kg per person in 2012. Today, in addition to the sugar we choose to use on our breakfast cereal, in our coffee, and in other ways, we are exposed to large amounts of sugar which have been added to the processed foods we eat and over which we have no control. For a number of years, many Canadians have been trying to decrease their consumption of sugar. For some, this has not been simply a matter of choice. Many

people have health conditions diabetes is probably the most common which prevents them from using sugar. But for many others, concerns about the dangerous health problems associated with excessive sugar consumption have prompted a desire for good tasting, but safer sugar substitutes. Until quite recently, only two compounds have been licensed for use as sugar substitutes, saccharin and cyclamates. Questions about the long-term health effects of both have been raised, and the latter was banned by the Canadian Food and Drug Administration in 1976. Saccharin is still permitted for human consumption, but now carries warnings that it “may be harmful to your health.” The search for a safe, good-tasting sugar substitute has, therefore been an intensive one for many years. One stage of the search came to an end in 1983 when the compound called aspartame was licensed for use as a sugar substitute. Aspartame consists of two amino acids. L-aspartic acid and L-phenylalanine, and is about 180 times as sweet as sucrose. Aspartame has completely revolutionized the soft-drink market. Colas that contain a sweet, safe, non-sugar product has attracted many consumers of soft drinks but also has appeal to millions who previously did not consume soft drinks. Aspartame is one of the most tested substances of all time. Still, all the problems of synthetic sweeteners have not been solved. For example, aspartame is very expensive to manufacture, about 20 times as much as saccharin- (another banned substitute). Finally there have been erroneous fear-mongering websites linking aspartame to brain damage in experimental rats and various health concerns with people. Clearly, the search for the “ideal” sweetener is far from over.

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BioChem Practice Quiz Matching: a. amino acid (or more than one) d. glycerol b. glucose (or more than one) e. fatty acid c. nucleotide (or more than one) f. both glycerol and fatty acid

1. _____ 2. _____

3. _____

4. _____ 5. _____

6. polysaccharide _____, quick energy _____, ribose_____, enzyme _____,

long-term energy storage _____, unsaturated _____, hydrocarbon _____, 7. When HCl, a strong acid, is added to water, the pH a) goes up b) stays the same c) goes down d) unknown

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8. When two non-metal oxygen atoms react with each other, they a) each give up 2 e- b) each take 2 e- c) each need 6 e- d) share 9. In this reaction, 2K + Cl2 --> 2KCl, chlorine has been reduced. a) true b) false 10. Circle the peptide bond 12. Which molecule below would be used repeatedly to form a nucleic acid?

a) b) c) d)

13. Which pair below is mismatched? a) amino acid……………protein b) glycerol………………..glycogen c) glucose………………...starch d) phosphoric acid…….nucleotide

14. What atoms are most often found in organic molecules? (use symbols)

_____ _____ _____ _____

15. Which atom from question 14 is unique to amino acids and nucleotides? _____ 16. What are the 4 major groups of organic compounds? ________________

_________________ __________________ ________________

17. Using your answers from question 16, which are most concerned with short-

term energy? _______________ Which form genes? ________________ Which ones form enzymes? ________________

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18. Provide a list of molecules that would be associated with “a” in the diagram

___________________ __________________ ___________________ __________________ Which molecules would be associated with “c” in the diagram? ___________________ __________________ ___________________ __________________

19. Write the words unsaturated and saturated beside the appropriate structure.

____________________ _____________________

20. Draw a dipeptide and circle the peptide bond.

21. The secondary level of structure for a protein has what shape? ______________

What type of bond is required to hold this shape? _________________. What does the tertiary level of protein structure require? _______________________________________________________ Name a molecule in your body that has the tertiary level of protein structure. _____________________

22. Draw and label a nucleotide below. Is ATP a nucleotide? _______

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23. Is this an organic compound? _______ How do you know? _____________ ____________________________________. This molecule is not an amino acid. Does it have an amino group? ______ Does this molecule have a carboxyl group? ______ Is this a fatty acid? ______ Is this a type of a sugar molecule? ______ How do you know? ______ Is this molecule an enzyme? ______ How do you know? ________________ ________________________________________________________ This molecule above is called urea, a waste compound produced by your liver. 24. This molecule repeats itself over and over in even longer chains than shown below. What type of molecule would this be?____________________ What level of structure is present? ______ Circle a peptide bond on the diagram. Draw a dotted line on the diagram to show the type of bond required to form the secondary level of this structure.

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OBJECTIVE SHEET ENZYMES 1. Define the following terms: metabolism, metabolic pathway, substrate, enzyme,

enzyme-substrate complex, competitive inhibitor, denaturation, activation energy, and Apo enzyme.

2. Describe the “Induced Fit” theory of enzymatic reaction. 3. Describe the role of enzymes in biochemical reactions. 4 Explain how pH, temperature, substrate concentration, enzyme concentration, and

heavy metals affect enzyme activity. 5. State the function of the following enzymes (based on their names): lactase,

maltase, sucrase, amylase, lipase, protease, and dehydrogenase. 6. Explain the three graphs below. Provide reasons for the shape of the graphs.

Discuss what is happening at the molecular level.

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Many chemical reactions that occur in the body require a large amount of energy in order for the reactants to come together to make products. This can be a problem in animals because the energy needed would require temperatures too great for most cells to function.

Evolution’s answer to this problem is the enzyme. Enzymes lower the activation energy needed for reactions to occur. This allows every critical reaction to occur at body temperature.

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ENZYMES

Enzymes are biological catalysts, that is they speed up the rate of chemical reactions without being used up in the reaction themselves. The Active Site of Enzymes This is the place on the enzyme where the substrate fits in. The active site is 3-dimensional and has a shape that is complementary to that of

the substrate. The Induced Fit Theory The old “Lock and Key” theory suggested that enzymes and substrates fit together like an inflexible key in a keyhole. Recent evidence suggests that the active site of an enzyme is flexible. Binding between the enzyme and the substrate temporarily alters the shape of the enzyme. This change in shape is thought to cause a strain on the chemical bonds in the substrate. Co-factors and Co-enzymes Some enzymes need a non-protein substance to help them function. These substances are called co-factors. There are two types: Inorganic metal ions such as Mg++, K+, and Ca++ Co-enzymes such as vitamins and NAD+

The protein part of the enzyme is called an Apo enzyme. It gives the enzyme its specificity.

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Cells Can Make Inactive Enzyme Forms for Cell Protection Some enzymes would destroy the very cells that produce them. To avoid this, cells make the enzyme in a temporary inactive form. Once the enzyme is outside of the cell, it is changed to the active form. i.e. HCl acid in the stomach converts pepsinogen (inactive form) into pepsin (active form) which then starts the digestion of protein in the stomach. Enyzme Reading: pg. 106-109 1. What is entropy? 2. List three functions of ATP. 3. Define energy of activation. What effect do enzymes have on the EA?

4. E + S ES E + P Explain this equation. 5. Diagram a simple enzyme and the molecule on which it will act. Label the active

site and the substrate. 6. What is the allosteric site? In noncompetitive inhibition, a molecule fits into the

allosteric site. What effect does this have on the speed of the reaction catalyzed by the enzyme? Why?

7. Explain how feedback inhibition (also called noncompetitive inhibition) controls

the amount of product made during a metabolic pathway. 8. Some enzymes cannot work alone, but need a molecule called a cofactor. What are

organic cofactors called? What effect do metals such as mercury or lead have on enzymes?

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TOOTHPICKASE ENZYME LAB Toothpickase is a very unique enzyme that usually has a molecular mass somewhere between 50 and 90 kg and has a shape similar to a human teenager. The substrate for this enzyme is the common toothpick upon which the enzyme acts to produce two smaller pieces (a broken toothpick). The active site of the enzyme is situated between the thumb and the forefinger, if the fingers are held close together. Being an enzyme, toothpickase cannot see its substrate, but instead it must blindly collide with it at random. You and your partner will conduct two experiments to gain some understanding of how enzymes work in the body. Experiment 1 Calculating the Enzyme Reaction Rate Place a pile of toothpicks on the table and have your ‘toothpickase’ break as many as possible (one at a time) in the allotted time. Fill your results in the table below recording results every 10 seconds as you go continuously. Graph your results. (put time on the x-axis)

Table 1 TIME

(seconds) # of broken toothpicks

0

10

30

60

Experiment 2 The Effect of Substrate Concentration Spread randomly only the allotted number of toothpicks on the table and allow your ‘toothpickase’ to work for only 10 seconds. Fill your results in the table below. Graph your results (put the # of toothpicks available on the x-axis)

Table 2 # of toothpicks

available # of toothpicks

broken in 10 sec. 0 2 4 6 8 10 12 14

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Graph #1 Toothpickase Reaction Rate

Calculate the reaction rate for toothpickase from the slope of the above graph. Rx rate = N2 – N1

________ Reaction rate = _______ toothpicks/sec.

T2 – T1

Graph # 2 Effect of Substrate Concentration on Reaction Rate

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Conclusions

On a sheet of paper titled TOOTHPICKASE, hand in the following:

By looking at your graphing results for experiment #1 (reaction rates) and #2 (effect of

substrate concentration) draw as many conclusions as possible to help explain a little about

how enzymes and substrates work together. Use point form answers.

Questions (read text references pages 106-109)

1. What would be the effect of adding finishing nails that were the same size as the

toothpicks? Why? (2)

2. What would the finishing nails be called if they were real molecules? (1)

3. Fully define what a catalyst is (2)

If toothpickase were a real enzyme, what factors would affect its reaction rate? Explain how

each factor acts.(5)

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The Amylase Enzyme Lab Enzymes are biological catalysts; that is, they speed up the rate of chemical reactions without being changed themselves. We are going to examine the reaction of salivary amylase on amylose (starch) under different pH and temperature conditions. Indicators When enzyme and substrate molecules work together they are too small to be seen. We need some sort of an indicator molecule such as iodine to allow us to see the results of this reaction. When iodine is added to starch, the normally reddish/brown iodine turns a deep purple/black colour. This is why iodine can be used as an indicator. It indicates the presence of starch by turning a different color. If we place the amylase enzyme in a sample of starch solution, the starch will be broken down into dextrins and finally into the disaccharide maltose by the enzyme. Adding iodine will indicate to us that the enzyme worked because the iodine will remain its characteristic reddish/brown colour. In a group of two you will test how pH or temperatures affect this process. The Temperature Experiment Put a couple drops of iodine in each of the spot plate wells. Prepare a test tube with 5mL of starch solution and 5mL of tap water mixed together. Have your partner prepare a second test tube with only 5 drops of enzyme solution in it. Notice on the side counter where there are 4 water baths of different temperature. Starting at any station, place both tubes into the water for 5 minutes. Use the test tube holders provided. After 5 minutes, pour the contents of the starch/water test tube into the test tube containing the enzyme drops and mix thoroughly. Put the test tube back into the water bath to keep the temperature constant. At one minute intervals, carefully pour a small amount of the test tube into one well of the spot plate. Return the test tube to the water bath to maintain the temperature. If the iodine stays reddish/brown, you are finished. You can go to the next station. The enzyme worked at that particular temperature in only 1 minute. If the enzyme didn’t work at this temperature, the well will turn black and you will try again in a new well at minute 2. Do a maximum of 12 minutes for each station. To test all 4 different temperatures your group will have prepared 8 test tubes in total. The pH Experiment Put a couple drops of iodine in each of the spot plate wells. Notice on the side counter where there are 4 pH buffer solutions. In a test tube you will add 5mL of one of the buffer solutions, (you will eventually do all the different solutions), 5mL of the starch solution and 5 drops of the enzyme solution. **The order that you mix them is important!!** Before you combine these 3 together in a test tube, write the order down on a piece of paper and show me. At one minute intervals, carefully pour a small amount of the test tube into one well of the spot plate. If the iodine stays reddish/brown, you are finished. You can go to the next station. The enzyme worked at that particular pH in only 1 minute. If the enzyme didn’t work at this pH, the well will turn black (starch is still present) and you will try again in a new well at minute 2. Do a maximum of 12 minutes for each station.

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OBJECTIVE SHEET CELL STRUCTURE (PLANT AND ANIMAL) 1. Compare and contrast the function of prokaryotic and eukaryotic cells. 2. Describe the structure and function of the following organelles: cytoskeleton (microtubule/filament) SER and RER golgi body nucleus lysosomes mitochondria plasma membrane cell wall chloroplast nuclear envelope vacuole vesicle nucleolus ribosome chromosome centriole flagella cilia 3. Identify the above organelles in a diagram and an electron micrograph. 4. Identify the functional interrelationships of cell structures. 5. Discuss the relationship and importance of surface area to volume ratio with

reference to cell size.

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Surface Area to Volume Ratio SA/V ratio Limits to Cell Size There are two main reasons why as organisms grow, their cells begin to divide rather than just having the cells get larger. The larger a cell becomes, the more demands the cell places on the DNA to control the cell. In addition, the cell has more trouble moving enough nutrients and wastes across the cell membrane. So making more cells and keeping them small is the best way to go. We talk about this relationship of cell size to the cell’s activity level as “Surface area to Volume ratio. As the length (or SA) of a cell increases, its volume increases even faster than its SA so we say that the cell’s SA to V ratio has decreased. If a cell is to metabolically active, being large is not good. Large cells have difficulty obtaining enough nutrients or removing enough waste by diffusion if they want to be metabolically active cells. As a cell grows larger, its SA/V ratio decreases Small, flat cells have the highest SA/V ratio and therefore can be very active If a cell finds itself with a poor SA/V ratio, it can compensate for this problem by:

1) Cyclosis (circulating nutrients) 2) Large vacuole (pushes contents to the outside near the cell membrane) 3) Convoluted membranes (twisted, folded membranes)

-as found in the brain, kidney nephrons, and small intestines.

42

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Micrograph Practice This exercise will help you interpret micrographs of plant and animal cell organelles. You will need to use chapter 3 from your text as a reference. Check your work when done. 1. What is the function of the cell membrane? _______________________ _____________________________________________________ 2. Below are two cell membranes from cells adjacent to each other. Between the cell

membranes is water. Each cell membrane has two black lines along the length of the membrane. What do you think the black lines represent?

_____________________________________________________

3. The structures below are all part of the cell’s _____________________

(hint: analogous to your bones)

Read text pages 58-59 and then list three components of the cytoskeleton. _______________________________________________________ _______________________________________________________

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Where are actin filaments found? ________________________________ _______________________________________________________ What do microtubules do? ____________________________________ 4. How many membranes surround the nucleus inside this cell? __________ Observe the nuclear envelope on text page 52. After reading, state a possible role for a nuclear pore. _______________________________________________________ Why does the nucleus in young cells appear larger than in older cells? _______________________________________________________ 5. Identify the name of the structures below. ______________

Would you expect the ribosomes not found on the ER (but loose in the cytoplasm) to be making protein for export out of the cell or for use inside the cell? ___________________________ What is ER called without ribosomes? ___________________________ State two important functions of smooth endoplasmic reticulum in the cell.

_______________________________________________________

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6. Name the “flattened pancake-like” structure that is outside the nucleus. _____________________ **Read page 54 and state the function of this structure. _______________________________________________________ _______________________________________________________ _______________________________________________________ 7. The special vacuoles (indicated with an arrow) contain digestive enzymes and is made in the golgi apparatus. What are these called and list two functions: __________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________

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8. What is the difference between a vacuole and a vesicle? _______________ _______________________________________________________ List the items found in plant vacuoles _____________________________ _______________________________________________________ State two functions of plant vacuoles ______________________________ _______________________________________________________ 9. Below is a mitochondrion. State its function.

What does the “C” in the diagram represent? __________________

_______________________________________________________ _______________________________________________________ Why do mitochondria have different DNA than the nucleus? ___________________________________________________________ ___________________________________________________________ ___________________________________________________________

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Read text pages 60-61. Many microorganisms contain cilia or flagella (including you!) Notice the “9+2 arrangement” of microtubules that make up the x.s.. 10. What does the following organelle do? _____________________ _____________________ _____________________ A stack of “coin-like” structures called a granum is where the pigment ____________________ is found. The stroma is between the “coin-stacks”. This is where glucose is made. 11. In this micrograph of a plant cell, note the large central vacuole. The large vacuole pushes the cell membrane and cytoplasmic organelles close to the cell wall. Why is this important? _______________________________________________________ _______________________________________________________

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12. In what organelle would you expect to see the following process occurring? _______________________ 13. The diagram below shows an electron micrograph of a layer found outside the cell membrane in a cell. Would this be outside of a plant or animal cell? ___________________. This layer is a polysaccharide called ________________________. Is this layer considered to be living? _________

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OBJECTIVE SHEET TRANSPORT ACROSS THE CELL MEMBRANE 1. Diagram the Fluid-Mosaic Model of the plasma membrane. 2. Explain why the plasma membrane is described as selectively permeable. 3. Identify the molecule(s), and the structure of the membrane for the movement

using the following processes:

Simple Diffusion Facilitated Diffusion Active Transport 4. Describe the difference between pinocytosis and phagocytosis. 5. Explain factors that affect the rate of diffusion across a cell membrane. 6. Predict the effects of tonicity on animal cells. 7. Define the following terms and recognize the following conditions: lysis, crenation,

plasmolysis, turgor pressure, Brownian motion, and bulk flow.

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A. B. C. D. E. F. G. H. I. J.

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Tonicity Practice Review

solute solvent solution hypertonic isotonic hypotonic diffusion osmosis permeable osmotic pressure selectively permeable A B 7% starch 5% starch 5% glucose 12% glucose membrane is impermeable to starch Use the diagram above to answer the following: Side A is ________________________ to side B at the start of the experiment. The membrane is classified as being ___________________________ since it allows some molecules through. This movement is called ___________________. Water will move toward side _____ by a process called ____________________. Starch will ____________________. The concentration of starch on side B will _________________ as the experiment runs. A possible reason for the behaviour of the starch molecules __________________________________________. The side that had the highest osmotic pressure in the beginning was side ________. Its OP has _______________________ as the experiment ran.

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Results of Osmosis All of the following occur due to the tendency of cells to become isotonic to their environment. Draw simple diagrams for #1 to 4 in the space provided. Make up concentrations for the cells and the solutions. Assume that the cell membrane is impermeable to the solute. Use arrows to indicate the direction of osmosis.

1. Plasmolysis –when a plant cell is placed in a solution that is hypertonic to it, water leaves the vacuole, the vacuole shrinks, allowing the cytoplasm and the cell membrane to move in away from the cell wall.

2. Turgor Pressure – when a plant cell is placed in a hypotonic solution, water enters the vacuole and pushes the cell contents against the cell wall, helping to support the cell. This outward pressure stops any more water from entering the cell.

3. Crenation – when animal cells are placed in a hypertonic solution, they lose water by osmosis and shrink.

4. Lysis – when animal cells are placed in a hypotonic solution, water enters and causes the cell to burst or lyse. When this occurs in red blood cells it said that they are in a condition of hemolysis.

Changing environments in or out of cells can cause these conditions. The

cellular conditions are created in cells as a result of osmosis.

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Conditions of Cells Exercise Make a slide of an epithelial cell from the inside of your cheek. Add methylene blue stain. Observe under H power. Diagram one cell. Include the labels, cell membrane, mitochondria, cytoplasm, and nucleus. Make a slide of onion cells with iodine. Observe under M or L power. Diagram several cells showing how they fit together. Look closely at the cytoplasm in your cells. Lift the cover slip and add a drop of salt solution. Observe one cell showing a change in the cytoplasm caused by adding the salt. Diagrams: all diagrams are drawn in pencil and must include: appropriate labels and magnification of the drawing.

Mag = DS Field diameters: L 4.4 mm or 44oo m

AS M 1.8 mm or 1800 m

H 0.44 mm or 4400 m Questions: 1. Describe the difference between a prokaryotic and eukaryotic cell. 2. List three structures present in a plant cell and an animal cell but are not visible in

your microscope. 4. Why did the stain move into the cheek cell but the cell contents can’t leave the cell? 5. Describe the salt solution in relation to the onion cell. How do you know for sure

that salt did not cross the cell membrane? 6. What condition was the onion cell in before the salt was added? After? Name the

movement that caused this condition. If pure water is added to your cheek cell, what condition would it be in?

7. Consider the beakers containing the following solute concentrations:

A 10% salt B 11% salt C 10% salt 5% sugar 4% sugar 8% sugar

COMPARE WITH RESPECT TO: SALT SUGAR TOTAL A to B hypotonic

A to C

hypotonic

B to C

hypotonic

7. If A and C were animal cells, what condition would C be in? What condition is A?

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How Materials Enter and Leave Cells Type of Movement Condition of Cell Cause of Condition 1. Passive Transport facilitated diffusion plasmolysis (plant) uses protein carriers cells in a hypertonic solution

No energy required. crenation (animal) Molecules move with simple diffusion concentration gradient. turgor pressure (plant)

osmosis cells in a hypotonic solution hemolysis (blood cell)

2. Active Transport cells accumulate materials

in a higher concentration

Requires energy from ATP. than its surrounding Materials move against the

concentration gradient using protein pumps.

3. Exocytosis vesicles from golgi bodies fuse with cell membranes secreting their contents 4. Endocytosis pinocytosis membrane folds to enclose liquids or small molecules

phagocytosis uses pseudopods to surround cell or cell parts 5. Bulk Flow whole blood moves in response to a pressure difference (like blood moving in response to a heart beat)

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Practice: Result of Movement in a Cell F.I.B. ______________________________ is the constant motion exhibited by all molecules. Because of this motion, three types of passive transport can occur in cells, __________________, _____________________, __________________ These three methods do not require ________________. Cells are able to build up accumulations of ions higher than that of their surroundings by the process known as ________________________. For some molecules, the protein channels open to allow easy entrance into the cell. When this happens it is called _______________ ________________. Large molecules are taken in by the process of __________ ________________. An onion cell, which is 0.2% sucrose is placed into a 4% sucrose solution. Which has a lower OP: the cell or the solution? __________________ The cell is _____________________ to the solution. The condition that the cell will end up in is ____________________. A red blood cell that is 0.9% glucose is put into pure water. The cell is _______________________ to the water and will end up in a condition known as _______________________. If this were a plant cell, the condition would be ________________________.

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Identify 2 molecules that cannot get through structure “f”. ___________________ _____________________ Identify 2 processes that could use structure “j”. What molecules would be associated with each of the processes you chose? ___________________________________________________________ ___________________________________________________________ What is the function of structure “i”? _________________________________ ___________________________________________________________

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Osmosis Potato Lab In this lab you will learn how cell membranes and cell walls function by experimenting with various sucrose solutions and potatoes. You will apply your knowledge of cell conditions, and the environments that cause them to understand how materials move in and out of typical cells. Purpose: To determine the concentration of solute in potato cytoplasm. Material: potato 1 mol/L sucrose solution distilled water 11 test tubes razor blade

ruler electronic balance #5 cork borer 10 mL graduated cylinder 100 mL beaker 10 mL pipette

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Procedure: A. Preparation of sucrose solutions Label 11 test tubes from 1 to 11 (label the test tube rack). Prepare 10 mL of each concentration of sucrose solution shown in column A in the table below. Use the information in the table to mix the solutions as follows: Add the amount of 1.0 M sucrose solution indicated in column B to the amount of distilled water indicated in column C to make a solution of the concentration shown in column A. Place each solution as it is prepared into the test tube rack making sure to keep them in order.

A B C D Concentration of sucrose solution required (mol/L)

Amount of 1.0 M sucrose solution required in mL

Amount of distilled water required in mL

Pour into test tube number shown below

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0.0

10

9

8

7

6

5

4

3

2

1

0

0

1

2

3

4

5

6

7

8

9

10

1

2

3

4

5

6

7

8

9

10

11

B. Preparation of potato sections Using a #4 or #5 cork borer, remove a section of potato. Using a razor blade, cut a 5 cm length (no skin) of potato section. Rinse the section with distilled water. Blot the section on a dry paper towel. Determine its mass to the nearest 0.1 g. Record this mass in data table #1 on the next page. Place this section into test tube #1. Remove and cut 10 more 5 cm lengths of potato section following the procedure above. Carefully record the initial mass of each section before placing it in a test tube. Allow each section to remain in its solution overnight. The next day, remove each potato section, blot dry and mass out to the nearest 0.1 g again. Record each mass in table #1 as “Final Mass”. Calculate if a gain or loss of potato mass has occurred in each section. Calculate the % change in mass for each potato section by using the following formula: Change in mass (+or-) (remember, use the change in mass rather than the final mass)

x 100% Initial mass

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Data Table: Name: ____________________________ Block:________ Percent Change in Mass

TEST TUBE Concentration of sucrose solution

mol/L

Initial Mass (g)

Final Mass (g)

Change in Mass (g)

add + or -

Percentage Change in Mass (%)

1

1.0

2

0.9

3

0.8

4

0.7

5

0.6

6

0.5

7

0.4

8

0.3

9

0.2

10

0.1

11

0.0

60

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Test 1 Practice Review sample questions

1. Atoms with the same atomic number but different weights are said to be a) isomers b) polymers c) isotopes d) bonds 2. Compounds containing H and C are a) inorganic b) acids c) organic d) bases 3. When calcium (20) joins with chlorine (17), calcium is a) reduced b) oxidized c) covalently bonded d) buffered 4. If a solution has a pH of 9, there would be a) more H+ than OH- b) more Na+ than H+ c) more Cl- than Na+ d) more OH- than H+ 5. A molecule is found to contain N. A valid conclusion is a) it must be an amino acid b) it must be a phospholipid c) it may be a carbohydrate d) it is not a fatty acid 6. Some hormones and all enzymes are composed of a) amino acids b) fatty acids c) carbohydrates d) nucleotides 7. Which of the following is found in a fatty acid? a) carboxyl group b) R group c) amino acid d) C=C

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8. Amino acids differ from one another in their a) hydrocarbon chain b) R groups c) peptide bonds d) double or single bonds 9. Energy storage molecules found in our liver are a) polysaccharides b) polypeptides c) disaccharides d) dipeptides 10. Cellulose and amylose are a) isomers b) polymers c) polyisomers d) monomers 11. Green plants use nitrates to make a) sugar b) protein c) fat d) starch 12. A molecule is found to contain C, H and O with two H present for every O. It must

be a(n) a) amino acid b) fatty acid c) carbohydrate d) phospholipid The following are True or False: 13. Water molecules are held together by H bonds. 14. Saturated fats have single bonds between the carbon atoms. 15. Polysaccharides are made from disaccharides by hydrolysis. 16. ADP is a nucleotide 17. Primary structure is determined by peptide bonds. 18. Carbohydrates are denatured by heat. 19. Fats contain more energy per gram than proteins. 20. All enzymes show secondary level of protein structure. 21. As substrate is added to a beaker of enzyme, the rx rate increases until all of the active sites are occupied at any given time. 22. Heavy metals denature enzymes.

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23. In an experiment, substrate S was added to a beaker containing equal amounts of

enzymes E1 to E7. The metabolic pathway in the diagram above shows the reactions that occurred. After 15 minutes a competitive inhibitor for E3 is added to the beaker and the reactions continue to completion. What would occur?

a) The rate of production of T would increase. b) The rate of production of Z would increase. c) The rate of production of X would increase.

d) The rate of production of E4 would decrease. 24.An enzyme’s ability to recognize a substrate is based on the enzyme’s a) molecular weight b) ability to buffer the pH c) ability to stabilize the temperature at optimum d) active site 25. As the pH of a catalyzed reaction is moved away from its optimum pH, the rx rate will slow due to a) molecules slowing down b) all of the enzymes being occupied at any given time c) there is less collisions between molecules d) denaturation occurs Put a check mark beside the pairs that are properly matched. 26. competitive inhibitor – increased reaction rate 27. enzyme – complementary shaped substrate 28. protein – coenzyme 29. substrate – active site 30. cellulase – cell wall

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The following are True or False. Use the diagram below: 31. W is the coenzyme 32. X is the product 33. Y is the coenzyme 34. Z is the Apo enzyme 35. Adenosine triphosphate would be used in a) osmosis b) facilitated diffusion c) phagocytosis d) diffusion 36. A cell that is engulfing bacteria would have many a) lysosomes b) ribosomes c) polysomes d) centrioles The following are True or False: 37. Water enters the cell by osmosis through the phospholipid bilayer. 38. Lipid molecules enter the cell by diffusion through the phospholipid bilayer. 39. In the cell membrane, hydrophilic tails point inward. 40 Cell fragments are taken into the cell by phagocytosis. 41. Which is represented by the diagram below? a) diffusion b) exocytosis c) pinocytosis d) phagocytosis