10- protein structure II Flashcards
what are tertiary structures, what are they the result of, and what do they contain?
- Overall three dimensional shape of a protein
- Result of interactions between non-adjacent regions
- Contains regions of order (secondary structure)
- Contains less ordered regions (Loops)
what are four examples of why tertiary structures are formed?
- Amino acid side chains or amide bonds on the backbone
- Two secondary structures (two helixes) are attracted to each other and fold back on themselves
- beta sheets coming together
- two loops of protein → interactions between amino acids that are very far from each other
what are the two different attractive forces that cause tertiary structures
- Attractions between secondary structures cause the secondary structures to fold back on themselves
- Mostly non-bonding interactions (hydrogen bonds, dipole, van der waals)
- Occasional covalent bond (common for proteins formed for more than one strand)
what is the strongest attractive force in tertiary structures?
covalent bond (most common type is disulphide bridge - the cysteine gets oxydized and end up forming a S-S bond)
explain ionic bonding in terms of being an attractive force in tertiary structures
- negatively charged on one strand gets attracted to positive charge on another
- electrostatic interactions, ionic bond, salt bridge
explain hydrogen bonding in terms of being a non-bonding interaction in tertiary structures
- hydrogen bond is typically formed by two groups capable of h-bond
- donor is the one that has the H on it, acceptor has lone pair that is able to interact with the H
- specialized dipole
- can occur between neutral or charged groups
explain van der waals forces in terms of being a non-polar interaction in tertiary structures
- weakest type
- involves interactions between non-polar side chains (alkyl and aromatic groups)
- extremely important for the 3D structure
- serve to amplify the other bonds
describe the protein shape in terms of polarity and non-polarity
- proteins tend to fold up into shapes that put the non-polar amino acids on the inside of the protein
- on the outside of the protein we find the polar chains → gives 3D conformation because they are able to interact with the water on the outside, stabilizing the structure
- non-polar groups do not interact with water, this excludes water from the inside of the protein and holds it together very well
- polar side chains is what makes some proteins able to dissolve in water
why is it important for the inside of a protein to be non-polar?
- helps to increase the strength of polar interactions that may occur within the protein
- if you put polar bonds inside the protein, they have a stronger electrostatic attraction than if they were outside (because there is no water for the electrostatic groups to interact with)
describe the difference in electrostatic attraction between the inside and outside of a protein
- on the outside of a protein, the electrostatic attraction is weaker due to the possible interactions the molecules can have with the water
- on the inside of a protein, the electrostatic attraction is stronger due to the lack of water molecules (non-polar environment)
what happens when two or more proteins bind together?
quaternary structures are formed (sub-modules can be same or different)
what are five reasons protein-protein interactions are very strong?
- Lots of surface contact area
- Lots of chemical interactions
- Exclusion of water from space between (called water exclusion, proteins only interact with each other and not with the water)
- Proteins stick together well
- Difficult to separate some protein (consequence for drug design)
explain the overall structure a protein
- Most of the molecule is a scaffold
- Only a small part is normally “functional”
- the scaffold is there to give the molecule a proper shape which allows the functional part to carry out its reaction
