If this packet is LOST, please

BSCS Packet #3 – Biochemistry and Digestion, Part 1 (Unit 3) Summer 2014

This Activity Packet belongs to: __________________________

At the end of the unit you will turn in this packet). Record the completion due dates in the chart below. You should expect a variety of quizzes: announced, unannounced, open-notes and closed-notes.

If this packet is LOST, please: drop it off at the BHS Science Dept. (rm 365) OR

drop it off in Ms.. Brunson’s classroom (rm 351) OR call the Science Dept. at (617) 713-5365.

Packet page Activity Points

Earned Avail. 2 Notes: Chemical Foundations of Life --- ---

3 Water: The Molecule of Life --- ---

4-6 Water Olympics 15

7-8 Lab: pH and Homeostasis 10

9 Molecular Modeling (Inorganic Molecules) 5

10-11 Organic Chemistry Notes --- ---

12-14 Molecular Modeling: How are atoms arranged in molecules of living things? 15

15-17 Nutrient Testing Lab 5+

18-20 Protein Folding 10

21-22 Enzyme Structure and Function 5

23-24 Biochemistry Test Review (Part 1) 20

Total 85

Notes: Chemical Foundations of Life Atoms and Elements Protons – Neutrons – Electrons – Elements – Atomic number – Mass number – Elements of Life Electrons and Bonding First 3 levels need how many electrons to be complete? ____, ____, ____ Compounds Molecules Ionic Bonds Covalent Bonds Nonpolar covalent bonds – Polar covalent bonds –

Water: The Molecule of Life Properties within a molecule of water (intramolecular) Properties between two molecules of water (intermolecular) Emergent Properties of Water Cohesion Surface Tension Adhesion Universal Solvent pH

Buffers

Water Olympics - An exploration of the properties of water 1. What is water’s chemical formula? _______________ 2. How many atoms make up a water molecule? _______ 3. What elements make up water (include the number of atoms of each of those elements in a single water

molecule)? ____________________________________ 4. Is water a compound? No Yes

Explain. _______________________________________________________________________________________ _______________________________________________________________________________________

5. What is a polar molecule? _________________________________________________________________ ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

6. Is water a polar molecule? No Yes 7. Sketch a water molecule. Include its polarity in your sketch. Investigation: Move from station to station following the procedures at each station. Answer all parts of each station. Station 1 – The Mystery of the Meniscus Fill the test tubes and graduated cylinder with 15 mL of water. Look closely at the water level. Notice the curve at the top of the water. You may remember from chemistry that the curve is called a meniscus. Explain why water forms that curve. ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ Station 2 – The Floating Paperclip Carefully fill the plastic cup as full as you possibly can without it spilling over. See if you can get the paperclip to float on the surface of the water. (Hint: make sure the paperclip is completely dry when you begin. You may put the paperclip on a fork and lower it in.) Use a magnifying glass to observe the surface of the water where it comes in contact with the paperclip. In the space below, describe (or draw) how this looks. Observations: Explain how that paperclip is able to float on the surface of the water:__________________________________ ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

Station 3 – Drops on a Penny Predict how many water drops will fit on a penny and put your prediction here: _______. Make sure the penny is completely dry, and slowly add water drops one by one. Count and record the number of drops. Be sure to look at the penny from table level before the water spills over. Water:

Average ______ Note observations: _____________________________________________________ __________________________________________________________________________________________________________________________________________

In the cleaning process, surface tension must be reduced so water can spread and wet surfaces. Chemicals that are able to do this effectively are called surfactants. Surfactants perform other important functions in cleaning, such as loosening, emulsifying (dispersing in water) and holding soil in suspension until it can be rinsed away. Everyday surfactants include soaps or detergents. Repeat this experiment with the water mixed with detergent. Water with detergent:

Average ______ Note observations: _____________________________________________________ __________________________________________________________________________________________________________________________________________

Explain why the drops cling to the penny when there is no detergent: __________________________________ ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ Station 4 – Pepper Designs Thoroughly rinse out the bowl, making certain there is no soap residue in the bowl. Sprinkle pepper lightly over the surface of the water. What happens with the pepper? Add one drop of soap and describe what happens with the pepper. The pepper is not repelled by the soap as it may appear. What actually happens is that the soap breaks the surface tension of the water. The pepper can only stay afloat where surface tension still exists. Station 5 – Water Drop Play Place a few drops of water around the wax paper. Use a toothpick and move the droplets around. Describe the behavior of the drops of water on the wax paper. Now, explain the behavior of the water drops.

Trial # # of drops 1 2 3

Trial # # of drops 1 2 3

Station 6 – Paper Towel Absorption Water is able to travel through the narrow spaces between the fibers of paper towels by capillary action. The attractive force between the water molecules and the paper fibers is greater than the cohesive force between the water molecules. This causes the water molecules to be pulled up the paper towel against the force of gravity. The attraction between unlike molecules is called adhesion. Predict which brand of paper towel will absorb more water: Brown White Place about 2-3 cm of water in the beaker and place the paper towel strip so it is partially in the water (just about 2 cm deep). Let the paper towels absorb water until the water stops rising. Use a ruler to measure the height absorbed above water level for each towel. Brown ___________ cm White ____________ cm Which towel was the most absorbent? Why? Analysis: Check off which water property/properties was/were working to make each phenomenon happen.

Event # Cohesion Adhesion Surface Tension 1 – Mystery of the Meniscus

2 – Floating Paperclip

3 – Drops on a Penny

4 – Pepper Designs

5 – Water Drop Play

6 – Paper Towel Absorption

pH and Homeostasis Mini-Lab Introduction∗ The pH scale measures how acidic or basic a substance is. The pH scale ranges from 0 to 14. A pH of 7 is neutral. A pH less than 7 is acidic. A pH greater than 7 is basic. There is a ten-fold difference between each number on the scale: 6 is ten times more acidic than 7, 4 is 100 times more acidic than 6, 8 is ten times more basic than 7 and 10 is 100 times more basic than 8. Pure water is neutral at 7. When polar or ionic chemicals are mixed with water, the solution can become either acidic or basic. Examples of acidic substances are vinegar and lemon juice. Lye, baking soda, and ammonia are examples of basic substances. Acids and bases are examples of poisons that react with tissue cells and break them down. Chemicals that are very basic or very acidic are highly reactive. Your body has mechanisms in place for controlling pH of cells and bodily fluids, which function best at a pH just above 7 (with a couple of exceptions). Compounds called buffers are maintained in the body to resist changes in pH. Buffers are molecules that can take up excess H+ ions when the body becomes too acidic or release H+ ions when the body becomes too basic. Lab activity In this mini-lab you will investigate the effects of acid on the pH of water, milk, and a buffer solution. Your first step, with your group, is to find the pH of each solution. To do this, take a drop of each solution and put on separate pH strips. Then compare the color of the strip to the scale on the side of the strip container. Then add HCl (acid) in 5-drop increments to water, buffer solution, and milk. After each 5-drop addition, swirl the beaker to mix it, then take a pH reading. When all groups have finished we will average the class data. Predictions (circle a choice for each) What do you think will happen to the pH of the water? Decrease Increase Stay the same What do you think will happen to the pH of the milk? Decrease Increase Stay the same What do you think will happen to the pH of the buffer? Decrease Increase Stay the same Data tables As HCl (acid) is added to water and milk solution:

Number of total drops added pH of water pH of milk Group data Class average Group data Class average

0 5 10 15 20

As HCl (acid) is added to buffer solution: Number of total drops added pH of buffer solution

– group data pH of buffer solution

– class average 0 5 10 15 20

∗ Modified from Virtual Chembook, C.E. Ophardt, Elmhurst College © 2003

Graph Construct a line graph to illustrate the class averages.

• Make sure individual data points are clearly visible. • You should have 3 lines in total – use a different color for each • Be sure to make a key/legend for your graph, label and scale your axes • Make a descriptive caption for your graph (as you would see in a textbook)

Caption: Analysis Answer the following questions IN COMPLETE SENTENCES on a separate piece of paper. Write very neatly or type your answers. 1. Identify the independent and dependent variables in this lab. Also describe what factors were controlled for

between all three substances. 2. Describe the changes in pH (use the class average) for water as each increment of HCl (acid) was added. 3. Describe the changes in pH (use the class average) for milk as each increment of HCl (acid) was added. 4. Describe the changes in pH (use the class average) for the buffer solution as each increment of HCl (acid)

was added. 5. Using your data, propose an explanation for why buffers are useful to have in our bodies. 6. Why do you think it is important to use a large (class average) data set rather than just use the data for your

own group? Do you think that your answers to 2-5 would be different if you used only your group data? Explain with at least one example from your graph.

Molecular Modeling – Inorganic Molecules Purpose: To observe the way in which certain atoms combine to form molecules, with a particular focus on elements relevant in Biology I. This should be review from Chemistry. Materials: Molecular Model Kits Procedure Part 1: 1. Get a molecular model kit. Identify the different colored spheres as carbon, hydrogen, oxygen, and

nitrogen atoms. Carbon= Hydrogen = Oxygen = Nitrogen =

2. Write the number of holes in the spheres that characterize each type of atom.

Carbon= Hydrogen = Oxygen = Nitrogen =

3. What do you think the “holes” represent? 4. How many bond(s) do the following atoms need to have in order to be “stable”? Think about

electrons and energy levels for each element (look at your periodic table). Carbon= Hydrogen = Oxygen = Nitrogen =

5. Atoms bond together to form a molecule. Each molecule is composed of two or more atoms. With

one oxygen and two hydrogen atoms, make a model of a water molecule. Connect the atoms (spheres) with connecting rods found in the kit. These rods will represent a pair of electrons or a COVALENT BOND. The oxygen atom shares electron pairs with two hydrogen atoms. Molecular formula of water = H2O Structural formula of water = O

H H

Ball and stick model = 6. The chemical formula of carbon dioxide is CO2

a. How many carbon atoms are in one carbon dioxide molecule? b. How many oxygen atoms are in one carbon dioxide molecule? c. Using the appropriate number of carbon and oxygen atoms, build a carbon dioxide

molecule. Get your teacher’s approval, then, draw its structural formula below. Conclusion Questions Part 1: 1. Describe the structure of an atom. 2. Why do atoms form molecules?

Draw a picture of your model:

Organic Chemistry Notes What do you think a “macromolecule” is? What is a “Monomer”? “Polymer”? What is an organic molecule? What are the four categories or types of organic molecules? Brainstorm Carbohydrates Proteins

Lipids Nucleic Acids

Carbohydrates

What are they – in simple terms?

What type of reaction builds up large carbohydrates? What is their function?

What type of reaction breaks large carbohydrates down?

What is the “monomer”?

What are examples in nature? In your diet?

What do they look like?

Nucleic Acids What are they – in simple terms?

What is its function?

Lipids

What are they – in simple terms?

What type of reaction builds triglycerides?

What is their function?

What type of reaction breaks down triglycerides?

Lipids don’t have monomers! What are the components of a triglyceride?

Saturated vs. Unsaturated

What do triglycerides look like?

What are examples in nature? In your diet?

Proteins

What is the “monomer”? What do the monomers look like?

What type of reaction builds up proteins?

What type of reaction breaks down proteins? What are some examples in nature (and what

are their functions)?

How can there be so many different proteins?

Molecular Modeling – How are molecules arranged in molecules of living things? Background: A molecule is composed of two or more atoms held together by covalent bonds. It is impossible to see a molecule because it is extremely tiny. It is possible, however, to obtain information concerning the arrangement of atoms in a molecule from the way in which the molecule reacts with other molecules and from special techniques such as x-ray diffraction. Using these techniques, scientists have measured the angles between bonded atoms and the distances between nuclei of bonded atoms. From these measurements, the shapes of molecules have been determined. The shapes of molecules in living things range from the very simple types such as oxygen or water to very complicated structures such as sugars and proteins. The shapes of molecules determine their functions. If a molecule’s shape is changed (denatured), it will no longer be able to function in its intended role. For example, hemoglobin is a protein found in red blood cells. It binds to oxygen and transports it in the blood. If the shape of the hemoglobin molecule is changed, it will no longer be able to bind to oxygen. Purpose: How do organic and inorganic compounds compare? What do the building blocks look like that make up organic molecules (carbohydrates, lipids, and proteins)? Recall that we described 3 ways to represent the molecules:

a. molecular formula: shows elements, #s of atoms and in what ratio, ex. H2O b. structural formula: shows how those atoms are connected, ex. c. ball-and-stick model: a picture showing your model, ex.

A. Carbohydrates 1. What are the building units (monomers) of carbohydrates? 2. What is the molecular formula for glucose? 3. Build a glucose molecule, using the (ring-shaped) structural formula below as a guide (2 are

shown). 4. Work with another group to carry on dehydration synthesis – use two glucose molecules to build a

larger molecule. Highlight/circle the atoms in the models above that needed to be removed to form the larger molecule.

a. What is this larger molecule called?

b. What do you need to remove in order to join the two glucose molecules?

5. Now carry on hydrolysis using the molecule that you created in the above step. a. What do you do in order to perform hydrolysis?

CHECK WITH THE TEACHER BEFORE MOVING ON TO THE NEXT PART. Teacher Initials:__________ B. Proteins 1. What are the building units (monomers) of proteins? 2. Build an amino acid molecule, using the structural formula on p66 of your book as a guide. Use a green ball for the variable (R) group. Label the three main parts of the amino acid below. 3. Take the amino acid and remove the green ball, replacing it with a hydrogen. This is the amino acid “glycine”. 4. Build a second amino acid (Do not take apart the 1st a.a.). Instead of putting a green ball for the R group, connect a carbon and 3 hydrogens. This is the amino acid “alanine”. Draw its structural formula. 5. Using your two amino acids, react them together to form a larger molecule. a. What is this larger molecule called?

b. What do you need to remove in order to join the two amino acids? (highlight or circle in the diagrams above)

c. The “joined” section of the larger molecule is called a ____________ bond. CHECK WITH THE TEACHER BEFORE MOVING ON TO THE NEXT PART. Teacher Initials:__________

R R

If you have time, do section C: (ask the teacher if you’re not sure) C. Lipids 1. Lipids are formed by combining one ____________ and three ___________ ________. 2. Build a glycerol (glycerin) molecule, using the structural formula below book as a guide. Label the

3 parts that can connect to a fatty acid. (Fig 4-10).

Conclusion Questions: 1. Write a paragraph in which you compare glucose (C6H12O6) to carbon dioxide (CO2). (Compare

size, number of atoms in each molecule, number of carbon-to-carbon bonds). 2. Explain: if a glucose molecule were broken down, how many carbon dioxide molecules could you

build? 3. How many carbon dioxide molecules would you need in order to build a glucose molecule? (This

is not necessarily the same answer as question #2.) 4. How are carbohydrates and lipids similar? How are they different?

5. How are proteins different from carbohydrates and lipids in terms of the elements that make up the

molecules?

Nutrient Testing Lab (13 pt) Purpose Question: What different kinds of organic molecules exist and how can we test different foods for the presence of these organic molecules? Introduction: As most foods are either made of cells, or made by cells, they contain the same organic compounds found within cells. Different kinds of cells (and therefore foods) contain mixtures of these compounds, called nutrients, some containing more of one than the others. These compounds are: carbohydrates (sugars and starches), proteins, fats, vitamins and minerals (which are inorganic). When testing a food for a nutrient, no matter how thoroughly the compounds are mixed with the other contents of the food, it will react to the test, as long as it is present in sufficient (high enough) quantities. In this exercise, you are going to use some of the standard chemical tests to find out what nutrients are present in some foods. As the tests for fats, sugar, vitamins and minerals are either too time-consuming or difficult, you are going to test for the 2 others: starch (a polysaccharide) and protein. Procedure: ***YOU MUST WEAR SAFETY GOGGLES FOR THIS ENTIRE EXPERIMENT*** Before you can use the chemical reagents (pronounced ree-a-gent) (which are the chemicals you use to do the tests) with confidence, you have to learn how they work. To do this, you will first do the test on foods that you know contain that nutrient, to see what color the reagent turns for a positive test. (A "+" test is one in which you had a reaction to prove the nutrient present; a "-" test is one in which you had no reaction and therefore found that nutrient not to be present.) These tests, or controls, will help you know that

a. the indicator reagent indeed tests for the nutrient you are looking for AND b. the indicator reagent ONLY tests for the presence of the nutrient you are looking for.

A. Testing Known Samples: This will be done together as a class. Nutrient tested for

Reagent used

Tested on well #1: Water

Tested on well #2: water + sugar

Tested on well #3: water + starch

Tested on well #4: water + protein

Starch iodine

(-) (-) (+) (-)

Protein Biuret

(-) (-) (-) (+)

Note: All reagents are found in dropping bottles. 1. STARCH TEST- Test your sample material by adding up to five drops of Lugol’s Iodine Reagent to the well. Look for and record the color. Repeat for other, non-food sample materials. 2. PROTEIN TEST- Test your sample material by adding up to five of Biuret Reagent to the well. Look for and record the color. Repeat for other, non-food sample materials.

Define/explain these terms as they relate to this experiment:(3 pt) Negative Control:

Positive Control:

Experimental Setup or Unknown: 1. Before you begin testing your food samples, identify them as being from either plant or animal.

Then, predict whether you think they will contain protein, starch, neither, or both. Discuss these predictions with the members of your lab group. Record a “+” if you think that the nutrient will be present; record an “–“ if you think the nutrient will be absent.

2. Now, your group will test the food samples on your tray. Record a “+” in the results column of your table if the food contains a given nutrient or an “-” in the same column if the food does not contain the nutrient.

3. Consult with at least two other lab groups (using the same indicator as you) to compare results. Make note of any inconsistencies in your data.

4. Wash your hands and clean up your lab table and put all materials back in the designated area. NO FOOD DOWN THE DRAIN, PLEASE!!

Data: (2 pt)

Name of Food Type of Food (Animal? Plant?)

STARCH PROTEIN Prediction Result Prediction Result

1.

2.

3.

4.

5.

6.

7.

8. Analysis Questions: Answer these questions on a separate sheet of paper. (8 pt) 1. In your own words, what is a negative control? (1 pt) 2. What were the three negative control groups used for iodine? (1 pt)

3. What is a positive control? What was the positive control used for iodine? Why was it important to test each indicator with a positive control? Be as specific as possible here. (1 pt)

4. As a class, how many trials did we use per treatment? Discuss the role of sample size (number of repeats) in an experiment. (1 pt)

5. What patterns emerge? In other words, did animal products tent to contain certain nutrients, but not others? What about plant products? (1 pt)

6. Describe how starch and protein are different macromolecules. Include a comparison of the following: (1 pt each)

a. the monomers of each b. the elements found in each (think of the SPONCH elements)

c. the function of each molecule in living organisms (What does starch do in plants? What is the role of proteins in living things?)

7. EXTRA CREDIT: Any successful experiment will control all variables other than the one actually being tested. In this experiment, our tested (experimental) variable was the type of food. Controlled variables included, for example, the amount of indicator added. All groups added 4 drops of each indicator to each well; thus, this variable was successfully controlled. Provide another example of a successfully controlled variable in this experiment. Describe what you did to successfully control it. (+1)

8. EXTRA CREDIT: Provide an example of a variable that we should have more effectively controlled, and specifically what we could have done to have better controlled it. (+1)

Proteins – What Determines Their Molecular Shape? Background: Proteins perform a wide variety of functions in living organisms. Hemoglobin is a protein in blood cells that transports oxygen from the lungs to the cells of the body. Enzymes act as biological catalysts to speed up reactions in every cell of the body. Proteins are a major part of muscles and are crucial for muscle contractions. Individual cells and whole organisms depend on proteins for structural support. Proteins are what make us unique individuals, providing the pigments in our skin, hair, and eyes. In order for a protein to perform its specific job, it needs to have a very specific shape. So what determines the shape of a protein? With only 20 different amino acids, how can there be so many different varieties of protein? You will explore these questions in this journal. Process and Procedure: 1. Take notes on the following topics:

Amino acid structure Hydrophobic vs. Hydrophilic Primary Structure (1°) Secondary Structure (2°) Tertiary Structure (3°) Quaternary Structure (4°)

2. Explore your amino acid kit. The long tube represents the carboxyl and amino groups of your amino acids. The smaller plastic pieces represent only the variable groups. Sort the amino acid variable groups on the magnetic board. Below are the categories to help you (the colors refer to the sticker on the base of the variable group – not the colors inside of the plastic).

Yellow = hydrophobic variable (R) group

White = hydrophilic variable (R) group

Red = negatively-charged, hydrophilic variable (R) group

Blue = positively=charged, hydrophilic variable (R) group

Green = hydrophilic variable (R) group with a sulfur atom

3. Look at the table and name the amino acid with the green variable group ____________________

4. Name 2 amino acids that have hydrophobic variable groups: ___________ and ____________

5. Name 2 amino acids that have hydrophilic, uncharged variable groups: __________ and _________

6. Name 2 amino acids that have hydrophilic, charged variable groups: ___________ and ____________

7. Find the following 15 amino acid variable groups and put them aside. These are the only 15 amino acids you will need for the rest of the journal, so you can put the others back in their bag.

Cysteine (2 of these) Methionine Arginine Valine

Lysine Aspartic acid Glutamic acid Asparagine

Serine Threonine Glycine

Alanine Leucine Tryptophan

8. Straighten out your tube and then arrange fifteen (15) clips on your tube. These clips should be evenly spaced. The foam tube represents what is called the backbone of the polypeptide (the non-R group parts of the polypeptide). The clips represent the locations of all 15 R groups of your protein, and onto them you will add your 15 variable groups that you and the other team chose.

9. Add one variable group to each clip. Try not to place a red too close to a blue, or the green too close to the other green, but otherwise the order is completely up to you.

10. This chain of 15 amino acids is a polypeptide molecule. Now, figure out how this molecule would fold if this were the amino acid sequence. Remember that you cannot shift the variable groups once they are on the tube. You may only bend the tube. Use the following rules:

r Fold up your tube so that all of the hydrophobic (yellow) variable groups are buried in the middle. Remember that these groups are repelled by water and that water surrounds the molecule on all sides.

r By bending the tube, move the red and blue variable groups so that they are within one cm of each other. Since they have opposite charges, they will attract and form a hydrogen bond.

r Make sure that your hydrophilic (white, red, blue, and green) variable groups are on the outside, where they can interact and hydrogen bond with water.

r Lastly, fold your molecule so that the two green variable groups can form a covalent disulfide bond. This is called a disulfide bridge and helps stabilize the protein. The two green groups must be within one centimeter of each other to form this covalent bond/disulfide bridge.

r Remember that you must simultaneously satisfy a-d (above)! Once all rules are simultaneously satisfied, you have a properly-folded protein molecule.

11. Once you think all of the above requirements have been met, call over your teacher to stamp or initial the page before moving on.

12. Compare your folded protein molecule to the protein molecules of the groups around you. Do you have the same 3D structure? Explain why or why not.

Conclusion Questions: 1. Now, draw a sketch of the tertiary structure of your protein (this question is asking you to sketch the 3D

structure of your protein). A rough sketch if fine – you don’t need to show any specific shapes for variable groups, BUT, using dashed lines, indicate the locations of the hydrogen bonds (the bonds between the red and blue variable groups). Also, using a BOLD line, show the location of the disulfide bridge (covalent bond).

2. ***You no longer need the model that you built. You should again place all of the amino acids on the chart and do a check to make sure that ALL amino acids are still present. If you are missing any, you will be docked points. Check your kit and put all pieces away before moving on to the next question. When you have checked your kit, call your teacher over to initial or stamp the box below.***

3. What type of reaction – degradation hydrolysis or dehydration synthesis – would you use to bond these 15 amino acids together? ___________________

4. Would you use water as a reactant or form water as a product when joining them? ___________ How many water molecules? _________

5. Is threonine’s variable group polar or nonpolar? ________ Hydrophobic or hydrophilic? _______ 6. Would you expect threonine to interact with or “hide” from water? _____________ 7. Cells are made of mostly water and proteins are found inside of cells. Given what you know about

threonine’s variable group would you expect to find the threonine amino acid on the outside of a large 3D protein, or hidden away in the middle of the protein? _____________

8. The 3D shape of the protein molecule is critical. If a protein is to work properly inside one of your cells, it must be folded correctly. If the 3D structure is incorrect, the protein may cease to function. Consider the following two scenarios: Scenario A: You substitute one hydrophilic amino acid for another hydrophilic amino acid, in the primary structure. Scenario B: You substitute one hydrophilic amino acid for a hydrophobic amino acid, in the primary structure. Predict which scenario will have a greater impact on tertiary structure of the protein and explain why you think so.

Enzyme Structure and Function Background: We’ve been talking about different kinds of reactions that occur in your body (like dehydration synthesis and hydrolysis) and how molecules change. Does this just happen on its own? If you leave a piece of meat in a Petri dish, will it just break down into amino acids all by itself? No! What will break down proteins? How do we break down the food that we eat? Enzymes! Part 1: Take notes on Enzyme structure and function below, and then complete the activity that follows. Key vocab words (make sure you define and highlight/underline) these words in your notes below: catalyst, activation energy, reactant, product, enzyme, substrate, active site, denature, induced fit Reactions in the body Catabolic (usually exergonic) Anabolic (usually endergonic) What are enzymes? What do enzymes do? Why are they important? What do enzymes look like?

How do enzymes work? (Induced Fit Model) Enzyme/Substrate specificity: What affects enzyme function? Temperature pH Substrate concentration Review Questions: 1. In the following equation, label the reactant(s), product(s), and enzyme(s):

oxygen water peroxidehydrogen catalase +⎯⎯ →⎯

2. Enzymes belong to which category of organic molecule?

3. What is the function of an enzyme?

4. What is activation energy?

5. What is a substrate?

6. Where is the active site located?

7. What happens to the substrate during the induced fit process?

Packet #3 Study Guide – Biochemistry (Part 1) Content of Exam: You are responsible for understanding the concepts from in-class activities, laboratory experiments, homework assignments, articles and readings. You should also be able to apply the concepts learned in this unit to new examples. All students must make a 3 x 5” index card, front and back, for use during the exam. Everyone is required to make one; you will turn this in on the day of the exam. It must be hand-written unless you have an accommodation (see me ahead of time). I suggest that as you study, identify concepts that give you the most difficulty and use the index card for those concepts. If you need an index card, let me know. Making your own study sheet – Please type your work (exceptions can be made for those who have very neat, easily readable handwriting). Do not attempt to cram everything into one page; expect it to be multiple pages. You do not need to write in complete sentences, but your answers should be thorough and clear. Please number your questions and do your best to answer them in order. You should incorporate the question into your answer OR download this document from the class website and place your answers after the questions and bring in a hard copy. Your study sheet should be made so that it will be useful to you for the final exam, so explain things such that when you are reviewing this sheet in six weeks, it will be clear to you in the future. The following list of questions is NOT comprehensive, but a starting point for your studying. Make sure you study all journals, labs, and notes sheets. Fundamentals of Life (atoms and bonds) 1. Draw the structure of an atom, including the locations of all three subatomic particles. 2. Describe the two types of bonds. Water properties (including pH lab) 3. How does the polarity of a water molecule contribute to its ability to form hydrogen bonds? 4. How does the ability of a water molecule to form hydrogen bonds contribute to water’s other

properties, like cohesion, adhesion, and surface tension? 5. What is the pH range of something that is acidic? Basic? 6. What is a buffer and where would you find one in nature? How are atoms arranged in molecules of living things and Organic Chemistry Notes 1. What is a monomer? Give one example for each of the macromolecule types. 2. Draw 2 amino acids. Show what happens when dehydration synthesis forms a dipeptide. 3. Draw the following molecules: Glucose, Amino Acid, Glycerol, Fatty Acid. 4. Circle and label the following groups on the above amino acid:

a. variable (R) group b. carboxylic acid group c. amine group

5. What is the difference between a saturated and unsaturated fatty acid? 6. Why is it better to consume unsaturated fatty acids than saturated fatty acids?

7. For lipids, carbohydrates, proteins, and nucleic acids: a. The structure/shape of the molecule b. The function or uses of the molecule in the human body c. The monomers and polymers of each d. The processes that break them apart (hydrolysis) and build them up (dehydration synthesis)

Nutrient Testing Lab 8. What is the purpose of a negative control? What were the negative control groups for Iodine in this

experiment? 9. What is the purpose of a positive control group? What were the positive control groups for Iodine

in this experiment? 10. What are controlled variables? What are some examples of controlled variables in this lab? 11. What kinds of food typically contain starch? Protein? 12. a. What indicator did you use to identify protein?

b. What change in color did you see? c. Name 2 substances that contain protein.

13. a. What indicator did you use to detect starch? b. What color change did you see? c. Name 2 substances that contain starch.

Protein Folding 14. Explain the four levels of protein structure. 15. What happens to a protein if a hydrophilic amino acid is replaced by a hydrophobic one? Discuss

the effects on the protein in terms of structure and function. What if a charged amino acid is replaced with a nonpolar one? What kind of bond holds one amino acid to another within a protein? What kind of bond holds the protein in its 3D structure?

Enzyme Structure and Function and Investigating Enzyme Activity 16. What is an enzyme? What is a substrate? What is an active site? 17. How do enzymes work? (general and detailed) 18. What would happen to enzyme activity if you heated the enzyme? What is happening to the

enzyme itself? 19. What would happen to the activity of enzymes if you cooled the enzyme? Why? 20. What would happen to the activity of an enzyme if you lowered the pH? Why? 21. What would happen to enzyme activity if you increased the surface area of the substrate? Why?

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