BIOMOLECULES. Organic molecules are carbon containing molecules and are central to living systems. CHAPTER OUTLINE. Chapter

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1 hapter 1 BIMLEULE LEAIG BJETIVE Understand that the polar nature of water and its physical and chemical properties are crucial in biological systems. Identify, describe and draw the molecular structure of proteins, carbohydrates, lipids, and nucleic acids. Distinguish between monomers and polymers. Describe the synthesis of macromolecules by condensation and their breakdown by hydrolysis. Identify the bonds formed or broken in each case. Understand and explain the structure and functional diversity of biomolecules. APTE UTLIE rganic molecules are carbon containing molecules and are central to living systems. Proteins, carbohydrates, lipids, and nucleic acids are four key groups of biological macromolecules. ondensation and hydrolysis reactions are important in building and breaking apart biological molecules. The molecular structure of these biological macromolecules and their building blocks determine their ability to interact with water molecule, that is essential to life. Depending on their hydrophobicity and hydrophilicity, biological macromolecules show functional diversity, and play different roles in living systems. Astrobiology studies the origins, evolution and distribution of life in the universe; the central goal of this new science is to find evidence of past or present life beyond Earth, if it ever existed. For decades AA and EA have sent orbiters, landers and rovers on Mars to increase their knowledge of the ed Planet and to search for specific biomolecules that would be conclusive evidence of life. The link between space exploration and astrobiology was first highlighted by the American molecular biologist Joshua Lederberg, who, even before the official foundation of AA, was studying the possibilities of finding life beyond Earth. In 1958 (the year in which AA was founded), Lederberg, aged 33, won the obel Prize for discoveries about bacterial genetics. 1

2 Unit 1 Amino Acids and Proteins Keywords: Protein Amino acid Zwitterion Isoelectric point Disulfide bridge Peptide linkage In this unit you will Learn about amino acids Discuss the chemical structure and properties of amino acids Find out how amino acids bind together to build proteins Discover terms, verbs and expressions related to this topic WAM UP PAI WK A. Define the chemical bonds (ionic and covalent), and describe the factors that favor their formation. Provide an example for each of them, and write their Lewis symbols. ompare and discuss your answers with your classmate. Ionic Bond Lewis symbol Definition Example.... ovalent Bond Lewis symbol Definition Example.... PAI WK B. The diagram shows the structural formula of the water molecule. Indicate its polarity, and explain the importance of its dipole nature in the chemistry of life. ompare and discuss your answers with your classmate PAI WK. Provide the definition of acid and base and write the reactions of an acid and a base in water. ompare and discuss your answers with your classmate. Acid (definition)... Acid Water... Base (definition)... Base Water... Interleukin 23 protein molecule. 2

3 EADIG AD LITEIG ead the text and listen to Track 1. Amino Acids and Proteins Introduction Proteins are large, complex molecules that consist of over 100 amino acid residues joined by peptide bonds. Depending on their chemical composition, proteins are defined as: imple proteins: they contain only amino acids and no other chemical groups. onjugated proteins: they function in interaction with other chemical groups attached by covalent bonding or weak interactions, such as lipids (lipoproteins), oligosaccharide chains (glycoproteins), and nucleic acids, either DA or A (nucleoproteins). Proteins play many critical roles in the body, and they do most of the work in cells and are required for the structure, function, and regulation of the body s tissues and organs. Proteins are classified by their biological function (see Table 1). TABLE 1 Proteins and Their Functions ategory Function Enzymes atalyze (speed up) biochemical reactions tructural proteins Provide physical stability and movement Defensive proteins ecognize and respond to nonself substances (e.g., antibodies) ignaling proteins ontrol physiological processes (e.g., hormones) eceptor proteins eceive and respond to chemical signals Membrane transporters egulate passage of substances across cellular membranes torage proteins tore amino acids for later use Transport proteins Bind and carry substances within the organism Gene regulatory proteins Determine the rate of expression of a gene LAGUAGE FU range in size from to (V) vary in size from... to... stretch from to allows for (V) enables something to happen consents attached to (V) joined, connected to something (not to be confused with... to attack (V) to damage: rust attacks metals) All proteins are polymers made up of 20 amino acids in different proportions and sequences. Proteins range in size from small ones such as insulin, which has 51 amino acids and a molecular weight of 5733 Daltons (Da), to huge molecules such as the muscle protein titin, with amino acids and a molecular weight of Da. Proteins consist of one or more polypeptide chains unbranched (linear) polymers of covalently linked amino acids. Variation in the sequences of amino acids in the polypeptide chains allows for the vast diversity in protein structure and function. Each chain folds into a particular three-dimensional shape specified by the sequence of amino acids present in the chain. α carbon 3 Amino group arboxyl group ide chain The tructure of Amino Acids Each amino acid has both a carboxyl functional group and an amino functional group (Figure 1) attached to the same carbon atom, called the a (alpha) carbon. Also, attached to the a carbon atom, are a hydrogen atom and a side chain, or group, designated by the letter. 3 α Figure 1 The tructure of an Amino Acid All amino acids have the same basic structure. 3

4 The a carbon is asymmetrical because it is bonded to four different atoms or groups of atoms. Therefore, amino acids can exist as optical isomers called D-amino acids and L-amino acids. D and L are abbreviations of the Latin terms for right (dextro) and left (levo). nly L-amino acids (with the configuration shown in Figure 1) are commonly found in the proteins of most organisms, and their presence is an important chemical signature of life. At the p levels typically found in cells (usually about p 7), both the carboxyl and amino groups of amino acids are ionized, forming a dipolar ion or zwitterion: LAGUAGE FU it is bonded to (V) it is held together by a chemical bond the carboxyl group has lost a hydrogen ion: and the amino group has gained a hydrogen ion: 2 3 Thus, amino acids show amphoteric behaviour (from the Greek word amphoteroi, which means both), i.e. amino acids can react both as an acid as well as a base. If you increase the p of a solution of an amino acid by adding hydroxide ions, the hydrogen ion is removed from the - 3 group: If you decrease the p by adding an acid to a solution of an amino acid, the -- part of the zwitterion picks up a hydrogen ion The isoelectric point is the p at which the amino acid has a net charge of zero, i.e. the zwitterion form is dominant. At p values below the pi, the amino acid carries a net positive charge; above the pi, it carries a net negative charge Low p igh p Isoelectric Point Every amino acid has a different isoelectric point: fifteen of the twenty amino acids have isoelectric points in the range of The lowest isoelectric point is 3.0 (aspartic acid) and the highest is 10.8 (arginine). 4

5 The side chains (or groups) of amino acids contain functional groups that are important in determining the three-dimensional structure and thus the function of the protein. As Table 2 shows, the 20 amino acids found in living organisms are grouped and distinguished by their side chains: Five amino acids have electrically charged (ionized) side chains at p levels typical of living cells. These side chains attract water (are hydrophilic) and attract oppositely charged ions of all sorts. Five amino acids have polar side chains. They are also hydrophilic and attract other polar or charged molecules. even amino acids have side chains that are nonpolar and thus hydrophobic. In the watery environment of the cell, these hydrophobic groups may cluster together in the interior of the protein. Three amino acids cysteine, glycine, and proline are special cases, although the side chains of the latter two are generally hydrophobic. LAGUAGE FU cluster (V) gather, assemble TABLE 2 The Twenty Amino Acids A. Amino acids with electrically charged hydrophilic side chains Positive egative Amino acids have both three-letter and single-letter abbreviations. 3 Arginine (Arg; ) istidine (is; ) 2 3 Lysine (Lys; K) The general structure of all amino acids is the same but each has a different side chain. Aspartic acid (Asp; D) Glutamic acid (Glu; E) B. Amino acids with polar but uncharged side chains (hydrophilic) erine (er; ) Threonine (Thr; T) Asparagine (Asn; ) Glutamine (Gln; Q) Tyrosine (Tyr; Y). pecial cases ysteine (ys; ) Glycine (Gly; G) 2 2 Proline (Pro; P) 2 2 D. Amino acids with nonpolar hydrophobic side chains Alanine (Ala; A) Isoleucine (Ile; I) Leucine (Leu; L) Methionine (Met; M) Phenylalanine (Phe; F) Tryptophan (Trp; W) Valine (Val; V)

6 The cysteine side chain, which has a terminal group, can react with another cysteine side chain in an oxidation reaction to form a covalent bond (Figure 2). This bond, called a disulfide bridge or disulfide bond ( ), helps determine how a polypeptide chain folds. ysteine can usually be synthesized by the human body, but it may also be obtained from the diet. Foods rich in proteins are an important source of cysteine: meat, eggs, dairy products and soy beans. This amino acid is an important source of sulfide in human metabolism. ysteine molecules in polypeptide chain ide chains 2 The groups of two cysteine side chains react to form a covalent bond between the two sulfur atoms resulting in the formation of a disulfide bridge. Figure 2 Disulfide Bridge Two cysteine molecules in a polypeptide chain can form a disulfide bridge ( ) by oxidation (removal of atoms). The glycine side chain consists of a single hydrogen atom,. It is the simplest amino acid and small enough to fit into tight corners in the interiors of protein molecules where larger side chains cannot fit. ince the side chain,, is a single hydrogen atom, glycine is a non-optical amino acid. Glycine is a non-essential amino acid, implying that our bodies are able to produce it. Most proteins contain small quantities of glycine, except for collagen, which contains almost 35% glycine. In the genetic code, glycine is coded by all codons starting with GG (GGU, GG, GGA and GGG). Proline possesses a modified amino group that lacks a hydrogen and instead forms a covalent bond with the hydrocarbon side chain, resulting in a ring structure. This limits both its hydrogen-bonding ability and its ability to rotate about the a carbon. Thus proline is often found where a protein bends or loops. Moreover, due to its rigidity, proline is abundant in the proteins of thermophilic organisms. 6

7 Peptide Linkages When amino acids polymerize, the carboxyl and amino groups attached to the a carbon are the reactive groups. The carboxyl group of one amino acid reacts with the amino group of another, undergoing a condensation reaction that forms a peptide linkage (also called a peptide bond). Figure 3 gives a simplified description of this reaction. Amino group Peptide linkage 2 arboxyl group The amino group of one amino acid reacts with the carboxyl group of another to form a peptide linkage. A molecule of water is lost (condensation) as each linkage forms. terminus ( 3 ) terminus ( ) 2 epetition of this reaction links many amino acids together into a polypeptide. terminus ( 3 ) terminus ( ) Figure 3 Formation of Peptide Linkages In living things, the reaction leading to a peptide linkage has many intermediate steps, but the reactants and products are the same as those shown in this simplified diagram. Just as a sentence begins with a capital letter and ends with a period, polypeptide chains have a beginning and an end. The capital letter marking the beginning of a polypeptide is the amino group of the first amino acid added to the chain and is known as the terminus. The period is the carboxyl group of the last amino acid added; this is the terminus. Two characteristics of the peptide bond are especially important in the three-dimensional structures of proteins: In the linkage, the adjacent a carbons (a- a-) are not free to rotate fully. In fact two resonance structures exist: LAGUAGE FU terminus () the last stop or station at the end of a bus or a train route adjacent (A) next to; touching 7

8 Thus, the bond between the carbonyl carbon and the nitrogen has a partial double bond character, and as a consequence rotation around this bond is restricted. Thus, the peptide unit is a rigid structure and rotation is restricted to the bonds involving the a carbon: otation possible otation restricted The oxygen bound to the carbon (=) in the carboxyl group carries a slight negative charge (δ ), whereas the hydrogen bound to the nitrogen ( ) in the amino group is slightly positive (δ ). This asymmetry of charge favours hydrogen bonding within the protein molecule itself and between molecules. These bonds contribute to the structures and functions of many proteins. In addition to these characteristics of the peptide linkage, the particular sequence of amino acids with their various groups in the polypeptide chain also plays a vital role in determining a protein s structure and function. EMITY EALL esonance tructures If more than one Lewis structure can be drawn for a specific compound, the molecule or ion is said to have resonance, and each individual Lewis structure is then known as a contributing resonance structure. esonance structures are used to show that electrons are delocalized, i.e. they are able to move between atoms to stabilize the molecule. Two or more resonance structures are used to describe the hybrid structure that is intermediate between the contributing Lewis structures shown below. By convention, the double-headed arrow shows contributing resonance structures. 8

9 Task 1a UDETADIG AD DEFIIG PAI WK A. Answer the questions; then compare and discuss your answers with your classmate. 1. Discuss the biological roles of amino acids. 2. Describe what makes each of the 20 amino acids found in proteins unique. 3. Explain the amphoteric behaviour of amino acids. 4. List the attributes that would make an amino acid s group either hydrophobic or hydrophilic. 5. Explain why cysteine, glycine and proline are considered special amino acids. 6. Describe the process by which amino acids are joined together. B. Fill in the blanks using the words given below. condensation isoelectric point proteins asymmetrical carbon peptide linkages polypeptide chains side chain amino acids zwitterion The functions of (a).... include support, protection, catalysis, transport, defence, regulation, and movement. Proteins consist of one or more (b).... which are polymers of (c)..... Four atoms or groups are attached to a central (d).... atom: a hydrogen atom, an amino group, a carboxyl group, and a variable group. The particular properties of each amino acid depend on its (e)...., or group, which may be charged, polar, or hydrophobic. The a carbon is (f).... because it is bonded to four different atoms or groups of atoms. The (g).... is the p at which the amino acid is neutral, i.e. the (h).... form is dominant. (i)...., also called peptide bonds, covalently link amino acids into polypeptide chains. These bonds form by (j).... reactions between the carboxyl and amino groups.. Provide a definition for the terms listed below. a) Protein... b) Amino acid... c) Zwitterion... d) Isoelectric point... e) Disulfide bridge... f) Peptide linkage... g) Glycine... 9

10 WAT AD AWE Video 1 The tructure of Amino Acids (15:32 min) Watch the online video and answer the following questions step by step. Task 1b UDETADIG A. Watch the first part of the video (to 06:27). After watching, answer the following questions. 1. Describe the function of haemoglobin. 2. Describe the function of cell tissues. 3. What are amino acids? ow many of them are there? 4. Label the structural formula below Explain why each of the twenty amino acids is different from each other. 6. What is a chiral carbon? Are there any exceptions among amino acids? B. ow watch the second part of the video (06:28 to 10:05). After watching, write down the two Fischer projections of the generic amino acids and explain the origin of the names and how to recognize the two molecules. L amino acid D amino acid PAI WK. Finally, watch the third part of the video (10:06 to the end), and complete the text that lists the main ideas discussed in the video. ompare your answers with your classmate. We are now going to review the main ideas that have been discussed in this video. Firstly, we have learnt where (a).... fit in a larger metabolic process, such as in the example of (b).... econdly, we have found out about the structure of an amino acid, and the fact that the central (c).... is a chiral carbon with (d).... activity. The only exception to this rule is the amino acid (e)...., which has the simplest side chain of a (f)...., and therefore cannot be considered a chiral molecule. Thirdly, we have learnt about the Fischer projections for amino acids, and the fact that the (g).... of an amino acid is the only one that can be found within the (h)

11 Task 2 APPLYIG A. After reading the text in task 1a or watching the video in task 1b, you are now familiar with the structure of amino acids. The table below shows the structural formulas of the twenty amino acids. ircle the unique side chain of each amino acid, and then group the amino acids into: - amino acids with electrically charged (ionized) side chains; - amino acids with polar side chains; - amino acids with non polar (and thus hydrophobic) side chains. Find and label cysteine, glycine and proline. B. The picture below shows the amino acid alanine. Write down the acidbase equilibria that lead to the three forms of the amino acid: at low p, at the isoelectric point, and at high p Pick two amino acids of your choice, and write down the structural formulas in the zwitterionic form. Write down the condensation reaction that leads to the formation of the peptide linkage between the two amino acids. GUP WK D. From a historical point of view, phenylalanine (pictured below in its molecular formula) is an interesting amino acid. earch the web and prepare a presentation with slides to point out: 1. The genetic codon(s) for phenylalanine and the historically relevant experiment that kick-started the discovery of the genetic code. 2. The role of phenylalanine in the human body. 3. The genetic disease caused by the inability to metabolize phenylalanine. pecify name, causes, effects and therapy of this metabolic disease. 11