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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