Biochemistry

BiochemistryChemistry of life!+BiochemistryAtoms: basic unit of matterElements: a group of a the same type of atom.Atom has three partsProton (positive portion of atom)Neutron (neutral portion of atom)Electron (negative portion of atom)

+Biochemistry

+Biochemistryhttps://www.youtube.com/watch?v=H8WJ2KENlK0&list=PL88CEDF4EEA6E940BThe study of all of the elements from the periodic table of elements that support life. These compounds are all based on carbon. The four molecules most important for organisms are carbohydrates, lipids, proteins, and nucleic acids. +Biomolecules There are four types of biomoleculesWhy are they important?Biomolecules are the building blocks for all organisms. They are what make organisms. Example: hair is made of a bunch of protein and protein is made of amino acids, which are made of biomoleculesWhere are they found?They found everywhere in any organism and are made in the cell or during cellular processes.+Cells make a huge number of large molecules from a limited set of small moleculesThe four classes of biological molecules contain very large molecules.They are often called macromolecules because of their large size.They are also called polymers because they are made from identical building blocks strung together.The building blocks of polymers are called monomers. 2012 Pearson Education, Inc.6Student Misconceptions and ConcernsGeneral biology students might not have previously taken a chemistry course. The concept of molecular building blocks that cannot be seen can be abstract and difficult to comprehend for such students. Concrete examples from our diets and good images will increase comprehension. Teaching Tips1. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Consider adding that as the train cars are joined, a puff of steam appearsa reference to water production and a dehydration reaction when linking molecular monomers.2. The authors note that the great diversity of polymers mainly results from the arrangement of polymers, the different sequences made possible by combinations or permutations of the same monomers. Consider illustrating this by simply asking students how many different ways can we arrange the letters A, B, and C, using each letter, and only once, to form 3-lettered words. The answer is 6 permutations: ABC, ACB, BAC, BCA, CBA, CAB (the factorial of 3). And if letters can be repeated, the answer is 27 (= 33): AAA, BBB, CCC, ABB, ACC, etc.

Cells make a huge number of large molecules from a limited set of small moleculesMonomers are linked together to form polymers through dehydration reactions, which remove water.Polymers are broken apart by hydrolysis, the addition of water.All biological reactions of this sort are mediated by enzymes, which speed up chemical reactions in cells. 2012 Pearson Education, Inc.Animation: Polymers

7Student Misconceptions and ConcernsGeneral biology students might not have previously taken a chemistry course. The concept of molecular building blocks that cannot be seen can be abstract and difficult to comprehend for such students. Concrete examples from our diets and good images will increase comprehension. Teaching Tips1. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Consider adding that as the train cars are joined, a puff of steam appearsa reference to water production and a dehydration reaction when linking molecular monomers.2. The authors note that the great diversity of polymers mainly results from the arrangement of polymers, the different sequences made possible by combinations or permutations of the same monomers. Consider illustrating this by simply asking students how many different ways can we arrange the letters A, B, and C, using each letter, and only once, to form 3-lettered words. The answer is 6 permutations: ABC, ACB, BAC, BCA, CBA, CAB (the factorial of 3). And if letters can be repeated, the answer is 27 (= 33): AAA, BBB, CCC, ABB, ACC, etc.A cell makes a large number of polymers from a small group of monomers. For example,proteins are made from only 20 different amino acids andDNA is built from just four kinds of nucleotides.The monomers used to make polymers are universal.Cells make a huge number of large molecules from a limited set of small molecules 2012 Pearson Education, Inc.8Student Misconceptions and ConcernsGeneral biology students might not have previously taken a chemistry course. The concept of molecular building blocks that cannot be seen can be abstract and difficult to comprehend for such students. Concrete examples from our diets and good images will increase comprehension. Teaching Tips1. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Consider adding that as the train cars are joined, a puff of steam appearsa reference to water production and a dehydration reaction when linking molecular monomers.2. The authors note that the great diversity of polymers mainly results from the arrangement of polymers, the different sequences made possible by combinations or permutations of the same monomers. Consider illustrating this by simply asking students how many different ways can we arrange the letters A, B, and C, using each letter, and only once, to form 3-lettered words. The answer is 6 permutations: ABC, ACB, BAC, BCA, CBA, CAB (the factorial of 3). And if letters can be repeated, the answer is 27 (= 33): AAA, BBB, CCC, ABB, ACC, etc.

Figure 3.3A_s1Short polymerUnlinkedmonomer9Figure 3.3A_s1 Dehydration reaction building a polymer chain (step 1)

Figure 3.3A_s2Short polymerUnlinkedmonomerDehydration reactionforms a new bondLonger polymer10Figure 3.3A_s2 Dehydration reaction building a polymer chain (step 2)Lipidsare water insoluble (hydrophobic, or water-fearing) compounds,are important in long-term energy storage,contain twice as much energy as a polysaccharide, andconsist mainly of carbon and hydrogen atoms linked by nonpolar covalent bonds.Lipids are made of fatty acidsThey are the fats and oils that are produced by the bodyThey are used for storage and also for all membranes found in living organismsThey can also make steroid hormones responsible for sex hormones in animals and natural anabolic steroids which are responsible for muscle growth.

+Fats are lipids that are mostly energy-storage moleculesA fatty acid can link to glycerol by a dehydration reaction.A fat contains one glycerol linked to three fatty acids.Fats are often called triglycerides because of their structure. 2012 Pearson Education, Inc.12Student Misconceptions and Concerns1. Students may struggle with the concept that a pound of fat contains more than twice the calories of a pound of sugar. It might seem that a pound of food would potentially add on a pound of weight. Other students may have never understood the concept of calories in the diet, simply following general guidelines of avoiding fatty foods. Furthermore, fiber and water have no caloric value but add to the weight of food. Consider class discussions that explore student misconceptions about calories, body weight, and healthy diets.2. Students might struggle to extrapolate the properties of lipids to their roles in an organism. Ducks float because their feathers repel water instead of attracting it. Hair on our heads remains flexible because of oils produced in our scalp. Examples such as these help connect the abstract properties of lipids to concrete examples in our world.Teaching Tips1. The text in Module 3.8 notes the common observation that vinegar and oil do not mix in this type of salad dressing. A simple demonstration can help make this point. In front of the class, mix together colored water and a yellow oil (corn or canola oil work well). Shake up the mixture and then watch as the two separate. (You may have a mixture already made ahead of time that remains separated; however, the dye may bleed between the oil and the water.) Placing the mixture on an overhead projector or other well-illuminated imaging device makes for a dramatic display of hydrophobic activity!2. The text notes that a gram of fat stores more than twice the energy of a gram of polysaccharide, such as starch. You might elaborate with a simple calculation to demonstrate how a persons body weight would vary if the energy stored in body fat were stored in carbohydrates instead. If a 100-kg man carried 25% body fat, he would have 25 kg of fat in his body. Fat stores about 2.25 times more energy per gram than carbohydrate. What would be the weight of the man if he stored the energy in the fat in the form of carbohydrate? (2.25 x 25 = 56.25 kg of carbohydrate + 75kg (nonfat body weight) = 131.25 kg, an increase of 31.25%)3. Margarine in stores commonly comes in liquid squeeze containers, in tubs, and in sticks. These forms reflect increasing amounts of hydrogenation, gradually increasing the stiffness from a liquid, to a firmer spread, to a firm stick of margarine. As noted in the text, recent studies have suggested that unsaturated oils become increasingly unhealthy as they are hydrogenated. Students might therefore remember that as margarine products increase in stiffness, they generally become less healthy. Public attention to hydrogenation and the health risks of the resulting trans fats are causing changes in the use of products containing trans fats.

Figure 3.8BFatty acidGlycerol13Figure 3.8B A dehydration reaction linking a fatty acid molecule to a glycerol molecule

Figure 3.8CFatty acidsGlycerol14Figure 3.8C A fat molecule (triglyceride) consisting of three fatty acids linked to glycerolLipid Molecule: C-H

Long chains of Carbon and Hydrogen

+CarbohydratesMade of a carbon group and a hydroxyl group and are usually identified with sugars. They are the most abundant of all the biomolecules. Carbohydrates range from small sugar molecules (monomers) to large polysaccharides.Sugar monomers are monosaccharides, such as those found in honey,glucose, andfructose.Monosaccharides can be hooked together to formmore complex sugars andpolysaccharides.Carbs are used to store energy for the cell to work, but also work as a building block for many of the processes that go on. For example: blood clotting, growing and developing, fertilization. +Carbohydrate Molecule: C-H-O

This is an example of a monosaccharide called glucose. It is a building block found in sugar.Another monosaccharide is fructose which is a sugar found in fruit. Also monosaccharide are monomers and when you put many of the together, they are polysaccharides or polymersProteinThe subunits which make-up Proteins are Amino Acids. The amino acids are joined together to form chains, which are hundreds of amino acids long; called proteins.Proteins function as enzymes or as structural units in cells. They do most of the "work" in a cell. Almost all of the exciting stuff; metabolism, memory, hormone action, and movement involves proteins.

+Proteins are made from amino acids linked by peptide bondsProteins areinvolved in nearly every dynamic function in your body andvery diverse, with tens of thousands of different proteins, each with a specific structure and function, in the human body.Proteins are composed of differing arrangements of a common set of just 20 amino acid monomers.

2012 Pearson Education, Inc.19Teaching Tips1. Many analogies help students appreciate the diversity of proteins that can be made from just 20 amino acids. The authors note that our language uses combinations of 26 letters to form words. Proteins are much longer words, creating even more diversity. Another analogy is to trains. This builds upon the earlier analogy when polymers were introduced. Imagine making different trains about 100 cars long, using any combination of 20 types of railroad cars. Mathematically, the number of possible trains is 20100, a number beyond imagination.2. The authors note that the difference between a polypeptide and a protein is analogous to the relationship between a long strand of yarn and a sweater knitted from yarn. Proteins are clearly more complex!

Figure 3.11AAminogroupCarboxylgroup20Figure 3.11A General structure of an amino acidProteins are made from amino acids linked by peptide bondsAmino acids havean amino group anda carboxyl group (which makes it an acid).Also bonded to the central carbon isa hydrogen atom anda chemical group symbolized by R, which determines the specific properties of each of the 20 amino acids used to make proteins. 2012 Pearson Education, Inc.21Teaching Tips1. Many analogies help students appreciate the diversity of proteins that can be made from just 20 amino acids. The authors note that our language uses combinations of 26 letters to form words. Proteins are much longer words, creating even more diversity. Another analogy is to trains. This builds upon the earlier analogy when polymers were introduced. Imagine making different trains about 100 cars long, using any combination of 20 types of railroad cars. Mathematically, the number of possible trains is 20100, a number beyond imagination.2. The authors note that the difference between a polypeptide and a protein is analogous to the relationship between a long strand of yarn and a sweater knitted from yarn. Proteins are clearly more complex!Proteins are made from amino acids linked by peptide bondsAmino acid monomers are linked togetherin a dehydration reaction,joining carboxyl group of one amino acid to the amino group of the next amino acid, andcreating a peptide bond.Additional amino acids can be added by the same process to create a chain of amino acids called a polypeptide. 2012 Pearson Education, Inc.22Teaching Tips1. Many analogies help students appreciate the diversity of proteins that can be made from just 20 amino acids. The authors note that our language uses combinations of 26 letters to form words. Proteins are much longer words, creating even more diversity. Another analogy is to trains. This builds upon the earlier analogy when polymers were introduced. Imagine making different trains about 100 cars long, using any combination of 20 types of railroad cars. Mathematically, the number of possible trains is 20100, a number beyond imagination.2. The authors note that the difference between a polypeptide and a protein is analogous to the relationship between a long strand of yarn and a sweater knitted from yarn. Proteins are clearly more complex!

Figure 3.11C_s1CarboxylgroupAminogroupAmino acidAmino acid23Figure 3.11C_s1 Peptide bond formation (step 1)

Figure 3.11C_s2CarboxylgroupAminogroupAmino acidAmino acidDipeptidePeptidebondDehydrationreaction24Figure 3.11C_s2 Peptide bond formation (step 2)At this position (the R-group) in an amino acid, different functional groups can be present. There are twenty different types of amino acids found in proteins. Each has a differenb R-group.There are twenty different types of amino acids found in proteins: with eight essential. Essential amino acids must be acquired in the diet; nonessential amino acids can be synthesized by the body.+The 8 essential amino acids are in orange.alaninecysteinehistidinemethioninethreoninearginineglutamic acidisoleucinephenyalaninevaline

tryptophan asparagineglutamine leucineprolinetyrosineaspartic acidglycinelysineserine

+ProteinsThe amino acids within a single protein chain can interact. These interactions lead to a twisting and folding of the amino acid chain (protein) that is very important to the function of the protein. Two things determine the primary structure of a protein: The number of amino acids in the chain, where each specific amino acid occurs in the chain. The folding of a protein determines its shape and function within a cell. 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.

+A proteins specific shape determines its functionProbably the most important role for proteins is as enzymes, proteins thatserve as metabolic catalysts andregulate the chemical reactions within cells.

2012 Pearson Education, Inc.28Student Misconceptions and ConcernsThe 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 livesperhaps flathead and Phillips screwdrivers that match the proper type of screws or the fit of a hand into a glove.Teaching TipsMost 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.

Nucleic AcidsNucleic acids store, transmit and express genetic information. Nucleic acids are composed of subunits called nucleotides. Nucleotides contain a phosphate group, a sugar and a nitrogenous base. Nucleotides are linked together by bonds between the phosphate group of one nucleotide and the sugar of the next one2 types:DNARNA+DNA and RNA are the two types of nucleic acidsThe amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene.Genes consist of DNA(deoxyribonucleic acid), a type of nucleic acid.DNA is inherited from an organisms parents.DNA provides directions for its own replication.DNA programs a cells activities by directing the synthesis of proteins. 2012 Pearson Education, Inc.30Student Misconceptions and ConcernsModule 3.14 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 TipsThe NA in the acronyms DNA and RNA stands for Nucleic acid. Students often do not make this association without assistance.

DNA and RNA are the two types of nucleic acidsDNA does not build proteins directly.DNA works through an intermediary, ribonucleic acid (RNA).DNA is transcribed into RNA.RNA is translated into proteins.

2012 Pearson Education, Inc.31Student Misconceptions and ConcernsModule 3.14 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 TipsThe NA in the acronyms DNA and RNA stands for Nucleic acid. Students often do not make this association without assistance.

Figure 3.14_s1GeneDNA32Figure 3.14_s1 The flow of genetic information in the building of a protein (step 1)

Figure 3.14_s2GeneDNATranscriptionRNANucleic acids33Figure 3.14_s2 The flow of genetic information in the building of a protein (step 2)

Figure 3.14_s3GeneDNATranscriptionRNAProteinTranslationAminoacidNucleic acids34Figure 3.14_s3 The flow of genetic information in the building of a protein (step 3)Nucleic acids are polymers of nucleotidesDNA (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, anda nitrogenous base.

2012 Pearson Education, Inc.35Teaching TipsWhen 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? (Answer: Four nucleotides, GCAT, are possible). Are these the same words used in RNA? (Answer: No. Uracil substitutes for thymine.)

Figure 3.15APhosphategroupSugarNitrogenousbase(adenine)36Figure 3.15A A nucleotide, consisting of a phosphate group, a sugar, and a nitrogenous baseNucleic acids are polymers of nucleotidesDNA nitrogenous bases areadenine (A),thymine (T),cytosine (C), andguanine (G).RNAalso has A, C, and G,but instead of T, it has uracil (U). 2012 Pearson Education, Inc.37Teaching TipsWhen 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? (Answer: Four nucleotides, GCAT, are possible). Are these the same words used in RNA? (Answer: No. Uracil substitutes for thymine.)Nucleic acids are polymers of nucleotidesA nucleic acid polymer, a polynucleotide, forms from the nucleotide monomers,when the phosphate of one nucleotide bonds to the sugar of the next nucleotide,by dehydration reactions, andby producing a repeating sugar-phosphate backbone with protruding nitrogenous bases. 2012 Pearson Education, Inc.38Teaching TipsWhen 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? (Answer: Four nucleotides, GCAT, are possible). Are these the same words used in RNA? (Answer: No. Uracil substitutes for thymine.)

Figure 3.15BATCGTNucleotideSugar-phosphatebackbone39Figure 3.15B Part of a polynucleotideNucleic acids are polymers of nucleotidesTwo polynucleotide strands wrap around each other to form a DNA double helix.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. 2012 Pearson Education, Inc.40Teaching TipsWhen 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? (Answer: Four nucleotides, GCAT, are possible). Are these the same words used in RNA? (Answer: No. Uracil substitutes for thymine.)