Proteins (aka polypeptides) 3.11-3.14 A. Polymer of amino acid monomers B. 1000s exist each with unique 3-D structure that corresponds to its function C. Role in everything a cell /organism does D. Functions: 1. Enzymes- chemical catalyst 2. Structural proteins- hair and fibers of connective tissues 3. Contractile proteins- muscle 4. Defensive proteins- antibodies 5. Signal proteins- chemical messenger communication between cells 6. Receptor proteins- transmit signals into cells 7. Transport protein- help move molecules 8. Storage proteins- source of aa

E. Every amino acid (20) has the following structure: group Carboxyl group F. Amino acids are classified as hydrophobic or hydrophilic nonpolar R group hydrophobic polar R group hydrophilic Figure 3.12A General structure of an amino acid.

Leucine (Leu) Serine (Ser) Aspartic acid (Asp) Hydrophobic Hydrophilic Figure 3.12B Examples of amino acids with hydrophobic and hydrophilic R groups. Leucine (Leu) Serine (Ser) Aspartic acid (Asp) Hydrophobic Hydrophilic

G. Amino acids are linked by dehydration reaction. Carboxyl group Amino group Amino acid Amino acid Figure 3.12C Peptide bond formation. As more and more amino acids are added, a chain of amino acids called a polypeptide results. The combination of amino acids is determined by expression of genes on DNA. Although there seems to be an unlimited number of combinations of 20 amino acids, the combinations are limited in an individual because of inheritance.

Peptide bond Carboxyl group Amino group Dehydration reaction Amino acid Amino acid Dipeptide Figure 3.12C Peptide bond formation. As more and more amino acids are added, a chain of amino acids called a polypeptide results. The combination of amino acids is determined by expression of genes on DNA. Although there seems to be an unlimited number of combinations of 20 amino acids, the combinations are limited in an individual because of inheritance.

3.13 A protein’s specific shape determines its function A polypeptide chain contains hundreds or thousands of amino acids linked by peptide bonds The amino acid sequence causes the polypeptide to assume a particular shape The shape of a protein determines its specific function Because of the molecular structure of specific proteins on brain cells, endorphins bind to them. This gives us a feeling of euphoria and pain relief. Morphine, heroin, and other opiate drugs are able to mimic endorphins and bind to the endorphin receptors in the brain. Because of the euphoria that results, we become addicted. Student Misconceptions and Concerns 1. The functional significance of protein shape is an abstract molecular example of form and function relationships, which might be new to some students. The binding of an enzyme to its substrate is a type of molecular handshake, which permits specific interactions. To help students think about form and function relationships, share some concrete analogies in their lives—perhaps flathead and Phillips screwdrivers that match the proper type of screws or the fit of a hand into a glove. Teaching Tips 1. Most cooking results in changes in the texture and color of food. The brown color of a cooked steak is the product of the denaturation of proteins. Fixatives such as formalin also denature proteins and cause color changes. Students who have dissected vertebrates will realize that the brown color of the muscles makes it look as if the animal has been cooked. Copyright © 2009 Pearson Education, Inc.

Groove Figure 3.13A Ribbon model of the protein lysozyme.

Groove Figure 3.13B Space-filling model of lysozyme.

3.14 A protein’s shape depends on four levels of structure A protein can have four levels of structure Primary structure Secondary structure Tertiary structure Quaternary structure For the BLAST Animation Alpha Helix, go to Animation and Video Files. Teaching Tips 1. Consider this assignment to review the organic molecules in our diets. Have students, working individually or in small groups, analyze a food label listing the components of a McDonalds’ Big Mac or other fast-food sandwich. Note the most abundant organic molecule class (perhaps by weight) found in each component. Copyright © 2009 Pearson Education, Inc.

3.14 A protein’s shape depends on four levels of structure primary structure- unique amino acid sequence The correct amino acid sequence is determined by the cell’s genetic information The slightest change in this sequence affects the protein’s ability to function Sickle cell disease is manifested by an inability of hemoglobin in red blood cells to carry oxygen, the primary function of hemoglobin. This blood disorder is the result of change in a single amino acid. Teaching Tips 1. Consider this assignment to review the organic molecules in our diets. Have students, working individually or in small groups, analyze a food label listing the components of a McDonalds’ Big Mac or other fast-food sandwich. Note the most abundant organic molecule class (perhaps by weight) found in each component. Copyright © 2009 Pearson Education, Inc.

Four Levels of Protein Structure Primary structure Amino acids Figure 3.14A Primary structure.

3.14 A protein’s shape depends on four levels of structure secondary structure- coiling or folding of the polypeptide as result of H bonds between areas of polypeptide chain Coiling results in a helical structure called an alpha helix Folding may lead to a structure called a pleated sheet Hydrogen bonding is an important component of the silk protein of a spider’s web. The many hydrogen bonds makes the web as strong as steel. Teaching Tips 1. Consider this assignment to review the organic molecules in our diets. Have students, working individually or in small groups, analyze a food label listing the components of a McDonalds’ Big Mac or other fast-food sandwich. Note the most abundant organic molecule class (perhaps by weight) found in each component. Copyright © 2009 Pearson Education, Inc.

Four Levels of Protein Structure Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Pleated sheet Figure 3.14A Primary structure. Figure 3.14B Secondary structure.

3.14 A protein’s shape depends on four levels of structure Tertiary structure- overall 3D shape of a protein results from interactions between the R groups of the various amino acids Shape stabilized by clustering of hydrophobic R groups, H bonds, and ionic & covalent bonds Teaching Tips 1. Consider this assignment to review the organic molecules in our diets. Have students, working individually or in small groups, analyze a food label listing the components of a McDonalds’ Big Mac or other fast-food sandwich. Note the most abundant organic molecule class (perhaps by weight) found in each component. Copyright © 2009 Pearson Education, Inc.

Four Levels of Protein Structure Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Pleated sheet Tertiary structure Figure 3.14A Primary structure. Figure 3.14B Secondary structure. Figure 3.14C Tertiary structure. Polypeptide (single subunit of transthyretin)

3.14 A protein’s shape depends on four levels of structure Quaternary Structure- occurs in proteins with more than one polypeptide; described as globular or fibrous

Four Levels of Protein Structure Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Pleated sheet Tertiary structure Figure 3.14A Primary structure. Figure 3.14B Secondary structure. Figure 3.14C Tertiary structure. Figure 3.14D Quaternary structure. Polypeptide (single subunit of transthyretin) Transthyretin, with four identical polypeptide subunits Quaternary structure

3.13 A protein’s specific shape determines its function If for some reason a protein’s shape is altered, it can no longer function Denaturation will cause polypeptide chains to unravel and lose their shape and, thus, their function Proteins can be denatured by changes in salt concentration and pH Excessive heat can also denature a protein. A good example is frying or boiling an egg. The proteins in the egg “white” become solid, white, and opaque upon denaturation. Student Misconceptions and Concerns 1. The functional significance of protein shape is an abstract molecular example of form and function relationships, which might be new to some students. The binding of an enzyme to its substrate is a type of molecular handshake, which permits specific interactions. To help students think about form and function relationships, share some concrete analogies in their lives—perhaps flathead and Phillips screwdrivers that match the proper type of screws or the fit of a hand into a glove. Teaching Tips 1. Most cooking results in changes in the texture and color of food. The brown color of a cooked steak is the product of the denaturation of proteins. Fixatives such as formalin also denature proteins and cause color changes. Students who have dissected vertebrates will realize that the brown color of the muscles makes it look as if the animal has been cooked. Copyright © 2009 Pearson Education, Inc.

3.16 Nucleic acids are information-rich polymers of nucleotides DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are composed of monomers called nucleotides Nucleotides have three parts A five-carbon sugar called ribose in RNA and deoxyribose in DNA A phosphate group A nitrogenous base Student Misconceptions and Concerns 1. Module 3.16 is the first time the authors present the concept of transcription and translation, discussed extensively in later chapters. The basic conceptual flow of information from DNA to RNA to proteins is essential to these later discussions. Teaching Tips 1. The “NA” in the acronyms DNA and RNA stands for “nucleic acid.” Students often do not make this association without assistance. Copyright © 2009 Pearson Education, Inc.

Nitrogenous base (adenine) Phosphate group Sugar Figure 3.16A A nucleotide, consisting of a phosphate group, sugar, and a nitrogenous base. Student Misconceptions and Concerns 1. Module 3.16 is the first time the authors present the concept of transcription and translation, discussed extensively in later chapters. The basic conceptual flow of information from DNA to RNA to proteins is essential to these later discussions. Teaching Tips 1. The “NA” in the acronyms DNA and RNA stands for “nucleic acid.” Students often do not make this association without assistance. Phosphate group Sugar

3.16 Nucleic acids are information-rich polymers of nucleotides a polynucleotide forms when the phosphate of one nucleotide bonds to the sugar of the next nucleotide DNA double helix-two polynucleotide strands wrap around each other The two strands are associated because particular bases always hydrogen bond to one another A pairs with T, and C pairs with G, producing base pairs RNA is usually a single polynucleotide strand Student Misconceptions and Concerns 1. Module 3.16 is the first time the authors present the concept of transcription and translation, discussed extensively in later chapters. The basic conceptual flow of information from DNA to RNA to proteins is essential to these later discussions. Teaching Tips 1. The “NA” in the acronyms DNA and RNA stands for “nucleic acid.” Students often do not make this association without assistance. Copyright © 2009 Pearson Education, Inc.

Base pair Figure 3.16C DNA double helix.

3.16 Nucleic acids are information-rich polymers of nucleotides A particular nucleotide sequence that can instruct the formation of a polypeptide is called a gene Most DNA molecules consist of millions of base pairs and, consequently, many genes These genes, many of which are unique to the species, determine the structure of proteins and, thus, life’s structures and functions Student Misconceptions and Concerns 1. Module 3.16 is the first time the authors present the concept of transcription and translation, discussed extensively in later chapters. The basic conceptual flow of information from DNA to RNA to proteins is essential to these later discussions. Teaching Tips 1. The “NA” in the acronyms DNA and RNA stands for “nucleic acid.” Students often do not make this association without assistance. Copyright © 2009 Pearson Education, Inc.

Mutations are alterations in bases or the sequence of bases in DNA 3.17 EVOLUTION CONNECTION: Lactose tolerance is a recent event in human evolution Mutations are alterations in bases or the sequence of bases in DNA Lactose tolerance is the result of mutations In many people, the gene that dictates lactose utilization is turned off in adulthood Apparently, mutations occurred over time that prevented the gene from turning off This is an excellent example of human evolution Mutations that lead to lactose tolerance are relativity recent events. The mutation was useful because it allowed people to drink milk when other foods were unavailable. In other words, it provided a survival advantage. Student Misconceptions and Concerns 1. The evolution of lactose tolerance within human groups in East Africa does not represent a deliberate decision, yet this evolutionary change appears logical. Many students perceive adaptations as deliberate events with purpose. As students develop a better understanding of the mechanisms of evolution, it will be important to point out that mutations arise by chance, with the culling hand of natural selection favoring traits that convey advantage. Organisms cannot plan evolutionary change. Teaching Tips 1. When discussing the sequence of nucleotides in DNA and RNA, consider challenging your students with the following questions based upon prior analogies. If the 20 possible amino acids in a polypeptide represent “words” in a long polypeptide sentence, how many possible words are in the language of a DNA molecule? (Four nucleotides, GCAT, are possible). Are these the same “words” used in RNA? (Answer: No. Uracil substitutes for thymine.) Copyright © 2009 Pearson Education, Inc.

Amino acids Primary structure Figure 3.14A Primary structure.

Amino acids Hydrogen bond Alpha helix Pleated sheet Figure 3.14B Secondary structure. Alpha helix Pleated sheet Secondary structure

Polypeptide (single subunit of transthyretin) Tertiary structure Figure 3.14C Tertiary structure. Tertiary structure

Transthyretin, with four identical polypeptide subunits Figure 3.14D Quaternary structure. Quaternary structure