proteins are vital for the normal function of a cell essentially a protein is at its simplest a very long chain of individual units called amino acids bound to each other by peptide bonds to form an amino acid chain they sort of resemble a string of beads and they get twisted and folded into a final protein shape to make a protein we need to get to know two things the ingredients which are the amino acids and the recipe or how the finished amino acid chain folds into the protein humans use 20 amino acids in our day-to-day protein making so we have alanine Arginine asparagine aspartic acid cysteine glutamic acid glutamine glycine histadine isol leucine Lucine lysine methionine phenol alanine Proline cine thionine tryptophan tyrosine and veine pH that's 20 one way to divide these is into the ones that we make ourselves and the ones that we cannot make ourselves there are five amino acids that are dispensable alanine asparagine aspartic acid glutamic acid and Cene because we can make them denovo ourselves at any time and in good quantity then there's six of them that we call conditionally essential because we can make them most of the time but not always and these are Arginine cysteine glutamine glycine Proline and tyrosine finally there are nine of them that we cannot make ourselves htin isoline Lucine lysine methionine phenol alanine threonine tryptophan and veine and as a result we have to obtain them from our diet we call these the essential amino acids all right so the amino acid just from the name you can tell they've got an amine group or nh2 and also an acid in this case a carboxilic acid group or Co the amine and carboxilic acid groups are both bound to the same carbon called the alpha carbon now at a physiologic pH of 7.4 the amine group has a positive electrical charge and the carboxy group has a negative charge having both a positive and a negative charge makes amino acids a type of zwitter ion which is German for hybrid or double ion now the alpha carbon also has a side chain sometimes marked as r and this side chain gives the amino acids certain properties which can play an important role in the overall protein structure first the side chain can be hydrophilic or hydrophobic so water loving or water hating hydrophobic amino acids have non-polar side chains this might be in the form of an alkal side group which is a saturated hydrocarbon seen in veine glycine alanine Lucine isol leucine methionine and Proline alternatively it can be in the form of an aromatic side group which involves a six carbon ring like in phenol alanine tyrosine and tryptophan now hydrophilic amino acids have polar side chains these polar side chains might be acidic like when their side chains contain additional carboxy groups like aspartic acid and glutamic acid other hydrophilic amino acids have polar side chains that are basic like lysine histadine and Arginine at physiological pH the acidic groups lose a hydrogen and the basic groups gain a hydrogen finally some polar side chains are neutral for example they can contain hydroxy groups like Cene theanine or tyrosine or suf hydral groups like cysteine or carboxamide groups like asparagine or glutamine now keep in mind that the charge and amino acid really depends on its side chain as well as the pH for example at a very low PH the amine group is positive while the carboxy group is neutral and at a very high pH the amine group is neutral and the caroal group has a negative charge and at a pH that's somewhere in between both groups are electrically charged and they cancel each other out resulting in no net charge for the amino acid the just right pH also known as the pi or isoelectric point is different for every amino acid and it depends on the specific side chains for amino acids to link up in a chain the carboxy group of one amino acid has to bind to the amine group on another amino acid creating a single peptide bond this is a condensation reaction meaning that two amino acids are basically smooshed together and the O from the carboxy group along with one of the hydrogens from the amine group get released as a water molecule in the formation of an amide Bond well technically being a single Bond it actually has the properties of a structurally stronger double bond thanks to the property of resonance now resonance is a property of a molecule where electrons get shared across the molecule while keeping the arrangement of atoms the same basically the electrons from neighboring functional groups in the amino acid are borrowed and that makes peptide bonds stronger and more stable so amino acids are essentially a carboxy group an amine group a side chain and a hydrogen all bound to an alpha carbon now there's an interesting geometric property here called chirality which means that each amino acid can exist in two forms that look like mirror images of each other these two forms are called en anomers of each other we have the left or level oriented amino acids as well as the right or dextro oriented amino acids while similar these are definitely not the same think of it like a pair of shoes even though they're made out of the same materials and generally look alike the left and the right shoe are not interchangeable at least not without a lot of pain involved as it turns out proteins are only made out of level oriented amino acids now protein production itself happens in cellular structures called ribosomes which use the messenger RNA which is essentially a blueprint that tells the ribosome exactly the order of amino acids that are needed at this point the protein is just a growing string of amino acids as it grows it's either being injected into another organel called the endoplasmic reticulum which will help the protein take shape or it's being translated directly into the cytool now the proteins have multiple levels of structure to them primary secondary tertiary and quinary structure creating a hierarchy as an analogy think about the alphabet it can be used to create Words which can make simple sentences which can further be made into complex sentences as an example the letters themselves would be considered the primary structure then simple words like exam and ours would represent secondary structures tertiary structure would be when the entire chain folds together maybe making a simple sentence like the exam is in 2 hours and the quadin structure might actually be a few peptide chains coming together to form a more complex protein making a complex sentence that says the exam is in 2 hours and I haven't slept at all when it comes to proteins the primary structure is simple enough it's just a linear sequence of amino acids connected through peptide bonds like a String of Pearls now the peptide bonds between the amino acids are very rigid but by comparison the single bonds connecting the amide functional group of the peptide bond to the alac carbon are flexible that allows significant freedom of rotation and through that rotation the protein can fold into one of the two types of secondary structure Alpha helix or beta pleated sheets the alpha Helix resembles a spring the helical structure brings the co of the first amino acid near the the NH of the fifth amino acid the second Co gets near the sixth NH and so on in other words each of these instances is separated by four amino acids having the O and H get close to one another allows for a strong hydrogen bond to form and that makes the alpha helical structure really stable beta pleated sheets also rely on hydrogen bonding but slightly differently imagine a neatly folded piece of paper in beta completed sheets hydrogen bonds form between the NH on one flap of paper and the co on another flap of paper and these bonds almost hold or glue the sheets together that makes beta ple sheets really stable as well now tertiary structure is the overall shape of the polypeptide chain and it includes the secondary structures as well as other features for example two sulfur containing cyes can bind to form a disulfide bridge also hydrophobic amino acids form bonds with one another and Orient themselves toward the inside of the protein in that way they avoid contact with water it's like the hydrophobic amino acids are being a bit shy basically the way a polypeptide chain twists and turns to form its tertiary structure is kind of like the way headphones get tangled up in your pocket quadrin structure is the final level and it's the level at which multiple polypeptide chains come together to form a larger protein structure a classic example involves the four polypeptide subunits that have come together to form a single hemoglobin protein which is roughly a tetrahedral Arrangement all right as a quick recap there are 20 amino acids five dispensable six conditionally essential and nine essential the primary structure of a protein is the linear sequence of amino acids the secondary structure includes both Al Alpha helix or beta pleed sheets both of which rely on hydrogen bonds the tertiary structure binds the secondary structures through various other Bond interactions like disulfide Bridges or hydrophobic reactions and the quadrin structure creates the final shape of a protein by connecting multiple polypeptides in the form of tertiary structures helping current and future clinicians Focus learn retain and Thrive Lear learn more