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S2018_Lecture06_Reading

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    Amino Acids

    Amino acids are the monomers that make up proteins. Each amino acid has the same core structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the alpha carbon known alternately as the R group, the variable group or the side-chain. 

    Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.

    Attribution: Marc T. Facciotti (own work)

    Note: Possible discussion

    Recall that one of the learning goals for this class is that you (a) be able to recognize, in a molecular diagram, the backbone of an amino acid and its side chain (R-group) and (b) that you be able to draw a generic amino acid. Make sure that you practice both. You should be able to recreate something like the figure above from memory (a good use of your sketchbook is to practice drawing this structure until you can do it with the crutch of a book or the internet).

    The Amino Acid Backbone

    The name "amino acid" is derived from the fact that all amino acids contain both an amino group and carboxyl-acid-group in their backbone. There are 20 common amino acids present in natural proteins and each of these contain the same backbone. The backbone, when ignoring the hydrogen atoms, consists of the pattern:

    N-C-C

    When looking at a chain of amino acids it is always helpful to first orient yourself by finding this backbone pattern starting from the N terminus (the amino end of the first amino acid) to the C terminus (the carboxylic acid end of the last amino acid).

    Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of the first amino acid is linked to the amino group of the second incoming amino acid. In the process, a molecule of water is released and a peptide bond is formed.
    Try finding the backbone in the dipeptide formed from this reaction. The pattern you are looking for is: N-C-C-N-C-C

    Attribution: Marc T. Facciotti (own work)

    The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration synthesis (condensation) reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water and creating the peptide bond.

    Amino Acid R group

    The amino acid R group is a term that refers to the variable group on each amino acid. The amino acid backbone is identical on all amino acids, the R groups are different on all amino acids. For the structure of each amino acid refer to the figure below.

    There are 20 common amino acids found in proteins, each with a different R group (variant group) that determines its chemical nature. R-groups are circled in teal. Charges are assigned assuming pH ~6.0. The full name, three letter abbreviation and single letter abbreviations are all shown.

    Attribution: Marc T. Facciotti (own work)

    Note: Possible Discussion

    Let's think about the relevance of having 20 different amino acids. If you were using biology to build proteins from scratch, how might it be useful if you had 10 more different amino acids at your disposal? By the way, this is actually happening in a variety of research labs - why would this be potentially useful?

     

    Each variable group on an amino acid gives that amino acid specific chemical properties (acidic, basic, polar, or nonpolar). You should be familiar with most of the functional groups in the R groups by now. The chemical properties associated with the whole collection of individual functional groups gives each amino acid R group unique chemical potential.

    For example, amino acids such as valine, methionine, and alanine are typically nonpolar or hydrophobic in nature, while amino acids such as serine and threonine are said to have polar character and possess hydrophilic side chains.

    Note: Practice

    Using your knowledge of functional groups, try classifying each amino acid in the figure above as either having the tendency to be polar or nonpolar. Try to find other classification schemes and think make lists for yourself of the amino acids you would put into each group. You can also search the internet for amino acid classification schemes - you will notice that there are different ways of grouping these chemicals based on chemical properties. You may even find that there are contradictory schemes. Try to think about why this might be and apply your chemical logic to figuring out why certain classification schemes were adopted and why specific amino acids were placed in certain groups.

     

    Proteins

    Proteins are class of biomolecules that perform a wide array of functions in biological systems.  Some proteins serve as catalysts for specific biochemical reactions. Other proteins act as signaling molecules that allow cells to "talk" with one another. Proteins, like the keratin in fingernails, can also act in a structural capacity. While the variety of possible functions for proteins is remarkably diverse, all of these functions are encoded by a linear assembly of amino acids, each connected to their neighbor via a peptide bond. The unique composition (types of amino acids and the number of each) and the order in which they are linked together determine the final three dimensional form that the protein will adopt and therefore, also the protein's biological "function". Many proteins can, in a cellular environment, spontaneously and often rapidly take on their final form in a process called protein folding.  To watch a short (four minutes) introduction video on protein structure click here.

    Protein structure

    Protein structures can be described by four different levels of structural organization called primary, secondary, tertiary, and quaternary structures.  These are briefly introduced in the sections that follow.  

    Primary structure

    The unique sequence of amino acids in a polypeptide chain is its primary structure (Figure 1). The amino acids in this chain are linked to one another other via a series of peptide bonds.  The chain of amino acids is often referred to as a polypeptide (multiple peptides).  

    Figure 1. The primary structure of a protein is depicted here as "beads on a string" with the N terminus and C terminus labeled. The order in which you would read this peptide chain would begin with the N terminus as Glycine, Isoleucine, etc., and end with Methionine.
    Source: Erin Easlon (own work)

     

    Due to the common backbone structure of amino acids, the resulting backbone of the protein has a repeating -N-Cα-C-N-Cα-C- pattern that can be readily identified in atomic resolution models of protein structures (Figure 2).  Be aware that one of the learning goals for this class is for you to be able to examine a model like the one below and to identify the backbone from the side chain atoms (e.g. create the purple trace and blue shading if there aren't any).  This can be done by finding the -N-Cα-C-N-Cα-C- pattern.  Moreover, another learning goal for this class is that you are able to create drawings that model the structure of a typical protein backbone and its side chains (aka. variable group, R group).  This task can be greatly simplified if you remember to start your model by first creating the -N-Cα-C-N-Cα-C- pattern and then filling in the variable groups.  

     

    Figure 2. A model of a short 3 amino acid long peptide.  The backbone atoms are colored in red.  The variable R groups are circled in light blue.  A purple line traces the backbone from the N-terminus (start) to the C-terminus (end) of the protein.  One can identify (in green) the repeated -N-Cα-C-N-Cα-C- ordered pattern by following the purple line from start to end and listing off the backbone atoms in the order that they are encountered.  
    Attribution: Marc T. Facciotti (own work)



    Secondary structure

    Due to the specific chemistry of the peptide bond the backbone between adjacent alpha-carbon atoms forms a highly planar structure (Figure 3). This means that all of the atoms linked by the pink quadrilateral lie on the same plane.  The polypeptide is therefore structurally constrained since very little rotation can happen around the peptide bond itself.  Rather, rotations occur around the two bonds extending away from the alpha carbons.  These structural constraints lead to two commonly observed patterns of structure that are associated with the organization of the backbone itself.  

    Figure 3. The peptide bond between two amino acids is depicted. The shaded quadrilateral represents planar nature of this bond.
    Attribution: Marc T. Facciotti (own work)

    We call these patterns of backbone structure the secondary structure of the protein. The most common secondary structure patterns occurring via rotations of the bonds around each alpha-carbon, are the α-helix, β-sheet and loop structures. As the name suggests, the α-helix is characterized by a helical structure made by twisting the backbone.  The β-sheet is actually the association between two or more structures called β-strands.  If the orientation (N-terminus to C-terminus direction) of two associating β-strands are oriented in the same/parallel direction, the resulting β-sheet is called a parallel β-sheet.  Meanwhile, if two associating β-strands are oriented in opposite/anti-parallel directions, the resulting β-sheet is called an anti-parallel β-sheet.  The α-helix and β-sheet are both stabilized by hydrogen bonds that form between backbones atoms of amino acids in close proximity to one another.  More specifically, the oxygen atom in the carbonyl group from one amino acid can form a hydrogen bond with a hydrogen atom bound to the nitrogen in the amino group of another amino acid.  Loop structures by contrast refer to all secondary structure (e.g. backbone structure) that can not be identified as either α-helix or β-sheet.  

     

    Figure 4. The α-helix and β-sheet are secondary structures of proteins that are stabilized by hydrogen bonding between carbonyl and amino groups in the peptide backbone. Note how the hydrogen bonds in an alpha-helix occur between amino acids that are relatively close to one another (about 4 amino acids apart in the amino acid chain) while the interactions that occur in β-sheets may occur between amino acids that are much farther apart in the chain.  

    Tertiary structure

    The backbone and secondary structure elements will further fold into a unique and relatively stable three-dimensional structure called the tertiary structure of the protein. The tertiary structure is what we typically associate with the "functional" form of a protein.  In Figure 6 two examples of tertiary structure are shown.  In both structures, the protein is abstracted into a "cartoon" that depicts the polypeptide chain as a single continuous line or ribbon tracing the path between alpha carbons of amino acids linked to one another by peptide bonds - the ribbon traces the backbone of the protein (Figure 5).  

    Figure 5. How protein "cartoon" figures are drawn.  Protein cartoons (like those shown in Figure 6) are perhaps the most common representation of three-dimensional protein structure.  These cartoon models help us visualize the major features of a protein structure by tracing the path from one alpha-carbon to the next along the polypeptide backbone.  This is depicted as a thick purple line.  In a longer polypeptide this line would continue and join to the next alpha carbon until the end of the polypeptide was reached.  While these models allow us to visualize the general structure of a protein, they leave out a lot of molecular-level detail.    

     

    The ribbon created by joining alpha-carbons can be drawn as a simple continuous line or it can be enhanced by uniquely representing secondary structural elements.  For instance, when an α-helix is identified, the helix is usually highlighted by accentuating/broadening the ribbon to make the helical structure stand out.  When a β-strand is present, the ribbon is usually broadened and an arrow is typically added to the C-terminal end of each β-strand - the arrow helps to identify the orientation of the polypeptide and whether β-sheets are parallel or anti-parallel.  The thin ribbon connecting α-helix and β-strand elements is used to represent the loops. Loops in proteins can be highly structured and play an important role in the protein's function.  They should not be treated lightly or dismissed as unimportant because their name lacks a Greek letter.

     

    two_proteins.png

    Figure 6. Examples of tertiary structures of proteins.  Secondary structure elements are colored as follows: β-sheet - yellow, α-helix - red; loop - green.  In panel A the structure of protein gamma crystallin (PDBID 1a45) - a protein found in the vertebrate eye - is depicted.  This protein is composed largely of  β-sheet  and loops.  In panel B the structure of the protein triose phosphate isomerase (PDBID 1tim) - a protein found in the glycolytic pathway - is composed of β-sheet, α-helix, and loops joining the secondary structural elements.  

    Attribution: Marc T. Facciotti (own work)

     

    The tertiary structure is the product of many different types of chemical interactions among amino acid R groups, backbone atoms, ions in solution and water.  These bonds include ionic, covalent, and hydrogen bonds and Van der Waals interactions.  For example, ionic bonds may form between various ionizable side chains.  It may, for instance, be energetically favorable for a negatively charged R group (e.g. an Aspartate) to interact with a positively charged R group (e.g. an Arginine).  The resulting ionic interaction may then become part of the network of interactions that helps to stabilize the three dimensional fold of the protein.  By contrast, R groups with like charges will likely be repelled by each other and be therefore unlikely to form a stable association thereby disfavoring a structure that would include that association.  Likewise, hydrogen bonds may form between various R groups or between R groups and backbone atoms. These hydrogen bonds may also contribute to stabilizing the tertiary structure of the protein.  In some cases covalent bonds may also form between amino acids. The most commonly observed covalent linkage between amino acids involves two cysteines and is termed a disulfide bond or disulfide linkage.  

    Finally, the association of the protein's functional groups with water also helps to drive chemical associations that help to stabilize the final protein structure.  The interactions with water can, of course, include the formation of hydrogen bonds between polar functional groups on the protein and water molecules.  Perhaps more importantly, however, is the drive for the protein to avoid placing too many hydrophobic functional groups in contact with water.  The result of this desire to avoid interactions between water and hydrophobic functional groups means that the less polar side chains will often associate with one another away from water resulting in some energetically favorable Van der Waals interactions and the avoidance of energetic penalties associated with exposing the non-polar side chains to water.  Indeed, the energetic penalty is so high for "exposing" the non-polar side chains to water that burying these groups away from water is thought to be one of the primary energetic drivers of protein folding and stabilizing forces holding the protein together in its tertiary structure.  

    Figure 6. The tertiary structure of proteins is determined by a variety of chemical interactions. These include hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages. This image shows a flattened representation of a protein folded in tertiary structure. Without flattening, this protein would be a globular 3-D shape.

    Quaternary structure

    In nature, the functional forms of some proteins are formed by the close association of several polypeptides.  In such cases the individual polypeptides are also known as subunits.  When the functional form of a protein requires the assembly of two or more subunits we call this level of structural organization the protein's quaternary structure.  Yet again, combinations of ionic, hydrogen, and covalent bonds together with Van der Waals associations that occur through the "burial" of hydrophobic group at the interfaces between subunits help to stabilize the quaternary structures of proteins.  

    Figure 7. The four levels of protein structure can be observed in these illustrations. 
    Source: Modification of work by National Human Genome Research Institute

    Denaturation

    As was previously described, each protein has its own unique structure that is held together by various types of chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, that change the nature of or interfere with the associations between functional groups, the protein's secondary, tertiary and/or quaternary structures may change, even though the primary structure remains the same. This process is known as denaturation.  While in the test tube denaturation is often reversible, in the cell the process can often be, for practical purposes, irreversible, leading to loss of function and the eventual recycling of the protein's amino acids.  Resistance to environmental stresses that can lead to denaturation vary greatly amongst the proteins found in nature. For instance, some proteins are remarkably resistant to high temperatures; for instance, bacteria that survive in hot springs have proteins that function at temperatures close to the boiling point of water. Some proteins are able to withstand the very acidic, low pH, environment of the stomach.  Meanwhile some proteins are very sensitive to organic solvents while others can be found that are remarkably tolerant of these chemicals (the latter are prized for use in various industrial processes).  

    Finally, while many proteins can form their three dimensional structures completely on their own, in many cases proteins often receive assistance in the folding process from protein helpers known as chaperones (or chaperonins) that associate with their protein targets during the folding process. The chaperones are thought to act by minimizing the aggregation of polypeptides into non-functional forms - a process that can occur through the formation of non-ideal chemical associations.

    Khan Academy link

    Protein structure.

     

     

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