Lecture 1 - Chemical Bonds and Macromolecules Flashcards
What elements make up most of the mass of the human body and why are they significant?
CHON - lightest elements capable of forming one, two, three, or four covalent bonds (based on number of valence electrons)
What are the hydrogen bond donors?
A hydrogen atom which is bonded to an N, O, or F. They are highly electronegative and give a positive charge to H and a negative charge to the donor
What are noncovalent bonds? Are they readily reversible? What are the main types?
Bonds which make a difference in aggregate, 1/10-1/25 as strong as covalent bonds. They are readily reversible and do not involve sharing electrons.
- Ionic
- Hydrogen - NOF
- van der Waals
How is the energy of an ionic interaction calculated?
E= (kq1q2) / (Dr)
Where k is Coulomb’s proportionality constant, converting to kcal/mol
D = dielectric constant
What influences the dielectric constant?
D is proportional to ability of the medium to loosen electrovalent bonds of reversed molecules.
This is very high in water ~80, because the lattice can be hydrated stabilizing the dissolved ion pair since water is a dipole.
Nonpolar character -> less dipole moment -> lower dielectric constant.
Why are cell membranes impermeable to ions?
Dielectric constant of lipid bilayer is ~3 which is very low, it is quite nonpolar. Energy barrier required for charged species to exist in bilayer is too high to permit the action
What is the hydrogen bond acceptor?
Partially negatively charged atoms with high electronegativity in an uncharged but polar moleccule
How does water affect hydrogen bonding between other molecules?
Water can disrupt other hydrogen bonds by competing to form them
What causes van der Waals attraction / repulsion and what is van der Waals contact?
Attraction - A transient dipole around one nucleus induces a transient opposite dipole in the nearby atom, attracting them
Repulsion - nuclei approach too close and start to repel, overlying electron clouds repel
van der Waals contact - when net attraction is maximal
What defines molecular volume?
the distance for van der Waals contact with the molecule - repulsion starts to occur when electron clouds repel.
How can a spontaneous reaction be defined? Formula?
Any reaction with a negative gibbs free energy, favored if the final state of the molecule has lost the capacity to perform work and gained freedom to occupy multiple states
(negative entropy and positive entropy change)
State function: delta G = delta H - T * delta S
Why does the hydrophobic effect occur?
Spontaneous clustering of nonpolar group limits their exposure to aqueous solvent, decreasing the ordering of water molecules and restoring some solvent H-bonds that were lost. This limits the negative impact on water entropy
What is an amido group?
R-Carbonyl-amino
What is a sulfhydryl / thiol group?
Hydroxyl group which is made from sulfur rather than oxygen
R-S-H
What is an acyl group?
An R-Carbonyl-R
Very general term, could include amido, acetyl, carboxylic acid, ketone, aldehyde
What is an acetyl group?
any R-Carbonyl-Methyl
How is an anhydride formed?
Two carboxylic acids react, and link together by an oxygen, they precipitate a water
What is an example of a mixed anhydride?
Carboxylic acid reacts with phosphoric acid, makes an acyl phosphate
Why are anhydrides and thioesters considered high energy?
The products released by cleavage of such bonds are stabilized through resonance
Why does hydrolysis of the thioester bond yield more energy than cleavage of oxygen ester?
Only oxygen esters have a significant resonance contributor which stabilizes them. Sulfurs in thioesters don’t form double bonds with carbons will since they have such a size difference
What are isomers?
Compounds with the same molecular formula but different structures - they have unique properties
What is a structural isomer? Example?
Molecules that differ in the order the atoms are arranged. Glucose / Fructose. Glucose is an aldo-sugar, fructose is a keto-sugar
What does an isomerase do?
Interconverts aldehydes + ketones
What does a mutase do?
Moves a functional group to a different position in a molecule
