bioch 200 lec 1
what are the 4 major classes of biomolecules
amino acids
carbs
nucleotides
lipids
what are the corresponding colours to these atoms? oxygen, carbon, hydrogen, nitrogen, sulphur
o - red, c -grey/black, H- white, N- blue, S- yellow
"directionality" means
all covalent bonds are in the same oreintation, there are two distinct ends that are not the same, this is a result of intrinsic asymmetry.
given the three building blocks name their polymer and bond type: amino acids, nucleotides, monosaccharides
amino acids--> protein (peptide bonds)
nucleotides--> nucleic acids (phosphodiester bond)
monosaccharides--> polysaccharides (glycosidic bond)
what is the universal solvent
water
why is water the universal solvent
1. water is polar (uneven charge distribution) where the oxygen is partially negative and the hydrogens are partially positive so each molecules can act like a tiny magnet and pull/dissolve other ions/molecules apart.
2. it can strongly interact with itself and form up to 4 hydrogen bonds, this allows it to make stable hydration shells around ions an dpolar molcules
3.it has a high dielectric constant (weakens the attraction between oppositley charged particles like nacl)
4. dissolves ionic compounds (Na+, Cl-) and polar covalent molecules (sugars, amino acids)
what cant water dissolve
non polar molecules (fats/oils)---> hydrophobic
what is a hydrogen bond
weak, non covalnet bonds, when a hydrogen (slightly positive) is shared between two electronegative atoms
who is the donor and acceptor in a hydrogen bond
the donor in a h bond is the electronegative atom covalently attached to the hyydrogen, the acceptor is the second electrogengative atom with an appropriate hybridized lone pair
what is a permanent dipole
one side of the moelcule is slightly positive th eother slighlty negative-- permanent seperation of charge
do bond dipoles cancel
no like in water the two polar oh bonds they add up and create one overall net dipole
what would be longer a covalent bond or hydrogen bond
a hydrogen bond would be longer and weaker where the covalent bond would be shorter and stronger
what is lattice structure
when water freezes the moelcules arrange themselves in a regular open structure called. lattice because of h bonds
how does a water molecules make 4 h bonds
2 through its hydrogens (donors), 2 through its lone pairs (on oxygen), forming a tetrahedral structure
why does ice float in water
hydrogen bonds locks the water molecules in place at specific angles so they cant pack tightly, they form rings with empty spaces. the lattice takes up more space--> less dense--> floats
non covalent interactions include electrostatic forces and hydrophobic effects. what are the 3 types of electrostatic forces
ionic interactions (- and +), H bonds, Vander walls
van der waals includes dipole-dipole interactions and london dispersion forces. explain these two.
dipole- dipole: attraction between two polar molecules--> permanent dipole (weaker than h bonds bc h is so small can get very close/ shorter distance also attached usually to a very electronegative atom)
london dispersion: between non polar molecules, weak temporary attraction between all molecules. (weaker than dipole dipole)
hydrogen bond, ionic, vander walls, covalent bonds. rank from strongest to weakest.
covalent>> ionic> hydrogen bond> Van der Waals interaction
how does electronegativty play apart in dipoles. F> O> Cl> N> Br> I> S> C> H
the bigger the differance-> creates a permanent dipole.
is CH3 typically a h bond donor
no it is usally a h bond acceptor because it has a lone pair in an appropriate hybrizied obrital. atoms that are h bond donor will have a h atom bonded to a strongly electronegative atom.
when does water solubility inc
with inc numbers of potential hydrogen bonding groups
how to count how many h bonds a molecule can form with water
count OH--> can donat 33
alone oxygen--> 2
what is the hydrophobic effect
the tendency of non polar molecules to cluster together in water because it helps the water stay happy (more disordered-move freely).
what actually happens when non polar molecules enter water
the water molecules have to form ordered cages around the non polar surface which means more order, lower entropy, less randomness, more energy-->unfavourable
why do the non polar compounds clump (coalesce) in water
so there is less surface area exposed to the water which increases the entropy of the water--> less order--> water happy
are amphiphilic and amphipathic synonymous terms
yes used to describe structures that have both non polar and polar regions--> experience hydrophillic interactions and the hydrophobic effect.
amphilic vs amphipathic
philic: used more for chemical behaviour (solubility) means can love and fear water at the same time
pathic: used more for structure--> has structural regions with both polar and non polar character
give me two points to summarize the hydrophobic effect
1. non polar molecules interrupt the hydrogen bonding pattern of water
2. water molecules that surround a less polar molcule are more restricted in theri interactions with other water molecules
xxxxx nuffin abut hydrophobic bonds