Proteins & Amino Acids, Study notes of Geometry

Download Proteins & Amino Acids and more Study notes Geometry in PDF only on Docsity! Proteins & Amino Acids 5 Many of the most important macromolecules in living systems are polymers. These polymers are composed of small building blocks that are linked together in long, linear chains. Three of the most important biological polymers are polysaccharides, polynucleotides, and polypeptides (Figure 1). Polysaccharides, such as starch, are composed of sugar subunits whereas polynucleotides, such as DNA and RNA (the subject of Chapter 8), are built from nucleotides. Here and in the next chapter we focus on polypeptides. Polypeptides are chains of subunits called amino acids that are joined together by peptide bonds. Short polypeptides are called peptides, and long polypeptides are typically called proteins. Proteins are composed of 20 kinds of amino acids, which are at once alike and dissimilar. They share common features that allow them to form peptide bonds with each other while also exhibiting distinctive chemical features. This diversity of amino acids and the sheer number of possible combinations in their linear order allow for tremendous dissimilarity in the chemical and physical properties of proteins (Figure 2). Furthermore, proteins do not exist as unstructured chains. Rather, they fold in on themselves to form three-dimensional architectures with unique features. Proteins have diverse functions Owing to their enormous diversity, cells employ proteins to perform numerous tasks (Figure 3). Some proteins function as enzymes, which catalyze chemical reactions by reducing ΔG‡. Nearly all enzymes are proteins, and as we saw in the previous chapter, cells are able to carry • explain why peptide bonds are polar and prefer the trans configuration. • explain how side chains confer distinct chemical and physical properties on amino acids. • draw a peptide of a given sequence at a specified pH. After this chapter, you should be able to To understand how common and dissimilar features of amino acids determine the chemical and physical properties of proteins. Objectives Goal Proteins & Amino AcidsChapter 5 2 O HO HO OH OH OH O O HO OH HO O O HO OH HO O O HO OH HO O O HO OOH HO HO O OH NH2 N H H N N H H N N H O O O O O OH S N NN N NH2 O OH O P O O O O OOP O O N N N N H2N O OOP O O O O OOP O O H N N N N O NH2 H N N O O Monomer Polymer Sugar Amino acid Deoxyucleotide Starch Protein DNA Ca rb oh yd ra te Pr ot ei n N uc le ic a ci d Figure 1 Polymers are macromolecules composed of small-molecule monomers linked together in chains Carbohydrates, proteins, and nucleic acids are examples of biological polymers. Each class of molecule is made of monomer subunits covalently linked together in chains. (A) (B) actin HIV protease Figure 2 Proteins exhibit unique structures and chemical properties Surface charge representation of the proteins actin (A) and HIV protease (B). Even though both proteins are chains of amino acids, they each feature distinct three-dimensional shapes with unique chemical properties, as evidenced by the unique distribution of surface charges on each molecule. Blue represents positive charge, red negative charge, and white neutral. out controlled chemical reactions because they use enzymes to modulate reaction rates and couple favorable processes with unfavorable ones. In fact, nearly all transformations that occur in the cell are mediated by enzymes, and without them, living systems would carry out virtually no chemistry. Enzymes catalyze a wide variety of reactions and are often categorized according to the chemistry that they perform. Most enzymatic reactions involve either the transfer of electrons (oxidation and reduction reactions), the transfer of functional groups, the cleavage or formation of bonds, the rearrangement of bonds within individual molecules, or the use of ATP to covalently connect molecules. We will have more to say about how enzymes lower ΔG‡ in subsequent chapters. While enzymes come in many shapes and sizes and facilitate a vast number of specific chemical reactions, proteins as a whole are even more diverse. Not all proteins are enzymes; some proteins play structural roles. Hair is made of such proteins, as are fingernails and the outer layers of the skin. Many familiar materials, such as wool, silk, and leather are also made of protein. These structural proteins have evolved to withstand particular Proteins & Amino AcidsChapter 5 5 beam of X-rays penetrates through the crystal lattice. Some of the X-rays are diffracted as they encounter the individual atoms that make up the molecules in the crystal lattice. The diffraction creates a characteristic pattern of reflections that is collected on an X-ray film and from which the arrangement of atoms can be reconstructed. This technique is a common method that scientists use to determine the structures of proteins and other molecules of life, and you will see many representations such as these throughout this book. Figure 4 shows the iconic double-helical structure of DNA. DNA is almost always a double helix regardless of its nucleotide sequence; it essentially always has the same three-dimensional shape. In contrast, the protein in Figure 4 looks quite different from the proteins in Figures 2 and 3. This is because the three-dimensional structures of proteins are highly varied. The ability of different proteins to assume a wide range of distinct three- dimensional conformations is in large part why they are so versatile; a protein’s shape determines its function. Conversely, DNA has just one function—genetic information storage—for which it assumes a single shape. The sequence of amino acids in a protein determines its folded structure The specific order of amino acids in a protein is known as its primary structure. It is this sequence that determines the three-dimensional architecture of a protein. A famous experiment that proves that all the information necessary for proper folding of a protein is contained in its primary structure is presented in the next chapter. Amino acids share common structural features All amino acids are composed of an amino group (-NH2), a carboxylic acid group (-COOH), and an intervening carbon atom to which these two groups are connected. The intervening carbon atom is the alpha (α) Box 1 You might imagine that changing a single amino acid in a protein consisting of a hundred or more amino acids would have little effect on the protein’s folded shape or function. Often this is the case, but sometimes a single change makes a profound difference. Figure 5 shows one example in which the substitution of a single amino acid significantly alters the protein. Hemoglobin, the oxygen carrier in red blood cells, contains the amino acid glutamate at position 6 in the primary sequence. Hemoglobin typically folds into a globular (i.e., roughly spherical) shape that associates to form a tetramer (a complex consisting of four molecules of hemoglobin). People who have sickle-cell anemia have a single amino acid substitution in their hemoglobin. The substitution is a switch from this glutamate to valine. This alteration causes hemoglobin molecules to clump, as reflected in a change in the shape of the red blood cells, which have a distorted, sickle shape. The sickle-shaped cells do not carry as much oxygen and therefore deliver less oxygen to the body’s tissues. These cells are also fragile and can break, causing painful “crises” because they disrupt blood flow. The sickle-cell mutation is recessive, but a single copy of the mutant allele enables people to resist infection by the malaria- causing pathogen Plasmodium, which propagates in red blood cells. This protection against Plasmodium explains why the allele is common in areas where malaria is endemic. Sickle-cell disease: one amino acid makes a difference Proteins & Amino AcidsChapter 5 6 N H NH HN H N O N H O HO O N NH O O O O Glutamate at position 6 Glutamate Normal red blood cell Normal hemoglobin N H NH HN H N O N H O HO O N NH O O Valine at position 6 Valine Sickled red blood cell Sickle-cell hemoglobin (A) (B) (C) mutation causes hemoglobin to clump Figure 5 Sickle-cell disease is caused by a single amino acid change in the hemoglobin protein (A) Line drawings of a portion of the hemoglobin (left) and sickle-cell hemoglobin (right) proteins. Normal hemoglobin contains the amino acid glutamate at position 6 in the primary sequence. In individuals with sickle-cell disease, this glutamate is replaced with the amino acid valine. (B) Computer-generated structure showing the charges present on the surfaces of hemoglobin (left) and sickle-cell hemoglobin (right). As we will see shortly in this chapter, some amino acids can be negatively or positively charged, while many others are neutral. In the figure, blue represents positive charge, red represents negative charge, and white represents neutral atoms. The substitution of the negatively charged amino acid glutamate at position 6 with the neutral valine removes a negative charge that is normally present in hemoglobin. (C) Computer-generated models showing the structures of the hemoglobin (left) and sickle-cell hemoglobin (right) proteins. The substitution of glutamate with valine causes hemoglobin tetramers to clump together. Proteins & Amino AcidsChapter 5 7 carbon. For 19 of the 20 amino acids, an additional chemical group, known as an R group or side chain, is attached to the α carbon. The twentieth amino acid, glycine, has two hydrogen atoms connected to the α carbon instead of an R group and a single hydrogen atom. The unique chemical and structural properties of each amino acid are determined by the identity of the R group. Amino acids are chiral A key feature of amino acids is that the α carbon is chiral. When a carbon atom is bound to four unique groups, it creates a chiral center (also known as a stereocenter). Simply put, a chiral molecule is one that cannot be superimposed with its mirror image. This is represented in Figure 7A by a cartoon in which four colored spheres represent the four different substituents of the α carbon of one of the 19 amino acids that have an R α “R” Group Alpha (α) Carbon Carboxylic Acid Group (-COOH) Amino Group (-NH2) Figure 6 Amino acids have four component parts Molecule A Molecule B (Mirror image of Molecule A) rotate 180° Molecule A Molecule B (rotated) orientation reversed; not superimposable superimposableMolecule C Molecule D (Mirror image of Molecule C) rotate 180° Molecule C Molecule D (rotated) (A) (B) Chiral cannot be superimposed with mirror image. Achiral can be superimposed with mirror image. Figure 7 Chiral molecules cannot be superimposed with their mirror images (A) Atoms that are bound to four unique substituents cannot be superimposed with their mirror images and are therefore chiral. (B) Atoms that are bound to fewer than four unique substituents can be superimposed with their mirror images and are therefore achiral. Proteins & Amino AcidsChapter 5 10 Peptide bonds are flat, polar, and not free to rotate The chemical properties of the peptide bond are important for determining the shape of the polypeptide chain. Some of the bonds of the peptide chain are free to rotate, but the peptide bond itself can only adopt certain conformations. To understand why, we return to the topic of the orbitals that surround atoms. When a covalent bond forms, the orbitals of the two bonded atoms overlap and mix, creating a bonding orbital that holds the shared pair of electrons. Bonding orbitals are a combination of atomic orbitals from each atom, and much like atomic orbitals, they describe where the shared electrons are likely to be found. A single bond [which we sometimes call a sigma (σ) bond] is composed of a cylindrically symmetrical orbital that joins two nuclei. A double bond consists of one σ bond as well as a second bond called a pi (π) bond. The π bond forms when the p orbitals of two nuclei overlap. Bonding orbitals can only hold two electrons. That means that single, double, and triple bonds must consist of one, two, and three bonding orbitals, respectively. In fact, single bonds always consist of one σ-orbital, double bonds always consist of one σ-orbital and one π-orbital, and triple bonds always consist of one σ-orbital and two π-orbitals. It turns out that this has an important consequence; bonds that contain π-orbitals cannot rotate freely. Sigma bonding orbitals have a cylindrical shape, and as such, single bonds can rotate freely without disrupting the orbital overlap that creates the bond. Conversely, the p orbitals that compose π-orbitals must be parallel with one another to overlap. If the π-bond were to rotate, the bond would break. Since breaking a covalent bond requires energy, the rotation of a π-bond has a high barrier. Because double bonds contain π-orbitals, they are not free to rotate. Shown in Figure 11 is the example of ethylene H N O N H H N OH O O O H2N R OH O N R' OH O H H H2N R O N R' OH OH-H2O + (A) (B) Peptide bond Proteins contain many peptide bonds Toward C-terminusToward N-terminus N-terminus C-terminus Figure 10 Amino acids are connected by peptide bonds to form polypeptide chains (A) Amino acids are connected by peptide bonds in proteins. The amino and carboxylic acid groups of any two amino acids can be covalently connected by a peptide bond, with the equivalent of the removal of a water molecule (shown in blue). The resulting amino acid chain has two ends, one with a free amino group, the N-terminus, and one with a free carboxylic acid group, the C-terminus. (B) Proteins are often made from very long polypeptide chains that typically contain hundreds of peptide bonds. Only four amino acid subunits of a protein are shown, as depicted by the squiggly lines (“spinach”) at each end. Proteins & Amino AcidsChapter 5 11 (C2H4), which contains a carbon-carbon double bond. Because this double bond contains a π-bonding orbital, the bond cannot rotate. Notice that the hydrogen and carbon atoms in ethylene are arranged in the same plane as one another, allowing the p orbitals to overlap and form the π-bonding orbital (see Box 2). We are still left with the question of why the peptide bond does not rotate. After all, we have drawn the peptide bond as a carbon-nitrogen single bond, so it should rotate freely. It turns out, however, that the peptide bond does not behave like a single bond because it has some double-bond character. The standard line drawing that we have shown for the peptide bond is somewhat misleading, as it fails to describe the bond’s properties in their C C H H H H C C H H H H p p π C C H H H H Figure 11 Double bonds cannot rotate because they contain π-orbitals Shown is the π-bonding orbital in ethylene (C2H4), which is formed by two overlapping p orbitals. The ethylene molecule is flat, and all of its atoms lie in the same plane because its π-bond can only exist when the p orbitals overlap. Box 2 As we have seen, ethylene is unable to rotate around its double bond due to its π bond. Another feature of ethylene is that its hydrogen and carbon atoms are in a planar configuration; they have a trigonal planar geometry. This means that the atomic orbitals linking the hydrogen and carbon atoms are pointing to the vertices of a triangle. The significance of this trigonal planar geometry is that it keeps the electrons in the three bonds to carbon maximally separated. How can σ- and π-bonds achieve this geometry? As you will remember, the s orbital is spherical and does not point in any specific direction. The three p orbitals are dumbbell shaped and are directed orthogonally (at right angles) to each other. So it seems that no combination of these four orbitals could allow carbon to bond to three other atoms in a trigonal planar fashion. Therefore, scientists came up with a mathematical manipulation known as hybridization that allows these orbitals to “mix” to produce an equal number of hybrid orbitals. In the case of the ethylene carbons, the s and two p orbitals mix to form three sp2 orbitals, which point at the three vertices of a triangle and allow bonding to two hydrogen atoms and one carbon atom, as shown below. Hybrid orbitals C C p p sp2 sp2 sp2 sp2 sp2 sp2C C H H H H H H H H Proteins & Amino AcidsChapter 5 12 entirety. The peptide bond behaves like ethylene in that the atoms attached to nitrogen and carbon are in the same plane and rotation is restricted. To understand this behavior, consider the bonding between nitrogen and the carbonyl carbon of the peptide bond. The nitrogen has a tendency to share its lone pair of electrons with the carbonyl carbon, delocalizing electrons among the nitrogen, carbon and oxygen atoms and creating a lower-energy state (Figure 12). Bonding in which electrons are delocalized and distributed among multiple atoms is referred to as resonance stabilization. Resonance stabilization does not mean that the peptide bond oscillates between the structures shown in Figure 12; rather, it exists as a hybrid of these two extremes. The distribution of electrons in this hybrid state is not, however, uniform. Rather, it is biased such that the single bond-like character of the carbon-nitrogen bond is slightly favored (60%) over its double bond-like character. Because the C-N bond has some double-bond character, the peptide bond is flat, meaning that the nitrogen and carbonyl carbon atoms both have trigonal planar geometries. Another consequence of resonance stabilization is that the peptide bond is polarized. As a result of resonance in this hybrid structure, the oxygen carries a partial-negative charge and the nitrogen a partial-positive charge. Because of the charge separation between oxygen and nitrogen, the peptide bond is polar. As we will see later, the partial-positive charge of the nitrogen and hydrogen and the partial-negative charge of the oxygen are important properties that influence how proteins fold. The backbone of polypeptide chains is not simply a continuous series of peptide bonds. Rather, it also consists of bonds between the amide nitrogens and α carbons and the bonds between the α carbons and carbonyl carbons. As we now explain, the peptide bonds within this framework are not free to rotate, whereas the other two bonds are. As in the example of ethylene from Figure 11, the double-bond character of the peptide bond causes it to be flat. All of the atoms immediately bound to the peptide bond are forced to be coplanar. The six coplanar atoms are the carbonyl carbon, the carbonyl oxygen, the peptide bond nitrogen, the hydrogen bound to that nitrogen, and the two adjacent α carbons. Each set of six coplanar atoms is highlighted as colored rectangles in Figure 13. Each rectangle is free to rotate relative to the adjacent coplanar sets of atoms. Notice that the α carbon is coplanar with two different (and differently colored) adjacent blocks of atoms. The requirement that sets of six atoms are coplanar rigidifies the polypeptide backbone and constrains it into a specific set of conformations, thereby influencing how the overall protein will fold. R N O H R' 60% R N O H R' 40% Figure 12 Resonance stabilization causes the peptide bond to have double-bond character The double-headed arrow signifies that the peptide bond is a hybrid of these two states. Proteins & Amino AcidsChapter 5 15 Some amino acids have ionizable side chains Some amino acids ionize (i.e., carry a full charge) at certain pH ranges (Figure 16). Aspartic acid and glutamic acid are acidic. They have side chains with pKa values well below physiological pH, and as a result, both amino acids exist predominantly in their deprotonated, negatively charged states under physiological conditions. Aspartic acid and glutamic acid go by a different set of names when they are deprotonated; when deprotonated, we call them aspartate and glutamate. You will often hear these names used interchangeably. Cysteine can also be deprotonated, as its pKa is about 8.0- 9.0. Although the neutrally charged, protonated form of cysteine is favored at physiological pH, its low pKa means that a significant amount of the deprotonated species is also present. Other amino acids, such as arginine and lysine, are basic, and at physiological pH they exist almost exclusively in their protonated, positively charged states. Histidine is also basic, but the pKa of its conjugate acid is close to physiological pH; as a result, it exists at physiological pH as a mixture of its positively charged, protonated form and its neutrally charged, deprotonated form. Since histidine’s pKa is about 6.0- 7.0, the neutrally charged state is slightly more abundant at physiological H3N O O NH2 O Asparagine Asn N H3N O O OH Serine Ser S H3N O O NH2O Glutamine Gln Q H3N O O OH Threonine Thr T H3N O O Alanine Ala A H3N O O Valine Val V H3N O O Isoleucine Ile I H3N O O Leucine Leu L H3N O O S Methionine Met M H3N O O SH Cysteine Cys C H3N O O H H Glycine Gly G H2 N O O Proline Pro P Nonpolar Polar Somewhat Polar H3N O O O O Aspartate Asp D H3N O O OO Glutamate Glu E Negatively Charged at pH 7.0 H3N O O HN Tryptophan Trp W H3N O O OH Tyrosine Tyr Y H3N O O Phenylalanine Phe F Aromatic Histidine His H H3N O O NH HN Arginine Arg R H3N O O NH H2 2N NH H3N O O NH3 Lysine Lys K Positively Charged at pH 7.0 Aect Peptide Shape Figure 15 The 20 amino acids can be grouped by their properties Shown are the twenty amino acids as they predominantly exist at pH 7. The side chain of each amino acid is shown in red, whereas the amino group, carboxyl group, and α carbon are shown in black Proteins & Amino AcidsChapter 5 16 pH. Because its pKa is so close to physiological pH, histidine is often used by enzymes to transfer protons during chemical reactions. Other amino acids, such as tyrosine and serine, can be deprotonated at high pH, but at physiological pH they largely exist in their protonated, neutrally charged states. In addition to side chains, the N- and C-termini of the polypeptide chain are ionized at physiological pH. The amino group at the N-terminus is basic, and its conjugate acid has a pKa of about 9.6. As a result, the amino terminus is predominantly protonated at physiological pH. The carboxyl group at the C-terminus is acidic and has a pKa of about 2.5. As a result, the carboxy terminus is predominantly deprotonated at physiological pH. The amide nitrogen in the peptide bond cannot be protonated in water due to the delocalization of its lone pair. Aspartic Acid/Aspartate Asp D 3.9-4.0 Glutamic Acid/Glutamate Glu E 4.0-4.5 Histidine His H 6.0-7.0 Cysteine Cys C 8.0-9.0 Tyrosine Tyr Y 10.0-10.3 Lysine Lys K 10.4-11.1 Arginine Arg R 12.5 O OH OHO NH HN SH OH NH3 H N NH2 NH2 OH O O OO NH N S O NH2 H N NH NH2 OSerine Ser S 13.0 N-terminus 9.6 C-terminus 2.5 AcidAmino Acid Conjugate Base pKa AcidTerminus Conjugate Base pKa NH3 R O NH2 R O OH OH N R O OH N R Figure 16 Amino acids contain ionizable functional groups The top portion of the table lists amino acids with ionizable side chains. The ionization state that predominantly exists at physiological pH is highlighted. The highlighted structures are highlighted in red if the indicated ionization form is at least 100 times more abundant than the other form and in purple if not. The bottom portion of the table describes the ionization of the free amino and carboxy groups at the termini of the polypeptide chain. Proteins & Amino AcidsChapter 5 17 Box 3 As an example, let us draw a peptide with the sequence NH3 +-WRM-COO− as it would predominantly exist at physiological pH. Drawing peptide structures S S Begin by drawing the peptide backbone. The backbone of each amino acid consists of the atoms nitrogen-carbon-carbon. Repeat this pattern three times since the peptide contains three amino acids. 1 2 3 Are you unsure about where to draw the carbonyl groups? Remember that the N-terminal free amino group must be bound to an alpha carbon, which is itself bound to a carbonyl carbon. Continue this pattern until you reach the C-terminus. Cα Ccarbonyl It’s easy to miscount the number of carbons in a side chain. Be sure to always double check. This linking carbon is found in ALL amino acids with rings in their side chains. Be sure not to omit it. Rings are commonly drawn incorrectly. Check the positions of atoms and bonds. H2N H N N H Except for proline, backbone nitrogen atoms always have one hydrogen atom. Draw in the C-terminus and backbone carbonyl groups. Draw in the side chains for each amino acid. H2N H N N HO O OH O H2N H N N HO O OH O HN HN H2N NH S Check for ionizable groups. Make sure that each group is drawn with the protonation state that matches the pH mentioned in the question. 4 Check for common mistakes. - Is the correct amino acid at the N-terminus? - Did you ionize the N-/C-termini? - Did you draw the side chains correctly? 5 H3N H N N HO O O O HN HN H2N NH2 pKa ~ 9.6; pKa > pH Protonated pKa ~ 12.5; pKa > pH Protonated pKa ~ 2.5; pKa < pH Deprotonated H3N H N N HO O O O HN HN H2N NH2 The peptide bond does NOT ionize. Proteins & Amino AcidsChapter 5 20 cysteines. Then the hair is curled around rollers, which places different sulfhydryl groups in close proximity, and finally, your hair is treated with an oxidizing agent, usually hydrogen peroxide, to form new disulfide bonds. Now instead of straight hair, you have curled hair. Amino acids often function cooperatively in proteins The amino acid side chains we have been describing are key functional components of proteins. Many proteins have enzymatic functions, and in these cases the side chains are directly involved in the reactions the enzymes catalyze. One class of enzymes, proteases, has evolved to catalyze the breakdown of peptide bonds in proteins. Many proteases contains a “catalytic triad” in which three amino acids in a precise arrangement work together to hydrolyze peptide bonds (Figure 19). The catalytic triad involves serine, histidine, and aspartate. The enzyme uses this catalytic triad to facilitate enzyme-catalyzed peptide bond hydrolysis. Of course, this can only occur because the folded protein precisely positions each of these amino acids in three dimensions, enabling the amino acids to interact with each other and with the substrate in just the right way. We will learn more about enzyme catalysis in later chapters, but before we do that, we need to examine the folded structures of proteins and the thermodynamics that underlie their formation. Ser His Asp Catalytic triad Chymotrypsin (a protease enzyme) Figure 19 Amino acid side chains are the functional components of proteins Amino acids often function cooperatively, especially in enzymes. As an example, chymotrypsin is an enzyme that cleaves peptide bonds. This chemical reaction is facilitated using a set of three amino acids—aspartate, histidine, and serine—that function cooperatively to form a “catalytic triad.” Proteins & Amino AcidsChapter 5 21 Summary Proteins are the most diverse and versatile macromolecules found in living systems. Proteins are polymeric chains of amino acid monomers connected by covalent peptide bonds. Unlike most other biological polymers, proteins fold into unique structures with distinct physical and chemical properties. As a result, cells use proteins for a broad range of structural, catalytic, regulatory, and transport functions. The folded structure of a protein is solely determined by its amino acid sequence, or primary structure. In fact, even small changes in the amino acid sequence can potentially alter a protein’s folded structure, as we saw in the example of sickle-cell disease. The amino acids that make up proteins all contain a central α carbon that is connected to an amino (-NH2) group, a carboxylic acid (-COOH) group, an R group (i.e., side chain), and a hydrogen atom. The chemical composition of the side chain determines the identity of the amino acid as well as its chemical properties. For all amino acids except glycine (for which the side chain is a hydrogen atom), the α carbon is chiral, meaning that it is not superimposable with its mirror image. Stereochemistry, which is the specific configuration at a chiral center, can have enormous effects on molecular properties. We use the term enantiomers to describe molecules that are mirror images of each other, and we refer to one enantiomer as “D” and the other as “L.” Living systems have evolved to use only the L-enantiomers of amino acids to construct proteins. Amino acids are connected by peptide bonds to form polypeptide chains. Polypeptides have two ends, one with a free amino group, the N-terminus, and one with a free carboxylic acid group, the C-terminus. At physiological pH, both of these termini are ionized. The amide in the peptide backbone, however, cannot be protonated in water. Peptide bonds are flat and polar, and they do not rotate freely. These properties influence the conformations that the peptide backbone can adopt, ultimately influencing how proteins fold. Furthermore, the conformations of the peptide backbone are influenced by amino acid side chains, which create steric clashes that bias the peptide backbone into specific conformations. Glycine and proline have a particularly strong influence on backbone conformation. Glycine can adopt a wide range of conformations since it lacks a side chain, and as a result, polypeptides rich in glycine tend to be more flexible. Proline, however, constrains the backbone into a narrower range of conformations. Due to the unique nature of its side chain, proline can sometimes take part in cis peptide bonds, which are generally disfavored for other amino acids. The amino acids found in proteins have a diverse range of properties that resist easy categorization. Some side chains are polar, some are nonpolar, and some are slightly polar. Several are positively or negatively charged at physiological pH. And yet others have ring structures that simultaneously have polar and nonpolar features. In the next chapter we will see how this diversity of amino acid properties influences the structure, folding, and myriad behaviors of proteins. Proteins & Amino AcidsChapter 5 22 Practice Problems 1. At physiological pH of 7.4, most amino acids are predominantly (>99%) present in one protonation state. Only histidine is substan- tially (>1%) present in two different protonation states. What are the charges of those two states? H3N H N N HO O O O NH HN SH H3N H N N HO O O O OH H3N H2 N N H2O O O O OO H3N H N N HO O OO OH3N O O O O H3N H N N H O O O O H3N H N N HO O O O OH NH3 a. NH2-His-Leu-Cys-COOH at pH 7.4 c. NH2-Ala-Glu-Gly-COOH at pH 7.4 e. NH2-Gly-Gly-Gly-COOH at pH 7.4 f. NH2-Val-Ser-Lys-COOH at pH 7.4 d. NH2-Asp-Gln-Glu-COOH at pH 7.4 b. NH2-Phe-Ser-Val-COOH at pH 7.4 (Solutions are located on the next page.) 2. A mistake was made when drawing each of the following peptides. For each peptide, identify the mistake and correct the drawing.