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Biology 12: Biochemistry (Chapter 3)

Text:

Vocabulary:

Acid (carboxyl) group, adenine, adenosine triphosphate (ATP), alpha helix, amine group, amino acid, beta pleated sheet, carbohydrate, cellulose, complementary base pairing, cytosine, dehydration synthesis, deoxyribonucleic acid (DNA), deoxyribose, dipeptide, disaccharide, double helix, glucose, glycerol, guanine, glycogen, hemoglobin, hydrolysis, lipid, lubricant, maltose, monomer, monosaccharide, neutral fat, nitrogenous base, nucleic acids, nucleotide, organic, peptide bond, phosphate, phospholipid, polymer, polypeptide, polysaccharide, primary structure, protein, quaternary structure, R-group, ribonucleic acid (RNA), ribose, saturated fatty acid, secondary structure, starch, steroid, sugar-phosphate backbone, tertiary structure, thymine, unsaturated fatty acid, uracil

Goals:1. Analyse the structure and function of biological molecules in living systems, including: carbohydrates,

lipids, proteins and nucleic acids

-Demonstrate a knowledge of dehydration synthesis and hydrolysis as applied to organic monomers and polymers

-Differentiate among carbohydrates, lipids, proteins, and nucleic acids with respect to chemical structure

-Recognize the following molecules in structural diagrams: adenosine triphosphate (ATP),, deoxyribonucleic acid (DNA), disaccharide, glucose, glycerol, hemoglobin, monosaccharide, neutral fat, phospholipid, polysaccharide (starch, glycogen, and cellulose), ribose, RNA, saturated and unsaturated fatty acids, steroids

-Rcognize the empirical formula of a monosaccharide as CnH2nOn

-List the main functions of carbohydrates

-Differentiate among monosaccharides (e.g., glucose), disaccharides (e.g., maltose), and polysaccharides

-Differentiate among starch, cellulose, and glycogen with respect to function, type of bonding, level of branching

-Describe the location, structure, and function of the following in the human body: neutral fats, steroids, phospholipids

-Compare saturated and unsaturated fatty acids in terms of molecular structure

-List the major functions of proteins

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

-Identify the peptide bonds in dipeptides and polypeptides

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-Differentiate among the following levels of protein organization with respect to structure and types of bonding: primary, secondary (alpha helix, beta pleated sheet), tertiary, quaternary (e.g., hemoglobin)

-List the major functions of nucleic acids (RNA and DNA)

-Name the four nitrogenous bases in ribonucleic acid (RNA) and describe the structure of RNA using the following terms: nucleotide (ribose, phosphate, nitrogenous base, adenine, uracil, cytosine, guanine), linear, single stranded, sugar-phosphate backbone

-Name the four nitrogenous bases in DNA and describe the structure of DNA using the following terms: nucleotide (deoxyribose, phosphate, nitrogenous base, adenine, thymine, cytosine, guanine), complementary base pairing, double helix, hydrogen bonding, sugar-phosphate backbone

-Compare the general structural composition of DNA and RNA

-Relate the general structure of the ATP molecule to its role as the “energy currency” of cells

Part A: Organic Chemistry

-The table right discusses some of the differences between organic and organic compounds. At a basic level, what else can be used to differentiate between them?

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-Think back to Grade 10. Why is carbon such an important element in the formation of organic compounds?

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1. Hydrocarbons

-Hydrocarbons are compounds made solely of a carbon skeleton and hydrogen. Notice the diverse compounds and shapes produced through the versatility of carbon.

*Complete Activity: Diversity of Carbon-Based Molecules (3.1)

-Do you remember your organic compound naming from Science 10? What does Butane mean? How is it different than Butene?

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-What does Propane mean?

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-Butane and Isobutane are isomers of each other. What does this mean?

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-The drug Thalidomide has two forms, one that has been used as a sedative and relief for nausea and one that causes birth defects. In the 1950’s, Thalidomide was prescribed to pregnant women to help with nausea. Unfortunately, doctors did not know that the benign form of Thalidomide transforms into the harmful version at pH levels that occur in the body. This resulted in many women losing their babies or the children being born with limb deformities.

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2. Functional Groups

-In addition to the size and shape of its carbon skeleton, the atoms attached to it also play a big role in determining the properties of an organic compound.

-Functional groups attach to carbon skeletons and the strong electronegativity of their O and N components make them polar. This makes compounds containing the functional groups hydrophilic.

-What would the advantage be on having hydrophilic organic compounds in living organisms?

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*Explore the chemical characteristics of each functional group through Activity: Functional Groups (3.2)

-Below is an illustration of the male and female steroid hormones. Notice the differences between their functional groups.

-Practice working with the different functional groups below!

a) Carboxylic Acids

-Organic compounds containing a COOH (Carboxyl) group. Referred to as Organic Acids.

-Some examples include:

b) Amines

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Aminoethan

-Organic compounds containing an NH2 (Amine) group.

-Amines are organic bases that raise the pH of solutions.

c) Alcohols

-Organic compounds containing an OH (Hydroxyl) group.

-The OH makes alcohol hydrophilic, which allows it to be soluble in water.

-Draw the structural formula of:

i) Ethanol (C2H5OH)

ii) Methanol (CH3OH)

iii) Make up another alcohol

d) Phosphate Group

-Phosphate groups are usually found in ADP, ATP, DNA and RNA.

e) Sulfhydryl Group

-Has an S-H (Sulfhydryl) group attached to the hydrocarbon molecule.

-The S-H group is important in stabilizing the 3-D shape of proteins.

Part B: Structure and Function of Macromolecules (Polymers)

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-What does the name macromolecule imply about carbohydrates, proteins and nucleic acids?

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-Examine the image right and explain how a macromolecule is formed.

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*Complete Activity: Making and Breaking Polymers (3.3) at home.

-Below are formulae illustrating the dehydration synthesis of the four main groups of organic molecules we are concerned with:

a) Carbohydrates

Monosaccharides Polysaccharides + H2O

b) Lipids

Fatty Acids + Glycerol Lipids + H2O

c) Proteins

Amino Acids Polypeptides + H2O

d) Nucleic Acids

Nucleotides Nucleic Acids + H2O

1. Carbohydrates

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-Carbohydrates can be easily recognized as they all have modifications of the following formula: CnH2nOn

a) Monosaccharides

-The diagram right shows the simple sugars (monosaccharides) that are the monomers of carbohydrates. They are recognized by their “ose” suffix.

-What is the difference between Triose and Pentose sugars?

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-What functional groups are present in monosaccharides?

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-Notice that Glucose, Galactose and Fructose have the same chemical formula. Do you think they will chemically act the same way?

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-Monosaccharides cannot always be drawn linearly as many form rings in aqueous solutions:

b) Disaccharides

-From its name alone, can you guess what a disaccharide might be?

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-How would our bodies break sucrose back into fructose and glucose?

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c) Polysaccharides

-What does “poly” indicate?

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-There are two types of polysaccharides:

i) Storage Polysaccharides

-What monosaccharide is produced by plants through photosynthesis? What happens to it?

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-Why is starch a better storage molecule than glucose?

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-Humans store glucose as glycogen in our liver and muscle cells. What do we use it for?

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ii) Structural Polysaccharides

-Cellulose is a structural component of plant cell walls, providing structure and support.

-Examine the image on the page above. How does the arrangement of glucose monomers vary between starch and cellulose?

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-The differences in glucose monomer arrangements is a product of starch and cellulose containing two different forms of glucose: Alpha or Beta.

-Which type of glucose can humans not digest?

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-Arthropods and Fungi use chitin as a structural protein.

2.

Lipids

-Lipids are very diverse, but all are hydrophobic. Does this make them polar or non-polar?

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-You need to know about three types of lipids:

a) Fats

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-Examine the image right. What are the components of a natural fat? How are they joined?

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-Which of the fatty acids depicted right is unsaturated? How do you know this?

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-Unsaturated fatty acids can be changed into saturated fatty acids by adding hydrogen. This creates trans fats.

-Trans indicates that the carbons bonded to the double bonded carbons are on opposite sides.

-Watch this video if you’re really interested in the difference between cis and trans.

-If you were interested in preserving your cardiovascular health, what types of fat should you avoid?

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-In June 2015 the FDA banned trans fats in processed foods.

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*Watch this video from the cassiopeiaproject on Lipid formation.

-Fat (adipose) cells are found under the skin and around internal organs. What are some of the positive benefits of fat in the human body?

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b) Phospholipids

-Compare a phospholipid molecule to a triglyceride (fat molecule). How are they different?

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-Why is our cell membrane called a phospholipid bilayer?

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_____________________________________________________________________________________*View Activity: Lipids (3.9) at home.

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c) Steroids

-Examine the diagram right. What is a steroid?

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-What are some important functions of cholesterol in animals?

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3. Proteins

a) Protein Functions

*Watch Activity: Protein Functions (3.11) and this video on protein functions.

-There are tens of thousands of proteins in your body. Some of their functions include:

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b) Protein Building Blocks

*Watch Activity: Protein Structure (3.14) and this video.

-Proteins are polymers made up of long chains of amino acids.

-All amino acids have an amino group, central carbon atom and R group.

-There are 20 different amino acids. Examine the diagram right. How are they different from one another?

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-If you were responsible for joining two amino acid monomers together, how would you do this?

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-If proteins (polypeptides) are made of many amino acids, how could you create different proteins?

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c) Protein Shape

-Proteins have many different levels of structure: Primary, secondary, tertiary and quaternary.

-Examine the image of the protein sucrose below. Why is structure important to proteins?

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i) Primary Structure

-What is the primary structure of a protein?

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-The table below shows how serious the effects of changing just one amino acid in the primary structure can be.

ii) Secondary Structure

-Examine the image right. What is the secondary structure of a protein?

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iii) Tertiary Structure

-The tertiary structure is the 3-D shape of the polypeptide created through interactions between R groups: hydrogen bonds, Van der Waals interactions, disulphide bridges (covalent) and ionic bonds.

iv) Quaternary Structure

-Many proteins are collections of polypeptide chains working as a macromolecule. They are held together by R group interactions.

-For example, haemoglobin is a cluster of 4 polypeptides that work as a transport protein in our blood.

-Summary of protein structures:

d) Protein Misfolding

-What is a consequence of the tertiary structure of proteins misfolding?

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-Some diseases caused by misfolded proteins include:

-Examine the diagram below. In addition to heat, what other factors do you think might cause proteins to denature?

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4. Nucleic Acids

a) Nucleic Acid Function

-Where does the primary structure of proteins come from?

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-Can DNA create proteins directly?

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b) Nucleic Acid Structure

*Watch Activity: Nucleic Acid Structure (3.16).

-Nucleic acid polymers are made of nucleotide monomers.

-Do you remember the difference between the monomers

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-Examine the image below. How is a DNA double helix held together?

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-Remember, RNA is single stranded but can pair with itself.

c) ATP

*Watch Activity: The Structure of ATP (15.3)

-ATP is a nucleotide created through cellular respiration that acts as an energy source for cells to do work.

-Hydrolysis of the bonds holding the phosphate groups together is an exothermic reaction that releases energy.

-The diagram below illustrates the type of work the cell uses the energy from ATP to do:

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