Jump to: navigation , search. Personal tools Log in. Namespaces Page Discussion. Views Read View source View history. This page was last modified on 20 October , at One final concept before we break down the individual amino acids, and that is the 3-dimensional protein structure.
In a biological system structure determines function , so understanding amino acid characteristics is key to understanding structure and ultimately protein function. Primary Structure of a 3-D Protein The first and more important determination factor of protein structure is the sequence of amino acids.
If the polypeptide chain is attached in a different order, you get a very different overall structure. Secondary Structure of a 3-D Protein The secondary structure comes from backbone hydrogen bonding interactions.
The peptide bond turns every former carboxyl and amino group into an amide functional group. The secondary structure of alpha helix and beta pleated sheets come from hydrogen bonding between the partially negative oxygen on the carbonyl and the partially positive hydrogen on the nitrogen.
THIS is where knowledge and understanding of amino acid side chains are critical. Many students confuse this with secondary structure, which is only backbone interactions. Quaternary Structure of a 3-D Multi-Polypeptide Protein Quaternary structure refers to the variable group interactions between different polypeptides to form a single larger protein.
Quaternary structures are not found in every protein. If the protein contains just a single amino acid strand, then the highest level of folding is its tertiary structure.
However, if the protein is made up of multiple polypeptide subunits, then the quaternary structure is what holds the different polypeptides together. This means you ignore any potential polarity on both the carboxyl and amino groups and ONLY look at the side chains. Hydrophobic, as the name implies is hydro — water , phobic — fearing. Hydrophobic amino acids have little or no polarity in their side chains. The lack of polarity means they have no way to interact with highly polar water molecules, making them water fearing.
However, if all you see are Cs and Hs you should automatically recognize a water-fearing amino acid. But glycine only has a hydrogen at its side chain position. Since hydrogen is non-polar, glycine is a hydrophobic amino acid. The Hydrogen side-chain makes glycine the smallest amino acid. Alanine is a simple amino acid which has just a methyl or CH3 group as its side chain.
Since you see nothing but carbon and hydrogen, Alanine is a non-polar hydrophobic amino acid. Valine is another simple amino acid with just an isopropyl variable group. Just like alanine, we see nothing but carbon and hydrogen, making valine a non-polar hydrophobic amino acid. You can recognize leucine as having the same variable group as valine but with an extra CH2 group.
Or you can simply recognize its isobutyl side chain. Isoleucine, as the name implies, is an isomer of leucine. The difference is the placement of the CH3 for a sec-butyl rather than a isobutyl side chain. Just like its isomer, isoleucine is nonpolar and hydrophobic. Methionine is the first potentially tricky amino acid. Since the difference in electronegativity is less than 0.
Pay attention to the structure of phenylalanine. It has a single carbon group with an attached benzene ring. Phenyl is the name for a benzene substituent, and this molecule has a benzene phenyl attached to the structure of alanine. Since phenylalanine has nothing but Cs and Hs in its aromatic side chain, it is nonpolar and hydrophobic. This is a tricky one. Notice the N-H in this side chain. N-H should be polar and capable of hydrogen bonding.
However, there are two reasons this amino acid is still non-polar and hydrophobic. The MCAT requires you to recognize that this is a large and bulky amino acid. Keep this in mind for med-school. The proline side chain is a 3-carbon chain that loops around and attaches back to the parent amino group. This means that unlike the other amino acids, proline does NOT have a hydrogen atom on its nitrogen when part of a polypeptide chain.
Since we just have 3 CH2 groups to analyze we get a nonpolar hydrophobic side chain. Pay attention to the presence of polar groups that are small compared to the overall sidechain, or very weakly polar and therefore hydrophobic. Cysteine has a slightly polar S-H, but its polarity is so mild that cysteine is unable to properly interact with water making it hydrophobic. Cysteine is a very important amino acid when it comes to tertiary and quaternary structure.
This covalent bond is much stronger and more permanent when compared to the standard tertiary and quaternary interactions. Take a close look at tyrosine. What do you see? On the one hand, we have a very polar and hydrogen-bond capable OH group, but on the other hand, the OH is tiny when compared to the size of the benzyl group CH2-phenyl.
Hydrophilic as the name implies comes from hydro-water and philic — loving. Polarity comes from a 0. The electronegativity difference is enough to create a slight separation of charge or polarity. And since like attracts like, these partially charged groups will be attracted to oppositely charged or partially charged groups such as water.
These groups will twist the polypeptide chain in order to interact with each other and with water. Hydrophobic groups will twist away from these side chains. Think of serine as alanine with an OH group attached. Unlike tyrosine, the OH is the majority in this molecule and its polarity is enough to influence the entire group. This makes series polar and very hydrophilic. There are multiple ways to look at this group. You can think of it as serine with an extra methyl group, or as valine but with an OH replacing one of the methyl groups.
If the side chain contains an amine functional group, the amino acid produces a basic solution because the extra amine group is not neutralized by the acid group. Amino acids which have basic side chains include: lysine, arginine, and histidine.
Amino acids with an amide on the side chain do not produce basic solutions i. Since an amino acid has both an amine and acid group which have been neutralized in the zwitterion, the amino acid is neutral unless there is an extra acid or base on the side chain. If neither is present then then the whole amino acid is neutral.
You need to look at the functional groups carefully because an amide starts out looking like an amine, but has the carbon double bond oxygen which changes the property. Amides are not basic. Even though tryptophan has an amine group as part of a five member ring, the electron withdrawing effects of the two ring systems do not allow nitrogen to act as a base by attracting hydrogen ions.
Amino Acid Molecular Structures. Elmhurst College. Amino Acid Structures. Chemistry Department. Amino Acid Review. Peptide Bonds. Virtual ChemBook. Structures of Amino Acids. Amino Acid Name. Structure of R group red. Neutral Non-polar. Neutral Polar. Acidic Polar. Neutral Slightly Polar.
Neutral Slightly polar. Characteristics and Properties of Amino Acids Introduction: Each amino acid has at least one amine and one acid functional group as the name implies. Principles of Polarity: The greater the electronegativity difference between atoms in a bond, the more polar the bond. Non-Polar Side Chains: Side chains which have pure hydrocarbon alkyl groups alkane branches or aromatic benzene rings are non-polar.
List all amino acids with non-polar side chains. Which amino acid is most insoluble in water: isoleucine or alanine?
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