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2.2: Structure & Function - Amino Acids

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• Kevin Ahern, Indira Rajagopal, & Taralyn Tan
• Oregon State University

Source: BiochemFFA_2_1.pdf . The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy

All of the proteins on the face of the earth are made up of the same 20 amino acids. Linked together in long chains called polypeptides, amino acids are the building blocks for the vast assortment of proteins found in all living cells.

"It is one of the more striking generalizations of biochemistry ...that the twenty amino acids and the four bases, are, with minor reservations, the same throughout Nature." - Francis Crick

All amino acids have the same basic structure, which is shown in Figure 2.1. At the “center” of each amino acid is a carbon called the α carbon and attached to it are four groups - a hydrogen, an α- carboxyl group, an α-amine group, and an R-group, sometimes referred to as a side chain. The α carbon, carboxyl, and amino groups are common to all amino acids, so the R-group is the only unique feature in each amino acid. (A minor exception to this structure is that of proline, in which the end of the R-group is attached to the α-amine.) With the exception of glycine, which has an R-group consisting of a hydrogen atom, all of the amino acids in proteins have four different groups attached to them and consequently can exist in two mirror image forms, L and D. With only very minor exceptions, every amino acid found in cells and in proteins is in the L configuration.

There are 22 amino acids that are found in proteins and of these, only 20 are specified by the universal genetic code. The others, selenocysteine and pyrrolysine use tRNAs that are able to base pair with stop codons in the mRNA during translation. When this happens, these unusual amino acids can be incorporated into proteins. Enzymes containing selenocysteine, for example, include glutathione peroxidases, tetraiodothyronine 5' deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases, and selenophosphate synthetase. Pyrrolysine-containing proteins are much rarer and are mostly confined to archaea.

Essential and non-essential

Nutritionists divide amino acids into two groups - essential amino acids (must be in the diet because cells can’t synthesize them) and non-essential amino acids (can be made by cells). This classification of amino acids has little to do with the structure of amino acids. Essential amino acids vary considerable from one organism to another and even differ in humans, depending on whether they are adults or children. Table 2.1 shows essential and non-essential amino acids in humans.

Some amino acids that are normally nonessential, may need to be obtained from the diet in certain cases. Individuals who do not synthesize sufficient amounts of arginine, cysteine, glutamine, proline, selenocysteine, serine, and tyrosine, due to illness, for example, may need dietary supplements containing these amino acids.

Table 2.1 - Essential and non-essential amino acids

Non-protein amino acids

There are also α-amino acids found in cells that are not incorporated into proteins. Common ones include ornithine and citrulline. Both of these compounds are intermediates in the urea cycle. Ornithine is a metabolic precursor of arginine and citrulline can be produced by the breakdown of arginine. The latter reaction produces nitric oxide, an important signaling molecule. Citrulline is the metabolic byproduct. It is sometimes used as a dietary supplement to reduce muscle fatigue.

R-group chemistry

Table 2.2 - Amino acid categories (based on R-group properties)

We separate the amino acids into categories based on the chemistry of their R-groups. If you compare groupings of amino acids in different textbooks, you will see different names for the categories and (sometimes) the same amino acid being categorized differently by different authors. Indeed, we categorize tyrosine both as an aromatic amino acid and as a hydroxyl amino acid. It is useful to classify amino acids based on their R-groups, because it is these side chains that give each amino acid its characteristic properties. Thus, amino acids with (chemically) similar side groups can be expected to function in similar ways, for example, during protein folding.

Non-polar amino acids

• Alanine (Ala/A) is one of the most abundant amino acids found in proteins, ranking second only to leucine in occurrence. A D-form of the amino acid is also found in bacterial cell walls. Alanine is non-essential, being readily synthesized from pyruvate. It is coded for by GCU, GCC, GCA, and GCG.
• Glycine (Gly/G) is the amino acid with the shortest side chain, having an R-group consistent only of a single hydrogen. As a result, glycine is the only amino acid that is not chiral. Its small side chain allows it to readily fit into both hydrophobic and hydrophilic environments.

• Glycine is specified in the genetic code by GGU, GGC, GGA, and GGG. It is nonessential to humans.
• Isoleucine (Ile/I) is an essential amino acid encoded by AUU, AUC, and AUA. It has a hydrophobic side chain and is also chiral in its side chain.
• Leucine (Leu/L) is a branched-chain amino acid that is hydrophobic and essential. Leucine is the only dietary amino acid reported to directly stimulate protein synthesis in muscle, but caution is in order, as 1) there are conflicting studies and 2) leucine toxicity is dangerous, resulting in "the four D's": diarrhea, dermatitis, dementia and death . Leucine is encoded by six codons: UUA,UUG, CUU, CUC, CUA, CUG.
• Methionine (Met/M) is an essential amino acid that is one of two sulfurcontaining amino acids - cysteine is the other. Methionine is non-polar and encoded solely by the AUG codon. It is the “initiator” amino acid in protein synthesis, being the first one incorporated into protein chains. In prokaryotic cells, the first methionine in a protein is formylated.

• Proline (Pro/P) is the only amino acid found in proteins with an R-group that joins with its own α-amino group, making a secondary amine and a ring. Proline is a non-essential amino acid and is coded by CCU, CCC, CCA, and CCG. It is the least flexible of the protein amino acids and thus gives conformational rigidity when present in a protein. Proline’s presence in a protein affects its secondary structure. It is a disrupter of α-helices and β-strands. Proline is often hydroxylated in collagen (the reaction requires Vitamin C - ascorbate) and this has the effect of increasing the protein’s conformational stability. Proline hydroxylation of hypoxia-inducible factor (HIF) serves as a sensor of oxygen levels and targets HIF for destruction when oxygen is plentiful.
• Valine (Val/V) is an essential, non-polar amino acid synthesized in plants. It is noteworthy in hemoglobin, for when it replaces glutamic acid at position number six, it causes hemoglobin to aggregate abnormally under low oxygen conditions, resulting in sickle cell disease. Valine is coded in the genetic code by GUU, GUC, GUA, and GUG.

Carboxyl Amino Acids

• Aspartic acid (Asp/D) is a non-essential amino acid with a carboxyl group in its Rgroup. It is readily produced by transamination of oxaloacetate. With a pKa of 3.9, aspartic acid’s side chain is negatively charged at physiological pH. Aspartic acid is specified in the genetic code by the codons GAU and GAC.
• Glutamic acid (Glu/E), which is coded by GAA and GAG, is a non-essential amino acid readily made by transamination of α- ketoglutarate. It is a neurotransmitter and has an R-group with a carboxyl group that readily ionizes (pKa = 4.1) at physiological pH.

Amine amino acids

• Arginine (Arg/R) is an amino acid that is, in some cases, essential, but non-essential in others. Premature infants cannot synthesize arginine. In addition, surgical trauma, sepsis, and burns increase demand for arginine. Most people, however, do not need arginine supplements. Arginine’s side chain contains a complex guanidinium group with a pKa of over 12, making it positively charged at cellular pH. It is coded for by six codons - CGU, CGC, CGA, CGG, AGA, and AGG.
• Histidine (His/H) is the only one of the proteinaceous amino acids to contain an imidazole functional group. It is an essential amino acid in humans and other mammals. With a side chain pKa of 6, it can easily have its charge changed by a slight change in pH. Protonation of the ring results in two NH structures which can be drawn as two equally important resonant structures.

• Lysine (Lys/K) is an essential amino acid encoded by AAA and AAG. It has an Rgroup that can readily ionize with a charge of +1 at physiological pH and can be posttranslationally modified to form acetyllysine, hydroxylysine, and methyllysine. It can also be ubiquitinated, sumoylated, neddylated, biotinylated, carboxylated, and pupylated, and. O-Glycosylation of hydroxylysine is used to flag proteins for export from the cell. Lysine is often added to animal feed because it is a limiting amino acid and is necessary for optimizing growth of pigs and chickens.

Aromatic amino acids

• Phenylalanine (Phe/ F) is a non-polar, essential amino acid coded by UUU and UUC. It is a metabolic precursor of tyrosine. Inability to metabolize phenylalanine arises from the genetic disorder known as phenylketonuria. Phenylalanine is a component of the aspartame artificial sweetener.
• Tryptophan (Trp/W) is an essential amino acid containing an indole functional group. It is a metabolic precursor of serotonin, niacin, and (in plants) the auxin phytohormone. Though reputed to serve as a sleep aid, there are no clear research results indicating this.
• Tyrosine (Tyr/Y) is a non-essential amino acid coded by UAC and UAU. It is a target for phosphorylation in proteins by tyrosine protein kinases and plays a role in signaling processes. In dopaminergic cells of the brain, tyrosine hydroxylase converts tyrosine to l-dopa, an immediate precursor of dopamine. Dopamine, in turn, is a precursor of norepinephrine and epinephrine. Tyrosine is also a precursor of thyroid hormones and melanin.

Hydroxyl amino acids

• Serine (Ser/S) is one of three amino acids having an R-group with a hydroxyl in it (threonine and tyrosine are the others). It is coded by UCU, UCC, UCA, UGC, AGU, and AGC. Being able to hydrogen bond with water, it is classified as a polar amino acid. It is not essential for humans. Serine is precursor of many important cellular compounds, including purines, pyrimidines, sphingolipids, folate, and of the amino acids glycine, cysteine, and tryptophan. The hydroxyl group of serine in proteins is a target for phosphorylation by certain protein kinases. Serine is also a part of the catalytic triad of serine proteases.

• Threonine (Thr/T) is a polar amino acid that is essential. It is one of three amino acids bearing a hydroxyl group (serine and tyrosine are the others) and, as such, is a target for phosphorylation in proteins. It is also a target for Oglycosylation of proteins. Threonine proteases use the hydroxyl group of the amino acid in their catalysis and it is a precursor in one biosynthetic pathway for making glycine. In some applications, it is used as a pro-drug to increase brain glycine levels. Threonine is encoded in the genetic code by ACU, ACC, ACA, and ACG.

Tyrosine - see HERE.

Other amino acids

• Asparagine (Asn/N) is a non-essential amino acid coded by AAU and AAC. Its carboxyamide in the R-group gives it polarity. Asparagine is implicated in formation of acrylamide in foods cooked at high temperatures (deep frying) when it reacts with carbonyl groups. Asparagine can be made in the body from aspartate by an amidation reaction with an amine from glutamine. Breakdown of asparagine produces malate, which can be oxidized in the citric acid cycle.
• Cysteine (Cys/C) is the only amino acid with a sulfhydryl group in its side chain. It is nonessential for most humans, but may be essential in infants, the elderly and individuals who suffer from certain metabolic diseases. Cysteine’s sulfhydryl group is readily oxidized to a disulfide when reacted with another one. In addition to being found in proteins, cysteine is also a component of the tripeptide, glutathione. Cysteine is specified by the codons UGU and UGC.

• Glutamine (Gln/Q) is an amino acid that is not normally essential in humans, but may be in individuals undergoing intensive athletic training or with gastrointestinal disorders. It has a carboxyamide side chain which does not normally ionize under physiological pHs, but which gives polarity to the side chain. Glutamine is coded for by CAA and CAG and is readily made by amidation of glutamate. Glutamine is the most abundant amino acid in circulating blood and is one of only a few amino acids that can cross the blood-brain barrier.
• Selenocysteine (Sec/U) is a component of selenoproteins found in all kingdoms of life. It is a component in several enzymes, including glutathione peroxidases and thioredoxin reductases. Selenocysteine is incorporated into proteins in an unusual scheme involving the stop codon UGA. Cells grown in the absence of selenium terminate protein synthesis at UGAs. However, when selenium is present, certain mRNAs which contain a selenocysteine insertion sequence (SECIS), insert selenocysteine when UGA is encountered. The SECIS element has characteristic nucleotide sequences and secondary structure base-pairing patterns. Twenty five human proteins contain selenocysteine.
• Pyrrolysine (Pyl/O) is a twenty second amino acid, but is rarely found in proteins. Like selenocysteine, it is not coded for in the genetic code and must be incorporated by unusual means. This occurs at UAG stop codons. Pyrrolysine is found in methanogenic archaean organisms and at least one methane-producing bacterium. Pyrrolysine is a component of methane-producing enzymes.

Ionizing groups

pKa values for amino acid side chains are very dependent upon the chemical environment in which they are present. For example, the R-group carboxyl found in aspartic acid has a pKa value of 3.9 when free in solution, but can be as high as 14 when in certain environments inside of proteins, though that is unusual and extreme. Each amino acid has at least one ionizable amine group (α- amine) and one ionizable carboxyl group (α- carboxyl). When these are bound in a peptide bond, they no longer ionize. Some, but not all amino acids have R-groups that can ionize. The charge of a protein then arises from the charges of the α-amine group, the α- carboxyl group. and the sum of the charges of the ionized R-groups. Titration/ionization of aspartic acid is depicted in Figure 2.10. Ionization (or deionization) within a protein’s structure can have significant effect on the overall conformation of the protein and, since structure is related to function, a major impact on the activity of a protein.

Most proteins have relatively narrow ranges of optimal activity that typically correspond to the environments in which they are found (Figure 2.11). It is worth noting that formation of peptide bonds between amino acids removes ionizable hydrogens from both the α- amine and α- carboxyl groups of amino acids. Thus, ionization/ deionization in a protein arises only from 1) the amino terminus; 2) carboxyl terminus; 3) R-groups; or 4) other functional groups (such as sulfates or phosphates) added to amino acids post-translationally - see below.

Not all amino acids in a cell are found in proteins. The most common examples include ornithine (arginine metabolism), citrulline (urea cycle), and carnitine (Figure 2.12). When fatty acids destined for oxidation are moved into the mitochondrion for that purpose, they travel across the inner membrane attached to carnitine. Of the two stereoisomeric forms, the L form is the active one. The molecule is synthesized in the liver from lysine and methionine.

From exogenous sources, fatty acids must be activated upon entry into the cytoplasm by being joined to coenzyme A. The CoA portion of the molecule is replaced by carnitine in the intermembrane space of the mitochondrion in a reaction catalyzed by carnitine acyltransferase I. The resulting acylcarnitine molecule is transferred across the inner mitochondrial membrane by the carnitineacylcarnitine translocase and then in the matrix of the mitochondrion, carnitine acyltransferase II replaces the carnitine with coenzyme A (Figure 6.88).

Catabolism of amino acids

We categorize amino acids as essential or non-essential based on whether or not an organism can synthesize them. All of the amino acids, however, can be broken down by all organisms. They are, in fact, a source of energy for cells, particularly during times of starvation or for people on diets containing very low amounts of carbohydrate. From a perspective of breakdown (catabolism), amino acids are categorized as glucogenic if they produce intermediates that can be made into glucose or ketogenic if their intermediates are made into acetyl-CoA. Figure 2.13 shows the metabolic fates of catabolism of each of the amino acids. Note that some amino acids are both glucogenic and ketogenic.

Post-translational modifications

After a protein is synthesized, amino acid side chains within it can be chemically modified, giving rise to more diversity of structure and function (Figure 2.14). Common alterations include phosphorylation of hydroxyl groups of serine, threonine, or tyrosine. Lysine, proline, and histidine can have hydroxyls added to amines in their R-groups. Other modifications to amino acids in proteins include addition of fatty acids (myristic acid or palmitic acid), isoprenoid groups, acetyl groups, methyl groups, iodine, carboxyl groups, or sulfates. These can have the effects of ionization (addition of phosphates/sulfates), deionization (addition of acetyl group to the R-group amine of lysine), or have no effect on charge at all. In addition, N-linked- and O-linkedglycoproteins have carbohydrates covalently attached to side chains of asparagine and threonine or serine, respectively.

Some amino acids are precursors of important compounds in the body. Examples include epinephrine, thyroid hormones, Ldopa, and dopamine (all from tyrosine), serotonin (from tryptophan), and histamine (from histidine).

Building Polypeptides

Although amino acids serve other functions in cells, their most important role is as constituents of proteins. Proteins, as we noted earlier, are polymers of amino acids.

Amino acids are linked to each other by peptide bonds, in which the carboxyl group of one amino acid is joined to the amino group of the next, with the loss of a molecule of water. Additional amino acids are added in the same way, by formation of peptide bonds between the free carboxyl on the end of the growing chain and the amino group of the next amino acid in the sequence. A chain made up of just a few amino acids linked together is called an oligopeptide (oligo=few) while a typical protein, which is made up of many amino acids is called a polypeptide (poly=many). The end of the peptide that has a free amino group is called the N-terminus (for NH2), while the end with the free carboxyl is termed the C-terminus (for carboxyl).

As we’ve noted before, function is dependent on structure, and the string of amino acids must fold into a specific 3-D shape, or conformation, in order to make a functional protein. The folding of polypeptides into their functional forms is the topic of the next section.

2.2: Structure and Function – Amino Acids

“It is one of the more striking generalizations of biochemistry …that the twenty amino acids and the four bases, are, with minor reservations, the same throughout Nature.” – Francis Crick

All amino acids have the same basic structure, shown in Figure 2.1. At the center of each amino acid is a carbon called the α carbon and attached to it are four groups – a hydrogen, a carboxylic acid group, an amine group, and an R-group, sometimes referred to as a variable group or side chain. The α carbon, carboxylic acid, and amino groups are common to all amino acids, so the R-group is the only variable feature. With the exception of glycine, which has an R-group consisting of a hydrogen atom, all of the amino acids in proteins have four different groups attached to them and consequently can exist in two mirror isomeric forms.

The designations used in organic chemistry are not generally applied to amino acid nomenclature, but a similar system uses L and D to describe these enantiomers. Nature has not distributed the stereoisomers of amino acids equally. Instead, with only very minor exceptions, every amino acid found in cells and in proteins is in the L configuration.

Figure 2.1 – General amino acid structure

There are 22 amino acids that are found in proteins and of these, only 20 are specified by the universal genetic code. The others, selenocysteine and pyrrolysine use tRNAs that are able to base pair with stop codons in the mRNA during translation. When this happens, these unusual amino acids can be incorporated into proteins. Enzymes containing selenocysteine, for example, include glutathione peroxidases, tetraiodothyronine 5′ deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases, and selenophosphate synthetase. Pyrrolysine-containing proteins are much rarer and are mostly confined to archaea.

Essential and non-essential

Nutritionists divide amino acids into two groups – essential amino acids and non-essential amino acids. Essential amino acids must be included in our diet because our cells can’t synthesize them. What is essential varies considerably from one organism to another and even differ in humans, depending on whether they are adults or children. Table 2.1 shows essential and non-essential amino acids in humans.

Some amino acids that are normally nonessential, may need to be obtained from the diet in certain cases. Individuals who do not synthesize sufficient amounts of arginine, cysteine, glutamine, proline, selenocysteine, serine, and tyrosine, due to illness, for example, may need dietary supplements containing these amino acids.

Table 2.1 – Essential and non-essential amino acids

Non-protein amino acids

There are also amino acids found in cells that are not incorporated into proteins. Common examples include ornithine and citrulline. Both of these compounds are intermediates in the urea cycle, an important metabolic pathway.

R-group chemistry

Table 2.2 – Amino acid categories (based on R-group properties)

Amino acids can be classified based on the chemistry of their R-groups. It is useful to classify amino acids in this way because it is these side chains that give each amino acid its characteristic properties. Thus, amino acids with (chemically) similar side groups can be expected to function in similar ways, for example, during protein folding. The specific category divisions may vary, but all systems are attempts to organize and understand the relationship between an amino acid’s structure and its properties or behavior as part of a larger system.

Non-polar amino acids

Amino acids in this group include:

• Alanine (Ala/A)
• Glycine (Gly/G)
• Isoleucine (Ile/I)
• Leucine (Leu/L)
• Methionine (Met/M)
• Valine (Val/V)

The amino acids in this group have nonpolar, hydrophobic R groups. When incorporated into globular proteins they tend to pack inward among other hydrophobic groups. In proteins that embed themselves into or through membranes, these amino acids can orient themselves toward hydrophobic portions of the inside of the membrane.

The small R groups here are more readily packed into tight formations. Proline is exceptional in that it has an R group that folds back and covalently bonds to the backbone of the amino acid, creating a more rigid element in a protein chain that reduces free movement of the polypeptide chain. Additionally, proline can undergo hydroxylation reactions, stabilizing the protein structure. This occurs in collagen with the aid of ascorbic acid (Vitamin C). One symptom of the vitamin C deficiency syndrome ‘scurvy’ is the reduced quality of collagen in tissues, including the skin and gums. This can lead to the deterioration and loss of teeth.

Figure 2.2 – Amino acid side chain properties Wikipedia

Figure 2.3 – Non-polar amino acids

Acidic Amino Acids (Carboxylic acid side chains)

• Aspartic acid (Asp/D)
• Glutamic acid (Glu/E)

Figure 2.4 – Carboxyl amino acids

These amino acids each contain a carboxylic acid group as part of the variable group. At physiological pH, these groups exist primarily in their deprotonated state. It is easy to be confused if they are drawn in this state, because their names include “acid” while the structure shows no ionizable proton and the charge on the R group is negative.

In addition to its role as a building block in proteins, glutamic acid (with the deprotonated form named “glutamate”) is a neurotransmitter. It also is recognized by a receptor in our mouths, contributing to a taste sensation described as “umami.” Many foods contain appreciable amounts of glutamate that are recognized by our taste receptors, and encourage us to eat these substances. Those foods frequently contain protein that has broken down to some degree: cooked meats, fermented sauces like Worcestershire or soy, tahini, broths, and yeast extracts.

Basic amino acids (Nitrogen-containing side chains)

Included in this group of amino acids are:

• Arginine (Arg/R)
• Histidine (His/H)
• Lysine (Lys/K)

Figure 2.5 – Amine amino acids

The variable group in each of these amino acids contains nitrogen, which imparts to the group the ability to exist in protonated and deprotonated states. They are frequently called basic, but also are often drawn in their protonated state which is more prevalent at physiological pH.

Arginine (Arg/R) is interesting due to the fact it is an essential dietary amino acid for premature infants, who cannot synthesize it. In addition, surgical trauma, sepsis, and burns increase demand for arginine and proper healing can require dietary intake.

Histidine contains a nitrogen-containing imidazole functional group that has a pKa of 6. This means it can pick up or donate hydrogen ions in response to small changes in pH. In proteins, histidine frequently has important roles participating directly in reactions involving hydrogen ion transfer.

The R group on lysine is frequently chemically modified in order for it to make unusual linkages to other chemical groups or to take part in specific chemical reactions. Lysine is often added to animal feed because it is a limiting amino acid and is necessary for optimizing growth of animals raised for consumption.

Aromatic amino acids

Figure 2.6 – Aromatic amino acids

Amino acids with aromatic side chains include:

• Phenylalanine (Phe/ F)
• Tryptophan (Trp/W)
• Tyrosine (Tyr/Y)

These amino acids are included in protein structures but also serve as precursors in some important biochemical pathways, leading to the production of hormones such as L-Dopa and serotonin.

Hydroxyl amino acids

This group includes

• Threonine (Thr/T)
• Serine (Ser/S)
• Tyrosine (already discussed as an aromatic amino acid)

The amino acids in this group contain alcohol groups, which can engage in hydrogen-bonding interactions. As part of protein molecules they are hydrophilic and can be oriented outward in watery environments. The alcohol group is subject to chemical reactions or modifications, for instance when carbohydrate groups are covalently linked to proteins.

Figure 2.7 – Hydroxyl amino acids

Figure 2.8 – Amino acid properties Wikipedia

Other amino acids

• Asparagine (Asn/N) is a polar amino acid. The amide on the functional group is not basic.
• Cysteine (Cys/C)
• Glutamine (Gln/Q)

Figure 2.9 – Other amino acids

Cysteine, which contains a thiol. Thiols can react with one another via oxidation, forming disulfide links containing two covalently-linked sulfur atoms. Variable groups on methionine in protein chains can undergo such reactions, covalently tying the chains to one another with a short tether. Such disulfide links or bridges restrict the mobility of protein chains and contribute to more defined structures.

• Selenocysteine (Sec/U) is a component of selenoproteins found in all kingdoms of life. Twenty five human proteins contain selenocysteine. It is a component in several enzymes, including glutathione peroxidases and thioredoxin reductases. It is not coded for by the standard genetic code.
• Pyrrolysine (Pyl/O) is a twenty second amino acid, but is rarely found in proteins. Like selenocysteine, it is not coded for in the genetic code and must be incorporated by unusual means.

Ionizing groups

Some, but not all amino acids have R-groups that can ionize. The charge of a protein then arises from the charges of the amine group, the carboxyl group, and the sum of the charges of the ionized R-groups. Titration/ionization of aspartic acid is depicted in Figure 2.10. Ionization (or deionization) within a protein’s structure can have significant effect on the overall conformation of the protein and, since structure is related to function, a major impact on the activity of a protein.

Figure 2.10 – Titration curve for aspartic acid Image by Penelope Irving

Building Polypeptides

Although amino acids serve other functions in cells, their most important role is as constituents of proteins. Proteins, as we noted earlier, are polymers of amino acids.

Amino acids are linked to each other by peptide bonds, in which the carboxyl group of one amino acid is joined to the amino group of the next, with the loss of a molecule of water. Additional amino acids are added in the same way, by formation of peptide bonds between the free carboxyl on the end of the growing chain and the amino group of the next amino acid in the sequence. A chain made up of just a few amino acids linked together is called an oligopeptide (oligo=few) while a typical protein, which is made up of many amino acids is called a polypeptide (poly=many). The end of the peptide that has a free amino group is called the N-terminus (for NH2), while the end with the free carboxyl is termed the C-terminus (for carboxyl).

Figure 2.16 Formation of a peptide bond

As we’ve noted before, function is dependent on structure, and the string of amino acids must fold into a specific 3-D shape, or conformation, in order to make a functional protein. The folding of polypeptides into their functional forms is the topic of the next section.

The alpha carbon in organic molecules refers to the first carbon atom that attaches to a functional group, such as a carbonyl. In amino acids the alpha carbon is the carbon adjacent to the carbonyl carbon.

Introductory Biochemistry Copyright © by Carol Higginbotham is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License , except where otherwise noted.

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10.0: Introduction to Amino Acids and Proteins

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• Page ID 474642

• Tim Soderberg
• University of Minnesota Morris

Proteins are polymers of amino acids , linked by amide groups known as peptide bond s. An amino acid can be thought of as having two components: a 'backbone', or 'main chain', composed of an ammonium group, an 'alpha-carbon', and a carboxylate, and a variable 'side chain' (in green below) bonded to the alpha-carbon.

There are twenty different side chains in naturally occurring amino acids, and it is the identity of the side chain that determines the identity of the amino acid: for example, if the side chain is a -CH 3 group, the amino acid is alanine, and if the side chain is a -CH 2 OH group, the amino acid is serine. Many amino acid side chains contain a functional group (the side chain of serine, for example, contains a primary alcohol), while others, like alanine, lack a functional group, and contain only a simple alkane.

The two 'hooks' on an amino acid monomer are the amine and carboxylate groups. Proteins (polymers of ~50 amino acids or more) and peptides (shorter polymers) are formed when the amino group of one amino acid monomer reacts with the carboxylate carbon of another amino acid to form an amide linkage, which in protein terminology is a peptide bond . Which amino acids are linked, and in what order - the protein sequence - is what distinguishes one protein from another, and is coded for by an organism's DNA. Protein sequences are written in the amino terminal (N-terminal) to carboxylate terminal (C-terminal) direction, with either three-letter or single-letter abbreviations for the amino acids (see amino acid table). Below is a four amino acid peptide with the sequence "cysteine - histidine - glutamate - methionine". Using the single-letter code, the sequence is abbreviated CHEM.

When an amino acid is incorporated into a protein it loses a molecule of water and what remains is called a residue of the original amino acid. Thus we might refer to the 'glutamate residue' at position 3 of the CHEM peptide above.

Once a protein polymer is constructed, it in many cases folds up very specifically into a three-dimensional structure, which often includes one or more 'binding pockets' in which other molecules can be bound. It is this shape of this folded structure, and the precise arrangement of the functional groups within the structure (especially in the area of the binding pocket) that determines the function of the protein.

Enzymes are proteins which catalyze biochemical reactions. One or more reacting molecules - often called substrates - become bound in the active site pocket of an enzyme, where the actual reaction takes place. Receptors are proteins that bind specifically to one or more molecules - referred to as ligands - to initiate a biochemical process. For example, we saw in the introduction to this chapter that the TrpVI receptor in mammalian tissues binds capsaicin (from hot chili peppers) in its binding pocket and initiates a heat/pain signal which is sent to the brain.

Shown below is an image of the glycolytic enzyme fructose-1,6-bisphosphate aldolase (in grey), with the substrate molecule bound inside the active site pocket.

(x-ray crystallographic data are from Protein Science 1999 , 8, 291 ; pdb code 4ALD. Image produced with JMol First Glance )

Intro to nucleic acids ⇒

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Amino acids: Chemical and Physical Properties

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Amino Acids

Jan 01, 2020

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Amino Acids. Structural Feature of Proteins. Proteins functionally diverse molecules in living systems such as: in the body are polymers made from 20 different amino acids. differ in characteristics and functions that depend on the order of amino acids that make up the protein.

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• amino acids
• side chains
• derived proteins
• simple proteins combined
• weakly basic amino groups

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Structural Feature of Proteins Proteins functionally diverse molecules in living systems such as: • in the body are polymers made from 20 different amino acids. • differ in characteristics and functions that depend on the order of amino acids that make up the protein. • perform many different functions in the body, such as provide structure, transport oxygen, direct biological reactions, control against infection, and even be a source of energy.

STRUCTURE OF THE AMINO ACIDS Amino acids are the molecular building blocks of proteins Each amino acid (except for proline) has: • A carboxyl group (-COO-) . • An amino group (-NH3+) . • Side chain ("R-group") bonded to the α-carbon atom. These carboxyl and amino groups are combined in peptide linkage.

Ionization of Amino Acids • In most body fluids the carboxylic group (−COOH) and the amino group (−NH2) are ionized. • An ionized amino acid that has a positive and negative charge is a dipolar ion called a zwitterion.

Classification of Amino Acids They classified according to the side chain: • Amino acids with nonpolar side chains. • Aromatic R Groups. • Amino acids with uncharged polar side chains. • Positively Charged (Basic) R Groups. • Amino acids with acidic side chains.

A- Nonpolar Side Chains • The side chains cluster in the interior of the protein due to hydrophobicity. • The side chain of proline and its α-amino group form a ring structure. • Proline gives the fibrous structure of collagen, and interrupts the α-helices found in globular proteins.

B- Aromatic (R) Groups • Their aromatic side chains, are nonpolar so that participate in hydrophobic interactions. • Tyrosine is an important in some enzymes. • Most proteins absorb light at a wavelength of 280 nm due to aromatic groups. • A property exploited by researchers in the characterization of proteins.

C. Uncharged polar side chains • More hydrophilic because they form hydrogen bonds with water. • includes serine, threonine, cysteine, asparagine, and glutamine. • Cysteine contains a sulfhydryl group (-SH), an important component of the active site of many enzymes. • Two cysteines can become oxidized to form a dimmer cystine, which contains a covalent cross-link called a disulfide bond (-S-S-).

D. Basic (R) Groups • The R groups have significant positive charge. • Lysine has a second positive amino group at the position on its (R) chain. • Arginine has a positively charged guanidino group. • Histidine has a positive imidazole group facilitates the enzyme-catalyzed reaction by serving as a proton donor/acceptor.

E. Acidic Side Chains • Aspartic and glutamic acid are proton donors. • At neutral pH, the side chains of these amino acids are fully ionized. • They have a negatively charged carboxylate group (-COO-) at physiologic pH.

Uncommon Amino Acids • Hydroxylysine and hydroxyproline, are found in the collagen and gelatin proteins. • γ-Carboxyglutamic acid is involved in blood clotting. • N-methylarginine and N-acetyllysine are found in histone proteins associated with chromosomes.

Optical Properties of Amino Acids • The α-carbon of a.a. is attached to four different chemical groups is a chiral or optically active carbon atom. • Glycine is the exception. • amino acids exist in two forms, D and L, that are mirror images of each other. • All amino acids found in proteins are of the L-configuration.

ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS • Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and weakly basic α-amino groups. • Each of the acidic and basic amino acids contains an ionizable group in its side chain. • Thus, both free and some of the combined amino acids in peptide linkages can act as buffers.

Amino acids join together in a long chain: N terminal end to C terminal end = a polypeptide.

FORMATION OF DIPEPTIDE

Protein classification • Proteins are classified based on their • Solubility and composition • Function • Shape & size

Classification based on solubility and composition • According to this classification, proteins are divided into three main groups as simple, conjugated and derived proteins. • Simple proteins • Simple proteins yield on hydrolysis, only amino acids. • These proteins are further classified based on their solubility in different solvents as well as their heat coagulability.

Albumins • Albumins are readily soluble in water, dilute acids and alkalies and are coagulated by heat. • Albumins may be precipitated out from solution using high salt concentration, a process called 'salting out'. • They are deficient in glycine. • Serum albumin and ovalbumin (egg white) are examples.

Globulins • They carry out synthesis, transport, and metabolism in the cells • Globulins are insoluble or sparingly soluble in water, but their solubility is greatly increased by the addition of neutral salts such as sodium chloride. • These proteins are coagulated by heat. • They are deficient in methionine. • Serum globulin, fibrinogen, myosin of muscle and globulins of pulses are examples.

Histones • Histones are small and stable basic proteins • They contain fairly large amounts of basic amino acid, histidine. • They are soluble in water, but insoluble in ammonium hydroxide. • They are not readily coagulated by heat. • They occur in globin of hemoglobin and nucleoproteins

Protamines • Protamines are the simplest of the proteins. • They are soluble in water and are not coagulated by heat. • They are basic in nature due to the presence of large quantities of arginine. • Protamines are found in association with nucleic acid in the sperm cells of certain fish. • Tyrosine and tryptophan are usually absent in protamines.

Prolamins • Prolamins are insoluble in water but soluble in 70-80% aqueous alcohol. • Upon hydrolysis they yield much proline and amide nitrogen, hence the name prolamin. Glutelins • Glutelins are insoluble in water and absolute alcohol but soluble in dilute alkalies and acids. • They are plant proteins e.g., glutenin of wheat.

Albuminoids • These are characterized by great stability and insolubility in water and salt solutions. • These are called albuminoids because they are essentially similar to albumin and globulins. • They are highly resistant to proteolytic enzymes. • They are fibrous in nature and form most of the supporting structures of animals. • They occur as chief constituent of exoskeleton structure such as hair, horn and nails.

Conjugated proteins • These are simple proteins combined with some non-protein substances known as prosthetic groups. • The nature of the non-protein or prosthetic groups is the basis for the sub classification of conjugated proteins.

Mucoproteins • These proteins are composed of simple proteins in combination with carbohydrates like mucopolysaccharides, which include hyaluronic acid and chondroitin sulphates. • On hydrolysis, mucopolysaccharides yield more than 4% of amino-sugars, hexosamine and uronic acid e.g., ovomucoid from egg white. • Soluble mucoproteins are neither readily denatured by heat nor easily precipitated by common protein precipitants like trichloroacetic acid or picric acid. • The term glycoproteins is restricted to those proteins that contain small amounts of carbohydrate usually less than 4% hexosamine.

Chromoproteins • These are proteins containing coloured prosthetic groups e.g., haemoglobin, flavoprotein and cytochrome. Lipoproteins • These are proteins conjugated with lipids such as neutral fat, phospholipids and cholesterol. Phosphoproteins • These are proteins containing phosphoric acid. • Phosphoric acid is linked to the hydroxyl group of certain amino acids like serine in the protein e.g., casein of milk.

Derived proteins • These are proteins derived by partial to complete hydrolysis from the simple or conjugated proteins by the action of acids, alkalies or enzymes. • They include two types of derivatives, primary-derived proteins and secondary-derived proteins. Primary-derived proteins These protein derivatives are formed by processes causing only slight changes in the protein molecule and its properties. There is little or no hydrolytic cleavage of peptide bonds.

Proteans • Proteans are insoluble products formed by the action of water, dilute acids and enzymes. • These are particularly formed from globulins but are insoluble in dilute salt solutions • e.g., myosan from myosin, fibrin from fibrinogen. Metaproteins • These are formed by the action of acids and alkalies upon protein. • They are insoluble in neutral solvents. Coagulated proteins Coagulated proteins are insoluble products formed by the action of heat or alcohol on natural proteins e.g., cooked meat and cooked albumin.

Secondary-derived proteins • These proteins are formed in the progressive hydrolytic cleavage of the peptide bonds of protein molecule. • They are roughly grouped into proteoses, peptones and peptides according to average molecular weight. • Proteoses are hydrolytic products of proteins, which are soluble in water and are not coagulated by heat. • Peptones are hydrolytic products, which have simpler structure than proteoses. • They are soluble in water and are not coagulated by heat. • Peptides are composed of relatively few amino acids.  They are water-soluble and not coagulated by heat.

Classification of proteins based on function Catalytic proteins – Enzymes • The most striking characteristic feature of these proteins is their ability to function within the living cells as biocatalysts. • These biocatalysts are called as enzymes. • Enzymes represent the largest class. • Nearly 2000 different kinds of enzymes are known, each catalyzing a different kind of reaction. • They enhance the reaction rates a million fold.

Regulatory proteins - Hormones • These are polypeptides and small proteins found in relatively lower concentrations in animal kingdom but play highly important regulatory role in maintaining order in complex metabolic reactions e.g., growth hormone, insulin etc. Contractile proteins • Proteins like actin and myosin function as essential elements in contractile system of skeletal muscle. Secretary proteins • Fibroin is a protein secreted by spiders and silkworms to form webs and cocoons.

Protective proteins - Antibodies • These proteins have protective defense function. • These proteins combine with foreign protein and other substances and fight against certain diseases. • e.g., immunoglobulin. • These proteins are produced in the spleen and lymphatic cells in response to foreign substances called antigen. • The newly formed protein is called antibody which specifically combines with the antigen which triggered its synthesis thereby prevents the development of diseases. • Fibrin present in the blood is also a protective protein.

Storage proteins • It is a major class of proteins which has the function of storing amino acids as nutrients and as building blocks for the growing embryo. • Storage proteins are source of essential amino acids, which cannot be synthesized by human beings. • The major storage protein in pulses is globulins and prolamins in cereals. • In rice the major storage protein is glutelins. • Albumin of egg and casein of milk are also storage proteins.

Transport proteins • Some proteins are capable of binding and transporting specific types of molecules through blood. • Haemoglobin is a conjugated protein composed of colourless basic protein, the globin and ferroprotoporphyrin or haem. • It has the capacity to bind with oxygen and transport through blood to various tissues. • Myoglobin, a related protein, transports oxygen in muscle. • Lipids bind to serum proteins like albumin and transported as lipoproteins in the blood.

Toxic proteins • Some of the proteins are toxic in nature. • Ricin present in castor bean is extremely toxic to higher animals in very small amounts. • Enzyme inhibitors such as trypsin inhibitor bind to digestive enzyme and prevent the availability of the protein. • Lectin, a toxic protein present in legumes, agglutinates red blood cells. • A bacterial toxin causes cholera, which is a protein. • Snake venom is protein in nature

Classification based on size and shape • Based on size and shape, the proteins are also subdivided into globular and fibrous proteins. • Globular proteins are mostly water-soluble and fragile in nature e.g., enzymes, hormones and antibodies. • They have compact, spherical shapes. • Fibrous proteins are tough and water-insoluble. • They are used to build a variety of materials that support and protect specific tissues, e.g., skin, hair, fingernails and keratin

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