If you haven't read part 1 and 2 of this series yet, I will put the links here and here for you! For this segment, we will talk about peptide bond formations and the 4 different types of protein structures. Now, if you've already known about amino acids, you will know that they are the building blocks that make up peptides and proteins. However, how do they come together to create these peptides? The answer is something called "peptide bonds".
Proteins are linear polymers of amino acids (monomers of protein) or "residues". When there are 2 amino acids "bound" to each other, we call them dipeptides. When there are 3, they are called tripeptides. And when there are more AAs subunits/residues being bind to each other, they are called polypeptides. These peptides are actually joined together by peptide bonds, which is a covalent amide that is formed between the carboxylic group (-COO-) of one AA and the amino group (-NH3+) of another amino acid.
FOUR TYPES OF PROTEIN STRUCTURES
Proteins have 4 levels of structure: Primary, secondary, tertiary, and quaternary.
A. Primary Protein Structure: The primary structure of a protein is basically the sequence of amino acids that's stabilized by the formation of covalent peptide bonds between the adjacent amino acids. The primary structure of the protein is determined the gene that corresponds to that protein. The linear amino acid sequence is important because it helps determine the native conformation of the protein. The free amino end at the left that has NH3+ is called the N-terminus and the free carboxyl end at the right is known as the C-terminus (COO-).
PEPTIDE BOND FORMATION
Peptide bond formation is the result of a dehydration synthesis reaction. First, the electrophilic carbonyl carbon on the first AA is attacked by the nucleophilic amino group on the second AA. Then, the hydroxyl group of the carboxylic acid is kicked off and this results in the formation of the peptide bond. To make it short and sweet, the carboxyl group of one molecule will attack the amino group on the other amino acid - releasing an H2O molecule (some water) as a byproduct. You now have a dipeptide!
HOW TO BREAK UP PEPTIDE BONDS
Peptide bonds can be broken in processes called hydrolysis and proteolysis. This can either be done with proteolytic enzymes or strong acids. Let's say you throw the polypeptide in a strong acid solution with some heat, then you will get a bunch of broken up amino acids in the mixture. It's therefore considered to be nonspecific because it doesn't discriminate where it cuts. If you add some proteolytic enzymes, however, they will cleave up the peptide bonds only at specific locations. Proteases don't just cleave anywhere. Oh no no no. Just think of them as being the pickier friends/cousins to strong acids. ^^ For example, trypsin, an enzyme that's produced by our pancreas, only cleaves at the carboxyl side of basic amino acids like lysine, arginine, and histidine. Therefore, if there's a polypeptide chain with those basic amino acids, they will cleave the right side/C-terminal of those side chains!
B. Secondary Protein Structure: A protein's secondary structure is held together by the intramolecular hydrogen bonding between the amino acids that are nearby. The 2 most common secondary structures are alpha helices and beta pleated sheets.
1) Alpha Helices: An alpha helix has a rod-like structure that coils clockwise around a central axis. The side chains are pointing away from the helix core. It's an important structure in keratin, the protein that is found in our hair, skin, and fingernails!
2) Beta Sheets: Beta pleated sheets are composed of parallel or anti-parallel peptide chains that lie alongside one another. They are held together by hydrogen bonds between the carbonyl oxygen atom of 1 chain to the amide hydrogen atom in the adjacent chain.
***Amino Acids that Interfere with Secondary Structures :
Proline: Due to its rigid structure, proline is rarely found in alpha helices and beta sheets because it introduces kinks in the structures. The reason why is because its side chain forms a second alkyl group to the amine. This causes the structure to have conformational rigidity and in return, it cannot act as a donor for hydrogen bonding. Interestingly enough, although proline introduces kinks to secondary structures like alpha helices, it can be commonly found in helices that cross the cell membrane as well as in between turns between the chains of a beta sheets.
Glycine also applies as well. However, I already explained about it so feel free to go back to part 1 of this series to read more about it!
C. Tertiary Structure: The tertiary structure of a protein has a 3-dimensional shape that is determined by hydrophobic and hydrophilic interactions between the AA's R groups. Because of their nature, hydrophobic AAs prefer to be in the interior of proteins and hydrophilic AAs prefer to be on the surface of proteins. An important component of tertiary structures is the presence of disulfide bonds, which can form when 2 cysteine molecule goes through the oxidation reaction (where 2 protons and 2 electrons are lost) to form cystine. These disulfide bonds create loops in the protein chain.
D. Quaternary Structure: These protein structures normally contain more than 1 polypeptide chain and they reflect the final composition/form of the protein. You can just imagine lots of tertiary structures coming together to create a quaternary structure if that makes it easier! Examples that we can find in our daily lives include hemoglobin as well as immunoglobulin G (igG) antibodies. They are held together by non-covalent interactions and tend to be: 1) More stable due to the reduced surface area; 2) Reduce the amount of DNA that's needed to encode the protein complex; 3) Bring catalytic sites closer together and thus speed up reactions; and 4) Induce cooperativity or allosteric effects.
E. Protein Folding and Denaturation
Now that you have a better understanding of protein structures and peptide bonds, let's go ahead and discuss HOW and WHY they conform a certain way! Have you ever questioned why not all proteins look alike? The answer has to do with something called hydrophobic interactions.
*** Non-covalent Interactions:
For a quick recap, in primary structures, the amino acids are held together by peptide bonds. In secondary structures, they are held together by hydrogen bonds. In tertiary and quaternary structures, the polypeptides are held together by something called hydrophobic interactions, which play an important part in a protein's conformational stability. It can come from van der Waals forces between nonpolar side chains as well as London dispersion forces.
1) Protein Folding and the Solvation Layer:
Okay, let's break it down: First, you need to know that hydrophilic residues like to accumulate on the surface of protein structures and hydrophobic residues occupy the interior of the proteins. For example, if you drop a hydrophobic solute into an aqueous solution, that solvent will form something that's called a solvation layer around that solute. Because of its polarity however, the water molecules in that solvation layer cannot form hydrogen bonds with the side chain. This means that the H2O molecules will have to rearrange themselves in order to maximize the number of hydrogen bonds between the solvent and the solute. Therefore, there will be a negative change in entropy and this makes the overall process non-spontaneous. On the other hand, if we put a hydrophilic solute into a polar solvent, the water molecules will have an easier time forming hydrogen bonds with the side chain and it will try to arrange itself so that the number of hydrogen bonds will be maximized. This increases the entropy and make the overall process spontaneous.
2) Protein Denaturation:
Think of this process as the opposite of protein folding. It is often irreversible and unfolded proteins cannot catalyzed reactions. For instance, when temperature increases to a high enough temp, then it can overcome the hydrophobic interactions and causing it to denature (unfold). This happens a lot in cooking. I mean, heat ==> increase in temperature ==> protein denaturing! Science is amazing guys (cue what Ash says in almost every single episode of Pokemon). ^_^ Besides heat, solutes like urea and SDS can also denature proteins by disrupting the disulfide bridges or the non-covalent bonds that hold the proteins together! Therefore, these solutes are often used to break up protein compounds.
I'm Linh - a science geek who loves experimenting and tinkering with recipes! I hope that this blog brings more ideas into your kitchens! Happy eating folks! XOXO