Biochemistry: The Chemistry of Living Things
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 The accepted procedure for completing this remedial assignment is to “save-as” to your own directory, complete the questions assigned, save and send via Email to rstevenson@papcs.com
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Of course, there are other ways … You could contribute to the murder of our forests and print the thing and then turn in … I leave it up to your good judgment. Do seek out clarification if any of this seems confusing.
 Note: There is much on this CD that is to be considered background chemistry. If you don’t have the background then you are encouraged to spend some time going through it. For the purposes of this remedial assignment I have chosen to focus on the organic chemistry material (the stuff of your curriculum … the stuff that you will be examined on … you get the picture).
Biochemistry (The essentials) o The structure of an atom (e.g., negative electrons occupy most of the space in the atom; neutrons and positive protons make up the nucleus of the atom; protons and neutrons are almost two thousand times heavier than an electron; the electric force between the nucleus and electrons holds the atom together) o The electron configuration of atoms governs the chemical properties of an element as atoms interact with one another by transferring or sharing the outermost electrons o Atoms may be bonded together into molecules or crystalline solids, and compounds are formed from chemical bonds between two or more different kinds of atoms o Chemical reactions can be accelerated by catalysts (e.g., enzymes) o The chemical reactions involved in cell functions (e.g., food molecules taken into cells are broken down to provide the chemical constituents needed to synthesize other molecules; enzymes facilitate the breakdown and synthesis of molecules) o The structures of proteins (e.g., long, usually folded chain molecules made of specific sequences of amino acids coded by DNA) and the role of proteins in cell function o The chemical and structural properties of DNA and its role in specifying the characteristics of an organism
(e.g., DNA is a large polymer formed from four kinds of subunits; genetic information is encoded in genes as a string of these subunits; each DNA molecule in a cell forms a single chromosome and is replicated by a templating mechanism to biological processes.
What is a hydrogen bond and how strong is it?
A hydrogen bond is a weak electrical attraction between an electronegative atom and a hydrogen atom bonded to another electronegative atom, such as oxygen or c and Inorganic Formulas
Biochemistry: View Scenes 18 – 21 and complete the exercise below.
Examine the chemical and structural formulas of organic and inorganic compounds.
Multimedia
Presentation

Scenes 18 – 19
1. Follow the Formula: this picture shows 3D models of various molecules, as well as chemical and structural formulas.
1a. What is the difference between a chemical formula and a structural formula?
A chemical formula shows the number of atoms of each element in a molecule. A structural formula shows, in addition, how atoms are bonded together.
1b. Explain the three types of covalent bonds and cite examples of each shown in this picture.
Single bond: methane and water; Double bond: Oxygen molecule and carbon dioxide; Triple bond: nitrogen molecule.
1c. How are covalent bonds represented?
The number of lines drawn between the bonded atoms indicates the type of bond.
Scenes 20 – 21
2a. What element is always found in organic compounds? What other elements are commonly found in organic compounds?
In all organic compounds carbon is an essential element. Also, hydrogen, oxygen, nitrogen, phosphorous and sulfur are commonly found in organic compounds.
2b. What produces organic compounds?
Organic compounds are essentially the stuff of life, produced by life and comprising life.
2c. Name some inorganic compounds that contain carbon.
Carbon monoxide and carbon dioxide
2d. Name some compounds essential to life that are not classified as organic compounds.
Water, carbon dioxide, various salts
Scenes 18 – 21
3. Are the basic chemical principles any different for organic and inorganic compounds? Explain.

No. The chemistry of organic and inorganic compounds follows the same principles. The distinction is simply a classification.
Biochemistry: Complete Interactive Tutorial #3
Identify chemical structures.
Interactive
Tutorial
Water
Biochemistry: View Scenes 22 – 28 and complete the exercise below.
You will learn in these scenes about the properties of water that are crucial to life.
Multimedia
Presentation
Scene 22
1. Why is water the most important compound for life on earth?
All living things need water to survive.
Scenes 23 – 24
2. Sticky Water: this picture shows water molecules bound together.
2a. What bond is formed between water molecules and what is the physical effect of these bonds?
Hydrogen bonds cause the water molecules to stick together so that water flows and forms drops.
2b. Describe how cohesion determines the ability of water to store heat without drastic changes in temperature. Why is this property important to life?
Hydrogen bonds absorb the increased movement of water molecules as heat is applied. Because organisms are mostly made up of water, this heat storage allows them to survive a wider range of temperatures.
Scenes 25 – 26
3a. These pictures illustrate ammonia and salt being added to water. Using these examples, explain how the property of adhesion makes water a good solvent.
Water adheres (clings many substances because of its polar molecules. Substances with polar molecules such as ammonia readily form hydrogen bonds with water, causing them to dissolve. Ionic compounds, such as table salt, are dissolved by the polar charges of water into positively and negatively charged ions.
3b. Why is the ability of water to dissolve ions

important to life?
The water of living cells contains a great variety of dissolved ions essential to life.
Scene 27
4. Define capillary action and cite an example in nature.
Capillary action is the tendency of water to move upward in a thin tube because of adhesion between the water molecules and the sides of the tube. Plants use capillary action to help transport water from the soil to the leaves.
Scene 28
5. Water ’s Slice of Cell Pie: this illustration shows a cell superimposed on a pie chart. Complete the table. cell component a. Water b. Organic compounds c. Minerals
% by weight
Carbohydrates
Biochemistry: View Scenes 29 – 32 and complete the exercise below.
Examine carbohydrate structure and formation.
Multimedia
Presentation
Scenes 29 – 30
1. Sugar Connection: this graphic shows structural formulas for glucose and maltose, and how sugar molecules can combine.
1a. What is the biological function of carbohydrates?
Carbohydrates are important energy storing compounds.
1b. A carbohydrate is composed of what elements in what ratio?

Carbohydrates are made of carbon, hydrogen and oxygen in a 1:2:1 ratio.
1c. What are the simplest carbohydrates called, what is the most common example of a simple carbohydrate, and what is its primary source in nature?
The simplest are monosaccharides (single unit sugars), the most common example being glucose, the sugar produced by plants during photosynthesis.
1d. What is dehydration synthesis?
Dehydration synthesis is the process by which sugar
(saccharide) molecules bond together (also known as condensation in some text b ooks).
1e. What kind of molecular facilitation is necessary for dehydration synthesis to occur?
Dehydration synthesis is brought about by the action of enzymes.
1f. When a dehydration synthesis bond occurs what is removed from the original sugars?
A hydrogen atom is removed from one sugar and a hydrogen and oxygen are removed from the other, molecule.
1g. Maltose is an example of what type of sugar?
Maltose is a disaccharide.
Scene 31 forming one water
2. Chains of Sugar: this diagram shows the chain structures and structural formulas for three different polysaccharides. (The carbons in the ring structures are not labeled.)
2a. Define polysaccharide .
Polysaccharide: a molecule formed when three or more simple sugars join.
2b. How long are polysaccharide chains?
They have no fixed size, and might contain hundreds or thousands of glucose units.
2c. The chain structure of cellulose differs in what way from the chain structures of starch and glycogen?
Cellulose polysaccharide chains do not branch.
2d. Complete the table, indicating where each polysaccharide is found and its function.
Starch
Glycogen
Cellulose
Where found
Scene 32
3a. Starch on the March: this graphic
Function

shows a starch polysaccharide chain. Define hydrolysis, including what must be present for hydrolysis to occur.
Hydrolysis is the process whereby disaccharides and polysaccharides are disassembled into simpler sugars. Water molecules must be available, and enzymes must be present to carry out the chemical reaction
3b. Where on the polysaccharide does hydrolysis take place?
Hydrolysis takes place at the oxygen atoms linking the rings together.
4. How is hydrolysis like dehydration synthesis and how is it different?
Lipids
Scene 33
1. Give several examples of lipids. What do all lipids have in common?
Fats, oils, waxes, phospholipids and steroids are lipids. Lipids are not water-soluble.
Scenes 34 – 36
2. Formulas For Fat: this diagram shows the structural formulas of a saturated fat (top) and a polyunsaturated fat (bottom). The shaded blocks are numbered below.
2a. Which numbered block includes the glycerol sugars?
Block 1
2b. Which numbered block includes the carboxyl groups?
Block 2
2c. Which numbered block includes the hydrogen and carbon chains of both molecules?
Block 3
2d. Which blocks include the fatty acids?
Blocks 2 and 3: the chains of carbon and hydrogen with an acid group, known as a carboxyl group, at one end.
2e. In a molecule of a simple fat, how many fatty acids are there and how many glycerol sugars?
A simple fat has three fatty acids and one glycerol sugar.
2f. What does letter a indicate?
A carbon-to-carbon single bond
2g. What does letter b indicate?
Two carbon-to-carbon double bonds
2h. When is an unsaturated fat considered polyunsaturated?
When it has more than one double or triple carbon-to-carbon bond in its fatty acids
2i. What is the importance of lipids and how do they compare to carbohydrates?
Lipids store energy, about twice as much per molecule as carbohydrates .
Scene 37
3. Fat Chance: this illustration shows sources of saturated and unsaturated fats.
3a. How do unsaturated and saturated fats differ in

their physical state at room temperature?
Unsaturated fats tend to be oil; saturated fats tend to be solid.
3b. Describe the process of hydrogenation.
Hydrogen atoms are added to an unsaturated fat, changing the double and triple bonds in the carbon chain to single bonds, thus converting an unsaturated fat into a saturated fat.
3c. What is the purpose of partial hydrogenation? Give an example.
Margarine is an example of partially hydrogenating oils so that they are solid at room temperature. Without any hydrogenation margarine would be fluid oil, and with complete hydrogenation it would be a brittle solid.
Scene 38
4. Heart of the Matter: this graphic shows a cholesterol molecule and the effect of cholesterol on the heart. What are the heath effects of saturated versus unsaturated fats?
Saturated fats increase blood cholesterol levels, causing deposits to build up on the walls of arteries (A and B), thus narrowing and hardening them and leading to heart disease.
Unsaturated fats tend to decrease blood cholesterol levels. Red meat
Biochemistry: Complete Interactive Tutorial #6
Bond formation in carbohydrates and lipids.
Interactive
Tutorial
Proteins
Biochemistry: View Scenes 39 – 43 and complete the exercise below.
Examine the structure and function of proteins.
Multimedia

Presentation
Scene 39
1. Proteins At Work: These images show various protein types. Complete the entries.
Type Function or example
Structural
Transport
Antibodies
Enzymes
Scene 40
2. Amino Architecture: this diagram shows amino acid building blocks. The questions correspond to the lettered labels.
2a. What is the nitrogen-containing group called?
An amino group
2b. What is the COOH group called?
A carboxyl group
2c. What is the “core” of an amino acid molecule?
A central carbon atom
2d. What building block is represented by R and what is its significance ?

Scenes 41 – 42
3. Peptide Preparation: this diagram shows amino acids joined by peptide bonds .
3a. Peptide bonds form between which two groups?
Peptide bonds form between the carboxyl group and the amino group.
3b. What is the byproduct of peptide bond formation, and what does it come from?
Peptide bond formation produces a water molecule, with an OH from the carboxyl group and an H from the amino group.
3c. You have seen this process previously. What is it called?
Dehydration synthesis (condensation reaction in some textbooks)
3d. What are two joined amino acids called?
A dipeptide
3e. What is a chain of joined amino acids called?
A polypeptide
Scene 43
4. Identify and explain the class of protein that facilitates chemical reactions.
Cells survive under conditions of temperature and pressure where certain essential chemical reactions could not take place unless catalyzed by the class of proteins called enzymes. Examples of enzyme action include the storage and release of energy,
Biochemistry: Complete Interactive Tutorial #5
Identify different chemical groups.
Interactive
Tutorial
Nucleic Acids

Biochemistry: View Scenes 44 – 49 and complete the exercise below.
Examine the structure of DNA and RNA.
Multimedia
Presentation
Scene 44
1. What are the two types of nucleic acid?
Deoxyribonucleic acid, or DNA, and Ribonucleic acid, or RNA
Scenes 45 – 46
2. Ladder of Life: this diagram shows structural parts of a DNA molecule.
2a. In the box on the left, what do the circle and the pentagon structures represent?
The circle shows a phosphate group and the pentagon shows the sugar, deoxyribose.
2b. In the box on the right, what are the four nitrogenous bases A, G, T and C?
The four nitrogenous bases: adenine, guanine, thymine and cytosine
2c. How are A and G classified?
As purines
2d. How are T and C classified?
As pyrimidines
2e. What is formed by the combination of a phosphate group, a deoxyribose and a nitrogenous base?
A nucleotide, the basic unit of DNA
2f. What is the importance of DNA?
DNA contains the hereditary information needed to form an organism’s proteins.
Scene 47
3a. The alternating deoxyribose and phosphate groups form what structural part of DNA?
The alternating deoxyribose and phosphate groups make up the side chains of the DNA double helix.
3b. What pairs do the bases form? Where are the base pairs situated in DNA?
Adenine links only with thymine and guanine links only with cytosine, forming base pairs bridging the two side chains.
3c. The DNA molecule in a human cell nucleus contains how many base pairs?
Nuclear DNA contains about three billion base pairs.

Scene 48
4. Messenger Molecule: the diagram shows structural components of RNA. The table shows essential differences between DNA and RNA. Complete the entries.
DNA number of chains type of sugar unique base
RNA
Biochemistry: Complete Interactive Tutorial #4
Now build a protein.
Interactive
Tutorial
Biochemistry: Complete Interactive Tutorial #7
Examine DNA structure.
Interactive
Tutorial

Test
Test: Biochemistry Comprehensive Exam
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