This entry in the Freelance Quizbowl University Series covers amino acids.
Amino Acids are neutral, zwitterionic (containing separate positive and negative charges) molecules that form a secondary code to the genetic code of DNA by being the building blocks for proteins. Amino acids are carried by tRNA (transfer RNA) to the ribosome, where they form a growing peptide (nonfunctional fragment of a protein). The tRNA equips an individual amino acid by recognizing a codon (three base pair sequence) of a single-stranded mRNA (messenger RNA) molecule, which in turn is transcribed from a double stranded DNA molecule and then subject to post-transcriptional modifications (most famously splicing of introns, leaving the functional exons, and addition of a 5’ cap and a poly-A tail). Often, more than one codon codes for an amino acid.
Amino acids interact with ATP to receive an adenyl and phosphate group. This resulting molecule then interacts with a tRNA molecule to form aminoacyl-tRNA. The amino acid itself consists of a central carbon atom bound to four kinds of groups. One of the groups bound to the carbon is a hydrogen atom. Another group bound to the carbon atom is an –NH2, or amino, group. Yet another group bound to the carbon atom is a –COOH, or carboxy, group. The final group is what distinguishes every amino acid from each other; this is the variable side chain. Side chains can be simple or relatively complex. Below is one way to classify the 20 different common amino acids. Each will be mentioned with its name, its three letter code, its single letter code, and some facts about why each is important.
Positively-Charged Amino Acids
These amino acids contain a positively-charged atom in their side chains. They are all bases.
Arginine (Arg, or R) – contains a guanidium group, is involved in the synthesis of nitric oxide, and stabilizes intermediates during enzymatic reactions.
Histidine (His, or H) – contains an aromatic imidazole group. Precursor for histamine synthesis. Forms a catalytic triad with serine and cysteine.
Lysine (Lys, or K) – contains a hydrocarbon chain ending with an amino group. Used in the synthesis of acetyl-CoA. Can be fitted with a pyrroline group to form pyrrolysine.
Negatively-Charged Amino Acids
These amino acids contain a negatively-charged atom in their side chains. They are all acids.
Aspartic Acid or Aspartate (Asp, or D) – participates in the urea cycle and gluconeogenesis. Modified to form the artificial sweetener Aspartame.
Glutamic Acid or Glutamate (Glu, or E) – structurally very similar to aspartic acid. Important nervous system excitatory neurotransmitter which interacts with AMPA or NMDA receptors.
Polar, Uncharged Amino Acids
These amino acids contain polar, hydrophilic oxygen atoms but don’t have charge.
Serine (Ser, or S) – shows up in many proteases (enzymes that cleave peptide bonds in proteins), used in purine and pyrimidine biosynthesis, part of the catalytic triad.
Threonine (Thr, or T) – one of two amino acids containing hydroxyl groups (the other is serine), which can be phosphorylated by kinases. Pretty much just like serine in every way.
Asparagine (Asn, or N) – contains an an amide side chain. It is present in asparagus and when metabolized by the body, leaves a characteristic smell in the urine
Glutamine (Gln, or Q) – structurally similar to asparagine. Free form is the most abundant amino acid in the bloodstream.
Hydrophobic Amino Acids
These amino acids contain mainly hydrocarbons, making them quite non-polar.
Alanine (Ala, or A) – second-simplest amino acid, with just a methyl side chain. Forms a cycle with glucose because it corresponds to pyruvate, the three-carbon product of glycolysis.
Valine (Val, or V) – branched-chain, just like many other hydrophobic amino acids. Substitutes for glutamic acid in hemoglobin, resulting in a misfolded protein that causes sickle-cell anemia.
Isoleucine (Ile, or I) – cannot be catabolized without the aid of biotin (vitamin B7). The isomer of leucine.
Leucine (Leu, or L) – stimulates muscle protein synthesis, activates the mTOR (mammalian target of rapamycin) pathway, and becomes toxic in maple syrup urine disease.
Methionine (Met, or M) – initiates protein translation, contains a sulfur atom, has a formyl- variety used for translation in bacteria
Phenylalanine (Phe, or F) – contains a phenyl group (benzene ring), metabolized improperly in PKU (phenylketourea), naturally found in breast milk
Tyrosine (Tyr, or Y) – contains a phenol group. Precursor to a group of hormones called catecholamines, donates electrons to chlorophyll in photosystem II in chloroplasts
Tryptophan (Trp, or W) – contains an indole ring, is the precursor to serotonin and the vitamin B3 (niacin), causes drowsiness post-Thanksgiving since it is found in turkey.
Unique Amino Acids
These amino acids are not like any others.
Cysteine (Cys, or C) – contains a thiol (alcohol with sulfur instead of oxygen), sulfur can be replaced with selenium to form selenocysteine. Two can be linked to form a disulfide bridge.
Glycine (Gly, or G) – simplest amino acid with hydrogen side chain. Only achiral amino acid since the central carbon is bonded to 2 Hs. Inhibitory central nervous system neurotransmitter.
Proline (Pro, or P) – amino acid with a five-atom ring connected to the amino group of the amino acid. First amino acid in alpha helix. Combines with hydroxyprolines in collagen.
The amino acids that need to be consumed in order to be present in the body are called essential. These amino acids are isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, histidine, and tyrosine. The other 10 amino acids are non-essential.
Amino acids have two angles, phi and psi, that are called dihedral. By plotting these angles in a Ramachandran diagram, one can determine which secondary structures are allowed by various amino acid sequences, whether it is an alpha helix or a beta chain.