Are you cramming for the MCAT and feeling a little overwhelmed by all of the amino acids? Don’t worry; we’ve got you covered! This MCAT Amino Acids Cheat Sheet will help you remember the most important information about these essential molecules. So you can put it up on a wall to help you stay focused during your study sessions.
Plus, if you want to take a deeper dive into Amino Acids, be sure to check out the Jack Westin Complete Guide to Amino Acids.
Introduction to Amino Acids
Mitochondria are the cell’s powerhouse and are probably directly behind Amino Acids, which are the building blocks of proteins. Amino acids are an extraordinarily high-yield topic on the MCAT. You probably remember some of their structures from your beginning biochemistry class.
If you scratch your head a little further, you might remember that amino acids can be categorized according to their various characteristics. Understanding proteins and amino acids are crucial for passing the MCAT because of how fundamental they are as a subject. This blog post will show you how to perform at your best while answering those protein questions on the MCAT. We’ll review how to read research sections on the subject as they appear on the MCAT at the end. But before we get started on the cheat sheet, you need to know some basics that we’ve listed below:
- The primary amino acid structure consists of a basic amino group, an acidic carbonyl group, and a variable “R” group that determines the characteristics of amino acids.
- The structure, name, one-letter code, three-letter abbreviation, and the class of each amino acid.
- A few amino acids have unique qualities that show up in particular kinds of inquiries.
- Primary, secondary, tertiary, and quaternary structures can be found in proteins.
- Various interactions play a role in tertiary structure protein folding, which is influenced by modifications that maximize entropy.
- Important laboratory methods for examining the structure and functionality of proteins include Western Blotting, SDS-PAGE, and isoelectric focusing.
Description of Amino Acid Structure
Alpha Carbon’s Absolute Configuration
The standard human genetic code contains 20 amino acid encodings. As the human body is unable to manufacture 10 of the amino acids, it is thought that these ten must be supplied through diet. But knowing which amino acids are necessary goes beyond what you need to know. You must know each amino acid’s name, side chain structure, three-letter abbreviation, and one-letter abbreviation.
The fundamental structure of each amino acid is the same. The glue that keeps an amino acid together is the core alpha (a) carbon. Four groups are bound to the alpha carbon of a free amino acid:
- an amino group (-NH2)
- a carboxyl group (-COOH)
- a hydrogen atom
- a distinct side chain (-R)
Remember, you need to have already taken the organic chemistry class to get the hang of amino acids on the MCAT. An alpha carbon attached to four different substituents must be chiral according to the notion of chirality. All amino acids are chiral, except for glycine, which defies the four unique substituent rules by having an additional hydrogen atom as its R-group.
An amino acid’s “R group,” which can fluctuate, makes it profitable. Because of this, each amino acid has unique characteristics that affect its size, polarity, charge, and interactions with other components of biological systems. See “Classifications” for more information.
There are D and L enantiomers, structurally identical molecules with opposed absolute configurations around the chiral carbon, for the 19 chiral amino acids. The human body solely produces proteins using L-amino acids, an evolutionary oddity. The amino group of L-amino acids is pointed to the left in a Fischer projection (see below). All 19 of the L-amino acids, except for cysteine, have an absolute configuration of S. Cysteine’s alpha carbon has the total configuration R.
Dipolar Ions of Amino Acids
The amino group (also known as the “N-terminus”) of an amino acid is a base that usually receives a positive charge when protonated in the pH 7.4 environment of the cell. An amino acid’s carboxylic acid functional group, often known as the “C-terminus,” is an acid that is usually deprotonated in the cell’s aqueous environment, leaving it with a negative charge.
Since the carboxyl and amino groups are both ionized in a physiologically relevant manner, they are conventionally represented as -NH3 and -C00. Any other ionizable residues are restricted to the acidic and basic amino acids. The uncharged (non-acidic/essential) amino acids are zwitterions because they have a plus one and a minus one charge under physiological conditions (ions whose accounts cancel out, producing a molecule with a net neutral amount).
Classifications for Amino Acids
Hydrophilic and hydrophobic interactions play a crucial role in a biological environment. Based on their distinct R-group, amino acids can be broadly divided into several types, significantly impacting how they operate. There are five categories into which amino acids can be categorized:
- nonpolar aliphatic
- nonpolar aromatic
- polar uncharged
- polar basic
- polar acidic.
Amino acids classified as nonpolar aliphatic have R-groups that have non-aromatic hydrocarbon chains. Another example is the plasma membrane of cells, which often consists of nonpolar amino acids rather than the hydrophilic amino acids that make up the exterior. Polar amino acids come in charged and uncharged varieties. The opposite side groups are highly hydrophilic and seek to optimize their interactions with other polar molecules, such as water, in contrast to the nonpolar amino acids.
They also have atoms that can form hydrogen bonds, improving water interactions. In contrast, amino acids with acidic residues have an additional negative charge. A notable exception is a histidine. Histidine is neutral at physiological pH because it contains an essential residue deprotonated under physiological circumstances. Below are the PKA values for the N and C termini and the acidic and basic residues. When stored in physiological settings, where the pH is around 7.4, amino acids are not always preserved.
What Are the Unique Qualities of Side Chains?
We will briefly review some of the most notable instances in which an amino acid side chain confers a particular feature, so learn each side chain and use its properties on exam day.
- A few side chains of amino acids naturally weaken proteins with helical structures. In particular, glycine and proline frequently destabilize (break down) the local alpha-helical secondary structure of proteins when they are introduced to them.
- Serine, threonine, and tyrosine are among the amino acids whose side groups are most frequently phosphorylated. A negatively charged phosphate is added to a molecule during phosphorylation, which often modifies the structure or function of the molecule. You’ll see that the hydroxyl functional group is present in these three amino acids. Although histidine is frequently a target of phosphorylation, the AAMC does not appear to use this information in its tests.
- Several amino acids resemble an irreversibly phosphorylated functional group. When used in place of serine/threonine/tyrosine, aspartic acid, and glutamic acid can simulate the presence of a phosphate group due to their structures being sufficiently close to those of phosphate. Therefore, changing an aspartic acid residue could result in an enzyme becoming permanently activated when it is phosphorylation-activated. The term “phosphomimetic effect” refers to this.
- The components of a polypeptide can occasionally form covalent disulfide connections with other cysteine residues, binding them together.
- Because of their appealing positive and negative charges, basic and acidic residues can interact to form salt bridges. Protein stabilization is greatly aided by salt bridges, an attractive interaction that combines acid/base interaction with hydrogen bonding.
Alpha-Amino Acid Synthesis
The Strecker and Gabriel syntheses are the two main techniques for creating amino acids in a lab setting and amino acid prototypes that you should have a basic understanding of. Don’t memorize specifics, but be aware of the big picture and certain vital lessons.
The Strecker Synthesis is a two-step process to manufacture various kinds of amino acids. In the first stage, an aldehyde (with a changeable R group – this is critical later) is combined with ammonia (NH3) to create an imine. Next, an alpha-aminonitrile is created by the nucleophilic charge of the cyanide ion on the imine.
The aminonitrile is hydrolyzed in the second stage, producing an alpha-amino acid. By changing the R group on the aldehyde, we can develop a range of alpha amino acids with unique R-groups. Notably, the Strecker synthesis results in a racemic mixture of L and D amino acids. That’s because the cyanide ion is added to the imine non-stereospecifically (in other words, 50 percent L and 50 percent D). Scientists must use an enantioselective technique to isolate only the Lor D enantiomer.
Due to the complexity of its synthesis, it is essential to understand the Gabriel Synthesis a little bit better. A diethyl bromomalonate is used to modify a phthalimide salt’s nitrogen.
This hydrogen may be deprotonated, and a molecule with a variable Regroup may alkylate the resulting anion (which allows for creating different amino acids). Base-catalyzed hydrolysis of the phthalimide produces a compound decarboxylated with heat and acid to produce a chiral amino acid.
Since the decarboxylation reaction in this instance is non-stereospecific yet nevertheless results in chiral amino acid, the result is also a racemic mixture of L and D amino acids. In other words, a racemic combination is produced by both the Strecker and Gabriel synthesis procedures.
Reactions to Amino Acids
Sulfur Linkage for Cysteine and Cystine
The sulfur-containing R groups of two cysteine molecules can create a covalent disulfide connection. Disulfide linkages between cysteine residues can impact the stability and folding of proteins.
Peptide Linkage: Polypeptides and Proteins
A molecule of two or more amino acids is called a peptide. Peptide bonds are what bind the two amino acids together. The two molecules are linked together, and a water molecule is released when the amino group of one amino acid nucleophilically attacks the carboxyl group carbon of another amino acid.
Peptide bonds can connect numerous amino acids to create long-chain polypeptides. Only hydrolysis, in which the bonds are severed by adding a water molecule, can break the peptide bond. This reaction is exergonic and spontaneous since it is the peptide bond formation’s opposite.
General Principles of Protein Structure
Let’s establish the framework for understanding amino acids’ higher-order counterparts, proteins, now that we’ve covered the fundamentals of amino acids.
Primary Protein Structures
From the N-terminus to the C-terminus, amino acids can be joined endlessly to create longer chains. The fundamental structure of a protein is its linear connection of amino acids. The sequence of amino acids that begins at an N-terminus and ends at a C-terminus is essentially what makes up a protein’s primary structure.
Proteins’ Secondary Structures
As soon as a single chain of amino acids is created, that chain will fold in a way that maximizes both the entropy and the stability of the protein. Smaller sections of a very long chain of amino acids will locally fold into unique structures, most frequently either beta sheets or alpha helices.
Proteins’ Tertiary Structures
A peptide chain’s tertiary structure is the overall three-dimensional structure that it folds into. A peptide will fold into its most energetically good confirmation once all its secondary structure components have folded; this best conformation is referred to as the peptide’s native state. The hydrophobic R groups of nonpolar amino acids usually reside in the core of the protein during protein folding in the aqueous environment of the body. In contrast, the hydrophilic R groups primarily live on the exterior of the protein.
Protein’s Quaternary Structure
A single amino acid chain will fold into a single peptide; the quaternary structure of a protein is the combination of several peptides or peptides with non-protein components. A polypeptide is created when many peptide subunits combine.
For describing the combination of several peptides, there are specific words. A monomer is a single peptide by itself; a dimer is two peptides joined together, a trimer is three peptides joined together, and so on.
When two peptides are combined, the prefix «homo-» is used if they are identical; otherwise, the prefix «hetero-» is applied.
Amino acids play a critical role in the body and are essential for MCAT success. The cheat sheet we’ve provided is just a starting point, but it should help you get comfortable with the different types of amino acids. To dive even deeper in Amino Acids, their structure, and what you can expect to see on the MCAT, check out the Jack Westin Complete Amino Acids Guide.