Ionic Bonds: Polar Charged amino acids Covalent Bonds: Same amino acid Hydrogen Bonds: Formed between polar (uncharged) amino acids Hydrophobic Interactions: Formed by nonpolar amino acids For each of the following, determine which types of bonds are involved in creating The bonds or structures in A. Covalent only B. Non-covalent only C. Both 5. Primary Structure A 6. Secondary Structure B 7. Tertiary Structure C 8. Di-sulfide bonds A. 9. Protein-protein interactions(typically) B Low affinity= High Kd High affinity= Low Kd Alpha Helix’s are formed by hyrdrogen bonds that occur every 4th amino acid, so the chain must be more than four to be able to have a structure. Two amino acids with the same charge, (positive-positive or negative-negative) Will repel each other and thus can not be right next to each other in a sequence or will disrupt the structure. Heat can break chemical bonds so species that thrive at high temperatures should have more disulfide bonds because they are not as sensitive to heat as others, non-covalent bonds are weaker than covelent bonds so they are easier to break so covalent bonds (like disulfide bonds) are better suited when an organism needs strong bonds When you heat an egg, it causes it to harder because of denaturing (unfolding) of the proteins around it, in doing so the hydrophobic amino acids are exposed and to avoid coming into contact with water, the protein condenses and hardens. Detergent is able to disolve the egg because it breaks the noncovalent bonds and the reducing agent breaks the disulfide bonds which can’t be broken by heat alone. How a protein will bind is determined by the number of bonds and the architecture of bonds that form between the ligand and the binding pocket of the protein.Holds ligand and protein together: Non-covalent bonds (hydrophobic interactions), vaander wals, and ionic bonds. Proteins and ligands come together through random movement throughout the cell ● Backbone Model ○ Shows: polypeptide chain without the R groups ○ Pro: Shows general shape ○ Con: Does not show secondary structure ● Ribbon Model ○ Pros: shows secondary structure of alpha and beta ○ Cons: does not show R groups ● Wire frame ○ Shows covalent bonds as sticks o Swizzle sticks show the bonds occurring between the R-groups ○ Pros: shows R groups and their interactions ○ Cons: hard to see secondary structure and overall backbone. ● Space full ○ Shows: each individual atom. ○ Pros: shows the radius and the relative size and surface shape of protein ○ Cons: you can’t tell the backbone structure and you can’t see past the surface. ● Nonpolar covalent bonds= hydrophobic ○ C-C ○ C-H ● Polar covalent bonds= hydrophilic ○ O-H ○ C-O ○ C-N ○ N-H Primary Structure Amino acid sequence (AA are linked by covalent peptide bonds) Secondary Structure: alpha helix • No R-group interactions here yet. • The main interactions here are noncovalent hydrogen bonds between atoms in the backbone of the amino acid • Helical structures formed between carbonyl group of one amino acid and the amino group of another amino acid 4 positions away on polypeptide • R groups stick out from helix • Because the H-bonds are formed by backbones of amino acids, the helices and sheets areubiquitous in protein structure. This is because it doesn’t matter what the R-groups or amino acids are individually; the bonds being formed are hydrogen bonds that are dependent on the backbones, not R-groups. (There is some role for R-groups, but this is not that important for our purposes). Secondary Structure: beta sheet • Hydrogen bonding between backbones of amino acids • Formed by hydrogen bonds between adjacent amino acids on polypeptide • Can run parallel or antiparallel to each other • R groups stick out above and below sheet Tertiary Structure •R-group interactions are very important here •The 3-D globular structure of a polypeptide due to folding as a result of R-group interactions. • It’s a single polypeptide here. • These interactions can include: Covalent bonds: Disulfide bridges (bonds) that can be formed between two cysteine amino acids. Noncovalent bonds: Include H-bonds, hydrophobic interactions, Van Der Waals, and ionic bonds. • In a cell, covalent bonds are much stronger than noncovalent bonds (with few exceptions) Quaternary Structure • Proteins have this structure when they are made up of more than one polypeptide. • You can find the same types of bonds here as you would in tertiary structure, but covalent bonds are pretty rare compared to noncovalent bonds. • Not all proteins have quaternary structure. • An example of a protein with quaternary structure is hemoglobin. It’s made up of four polypeptide chains, which are two alpha subunits and two beta subunits. (We call each polypeptide in a protein made up of more than one polypeptide a subunit). Proteins usually use noncovalent bonds because they are more flexible. Disulfide bonds are used when the struture needs to be stabalized. Covalent bonds Peptide bond: primary structure. Disulfide bond: tertiary and quaternary structure. ● Anything that disrupts noncovalent bonds can affect protein folding. Heat, light, pH, salt concentration, and detergent can all do this at the right amounts.○ Heat: Most proteins have their ideal temperature at which they work best, which is usually the body temperature of the organism they are in, if that temperature drops too low or raises too high, it would disrupt protein folding ○ Lights at the higher energy wavelengths could definitely disrupt protein folding. (Which is whylasers and UV rays damage our eyes). ○ Acidity and basicity can definitely play a role. Salt can too. ○ Detergents are able to disrupt noncovalent interactions very well. Which is why they’re good for cleaning. ○ Every protein is different and prefers different environmental conditions. Misfolded PrPSC will cause other PrPC to misfold. It will not cause other proteins (non PrP proteins) to misfold Protein-Ligand Interactions • Primarily dependent on non-covalent bonds (hydrogen/ionic/hydrophobic/V.D.W). • Mostly reversible. • The right R-groups have to be arrayed at the right angles and places at the binding pocket. • Interactions don’t always involve a binding “pocket”. There could be a flat interface. Kd= [P][L]/[C], where P is unbound protein, L