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Amino Acid Structures: Part I

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Amino Acid Structures: Part I

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AMINO ACID Structures: Part 1

Overview

There are 20 amino acids coded for in our genome

General structure

Central (alpha) carbon bound to:

  • Hydrogen atom
  • Carboxylic acid group
  • Amino group
  • Variable R group (differentiates AA)

AMINO ACID CLASSES

We divide amino acids into 4 general categories and 2 special cases.

  • Hydrophobic, which have nonpolar side chains that are usually aliphatic. Aliphatic means the side chains they have only have carbon and hydrogen atoms in their R groups (and no resonance).
  • Aromatic, which have one or more aromatic rings in the side chains.
  • Polar, which have polar, uncharged side chains.
  • Charged, which have either positively or negatively charged side chains
  • And the special cases: glycine (its R group is a hydrogen atom) and proline

In part 1, we learn the special cases and the hydrophobic amino acids:

SPECIAL CASES

Glycine (Gly, G)

  • Has the simplest R group: a hydrogen atom.
  • Glycine's fake R-group gives it many possible angles of rotation, which makes it unfavorable in some protein structures.

Proline (Pro, P)

  • The Proline "R group" is a ring structure that includes the amino group and the alpha carbon, which is different from the other amino acids.
  • Proline uses a pentagon (an imino ring) to connect the central carbon to the nitrogen atom of the amino group.
  • Proline is unfavorable (like glycine) but for the opposite reason: its bulky imino ring constrains its flexibility.

Hydrophobic

Alanine (Ala, A)

Valine (Val, V)

  • Beta branching; branch at the beta carbon

Leucine (Leu, L)

  • Branch on gamma carbon

Isoleucine (Ile, I)

  • Beta branching
  • Isomer of leucine (same formula, different arrangement of atoms)

Methionine (Met, M)

  • Contains sulfur atom

Full-Length Text

  • Here, we'll learn the structure of the 20 amino acids coded for in our genome.
    • To do this, we will group the amino acids in broad categories based on their characteristics.
    • This exercise is as fundamental to biochemistry as the learning the alphabet is to being able to read.
  • First, start a table.
  • Denote that amino acids have a general structure of a central carbon atom with four different atoms or groups bound to it.
    • Hydrogen atom
    • Carboxylic acid group
    • Amino group
    • Variable, R, group, which differentiates amino acids from each other.

There are 23 different R groups; they present the various unique side chains for each amino acid. However, we only have to learn the 20 genetically encoded ones; the 3 others are not encoded in our DNA and therefore are not classically taught.

  • Each amino acid has a name, a three-letter code and a one-letter code.  The codes are usually closely related to their amino acid name, which makes them easy to learn.
  • Here, we'll divide amino acids into four general categories (with two special cases).
    • Hydrophobic, which have nonpolar side chains that are usually aliphatic, meaning they only have carbon and hydrogen atoms in their R groups (and no resonance).
    • Aromatic, which have one or more aromatic rings in the side chains
    • Polar, which have polar, uncharged side chains
    • Charged, which have either positively or negatively charged side chains
    • And the special cases: glycine and proline

First, let's review the general structure of an amino acid.

  • Draw a carbon atom with four lines to represent its bonds in north, south, east, west orientation.
    • North, draw a hydrogen atom.
    • East, draw a carboxylic acid (COOH) group.
    • South, draw an R to represent the variable side chain.
    • West, draw an amino (NH2) group.

Because of the complexity of some of our R groups, we will use stick structures for most of our amino acid drawings.

Now, let's turn our general structure into a stick structure as follows:

  • First, start with an NH2 group.
    • Use lines to add a chain of two carbon atoms.
  • To the carbon atom nearest to the NH2 group, attach an R to represent the variable side chain.
  • To the other carbon atom, add a double-bonded O and a single-bonded OH group to transform it into a carboxylic acid group.
    • We've shown the amino group, carboxylic acid group, and R group.
    • What haven't we shown?... Hydrogen.  And we shouldn't, because in this format, we don't show hydrogen atoms attached to carbon atoms.
  • Note that our central carbon is also called the alpha carbon, and that carbon attachments on the side chains are also given Greek letters.
    • This means that the first carbon in an R group is called the beta carbon, the next is called the gamma carbon, and so on.

Let's draw the amino acids, now, beginning with the special cases: glycine and proline.

Begin with glycine, which has the simplest R group: a hydrogen atom.

  • Draw our general amino acid stick structure with a hydrogen atom as the R group.
    • Although hydrogen atoms are not usually shown, we do show this one because it is the R group.
  • Indicate that glycine's three and one letter codes are Gly and G.
    • Glycine's R-group gives it many possible angles of rotation, which makes it unfavorable in some protein structures.

Next, let's draw proline; its "R group" is a ring structure that includes the amino group and the alpha carbon, which is different from the other amino acids.

  • Indicate that proline is also denoted as Pro, or P.
  • Draw our general amino acid stick structure but omit one of the hydrogen atoms of the amino group.
  • Now, use a pentagon to connect the central carbon to the nitrogen atom of the amino group.
    • This is called an imino ring, and it gives proline its unique features.
    • Proline is unfavorable (like glycine) but for the opposite reason: its bulky imino ring constrains its flexibility.

At this point its best if you stop and re-draw these amino acids from memory before moving on.

Now let's draw the hydrophobic, non-polar amino acids, which includes alanine, valine, leucine, isoleucine and methionine. We will draw them in order of increasing complexity; their similar structures will reduce our memory burden.

  • Let's start with alanine, also written as Ala or A.
  • Draw a general amino acid stick structure and replace the R with a line.
    • Remind ourselves: what does the line represent? A methyl (CH3) group.
    • Alanine is considered to be the simplest amino acid (even though glycine has a simpler R group) because its R group is large enough to give it some steric constraints, but small enough to prevent major changes in protein structure.

Next we will build valine from the structure of alanine.

  • Write that valine's code forms are Val and V.
  • Draw another alanine stick structure and at the end of the methyl group, add two more methyl groups attached to the same carbon atom.
    • This looks like an upside-down wide V (or a rooftop) and represents an isopropyl group.
    • Notice that valine has beta-branching, since it has a branch at the beta carbon.

Now let's draw leucine (Leu or L) as follows:

  • Re-draw our alanine molecule, and add an isopropyl group.
    • What does this amino acid resemble? This molecule looks very similar to valine, except that it has an extra carbon atom before the branch.
    • Leucine does not have beta-branching, since the branched chain is on the gamma carbon.

Now let's draw isoleucine, which is closely related to both valine and leucine in structure.

  • Write that isoleucine is also written as Ile or I.
  • Draw another valine stick structure and add a methyl group to one end of the rooftop.
    • Like valine, isoleucine has beta-branching. Isoleucine has the same general formula as leucine, but the atoms are arranged differently, making it an isomer of leucine, hence the name isoleucine.

The final molecule in this group is methionine, which is also denoted as Met or M. Let's go back to our general amino acid stick structure.

  • First, add to our general structure, a two-carbon group (an ethyl group).
  • To the end of this group, we will add a sulfur (S) molecule.
  • Then, add a methyl group on the end.
  • Our completed R group is CH2-CH2-S-CH3.
    • Methionine is one of two sulfur-containing amino acids, but because the sulfur atom is sandwiched between alkyl groups, it is fairly unreactive.

Review: we now know seven amino acids: G, P, A, V, L, I and M. Grab a blank sheet of paper and test yourself by spelling the words GLAM and VIP as polypeptide chains.