Notes
Amino Acid: Chemistry Fundamentals
Sections
Amino Acid Fundamentals
Overview
AMINO ACIDS
- Building blocks of proteins
- 20 AA encoded in the human genome
- Few other AA not encoded in our genome: converted from other AA residues
CHIRALITY
Chiral carbon
- Carbon atom with 4 different attachments
Amino acid chirality
- Almost all AA have chiral carbon as central atom
- Exception: glycine (R-group = H-atom)
CORN: use to distinguish L & D-form AA
- Forms refer to optical properties
ZWITTERIONS & ISOELECTRIC POINT
Zwitterions
- Neutral w/ counterbalancing +/- charges
- Can both accept and donate protons
- AA's are zwitterionic under physiologic conditions: NH3+ and COO- = 0 net charge
Isoelectric point (pI)
- No net charge
- For most AA: zwitterionic state = isoelectric point
- Charged amino acids (aspartic acid & arginine): isoelectric point may favor more acidic or more basic form of molecule
PEPTIDE BOND FORMATION:
- Condensation reaction: amino acids join & form polypeptide chains
- Water eliminated for each bond formed
R GROUP ORIENTATION
- R groups face alternating directions (eg, east-west)
- Reduces strain
Full-Length Text
- Here we will learn about the fundamentals of amino acids, which are the most basic units of proteins and have several unique structural features that enable their function.
- Let's start a table.
- Denote the following characteristics of amino acids:
- amino acids are the building blocks of proteins.
- there are 20 amino acids encoded in the human genome and used for protein synthesis.
- there are a few other amino acids that are not encoded in our genome but are instead converted from other amino acid residues during or after translation.
Now, let's create drawings to depict the basic characteristics of amino acids.
- First, we will illustrate chirality in amino acids.
- Draw a carbon atom with four lines to represent its bonds; a chiral carbon is a carbon atom that has four different attachments.
- We draw them here in a north, south, east, west configuration; however, we should remember that atoms occupy a three dimensional arrangement in space, and are attached to the carbon atom in a tetrahedral arrangement.
- On the "north" side bond, attach a hydrogen atom.
- On the "east" side bond, add the carboxylic acid group (COOH).
- On the "south" side bond, attach an "R" to represent the variable side chain.
- On the "west" side, add the amino group (NH2).
- Notice that our carbon atom has four different groups attached to it.
- Almost all amino acids have a chiral carbon as their central atom with the exception of glycine; its "R group" is a hydrogen atom.
- Next, in order to understand how chirality causes the formation of amino acid isomers, draw another amino acid but here place the R group on the "north" side and the hydrogen atom on the "south" side.
- On the outside of the first amino acid, draw a curved arrow in clockwise direction (meaning, from the carboxylic acid group, past the variable side chain, the amino group, to the hydrogen).
- On the outside of the second amino acid, draw a curved arrow in counterclockwise direction.
- Notice that in both amino acids, the direction of the arrow forms the acronym "CORN": CO for the carboxylic acid group, R for the variable side chain, and N for the amino group.
- Indicate that the amino acid with the clockwise arrow is the "L-form" of the amino acid
- Next, indicate that the amino acid with the counter-clockwise arrow is the "D-form" of the amino acid
- We use the acronym CORN and the arrows to help us distinguish between the L and D forms.
- Write that all amino acids with chiral atoms exist naturally as their L-form.
Now let's depict two key features of amino acids: zwitterions and the isoelectric point. Amino acids are zwitterions, meaning that these molecules can be neutral with counterbalancing positive and negative charges, because they can both accept and donate protons.
- Draw another L-form amino acid but this time be sure to draw the individual atoms on the carboxylic acid and the amino group, which means on the carboxylic acid group, draw the carbon double-bonded to an oxygen atom and single-bonded to an oxygen atom, and show that this oxygen is bonded to a hydrogen atom.
- Similarly, on your amino group, draw the nitrogen atom with single bonds to two hydrogen atoms.
- Now, draw a proton going towards to the N atom of the amino group in order to illustrate that the amino group can accept a proton to become positively charged.
Next, let's draw a second amino acid to show this change in charge.
- Draw another amino acid except here attach 3 hydrogens to the amino group.
- Notice that the nitrogen atom is now positively charged.
- Next, circle the H atom of the carboxylic acid group with an arrow to show it leaves the molecule to illustrate that the carboxylic acid group can donate a proton to become negatively charged.
- Now, draw a third amino acid with the three hydrogens on the amino group, and the carboxylic acid group without the hydrogen atom.
- Notice that the oxygen atom is now negatively charged, but this counterbalances the positive charge of the nitrogen atom, giving the molecule a net charge of zero.
- This is the zwitterion form of an amino acid.
- Write that under physiological conditions, amino acids exist in their zwitterionic state with the amino group as NH3+ and the carboxylic acid as COO-.
- Because of this distinct feature, write that each amino acid has an isoeletric point (pI) at which it has no net charge.
- Write that for most amino acids, the isoelectric point is the zwitterionic state, but for charged amino acids, such as aspartic acid and arginine, the isoelectric point may favor a more acidic or more basic form of the molecule.
Finally, let's depict the formation of peptide bonds. Amino acids bind to each other to make polypeptide chains via a condensation reaction, which involves the elimination of a water molecule for each bond formed.
- Draw two amino acids next to each other with the carboxylic acid group of the first amino acid next to the amino group of the second amino acid.
- Now, encircle both the hydroxyl group of amino acid 1 and also one of the hydrogen atoms on the amino group of amino acid 2.
- With an arrow, indicate that these molecules are being eliminated as H2O.
- Now draw your two amino acids joined together with the carboxyl C from amino acid 1 single-bonded to the N from amino acid 2.
- Because of sterics, R groups in amino acid chains face alternating directions (eg, east-west).
- Functional groups will arrange themselves around the central atom to reduce the strain placed on the bonds by the sizes of attachments and by interactions between atoms.
Let's illustrate this using a stack of binders.
- Draw a stack of binders with an R group attached to the spine of each binder, and all the binders facing the same direction.
- Notice that after a few binders are stacked like this, the binders will start to slide off the top of the pile.
- Now redraw the stack of binders with the binders going in opposing directions.
- Now the stack of binders is much more stable.
- Notice that in this configuration the R groups now face opposite directions too.