Topic 3 Flashcards
Intramolecular interactions
Atoms interacting both within the atoms
Intermolecular interactions
Atoms interact between molecules
Covalent bonds
- hold atoms together in a molecule (intramolecular)
-formed by the sharing of electrons between atoms - strong bonds
-short length - typical C-C bond distance is 1.54A
- typical C-C bond energy is 357kJ/mol
- the most stable of bonds
- each atom type forms a characteristic number of covalent bonds with other atoms, depending on the number of free (bonding) electrons in the outer orbital
- elements like N and O also have non-bonding electron pairs or “lone pairs”
Noncovalent interactions
- weaker, readily reversible - require 1-30 kJ.mol to break
- distances between atoms is greater
- intramolecular or intermolecular
1. Hydrogen bond (weak forces)
2. Electrostatic interaction (salt bridges)
3. Van der Waals interaction
4. Hydrophobic interaction (forcing water to be more disordered in system)
Bond energy
- the amount of energy required to break a chemical bond (As well as the energy released when the bond is formed)
- can be measure/reported in kJ/mol, kcal/mol
What do covalent bonds hold together?
-hold atoms together in building blocks
- hold building blocks together in proteins and nuclei acids
Phosphodiester Bonds
- specialized covalent bond within molecules that hold phosphates together
- also hold nucleotides together in DNA/RNA strands
glycosidic bond
Joins the ribose to the base in ATP
Peptide bonds
- covalent bonds that hold amino acids together in polypeptide or protein
Disulfide bonds (disulfide bridges)
- covalent bonds between thiol groups on the side chains of the amino acid cysteine that hold different parts of the polypeptide backbone together
- stabilize the protein fold (usually most interactions that stabilize a protein fold are non-covalent)
Weak chemical interactions
- ie. non-covalent bonds
- stabilize the fold of proteins
- Hold DNA duplexes together
- induce folding of RNA
- bring macromolecules together for structures, reactions
Weak bonds:
- break and reform at room temp - are transient
- require much less energy to break than fo covalent bonds
- thermal energy at room temp = ~2.5 kJ/mol so weak bonds can be broken due to thermal motion
- are crucial for most cellular processes ie DNA replication, protein folding, protein-protein interactions
- transient interactions allow for very dynamic systems
- individually these bonds are weak, but all together can be very strong
Hydrogen Bonds
- from between a H atom covalently attached to an electronegative atom ( a hydrogen bond donor, usually O or N) and a second electronegative atom that serves as H bond acceptor
- the H-bond forms between the hydrogen atom on the donor and a lone electron pair on the acceptor
- bond energies range from ~10 - 30 kJ/mol - strongest of the weak non-covalently interactions
- the length of a H-bond is measured form the atom centres of the donor and the acceptor (~3A)
- H-bonds have directional property - won’t form if atoms aren’t oriented properly (in line with non-bonding electrons on acceptor atom)
- requiring a H bond donor and acceptor so are more specific than van der Waals bonds
- a H-bond is partially covalent bond
Hydrogen bonding in macro molecular structures
- Example can be seen in proteins within the polypeptide backbone
- H-bonds along the backbone hold the polypeptide in an helical conformation
- such interactions are essential for protein folding
- H-bonds hold bases together in duplex DNA, folded RNA
What is the key to water’s properties?
- hydrogen bonds are key to water’s properties and this role as a solvent
- water is highly polar: electrons are not shared equally between H and O in the covalent H-O bonds
- electronegative O pulls the electrons toward it, giving it a partial negative charge and giving the H’s partial positive charge
- the O has two lone pairs
What makes water different when compared to other solvents?
- has a very high melting point, boiling point and heat of vaporization compared to other solvents
- due to the hydrogen-bonding tendency which hold the molecules together requiring significant energy input to separate them
What does each water molecule have in ice?
The potential to H-bond to 4 other water molecules
- one for each hydrogen, two for each oxygen (one for each lone pair) to create a crystal lattice
Is water a solvent?
Yes
- is highly polar, thus an excellent solvent for ionic and nonionic-but-polar compounds
- water hydrates ions by electrostatic interactions
Dipole interactions
its partially positivity-charges Hs interact with negatively-charged ions, its partially negatively-charges O’s interact with positively-charged ions
The ability of water to hydrate ions is ______ than tendency to opposite ions to attract one another
Greater
Dielectric constant, D
- the ability of a solvent to interact with a solute and decrease the electrostatic interactions between ions is a measure of its dielectric constant, D
- a measure is the ability of a solvent to surround ions in dipole interactions, diminishing their attraction to another
- the greater is is, then lower that force between two charges in that particular solvent
How can water solubilize polar compounds?
By forming H-bonds with these solutes
What does water form around ions, proteins, and other macromolecules?
Hydration spheres
Hydrophilic
Love water
Why does water have one of the highest dielectric constants of any pure liquid?
Due to its polar nature
How do D constants indicate the reduction in attraction?
- indicate the reduction in attraction between two oppositely-charged ions in a given solvent relative to heir attraction in vacuum
Electrostatic interactions
- transient electrostatic interactions between opposite charges
- also called an ionic bond or a salt bridge
- electrostatic interactions between charged amino acid side chains contribute to stabilizing a protein structure
- specific interaction -> amino acid sequence drives protein folding
What does the attraction between two charged species depend on?
The nature (ie charge) of interacting species, q1 and q2, and the distance, r, between them
Coulomb’s Law
The energy of an electrostatic interaction between two point charges is directly proportional to the magnitudes of each charge and inversely proportional to the distance between the charges
The strong the energy of the interaction is when
The larger the (opposite charges) and the smaller the distance
What is also effected by the solvent, hence the D constant
Energy
Van der Waals
- include all intermolecular forces that act between electrically neutral molecules
- create interactions that are constantly forming and breaking at physiological temperatures in less their cumulative number imparts stability by collective action (ie in the case of hydrogen bonding and base stacking to hold the DNA duplex together)
- exist because the electron cloud of every atom fluctuates, yielding a transient electric dipole
Transient dipole
- the dipoles of one atom can influence the electron distribution in another, inducing a transient dipole in that atom
Dipole interactions - permanent dipoles
- polar molecules interact weakly with negative poles attracted to positive poles
- H-bonds are a specialized type of dipole-dipole interaction
Dipole-induced dipole interactions
A permanent dipole (or a charged group) can induce a dipole in a neighbouring group that’s neutral by distorting its electron distribution
London dispersion forces
- nonpolar groups can polarize electrons in a neighbouring group due to rapid fluctuation of their electron -> attraction
- extremely weak, transient, fall off rapidly with distance
What are van der Waals forces?
- the same of dipole-dipole attraction and repulsion
Van der Waals contact distance
- the attraction between the two atoms increase as r between the atoms decreases until they each optimal distance (van der Waals contact distance)
- at this distance the attractive forces are highest
- if atoms get closer than this optimal distance they will repel each other due to overlap between their electron clouds
-rw = 0.5r - r is longer than ac valent bond radius where orbitals overlap in a covalent bond radius
- each atoms has one that reflects the volume the atom -neutron, protons, electrons- occupies
Hydrophobic interactions
- not a true force but a consequence of the energy needed to insert a nonpolar molecule unto water
- water naturally forms a hydrogen bond network
- these bonds must be broken in order to insert nonpolar molecules
- nonpolar molecules form can der Waals interactions among themselves and do not H-bond with water - difficult to solvate/solubilize
- dissolving such nonpolar solutes requires organization of water molecules which surround them, resulting in cage-like structures known as clathrates
- this ordered arrangement of water molecules around each hydrophobic molecule is thermodynamically unfavourable - when the hydrophobic molecules associate with each other, this liberates part of the hydration shell, increasing the entropy (disorder) of the system, which is thermodynamically favorable
clathrates
Structure in which water molecules under certain conditions bond to form complex networks of molecules forming cage-like structures that encapsulate a guest molecule, which is a gas
Hydrophobic effect
- the attraction between non-polar molecules in an aqueous environment
- not so much an attraction but a default to a lower energy state
- draws non-polar molecules together in aqueous solution
- nonpolar molecules spontaneously aggregate in an aqueous solution, reducing the number of H2O molecules involved in ordered clathrate structures, thereby, increasing the disorder or entropy of the system -> more favourable situation energetically
Protein folding
- driven in part by the hydrophobic effect
- in unfolded protein nonpolar or hydrophobic regions are exposed to water, which much organize inter self around them
- in folded protein hydrophobic regions often associate with each other and are thus shielded from the aqueous solvent
- less order is required for the water molecules to solubilize the protein, which is more favourable energetically
- thus, protein folding occurs because a orderly folded protein is more thermodynamically stable than an unfolded protein in aqueous solution
