On Protein Structures
First of all learn the 20 amino acids used in protein synthesis. Amino acid memorization is made easier here. Proteins are made from amino acids and they’re also used in metabolism, so it’s good to learn them now. Plus you might be tested on it.
Know amino acid ionizations. Example, if there is a carboxyl group the acid version is the one with the hydrogen (R-COOH) and the basic version is the one with the hydrogen dissociated so it would just be oxygen with a negative charge(R-COO-). It’s the same concept with sulfer groups. Amine groups have (R-NH3+) and (R-NH2). Nitrogen has a lone pair of electrons when it’s R-NH2.
Learn to draw out peptides so you know how amino acids bind to each other. Start with the amino side. When making the bond the 1st amino acid loses the single bond oxygen in the R-COO- and attaches to the 2nd amino acid’s nitrogen (N). The 2nd amino acid’s nitrogen loses 2 of its hydrogen. Wateris the byproduct.
Post-translational process can produce other amino acids. Proteins can be covalently modified by the addition of other groups other than amino acids, this changes their function. Acetyl groups are attached to amino termini of certain proteins to resist degregation. Hydroxyl groups is added to proline residues to stabilize fibers of newly synthesized collagen. γ-carboxyglutamate is an amino acid that’s modified Vitamin K deficiency (insufficient carboxylation of gluamate in prothrombin, a clotting factor, leads to hemorrhage). Fatty acids, are added to proteins to make them more hydrophilic. Phosphorylation of proteins by hormones are reversible and changes function of protein.
On Protein structure:
Primary structure of a protein is the linear sequence of amino acids in the protein. This is unique for each protein, and comes from the sequences in DNA. The secondary structure is repeated small-scale structure. The 2 most common ones are alpha-helicies and beta-sheets. Secondary structures are usually stabilized by hydrogen bonds involving peptide backbone groups (not -R). Fibrous proteins are all secondary structures: alpha-keratin and collagen. Tertiary structures is the large-scale non-3D folding. It makes a protein go from a linear chain to a globular one. Myoglobin is nearly all alpha helical secondary structure. CD4 is nearly all beta. Both contain a hydrophobic interior. Porin is a membrane protein where the inside is hydrophilic because polar substances go through it. Proteins with multiple subunits, non-covalently associated is a quaternary structure.
(Extra stuff to know)
On post-translational modifications: proteins can be cleaved and trimmed after synthesis to make them active. They can be activated by peptide bond cleavage. Example, Inactive protein stored in pancreas. Pancreas releases the inactive enzyme to intestine and the intestine cleaves and activates the proteins. Example 2, blood clotting- Coluble fibrogen becomes insoluble fibrogen through cleavage and trimming.
On hyroxyl groups: If you’re deficient in vitamin C (leads to insufficient hydroxylation) the collagen won’t be able to maintain tissue strength.
Protein misfolding and aggregation are associated with some neurological diseases. Bovine spongiform encephalopathy (mad cow disease), and Creutzfeldt-Jakob disease are due to protein misfolding caused by agents called prions.
Prp proteins contain mostly alpha-helices. In an aggregate form, the alpha-helices have been converted into beta-strands. The misfolded proteins then form fibrous aggregates called amyloid forms.