Units which compose proteins

Sphere Stick Rotate. The term lipid refers to a wide variety of biomolecules including fats, oils, waxes and steroid hormones. The hydrophobic nature of the lipids dictates many of their uses in biological systems. Fats are a good source of stored energy while oils and waxes are used to form protective layers on our skin, preventing infection.

Some lipids, the steroid hormones, are important regulators of cell activity. We will revisit this during our discussion of the information flow in cells. The activities of steroid hormones such as estrogen have been implicated in cancers of the female reproductive system. Treatments based on this knowledge will be discussed in detail in the treatment section of the site.

Depicted above is an example of a triacylglycerol , or fat. The three long chains are composed only of carbon and hydrogen and this gives the molecule its hydrophobic properties. When you read about saturated and unsaturated fat content on a food label, they are referring to differences in these long hydrocarbon chains. A main function of lipids is the formation of biological membranes. Cells are surrounded by a thin layer of lipids. The layer is made up of a special type of lipid that has both hydrophobic and hydrophilic properties.

The hydrophilic ends of these molecules face the water-filled environment inside the cells and the watery environment outside the cells. A hydrophobic region exists inside the two layers. The membrane that surrounds the cells is rich in proteins and other lipids such as cholesterol. Most chemicals can not cross the lipid bilayer.

Water and some other small molecules can freely pass through the membrane while other molecules must be actively transported via protein channels embedded in the membrane. Membranes also contain a combination of the biomolecules that have been described so far.

As seen above, proteins may be coupled to carbohydrates to form glycoproteins. Glycoproteins are important in the cell:cell interactions discussed previously, and changes in the amounts or types of these proteins are seen in cancer. Similarly, a combination of lipids and carbohydrates lead to the formation of glycolipids. Both of these molecules are polymers. They are composed of monomer subunits like the carbohydrates and proteins described previously. The monomers used to build nucleic acids are called nucleotides.

Like all of the monomers described so far, the monomers used to build DNA are similar to each other but are not exactly alike. Thus, for simplicity sake, the 20 amino acids used for protein synthesis have both three letter and one letter code abbreviations Table 2. These abbreviations are commonly used to delineate protein sequences for bioinformatic and research purposes.

Answer: Tryptophan contains an indole ring structure that includes the amine functional group. However, due to the proximity of, and electron withdrawing nature of the aromatic ring structure, the lone pair of electrons on the nitrogen are unavailable to accept a proton.

Instead they are involved in forming pi- bonds within several of the different resonance structures possible for the indole ring. Conversely, within the immidazole ring structure found in histidine, there are two nitrogen atoms, one of which is involved in the formation of resonance structures Nitrogen 1 in Figure 2.

A Shown are four resonance structures of the indole ring structure demonstrating that the lone pair of electrons on the nitrogen are involved in the formation of pi -bonds. B The immidazole ring structure has one nitrogen 1 that is involved in resonance structures not shown and is not available to accept a proton, while the second nitrogen 3 has a lone pair of electrons available to accept a proton as shown.

Given the example above, describe using a chemical diagram, why the amide nitrogen atoms found in asparagine and glutamine are not basic. If you examine the structure of the alpha carbon within each of the amino acids, you will notice that all of the amino acids, except for glycine are chiral molecules Figure 2.

Like left and right hands that have a thumb, fingers in the same order, but are mirror images and not the same, chiral molecules have the same things attached in the same order, but are mirror images and not the same. The mirror image versions of chiral molecules have physical properties that are nearly identical to one another, making it very difficult to tell them apart from one another or to separate.

Because of this nature, they are given a special stereoisomer name called enantiomers and in fact, the compounds themselves are given the same name! These molecules do differ in the way that they rotate plain polarized light and the way that they react with and interact with biological molecules.

Molecules that rotate the light in the right-handed direction are called dextrorotary and are given a D- letter designation. Molecules that rotate light in the left-handed direction are called levorotary and are give an L- letter designation to distinguish one enantiomer from the other.

The D- and L- forms of alanine are show in Figure 2. Although most amino acids can exist in both left and right handed forms, life on Earth is made of left handed amino acids, almost exclusively.

Proteogenic amino acids incorporated into proteins by ribosomes are always in the L-conformation. Some bacteria can incorporate D-amino acids into non-ribosomally encoded peptides, but the use of D-amino acids in nature is rare.

Interestingly, when we will discuss the structure of sugars in Chapter XX, we will find that sugars that are incorporated into carbohydrate structures are almost exclusively in the D-conformation. No one knows why this is the case. However, Drs. John Cronin and Sandra Pizzarello have shown that of the amino acids that fall to earth from space on meteorites, more are in the L-conformation than the D-conformation. Thus, the fact that we are made predominantly of L-amino acids may be because of amino acids from space.

Why do amino acids in space favor the L-conformation? No one really knows, but it is known that radiation can also exist in left and right handed forms. So, there is a theory called the Bonner hypothesis , that proposes that the predominant forms of radiation in space ie. This is still speculative, but recent findings from meteorites make this hypothesis much more plausible.

Except for the simplest amino acid, glycine, all of the other amino acids that are incorporated into protein structures are chiral in nature. A Demonstrates the chirality of the core alpha amino acid structure when the non-specific R-group is used. B The D- and L-Alanine enantiomer pair, upper diagram represents the ball and stick model and the lower diagram represents the line structure. Note that the D- and L-designations are specific terms used for the way a molecule rotates plain polarized light.

It does not denote the absolute stereo configuration of a molecule. An absolute configuration refers to the spatial arrangement of the atoms of a chiral molecular entity or group and its stereochemical description e.

R or S , referring to Rectus , or Sinister , respectively. Absolute configurations for a chiral molecule in pure form are most often obtained by X-ray crystallography. Alternative techniques are optical rotatory dispersion, vibrational circular dichroism, use of chiral shift reagents in proton NMR and Coulomb explosion imaging. When the absolute configuration is obtained the assignment of R or S is based on the Cahn—Ingold—Prelog priority rules, which can be reviewed by following the link and in Figure 2.

All of the chiral amino acids, except for cysteine, are also in the S-conformation. Cysteine, contains the sulfur atom causing the R-group to have higher priority than the carboxylic acid functional group, leading to the R-conformation for the absolute stereochemistry. However, cysteine does rotate plain polarized light in the levorotary or left-handed direction.

Thus, the R- and S-designations do not always correspond with the D- and L- conformation. In the Cahn Ingold Prelog system for naming chiral centers, the groups attached to the chiral center are ranked according to their atomic number with the highest atomic number receiving the highest priority A in the diagram above and the lowest atomic number receiving the lowest priority D in the diagram above. The lowest priority is then pointed away from the viewer to correctly orient the molecule for further evaluation.

The path of priorities 1, 2, and 3 corresponding to A, B and C above are then traced. If the path is is in the clockwise direction, the chiral center is given the R-designation, whereas if the path is counterclockwise, it is given the S-designation.

Image from Wikipedia. In chemistry, a zwitterion is a molecule with two or more functional groups, of which at least one has a positive and one has a negative electrical charge and the net charge of the entire molecule is zero at a specific pH. Because they contain at least one positive and one negative charge, zwitterions are also sometimes called inner salts.

The charges on the different functional groups balance each other out, and the molecule as a whole can be electrically neutral at a specific pH. The pH where this happens is known as the isoelectric point. Unlike simple amphoteric compounds that may only form either a cationic or anionic species, a zwitterion simultaneously has both ionic states. Amino acids are examples of zwitterions Figure 2. These compounds contain an ammonium and a carboxylate group, and can be viewed as arising via a kind of intramolecular acid—base reaction: The amine group deprotonates the carboxylic acid.

An amino acid contains both acidic carboxylic acid fragment and basic amine fragment centres. The isomer on the right is the zwitterionic form.

Because amino acids are zwitterions, and several also contain the potential for ionization within their R-groups, their charge state in vivo , and thus, their reactivity can vary depending on the pH, temperature, and solvation status of the local microenvironment in which they are located.

The chart of standard pK a values for the amino acids is shown in Table 2. However, it should be noted that the solvation status in the microenvironment of an amino acid can alter the relative pK a values of these functional groups and provide unique reactive properties within the active sites of enzymes Table 2.

A more in depth discussion of the effects of desolvation will be given in Chapter XX discussing enzyme reaction mechanisms. Printable Version of pKa Values. As seen in Table 2. Recall that the pK a is defined as the pH at which the ionized and unionized forms of an ionizable functional group within a molecule exist in equal concentrations.

Thus, as a functional group shifts above or below its pK a value, there will be a shift in the concentrations of the ionized and unionized forms favoring one state over the other.

Within all amino acids both the carboxylic acid functional group C-terminus , and the amine functional group N-terminus are capable of ionization. In addition, seven amino acids aspartic acid, glutamic acid, arginine, histidine, lysine, tyrosine, and cysteine also contain ionizable functional groups within their R-groups.

Typically an ionizable group will favor the protonated state in pH conditions below its respective pK a values and will favor the deprotonated state in pH conditions above its respective pK a value. For example, if we look at a titration curve for the basic amino acid, histidine Figure 2. As each pK a is reached, the charge state of the amino acid is altered to favor the deprotonated state.

A Titration curve of histidine from low pH to high pH. Each equivalence point pK a is indicated. B Shows the favored ionization state of histidine following the passage of each pK a value. Image adapted from L. Van Warren. Cysteine is also a unique amino acid as this side chain is capable of undergoing a reversible oxidation-reduction redox reaction with other cysteine residues creating a covalent disulfide bond in the oxidized state Figure 2.

Recall that when molecules become oxidized that they are losing electrons and that when molecules are reduced that they are gaining electrons. During biological redox reactions, hydrogen ions protons are often removed with the electrons from the molecule during oxidation, and are returned during reduction.

Thus, if a reaction is losing or gaining protons, this is a good indication that it is also losing or gaining electrons and that a redox reaction is occurring. Thus, proton gain or loss can be an easy way to identify this reaction type. Disulfide bonds are integral in the formation of the 3-dimentional structure of proteins and can therefore highly impact the function of the resulting protein.

Disulfide bonds will be discussed in further detail section 2. During disulfide bond formation, two cysteines are oxidized to form a cystine molecule. This requires the loss of two protons and two electrons. Within cellular systems, proteins are linked together by a large enzyme complex that contains a mixture of RNA and proteins. This complex is called the ribosome.

Thus, as the amino acids are linked together to form a specific protein, they are placed within a very specific order that is dictated by the genetic information contained within the messenger RNA mRNA molecule. The translation mechanism used by the ribosome to synthesize proteins will be discussed in detail in Chapter XX.

The primary sequence of a protein is linked together using dehydration synthesis loss of water that combine the carboxylic acid of the upstream amino acid with the amine functional group of the downstream amino acid to form an amide linkage Figure 2. Similarly, the reverse reaction is hydrolysis and requires the incorporation of a water molecule to separate two amino acids and break the amide bond.

Notably, the ribosome serves as the enzyme that mediates the dehydration synthesis reactions required to build protein molecules, whereas a class of enzymes called proteases are required for protein hydrolysis. Within protein structures, the amide linkage between amino acids is known as the peptide bond. Subsequent amino acids will be added onto the carboxylic acid terminal of the growing protein. Thus, proteins are always synthesized in a directional manner starting with the amine and ending with the carboxylic acid tail.

New amino acids are always added onto the carboxylic acid tail, never onto the amine of the first amino acid in the chain. The directionality of protein synthesis is dictated by the ribosome and is known as N- to C- synthesis. The addition of two amino acids to form a peptide requires dehydration synthesis. As noted above in the zwitterion section, amide bonds have a resonance structure that will not allow the nitrogen lone pair of electrons to act as a base Figure 2.

During amide resonance, the lone pair electrons from the nitrogen are involved in pi -bond formation with the carbonyl carbon forming the double bond. Thus, amide nitrogens are not basic. In addition, the C-N bond within the amide structure is fixed in space and cannot rotate due to the pi- bond character.

Image from V. Instead, they are involved in pi- bond formation with the carbonyl carbon. Furthermore, the C-N bond within the amide structure is fixed in space and cannot rotate due to the pi- bond character.

This creates fixed physical locations of the R-groups within the growing peptide in either the cis or trans conformations.

Because the R-groups can be quite bulky, they usually alternate on either side of the growing protein chain in the trans conformation. The cis conformation is only preferred with one specific amino acid, proline. This is due to the cyclic structure of the proline R-group and the steric hindrance that is created when proline adopts the trans conformation Figure 2.

Thus, proline residues can have a large impact on the 3-D structure of the resulting peptide. The upper diagram displays the cis and trans conformations of two adjacent amino acids noted as X and Y which indicate any of the 20 amino acids, except for proline. In the trans conformation the R-group from amino acid X is rotated away and on the other side of the molecule when compared with the R-group from amino acid Y.

This conformation gives the least amount of steric hindrance compared with the cis conformation where the R-groups are located on the same side and in close proximity to one another.

In the lower diagram, any amino acid, X is positioned upstream of a proline residue. Due to the cyclization of the proline R-group with the amide nitrogen in the backbone, this shifts the position of the proline R-group to be in closer proximity to the R-group from amino acid X when it adopts the trans conformation.

Thus, proline favors the cis conformation which has less steric hindrance. Proteins are very large molecules containing many amino acid residues linked together in very specific order. Proteins range in size from 50 amino acids in length to the largest known protein containing 33, amino acids. Macromolecules with fewer than 50 amino acids are known as peptides Figure 2.

The order and nature of amino acids in the primary sequence of a protein determine the folding pattern of the protein based on the surrounding environment of the protein ie if it is inside the cell, it is likely surrounded by water in a very polar environment, whereas if the protein is embedded in the plasma membrane, it will be surrounded by very nonpolar hydrocarbon tails.

Due to the large pool of amino acids that can be incorporated at each position within the protein, there are billions of different possible protein combinations that can be used to create novel protein structures!

For example, think about a tripeptide made from this amino acid pool. At each position there are 20 different options that can be incorporated. Thus, the total number of resulting tripeptides possible would be 20 X 20 X 20 or 20 3 , which equals 8, different tripeptide options! Now think about how many options there would be for a small peptide containing 40 amino acids. There would be 20 40 options, or a mind boggling 1.

Each of these options would vary in the overall protein shape, as the nature of the amino acid side chains helps to determine the interaction of the protein with the other residues in the protein itself and with its surrounding environment. The character of the amino acids throughout the protein help the protein to fold and form its 3-dimentional structure. Essential amino acids refer to those necessary for construction of proteins in the body, although not produced by the body; which amino acids are essential varies from organism to organism.

Figure 3. Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the amino group of the incoming amino acid. In the process, a molecule of water is released. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction.

The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond Figure 3.

The products formed by such linkages are called peptides. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide.

Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function.

After protein synthesis translation , most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require the addition of other chemical groups. Only after these modifications is the protein completely functional. Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally found in the cellular organelle, the mitochondrion.

This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized during electron transfer.

Scientists have determined that human cytochrome c contains amino acids. For each cytochrome c molecule from different organisms that has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c.

This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position. As discussed earlier, the shape of a protein is critical to its function. For example, an enzyme can bind to a specific substrate at a site known as the active site.

If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

The unique sequence of amino acids in a polypeptide chain is its primary structure. For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine, whereas the C terminal amino acid is asparagine Figure 4. The sequences of amino acids in the A and B chains are unique to insulin.

Figure 4. Bovine serum insulin is a protein hormone made of two peptide chains, A 21 amino acids long and B 30 amino acids long. In each chain, primary structure is indicated by three-letter abbreviations that represent the names of the amino acids in the order they are present. The amino acid cysteine cys has a sulfhydryl SH group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulfide S-S bond. Two disulfide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape.

Note that all disulfide bonds are the same length, but are drawn different sizes for clarity. The unique sequence for every protein is ultimately determined by the gene encoding the protein. Hydrophobic side chains interact with each other via weak van der Waals interactions. The vast majority of bonds formed by these side chains are noncovalent.

In fact, cysteines are the only amino acids capable of forming covalent bonds, which they do with their particular side chains.

Because of side chain interactions, the sequence and location of amino acids in a particular protein guides where the bends and folds occur in that protein Figure 1. Figure 1: The relationship between amino acid side chains and protein conformation The defining feature of an amino acid is its side chain at top, blue circle; below, all colored circles. When connected together by a series of peptide bonds, amino acids form a polypeptide, another word for protein. The polypeptide will then fold into a specific conformation depending on the interactions dashed lines between its amino acid side chains.

Figure Detail. Figure 2: The structure of the protein bacteriorhodopsin Bacteriorhodopsin is a membrane protein in bacteria that acts as a proton pump. Its conformation is essential to its function. The overall structure of the protein includes both alpha helices green and beta sheets red.

The primary structure of a protein — its amino acid sequence — drives the folding and intramolecular bonding of the linear amino acid chain, which ultimately determines the protein's unique three-dimensional shape.

Hydrogen bonding between amino groups and carboxyl groups in neighboring regions of the protein chain sometimes causes certain patterns of folding to occur. Known as alpha helices and beta sheets , these stable folding patterns make up the secondary structure of a protein. Most proteins contain multiple helices and sheets, in addition to other less common patterns Figure 2.

The ensemble of formations and folds in a single linear chain of amino acids — sometimes called a polypeptide — constitutes the tertiary structure of a protein. Finally, the quaternary structure of a protein refers to those macromolecules with multiple polypeptide chains or subunits. The final shape adopted by a newly synthesized protein is typically the most energetically favorable one.

As proteins fold, they test a variety of conformations before reaching their final form, which is unique and compact. Folded proteins are stabilized by thousands of noncovalent bonds between amino acids. In addition, chemical forces between a protein and its immediate environment contribute to protein shape and stability. For example, the proteins that are dissolved in the cell cytoplasm have hydrophilic water-loving chemical groups on their surfaces, whereas their hydrophobic water-averse elements tend to be tucked inside.

In contrast, the proteins that are inserted into the cell membranes display some hydrophobic chemical groups on their surface, specifically in those regions where the protein surface is exposed to membrane lipids. It is important to note, however, that fully folded proteins are not frozen into shape. Rather, the atoms within these proteins remain capable of making small movements. Even though proteins are considered macromolecules, they are too small to visualize, even with a microscope.

So, scientists must use indirect methods to figure out what they look like and how they are folded.