Covalent and Noncovalent Interactions Flashcards
Learning Objectives - Review the electronic structure of an atom - Describe the different types of noncovalent interactions - Understand the consequences of noncovalent interactions in the behavior of biomolecules
What are covalent bonds?
- Atoms share a single pair of electrons
- Multiple covalent bonds occur when atoms share multiple pairs of electrons (double and triple bonds)
List the 4 major types of noncovalent bonds.
- Ionic bonds
- Hydrogen bonds
- van der Waals interactions
- Hydrophobic effect
What noncovalent interactions are the primary contributors to protein complex formation?
- Hydrogen bonding
- Electrostatics
- van der Waals interactions
- Hydrophobic effect
What are electrostatic interactions?
- Interactions between electrically charged groups must be balanced to stably bring two protein surface together
- Example: positive side chain of one protein interacts with the negative side chain of another protein
Describe factors that impact the strength of interactions between opposite charges?
- An increase in the magnitude of charges increases the strength of the interaction
- An increase in the distance between 2 charges weakens the interactions
What is hydrogen bonding?
- A hydrogen atom is partially shared between two electronegative atoms
- Example: a hydrogen atom is bonded to an oxygen atom and a nitrogen atom (could also be fluorine)
- Partial charges involved (think of dipoles)
- Positive partial charge of H is attracted to partial negative of atoms like N, O, and F
What is the hydrogen donor in a hydrogen bond?
- The electronegative atoms that a hydrogen is chemically bounded to
- Think of the oxygen atom in a water molecule
What is the hydrogen acceptor in a hydrogen bond?
- The electronegative atom that the hydrogen points towards
- Has a lone pair of electrons
How does a partial charge compare to the charge of a proton or electron?
Weaker!
What are van der Waals interactions?
- The basic attraction between atoms as they approach or are in close proximity with each other
- Forces are weak at long distances and stronger at shorter distances
- Weakest forces
How do van der Waals interactions react at VERY short distances?
- A repulsion force keeps the atoms from occupying the same space
- Electron clouds overlap and push atoms further apart
- There is a point (VDW radius) where the force is optimal!
What is the source of van der Waals forces?
- The electron cloud on one side of an atom can be more positively charged than another side
- Asymmetric charge distribution creates a dipole moment and creates an attraction between atoms
Describe the primary driving force in protein folding.
Hydrophobic effect
- The hydrophobic surfaces of the protein are buried into the protein’s core and hidden from water molecules
- Water molecules would be forced arrange themselves in a very specific manner when lining a hydrophobic surface, limiting their ability to move and rotate and bond with one another
What does the hydrophobic effect explains in terms of nonpolar molecules?
Why nonpolar molecules or the nonpolar sections of molecules aggregate
What makes nonpolar molecules hydrophobic?
- No charged groups
- No dipole moment
- Do not become hydrated
- Not soluble in water
Why do cages of water molecules form around nonpolar substances?
- Water wants to maintain a network of hydrogen bonding
- Attempt to minimize contact with the nonpolar substance
- Water molecules around the cage are free to remain less ordered (more energetically favorable)
How do weak interactions cause proteins to bind together so tightly?
As structurally complementary molecules collide, they form several noncovalent interaction at a close range
