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BCLN BIOLOGY 12 – Rev July 2014

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Unit 2 ~ Learning Guide Name:________________ INSTRUCTIONS Complete the following notes and questions as you work through the related lessons. You are required to have this package completed BEFORE you write your unit test. Do your best and ask questions about anything that you don't understand BEFORE you write the unit test. U2L1 NOTES: INTRODUCTION (web notes) Carbon ________________ is the basic element for life. It is a non-metal that must bond with other non-metals to become stable. When two non-metals bond together they form covalent bonds. Covalent bonds are formed when a pair of atoms share electrons (_______________________________________________________). Atoms will share electrons in order to complete the complement of electrons in their outermost electron shell. Carbon can share electrons with as many as 4 other atoms to form chains or rings.

IF YOU HAVE NOT COMPLETED CHEMISTRY 11 or 12 IN THE PAST YEAR YOU SHOULD VIEW THE TUTORIAL ON COVALENT

BONDING BEFORE PROCEEDING ANY FURTHER! Drawing each bond in a molecule as two dots gets old very fast. To save time chemists usually depict a bond as a line drawn from ______________________________ to another. Such representations are called_____________ structures rather than Lewis electron dot structures. Rings can also form: ______________________________________________________________________________ for the unit molecules, which make up the life compounds. On the right is a carbon ring which is classified as a carbohydrate. Examples: of life compounds are _________________, ____________________, ______________________ and Nucleic Acids.


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Dehydration Synthesis Unit molecules join together to form larger molecules called Polymers. _________________, ________________________, _______________, and ___________________________are all polymers. To join the unit molecules (or building blocks) together, a molecule of ___________ must be removed. _____ is taken from 1 molecule and ______ from the other molecule. This process is called _____________________________________________ and energy is required. To help remember this chemical reaction, think of what is happening to you as you lose water - you dehydrate. The word synthesis means to make. So we are making something by taking water away.

Hydrolysis If instead of making a larger molecule from smaller units we want to break down a polymer, a molecule of ______________ must be ________________. This process is called ______________________ and energy is required. Sometimes breaking words down will help you understand them. Hydro - refers to water and lysis means to break apart. The diagram on the right compares dehydration synthesis to hydrolysis. Note that condensation synthesis in the diagram refers to dehydration synthesis.


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U2L1 PRACTICE: INTRODUCTION

1. List the 4 major classes of carbon-containing life molecules that will be studied in this unit and throughout the course? a. ______________________________

b. ______________________________

c. ______________________________

d. ______________________________

2. Define the following terms: a. monomer

b. polymer

c. dehydration synthesis

d. hydrolysis


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U2L2 NOTES: CARBOHYDRATES (web notes) Carbohydrates: are sugars. We will look at 3 groups of carbohydrates;; the monosaccharides (mono - meaning one), the disaccharides (di-meaning two), and the polysaccharides (poly - meaning many). The elements in all carbohydrates are: _______________________, ____________________, and ______________________. The ratio of hydrogen atoms to oxygen atoms is always ___________ and the empirical formula for carbohydrates is _____________ 1. Sugars: ________________________________________________________. We will start by looking at the monosaccharides of which there are two groups. There are 5 carbon sugars (pentoses) and the 6 carbon sugars (hexoses). For the purpose of this unit we are only concerned with the hexose monosaccharides, but below are some examples of the pentose sugars. Note the 5 carbon rings.

a) __________________________: 5 or 6 carbon sugars (simple sugars)

i) Pentoses: _____________________________________

Examples: Ribose and Deoxyribose (1 less oxygen than ribose)

RIBOSE (in RNA) DEOXYRIBOSE (in DNA)

As chains. As rings.


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ii) Hexoses: ___________________________ (note the six carbon rings to the right)

3 example of hexoses that you need to know for this course are: fructose, glucose, and galactose.

Fructose Glucose Galactose

All have the formula ____________________, however if you examine their structural formulas, you will find the difference in the organization of ________________________. Looking at the 3 diagrams. You will see that all 3 monosaccharides have the exact same number of carbon to hydrogen to oxygen atoms. The difference between the 3 monosaccharides is the way these atoms are arranged. They are called ______________________. There Are Three Ways to Represent the Structure of Glucose (shown below)

YOU SHOULD WATCH THE MONOSACCHARIDES VIDEO BEFORE PROCEEDING ANY FURTHER!


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b) Disaccharides: are _____________________________________________ ________________________________________________________________

They have the common formula C12H22O11 3 Common Disaccharides along with their building blocks that you will need to know for this course are:

i) Maltose: _______________________________________ ii) Sucrose: ______________________________________ iii) Lactose: ______________________________________

YOU SHOULD WATCH THE DEHYDRATION SYNTHESIS OF TWO MONOSACCHARIDES VIDEO AND THE DISACCHARIDES VIDEO

BEFORE PROCEEDING ANY FURTHER!

c) Polysaccharides: The 3 common polysaccharides that you need to know for this course are: ____________________, _____________________, and __________________________ (be sure that you can recognize a diagram of their structure and know the function of each of these)

- the polysaccharides are long chains of glucose molecules bonded together (simple sugars) - the basic formula for these polymers is (C6H10O5)n

n = dozens to thousands of glucose units

i) Starch: Is the ___________________________________ _____________________________________________________________ -starch is made up of many glucose molecules bonded together in long chains with a ________________________.

Structure of Starch


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ii) Glycogen: Is the "_________________________" (in other words excess glucose in animals is stored as glycogen) in liver and muscle tissue.

- like starch Glycogen is also made up of long chains of glucose molecules, however it has ________________________________ instead of just a few

Structure of Glycogen Between meals - as [glucose] in blood decrease, the

________________________________________________________ ________________________________________________________ ________________________________________________________ to raise blood [sugar] to 0.1%. -After meals - [glucose] in the blood increase as food is digested. The excess glucose is converted into glycogen and stored in the liver and muscle tissues for later use.

iii) Cellulose: Is ________________________________________________ __________________________________________.

-Cellulose is formed in the cell walls of plants and gives pants their structure -Cellulose is made of long chains of glucose molecules with ____________________________________________ -There is a different type of linkage between the sugars found in cellulose as compared to starch or glycogen.


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Our digestive system is ___________________ to digest this linkage. Cellulose passes through our system as _________________________________________. It may be important for good health and prevention of colon cancer.

Structure of Cellulose Please note that each successive "glucose" is "flipped" relative to the previous one and that our body is unable to break this bond and thus, is unable to digest cellulose. As a result, cellulose serves simply as "roughage" in our diet. Functions of Carbohydrates

a) ___________________________________________________________ _____________________________ (all carbohydrates)

-Energy is released as the carbohydrates are broken down by hydrolysis

b) ______________________________________________ (cellulose) c) ___________________________________________________________ ____________________________ (starch/glycogen)

U2L2 PRACTICE: CARBOHYDRATES 1. What is the empirical formula for carbohydrates? _____________


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2. Define the following terms and give two examples of each.

Monosaccharide-

Disaccharide-

Polysaccharide-

3. Name the three disaccharides that you need to know for this course.

4. Identify the building blocks or monomers that come together to form each of the disaccharides that you listed above.

5. Name the three polysaccharides that you need to know for this course.


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6. Describe how you can distinguish the structures of each of these polysaccharides. Look at the examples closely and come up with a way to memorize which is which and then explain it (do not just simply draw each structure).

7. State the functions of each of these polysaccharides.

8. Why is cellulose considered "roughage" in our diets?


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U2L3 NOTES: LIPIDS (web notes and video) Lipids: _______________________________________________________________ We eat lipids as part of our food group. Our bodies are capable of producing them as well as metabolizing them. Next to glucose, _____________________ ___________________________________________________ for us. Unforunately, we store them in adipose (________) cells. They function as a _____________________________________, _______________________________, and ______________________. The three lipids you need to know for this course are the fats, phospholipids and steroids. Lipids such as those shown above typically contain the elements: Carbon, hydrogen, and oxygen but, in contrast to carbohydrates, the H:O ratio is greater than 2:1. ____________________________ are one of the two building blocks of neutral fats and are non-polar chains of carbon and hydrogen with a carboxylic acid end. A tremendous number of variations exist between fatty acids (be sure that you can recognize a diagram of both saturated and unsaturated fatty acids as shown below). Saturated fatty acids those compounds ______________________________________ between the carbon atoms. In other words these molecules are holding all the hydrogen atoms that they can. Other fatty acids are unsaturated (compound with _____________________________________________________________________).

Structure of a Saturated versus Unsaturated Fatty Acid Chain.

Please note that the circled atoms represent the carboxylic acid end to the fatty acid while the squared bonds represent the double bond or unsaturated point of the

unsaturated fatty acid chain.


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Neutral Fats Basic Structure of a Neutral Fat: __________________________________________ _____________________________________________________________________.

Dehydration synthesis of a triglyceride.

Please note that X represents the glycerol backbone and Y represents the three fatty acid chains that come together to form the triglyceride.

§ Monoglyceride - one fatty acid attached to a glycerol. § Diglyceride - two fatty acids attached to a glycerol. § Triglyceride - three fatty acids attached to a glycerol.

A) Fats (saturated fats): Usually of animal origin and are ___________________ _____________________________. Examples: Adipose tissue, Lard, Butter

YOU SHOULD WATCH THE NEUTRAL FATS VIDEO

BEFORE PROCEEDING ANY FURTHER! Oils, Waxes, and Steroids

B) Oils (unsaturated fats): Usually of plant origin and are __________________ _________________________________________________________________.

- Polyunsaturated fats have many double bonds therefore few hydrogen bonds. Examples: Vegetable oils

C) Waxes: Relatives of fats, they have fatty acids joined to a long _____________ _________________________________________________________________. D) Sterolds: Compounds such as sex hormones, cholesterol, and some of the ingredients of bile. Instead of a straight chain of carbon, steroids are non-polar ring


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structures. They are insoluble in water therefore considered a lipid.

Example: ______________________- important part of cell membrane and the protective cover around nerve fibres.

Note: Cholesterol is important, but too much results in __________________________ ____________________________________. This narrows the pathway for blood so the heart has to pump harder to push the blood through the body (i.e., increase ___________________________). Cholesterol is the imporant part of the cell membrane and the protective cover around nerve fibres. ___________________ such as _____________________________ are able to pass through cell membranes and combine with receptors in the cell. The steroid receptor complex activates certain genes leading to ____________________________. Increase protein synthesis is better for the athlete for muscle development.

YOU SHOULD WATCH THE STEROIDS VIDEO BEFORE PROCEEDING ANY FURTHER!

Phospholipids

E) Phospholipids Phospholipids are a variation of a triglyceride where one of the 3 fatty acids is replaced with a _______________________________________________ ________ group. (Note the glycerol backbone and 2 fatty acids along with the phosphate group)

Structure of a Phospholipid.

Note that the phosphate and nitrogen containing group is circled. This creates a polar region and consequently phospholipids can mix with both polar (likes water) and non-polar (dislikes water) materials.


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Phospholipids are very important in cells as they form much of the cell membrane.

The Heads of phospholipids are polar and are said to be water loving. (________________) The Tails of the phospholipids are non polar and are said to be water hating. (____________________). Because they have water soluble heads and water insoluble tails they tend to form a thin film on water with their tails in the air like above.

YOU SHOULD WATCH THE PHOSPHOLIPIDS VIDEO BEFORE PROCEEDING ANY FURTHER!

U2L3 PRACTICE: LIPIDS 1. What are the three major types of lipids that you need to know for this course?

2. Fill in the lipid summary table found below.

Lipid Chemical Structure Biological Function

Neutral Fat


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Phospholipid

Steroids

3. How do the bonds differ in a saturated versus unsaturated fatty acid tail?

4. The diagram below represents an important type of lipid: a. What type of lipid does the diagram represent?

b. What cell structure is this lipid primarily responsible for forming?

c. Please place a circle/oval ( ) around the glycerol backbone, a rectangle ( ) around the fatty acid tails and a cloud ( ) around the phosphate/nitrogen group.

d. Identify/label which portion of the molecule is hydrophobic and which portion is hydrophilic.


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e. Define hydrophobic and hydrophilic.

Diagram for Question 4

5. Steroids have a very different structure than the other types of lipids: a. Please describe the characteristic structure of a steroid.

b. Please explain why steroids are classified with other lipids.


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c. Please identify two important steroids in the human body and briefly explain their functions.

U2L4 NOTES: PROTEINS (web notes and video) Proteins

• Made of the elements: Carbon, hydrogen, oxygen and nitrogen. Sulfur is often present and phosphorus and iron are sometimes included.

• The Basic structure of all proteins are: long __________________________ _____________________________________ (or what is called a polypeptide)

• Amino acids - there are __________________________________________________ with the general structure like the one below

Be sure that you can identify the different parts of an amino acid. Note the amine group, the carboxylic acid, the central carbon bonded to a hydrogen and finally the radical (R) group. R = A variety of other atoms that distinguish one amino acid from another. There are 20 different amino acids so there 20 different R groups.


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YOU SHOULD WATCH THE BUILDING BLOCKS OF PROTEINS VIDEO

BEFORE PROCEEDING ANY FURTHER! Dehydration Synthesis ______________________________________ of amino acids will result in the bonding of amino acids together and the release of ___________________________________. If we consider the amino acids glycine and alanine, they will bond together and produce the dipeptide "glyala". A.A are joined by a ______________________________. A dipeptide has one peptide bond where a Tripeptide has two peptide bonds holding three amino acids together and so on. The order and combination of these A.A determines the type of __________________ that is produced. The term ___________________________ means numerous peptide bonds that join many amino acids together. Levels of Protein Structure - Primary Proteins This refers to the way in which a protein molecule is assembled and the factors that cause its specific three dimensional shape. There are four levels to protein structure of which you need to know the first 3 including the bonds that hold them in these shapes. Remember that chains of amino acids (the subunits or building blocks) which make up a protein are called _________________________.


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The first, or primary structure as it is called, is simply a straight __________________ _______________________________________. Note the ______________________ ________________ that bind these amino acids together. Because there are twenty different amino acids, it is easy to realize that there are literally millions of different variations of amino acid sequences - each with many (some with hundreds of) amino acids. Consequently, there are millions of proteins. Secondary Structures As the chains of amino acids get longer they begin to _____________________________ _____________________________ ____________________________. This is a result of the stress on the bond angle. ______________ ___________ form between the Hydrogen of one amino acid and an Oxygen further down the chain. An alpha helix contains 3.6 amino acids per spiral. There are other secondary structures, but the alpha helix is the most common and the one you will need to know for this course. Protein Structure - Tertiary and Quaternary Structures The third level is described as _____________________________ _____________________________________________________ _______________________________________________. As the helix gets longer there are some amino acids that cannot fit the configuration and therefore cause ___________. New bonds can form to hold it into a three-dimensional shape. The types of bonds are __________________________________________________ _____________________________________________________. It occurs in some protein systems, _______________________________, where different three-dimensional configurations are associated with and function with each


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other. _______________________ is a well-known protein that is actually made up of the association of four 3 dimensional shapes around a central heme (iron containing) component. YOU SHOULD WATCH THE LEVELS OF PREOTEIN STUCTURE VIDEO BEFORE PROCEEDING ANY FURTHER! Denature The weaker hydrogen and ionic bonds of the tertiary structure ____________________. They are very sensitive to thing like _________________________________________ _____________________________________________________________________ ___________________________________________________. If a protein's normal shape is destroyed because of such environmental conditions, it is said to be __________________________ (it will not work). Without the enzyme's normal shape, the enzyme is unable to combine efficiently with its substrate and therefore, no chemical reaction will occur. Examples we can see:

• This is what happens when milk spoils. The protein in milk, Caesin, denatures and becomes insoluble, forming floating lumps.

• Egg white is protein. Excess heat denature the protein. (fried or poached) • Cooking Liver.


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Be sure you understand these 4 important points about protein/enzyme denaturing:

1. The enzyme loses its normal three dimensional shape, changing the shape of it's active site

2. Due to the change in the shape of the enzyme's active site the enzyme can no longer bind to it's substraight

3. Because the protein (or enzyme) can no longer bind to it's substrate the enzyme cannot perform it's normal function

4. Therefore, _______________________________________________________. When enzymes in the human body denature, the biochemical pathway they work in no longer functions and the result is desease or possibly even death.

YOU SHOULD WATCH THE DENATURE VIDEO BEFORE PROCEEDING ANY FURTHER!

Functions of Proteins 1. FUNCTIONAL

• Enzymes (__________________________________________), reactions that will take 7 hours will take only a fraction of a second.

1. Maltase - Converts maltose to glucose and glucose 2. Carbonic Anhydrase: In blood, maintains blood pH

• ________________________________ - Hemoglobin - Transports O2, CO2, and H+

• Infection fighting - ______________________________________________

2. STRUCTURAL -___________________________________ ____________________________________

Keratin - ____________________________ Collagen - ___________________________ Actin/myosin - muscle fiber for movement


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U2L4 PRACTICE: PROTEINS 1. Identify the basic building block (monomer) of all proteins.

2. Draw the generic structure of the basic building block of proteins and clearly labeling its 4 key parts.

3. A dipeptide is: a. formed by what type of reaction?

b. held together by what type of bond? c.

4. Please describe the following levels of protein structure including the types of bonds that are involved: a. Primary

b. Secondary


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c. Tertiary and Quaternary 5. Describe what is meant when we say a protein/enzyme is denatured.

6. Identify at least three factors that can denature proteins/enzymes.

7. Define enzyme and give two examples of enzymes and their functions in the human body.

8. Describe what is meant by a structural protein and provide two examples in the human body.


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U2L5 NOTES: NUCLEIC ACIDS (web notes and video) Nucleic Acids - are made up of ___________________ ____________________________. A nucleotide has 3 components to it, a sugar, a phosphate group, and a nitrogenous base. Be sure that you can label and recognize and label a nucleotide's structure. DNA and RNA There are three types of nucleic acids. _____________________ are the genetic material and are involved in the functioning of chromosomes and protein synthesis and ATP. We will study DNA and RNA in more detail in a later unit. ATP (______________________________________________________)

• One particularly important nucleic acid is the modified nucleotide known as ATP.

• ATP is quite simply an RNA nucleotide with an adenine base ________________________________________________________________ _____________________________________________. Note the ~ line in between the phosphate groups used to indicate high energy bonds.


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Phosphate bonds are unique in that they are very rich in energy. Cells store energy as Chemical energy in this way. In order to release the energy, an enzymes, ATPase, breaks one of the bonds, thus producing ADP (adenosine diphosphate) and energy. ADP can be recycled. We can add a phosphate group back to the ADP with a small input of energy and we get an ATP molecule back.

• In this way, ATP is often called the energy currency of a cell (because cells make and "spend" ATP). We can use the analogy that various forms of molecules in our body are like various forms of monetary currencies in the world such that: Molecules of the body…

à à à

…are comparable to monetary currencies …

Savings Bond à Bank Account à Piggy Bank à Pocket Cash


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ATP ADP + P + Energy (7 Kcal per mole)

• ATP molecules can be moved all over the body. When energy is needed, the 3rd phosphate group is broken off. This results in Adenosine Diphosphate (ADP) and the release of heat energy. _________________________________________ _________________________________________________.

YOU SHOULD WATCH THE NUCLEIC ACID VIDEO

BEFORE PROCEEDING ANY FURTHER! U2L5 PRACTICE: NUCLEIC ACIDS 1. Identify the basic building block (monomer) of nucleic acids.

2. Draw the generic structure of the basic building block of nucleic acids and label its three key parts.

3. ATP is a key nucleotide in the human body: a. What does "ATP" stand for?

b. What is ATP's primary function?


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c. Does ATP release energy when it is being formed (dehydration synthesis) or broken down (hydrolysis)?

~ END OF UNIT 2 LEARNING GUIDE ~


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UNIT 2 ANSWER KEY U2L1 PRACTICE: INTRODUCTION

1. List the 4 major classes of carbon-containing life molecules that will be studied in this unit and

throughout the course?

a. ______________________________

b. ______________________________

c. ______________________________

d. ______________________________

2. Define the following terms :

a. monomer

b. polymer

c. dehydration synthesis

d. hydrolysis

U2L2 PRACTICE: CARBOHYDRATES 1. What is the empirical formula for carbohydrates? _____________


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2. Define the following terms and give two examples of each.

Monosaccharide-

Disaccharide-

Polysaccharide-


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3. Name the three disaccharides that you need to know for this course.

4. Identify the building blocks or monomers that come together to form each of the disaccharides that you listed above.

5. Name the three polysaccharides that you need to know for this course.

6. Describe how you can distinguish the structures of each of these polysaccharides. Look at the examples closely and come up with a way to memorize which is which and then explain it (do not just simply draw each structure).

7. State the functions of each of these polysaccharides.


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8. Why is cellulose considered "roughage" in our diets? U2L3 PRACTICE: LIPIDS

1. What are the three major types of lipids that you need to know for this course? (3 marks)

2. Fill in the lipid summary table found below.

Lipid Chemical Structure Biological Function

Neutral Fat


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Phospholipid

Steroids

3. How do the bonds differ in a saturated versus unsaturated fatty acid tail?


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4. The diagram below represents an important type of lipid:

a. What type of lipid does the diagram represent? (1 mark)

b. What cell structure is this lipid primarily responsible for forming? (1 mark)

c. Please place a circle/oval ( ) around the glycerol backbone, a rectangle ( ) around the fatty acid tails and a cloud ( ) around the phosphate/nitrogen group.

d. Identify/label which portion of the molecule is hydrophobic and which portion is

hydrophilic.

e. Define hydrophobic and hydrophilic.

Diagram for Question 4

5. Steroids have a very different structure than the other types of lipids:

a. Please describe the characteristic structure of a steroid.


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b. Please explain why steroids are classified with other lipids.

c. Please identify two important steroids in the human body and briefly explain their functions.

U2L4 PRACTICE: PROTEINS

1. Identify the basic building block (monomer) of all proteins.

2. Draw the generic structure of the basic building block of proteins and clearly labeling its 4 key parts.

3. A dipeptide is:


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a. formed by what type of reaction?

b. held together by what type of bonds

4. Please describe the following levels of protein structure including the types of bonds that are involved:

a. Primary

b. Secondary

c. Tertiary and Quaternary


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5. Describe what is meant when we say a protein/enzyme is denatured?

6. Identify at least three factors that can denature proteins/enzymes.

7. Define enzyme and give two examples of enzymes and their functions in the human body.

8. Describe what is meant by a structural protein and provide two examples in the human body.


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U2L5 PRACTICE: NUCLEIC ACIDS

1. Identify the basic building block (monomer) of nucleic acids.

2. Draw the generic structure of the basic building block of nucleic acids and label its three key parts

3. ATP is a key nucleotide in the human body:

a. What does "ATP" stand for?

b. What is ATP's primary function?


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c. Does ATP release energy when it is being formed (dehydration synthesis) or broken down (hydrolysis)?

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