Information

Difference in Basic Amino Structures


I'm having a hard time understanding why my slides in my biology course have two different representations of the "basic structure" of the amino acid:

1:

2:

The top one seem like what I would expect. The bottom one, it looks like the amine group gained a Hydrogen ion and the Carboxyl group lost one. Also, the center carbon gained an H. I honestly don't know if this description is even correct or not.

I'm extremely new to this level of biology, so very simple explanations are much appreciated. I just don't totally understand why there are two versions of the basic structure.

Also, I apologize if the tag is wrong, again, this isn't my major, so I'm very new to this material.


Your description is more or less correct, but so are both images. The bottom images shows the predominant form the amino acid would take at neutral pH (or any pH between ~2 and ~9.5). This is because the caroboxylic acid (-COOH) and amino (-NH2) groups are a weak acid and base and can lose or gain a proton (hydrogen cation), respectively. pH below the pKa of the functional group (~2 for carboxylic acid and ~9.5 for amino) favours protonation whereas pH above the pKa favours deprotonation. Also note that the "centre carbon" (the α-carbon) did not gain a proton in the second image, it's just drawn differently.

You could try this website for an overview of acid/base chemistry and perhaps these Wikipedia sections on zwitterions and isoelectric points with respect to amino acids, though there are many alternative sources of material available if you search for them. This question and answer may also be useful for you, at least eventually.


SDS-PAGE

SDS-PAGE (sodium dodecyl sulphate–polyacrylamide gel electrophoresis), is a discontinuous electrophoretic system developed by Ulrich K. Laemmli which is commonly used as a method to separate proteins with molecular masses between 5 and 250 kDa. [1] [2] The combined use of sodium dodecyl sulfate (SDS, also known as sodium lauryl sulfate) and polyacrylamide gel allows to eliminate the influence of structure and charge, and proteins are separated solely on the basis of differences in their molecular weight.


Structure, Nomenclature, and Properties of Proteins and Amino Acids

In aqueous solutions, amino acids are easily ionized. The most abundant ionic species present when amino acids are dissolved in an aqueous medium at neutral pH are shown in Figure 5-1, and the pK a s for all dissociable groups are shown in Table 5-1. The acid dissociation constant K a is used to define characteristics of titratable groups in organic acids and amines. The negative log of the dissociation constant K a is called the pK a of the titratable group. In a practical sense, this means that when the pH is equal to the pK a , the associated (AH, protonated) and dissociated (A – , unprotonated) species will be present in equal molar concentrations.



























































































































































AMINO ACID MOLECULAR MASS (g/mol) pK a α-COOH pK a α-NH 3 + pK a R GROUP HYDROPATHY INDEX (KYTE-DOOLITTLE SCALE)
Hydrophilic amino acids (charged and very polar) Arginine 155 2.17 9.04 12.48 −4.5
Lysine 146 2.18 8.95 10.53 −3.9
Asparagine 132 2.04 9.82 −3.5
Aspartate 133 2.09 9.82 3.86 −3.5
Glutamine 146 2.17 9.13 −3.5
Glutamate 147 2.19 9.67 4.25 −3.5
Histidine 174 1.82 9.17 6.0 −3.2
Amino acids with intermediate hydrophobicity (Tyr and moderately/weakly polar amino acids) Tyrosine 181 2.20 10.07 9.11 −1.3
Tryptophan 204 2.38 9.39 −0.9
Serine 105 2.21 9.15 −0.8
Threonine 119 2.63 10.43 −0.7
Glycine 75 2.34 9.60 −0.4
Proline 115 1.99 10.6 (NH 2 + ) 1.6
Alanine 89 2.34 9.69 1.8
Methionine 149 2.28 9.31 1.9
Cysteine 121 1.71 10.78 8.33 2.5
Hydrophobic amino acids (uncharged and nonpolar) Phenylalanine 165 1.83 9.13 2.8
Leucine 131 2.36 9.68 3.8
Valine 117 2.32 9.62 4.2
Isoleucine 131 2.36 9.68 4.5

Jack Kyte and Russell Doolittle (1982) proposed a hydropathy index that is now widely used to predict aspects of protein structure this scale assigns negative numbers to the most hydrophilic side chains and positive numbers to the most hydrophobic side chains (see Table 5-1). Other scales have been developed, some of which assign quite different values to some of the amino acids. Efforts to develop better methods of predicting protein structure continue. An example of the use of a hydropathy index to predict the transmembrane segments of a protein sequence is shown in Figure 5-4. Transmembrane segments of transmembrane proteins can be predicted from the average hydrophobicity scores for small regions of the polypeptide chain (e.g., segments of 9 to 19 amino acids). Transmembrane regions of proteins, which must pass through the lipid bilayers of cell membranes, tend to have high hydropathy scores (greater than 1.6 units).


Biochemistry


An illustration showing the biochemical structures present in a T Cell Receptor (image by Michelle Mischke).

This unit will introduce the course and cover the basics of biochemistry and cell composition. First, we will introduce the levels of organization of life, and the different types of organisms. We will then cover the structure of biological molecules and the molecular forces involved in the formation of these molecules. We will learn about the general structure and function of lipids, carbohydrates, and nucleic acids, as well as the composition, structure, and function of proteins. After learning about the major groups of macromolecules, we will explore their interactions within a cell, starting with metabolism, Gibbs free energy, biochemical reactions, enzymes and ATP as the energy currency. We will outline the cellular mechanisms for harvesting energy from glucose and related sugars, briefly outline glycolysis as a mechanism to generate ATP, and discuss the fate of the pyruvate produced in glycolysis under anaerobic and aerobic conditions. Finally, we will cover the general ideas of both cyclic and non-cyclic photophosphorylation and how these two processes are used by cells to generate the ATP and the NADPH needed for the Calvin Cycle in photosynthesis.

During this unit, you will describe both the chemical and molecular composition of a cell, and define the basic components of biological macromolecules. You will identify the forces that act in biological systems: covalent bonds, ionic bonds, hydrogen bonds, van der Waal's forces, and hydrophobicity. You will draw a generic amino acid and categorize each of the 20 amino acids appropriately based upon the nature of the side chain. You will also apply the general laws of thermodynamics to biological reactions. In addition, you will define Gibbs free energy, determine the Gibbs free energy change associated with a biochemical reaction, and identify spontaneous and non-spontaneous reactions.

At the end of this unit, you will be familiar with the different levels of organization of life, and the differences between eukaryotic and prokaryotic cells. You will understand the structures and properties of the major groups of macromolecules, including lipids and phospholipids, carbohydrates nucleic acids, and proteins, as well as their functions in the cell. You will be familiar with primary, secondary, tertiary, and quaternary levels of protein structure and know what types of bonds and forces stabilize each level. In addition, you will understand the effect of an amino acid substitution on the general structure and function of a protein. You will know how ATP provides the energy to power cellular work.

Finally, you will have a greater understanding of the reactions in cellular respiration and photosynthesis, when they occur, and why they are important. You will understand the relationships between cellular respiration and photosynthesis.

Looking for something specific in this course? The Resource Index compiles links to most course resources in a single page.


NAG and NAM are two amino sugars present in the peptidoglycan layer of bacteria. The NAG is an amide composed of glucosamine and acetic acid. The NAM is an ether of lactic acid and N-acetylglucosamine. NAM molecule has a peptide chain attached to it which facilitates cross-linking between oligopeptides of the peptidoglycan layer. On the other hand, NAG does not have a peptide chain attached to it. Instead, NAG locates between two NAM molecules and provides the structure to the peptidoglycan layer. This is the key difference between NAG and NAM


Peptide, Protein and Enzyme Design

M. Chino , . A. Lombardi , in Methods in Enzymology , 2016

1.2 Designing Functional Four-Helix Bundle Proteins

The four-helix bundle can be viewed as an α-helical coiled coil, which is, more generally, a super-secondary structure made up of α-helices packed together in a parallel or antiparallel orientation. Coiled coils amino acid sequences are usually described in terms of seven residues (heptad) repeats, since seven residues are present per two turns of the α-helix ( Kohn & Hodges, 1998 ). This scaffold is very robust and thermodynamically stable, since it is able to tolerate multiple residue substitutions without disrupting the global three-dimensional fold. As a consequence, the four-helix bundle scaffold is of great interest in the field of protein design, as it represents a useful template for structure-to-function relationship analysis and for developing novel artificial metalloenzymes ( Chino et al., 2015 Peacock, 2016 ). In principle, active site environment (first and second coordination sphere) can be modified to induce metal-binding selectivity and to finely tune the chemistry of the cofactor to achieve specific functions. This task often involves introducing asymmetry around the metal environment, thus representing a difficult challenge in the de novo design of α-helical coiled coils.

One possible strategy for developing an asymmetric four-helix bundle involves the noncovalent heterodimerization of four single α-helices or two helix–loop–helix (α2) domains ( Fig. 1 A and B ). This approach requires establishing a large energy gap to stabilize the desired heteromeric form respect to both homooligomeric folds, and any undesired heteromeric topology. Thus, the design methodology should include specific elements of both positive and negative design, to prevent alternate topologies from occurring ( Grigoryan, Reinke, & Keating, 2009 Havranek & Harbury, 2003 Hill, Raleigh, Lombardi, & DeGrado, 2000 ). Even though the “rules” that guide oligomerization are now well established, all the interactions responsible for the pairing specificity are strictly dependent on slight variations of pH, ionic strength, and other physicochemical conditions of the environment ( Fairman et al., 1996 Fry, Lehmann, Saven, DeGrado, & Therien, 2010 Marsh & DeGrado, 2002 Zhang et al., 2015 ). The noncovalently assembled complexes are generally not suitable for structural characterization, since it is difficult to completely avoid the presence of alternatively assembled species. On the other hand, heteromeric systems consisting of disconnected helices, which can be separately synthesized, purified, and combinatorially assembled, are well suited for the production of an array of any desired helical bundles from a significantly smaller number of peptides ( Calhoun et al., 2005 ). A variety of de novo designed heteromeric two-stranded coiled coils ( Litowski & Hodges, 2002 Thomas, Boyle, Burton, & Woolfson, 2013 ), three-helix ( Chakraborty, Iranzo, Zuiderweg, & Pecoraro, 2012 Dieckmann et al., 1997 ), and four-helix bundles ( Kaplan & DeGrado, 2004 Summa, Rosenblatt, Hong, Lear, & DeGrado, 2002 ) have been successfully developed and reported to date.

Fig. 1 . Possible strategies for developing antiparallel four-helix bundles. (A) Tetramerization of four single α-helices. (B) Dimerization of two helix-loop-helix motifs. (C) Single-chain construct.

An alternative strategy to mimic the asymmetry of natural proteins in the context of designed coiled coils uses a single polypeptide chain ( Fig. 1 C), in which helices are connected by loops ( Calhoun et al., 2003 Chakraborty et al., 2011 Smith & Hecht, 2011 ). Such proteins have generally unambiguous three-dimensional structures, thus greatly facilitating structural analysis. Nevertheless, the design of large proteins requires methods that are computationally intensive. In particular, the choice of interhelical loops is crucial, since it greatly affects both the stability and flexibility of the bundle. Further, the complexity of a single-chain construct limits its applicability for catalytic screening purposes, aimed at evaluating how systematic changes in the sequence affect structure, substrate-binding, and catalytic properties.

A third exploited strategy to obtain heteromeric four-helix bundles involves the covalent binding onto a predefined molecular scaffold. Mutter and colleagues introduced the concept of template assembled synthetic proteins (TASP) ( Mutter, 2013 Mutter & Tuchscherer, 1997 ), which have been successfully adopted as scaffold for recognition and coupling of exogenous ligands ( Monien, Drepper, Sommerhalter, Lubitz, & Haehnel, 2007 Rau, DeJonge, & Haehnel, 2000 Rau & Haehnel, 1998 ). Following the pioneering works of Mutter and coworkers, which adopted a properly designed cyclic decapeptide as template for assembling a variety of tertiary structures ( Mutter et al., 1988 ), Haehnel and coworkers developed modular organized proteins (MOPS), for selectively binding metal cofactors, such as heme and copper ion ( Monien et al., 2007 Rau, DeJonge, & Haehnel, 1998 Rau et al., 2000 Rau & Haehnel, 1998 Schnepf, Haehnel, Wieghardt, & Hildebrandt, 2004 ). A suitable chemoselective synthetic strategy was developed in order to control the identity and directionality of the helical segments, and obtain the desired heteromers.

A further approach for the design of heteromers retraces the way chosen by Nature, by building side chain/side chain covalent ligation through disulfide bond formation. Several computational methods have been developed so far, for predicting which pairs of residues, once mutated to cysteines, are suitable to form a disulfide bond. The used algorithms are derived from the analysis of side chains packing preferences of cysteine pairs involved in disulfide bonds, as found in crystal structures ( Burton, Oas, Fterke, & Hunt, 2000 Craig & Dombkowski, 2013 Hazes & Dijkstra, 1988 Pabo & Suchanek, 1986 Sowdhamini et al., 1989 ). Despite inspired by Nature, the applicability of this strategy is limited, due to the stringent geometrical requirements for disulfide bond formation.

Recently, we implemented a novel design method to obtain an asymmetric four-helix bundle through the covalent heterodimerization of two different α-helical hairpins ( Chino et al., 2016 ). This strategy aims at realizing an easy-to-screen system in a robust covalent framework, thus merging the advantages of using self-assembled monomers and single-chain constructs. We selected an efficient and orthogonal chemistry, to properly bind two different monomers in native conditions. In 2001 Kolb, Finn, and Sharpless published their seminal paper on the application of powerful and selective reactions to join small units through heteroatom links, and coined the term “Click Chemistry” ( Kolb, Finn, & Sharpless, 2001 ). Several research groups explored the different applications of the Click Chemistry in numerous fields, such as drug discovery and synthesis ( Galibert et al., 2010 Góngora-Benítez, Cristau, Giraud, Tulla-Puche, & Albericio, 2012 Valverde, Vomstein, Fischer, Mascarin, & Mindt, 2015 ) and polymer bioconjugation ( Marine, Song, Liang, Watson, & Rudick, 2015 Rachel & Pelletier, 2016 Shu, Tan, DeGrado, & Xu, 2008 ). In particular, the use of Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) has been largely employed as amide bond surrogate in the generation of α-helical and β-turn pseudopeptides ( Beierle et al., 2009 Horne, Yadav, Stout, & Ghadiri, 2004 ), in TASP based molecular assemblies ( Avrutina et al., 2009 ), as well as in strategies of peptide stapling, a macrocyclization process, where an intramolecular linkage is introduced to constrain the peptide in the desired α-helical conformation ( Jacobsen et al., 2011 Lau, Wu, de Andrade, Galloway, & Spring, 2015 Scrima et al., 2010 ). Finally, it is also notable the work of Kolmar and coworkers ( Empting et al., 2011 ), who constructed a triazole bridge, in replacement of a disulfide bond, employing the Ru(II)-catalyzed azide–alkyne cycloaddition (RuAAC).

The wide range of Click Chemistry applications prompted us to test this reaction in the selective intermolecular chemical ligation of two functionalized α2 peptides, to generate heterodimeric proteins. One of the major advantages of the Click Chemistry-based methodology relies on its orthogonality to the chemistry involved in solid-phase peptide synthesis. Once chosen the binding positions, the peptides to be ligated can be easily functionalized during the synthetic step, by introducing noncanonical amino acids bearing the azide and alkyne moieties in their sequences ( Fig. 2 ). CuAAC provides a simple to perform coupling process, leading to a thermally and hydrolytically stable triazole connection between the peptides. Moreover, the triazole ring of the linker could be introduced as a ligand in the metal-binding site.

Fig. 2 . Copper catalyzed 1,3-dipolar cycloaddition.

Finally, given the large number of commercially available azide and alkyne building blocks, the designer can finely control the length and flexibility of the linker by choosing different pairs of functionalized amino acids.

In this chapter, we describe the developed computational protocol, first applied to the DF3 structure, as a specific case study. As logical extension of the method, a more general protocol is also reported, aimed at including the construction of several linkers, in different protein positions, and at fulfilling as many as possible designer needs.


Oligosaccharides (dissaccharides) – the simplest form of carbohydrate polymers

Oligosaccharides are second type of carbohydrates.

Usually oligosaccharides contain two or three simple sugars attached to one another by covalent bonds called glycosidic linkages.

Glycosidic bonds can be of the alpha or the beta type.

Examples of important disaсcharides are:

Chemical structure of maltose is composed of two α - ring structures of glucose molecules held together by a 1-4 glycosidic linkage.

Maltose can be found in grains which is used in the production of beer.

Sucrose molecular structure consists of α - ring structure of glucose and α - ring structure of fructose with a 1-2 glycosidic linkage between them.

Sucrose is the most known as common table sugar.

Molecular structure of lactose is composed of such monomers of carbohydrates as α - ring structure of glucose and α - ring structure of galactose.

Lactose is normally found in milk.


Fatty Acids

Fatty acids are chain-like molecules that are important components of several types of lipids. The illustrations below show two different fatty acid molecules. Each has a characteristic carboxyl group (the -COOH) attached to a chain of carbons with hydrogen atoms attached to the carbon chain. Two things are noteworthy. First, the hydrocarbon chain is very non-polar and therefore doesn't dissolve in water very well. However, hydrocarbon chains do associate with each other readily. Second, note that the unsaturated fatty acid has two hydrogens removed, and this allows formation of a double bond, i.e., a stronger bond between two of the carbon atoms. Note also that the double bond tends to produce a bend or a kink in the fatty acid. The illustration to the right shows two other common fatty acids: stearic acid, which is a straight 18 carbon chain with no double bonds, and oleic acid, which is an 18 carbon chain with a single double bond, which cause a bend in the carbon chain.


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Difference in Basic Amino Structures - Biology

Molecular Structure of Proteins

Course: Living Environment (New York State Curriculum) or Honors Biology

Unit: Cellular Structure and/or Protein Synthesis

Objective: Students will develop a concept of how a watery environment such as the cell cytoplasm, affects the shape of a protein. In the first activity, the students will construct and test how certain molecules like water while others hate water. Then using molecular modeling, the second activity will explore how the concept of water loving and water hating help to form the shape of a protein.

Background Information: Proteins are long chains of amino acids that are linked together by peptide bonds. There are 20 different types of essential amino acids each of which has its unique side chain with its unique chemical property. The shape or three-dimensional folding pattern of a protein is derived from not only the sequence of amino acids but also the type of side chain that the amino acid contains and the interaction of these side chains with their environment.

The folded structure of a protein is actually thermodynamically less favorable because it reduces the disorder or entropy of the protein. So, why do proteins fold? One of the most important factors driving the folding of a protein is the interaction of polar and nonpolar side chains with the environment. Nonpolar (water hating) side chains tend to push themselves to the inside of a protein while polar (water loving) side chains tend to place themselves to the outside of the molecule. In addition, other noncovalent interactions including electrostatic and van der Waals will enable the protein once folded to be slightly more stable than not.

When oil, a nonpolar, hydrophobic molecule, is placed into water there is a reduction in disorder of the water molecules around the oil, that is, water molecules do not interact with the oil but instead have to be structured around the oil. This interaction lowers the entropy. By contrast if you remove the oil molecule from the water there will be an increase in disorder or entropy of the water molecules. Now if you take oil molecule and mechanically disperse it through out the water by stirring, it will eventually reform a globular shape. This globular shape allows for the reduction in the number of nonpolar molecules being exposed to water and actually slightly increases entropy as water molecules are liberated by the burying of nonpolar molecules to the center of the globular structure.

Since proteins have nonpolar side chains their reaction in a watery environment is similar to that of oil in water. The nonpolar side chains are pushed to the interior of the protein allowing them to avoid water molecule and giving the protein a globular shape. There is, however, a substantial difference in how the polar side chains react to the water. The polar side chains place themselves to the outside of the protein molecule which allows for their interact with water molecules by forming hydrogen bonds. The folding of the protein increases entropy by placing the nonpolar molecules to the inside, which in turn, compensates for the decrease in entropy as hydrogen bonds form with the polar side chains and water molecules.

Overview of Activities: There are two sets of activities within this lesson. The first activity involves the students forming 3-dimensional models of simple compounds including water, ethyl alcohol, and methyl alcohol. Upon completing these models students will examine how these 3 polar molecules interact with each other and with non-polar molecules. Students will be allowed to develop their own idea of how these molecules are related or not related and then test that concept. This is a 60 to 80 minute activity. Time for this activity can be reduced by having molecular models prepared for students to observe, and not allowing students to build the molecules.

In the second activity students will construct a model of protein. Although there are multiple rules about how a protein will fold, this activity will only focus on the side chains that are either water loving (polar) or water hating (nonpolar). This is a 45 minute activity which should either follow the first activity or a discussion of water loving or water hating molecules. For an advance class it is strongly suggested that acid/base side chains be included.


Something Called Side Groups

The side groups are what make each amino acid different from the others. Of the 20 side groups used to make proteins, there are two main groups: polar and non-polar. These names refer to the way the side groups, sometimes called "R" groups, interact with the environment. Polar amino acids like to adjust themselves in a certain direction. Non-polar amino acids don't really care what's going on around them. The polar and nonpolar chemical traits allow amino acids to point towards water (hydrophilic) or away from water (hydrophobic). The growing chains can then begin to twist and turn when they are being synthesized.