Biochemistry Midterm 1 Flashcards
What is the definition of a hydrogen bond?
dipole-dipole/charge-dipole interactions that arise between covalently bonded H atom and a lone pair of electrons on an electronegative atom
average number of bonds in liquid water vs ice
3.4 vs 4
why do micelles form?
by clustering non-polar tails together as a result of the hydrophobic effect, entropy is increased compared to if the hydrophobic regions were all separately interacting with water (minimized to ordered shell around micelle)
define van der waals interactions
weak interactions between atoms at the maximum between attraction (due to polarity and dipole) and repulsion (due to atom size)
van der waals qualities
between any 2 atoms, determine steric compatibility, individually easily broken, strong in numbers, stabilize macromolecules
colligative vs non colligative properties
colligative properties are only dependent on solute concentration and not on solute nature: boiling point, melting point and osmolarity
non colligative properties are dependent on solute nature: viscosity, surface tension, taste, color
adhesion vs cohesion
adhesion - binding between unlike molecules
cohesion - binding between like molecules (water surface tension)
water dissociation constant and dissociation at 25°
1.0 x 10^-14 M^2, at 25° 2 in every 10^9 molecules is dissociated
proton hopping definition
protons moving between hydrogen bonded water molecules causing net movement of a photon over long distance quickly`
ionic product of water
Kw = [H+][OH-]
A strong acid Ka and pKa
high Ka and low pKa
buffering capacity is greatest when
pH = pKa which is also when the acid is 50/50 concentration
buffer systems in vivo
phosphate, bicarbonate, histidine
peptide bonds are formed
through condensation reaction between carboxyl group and amino group of two amino acids
2 cysteine amino acids that form a disulfide bond is
cystine
histidine properties
not actively positively charged R group called imidazole but often involved in reactions as a proton donor. Imidazole is cyclic
uncommon amino acid that can be incorporated by ribosomes
selenocysteine
how do modified amino acids arise?
post-translational modifications, permanent or transient
high pH vs. low pH charged of amino acids
low pH amino acids will be positively charged (H is still attached to carboxyl group). High pH amino acids will be negatively charged (H is donated and NH2 is formed)
zwitterion
net 0 charge of amino acid, both negative and positive charges on amino acid. This occurs at pI for amino acid
how to calculate pI
without ionizable R group: average of pka1 and pka 2
with ionizable R group: average of pka closest to pkaR and pkaR
protein structures are stabilized by
non covalent forces: H bonds, ionic bonds, van der waals interactions, hydrophobic effect
why are disordered regions important
for interactions with other proteins - gives flexibility and ability for conformational change
common protein structural patterns
alpha helices, beta turns, beta sheets
why doesn’t the peptide bond rotate?
it is a resonance structure between O=C-N
phi vs. psi angle around alpha carbon
phi is amide nitrogen bond side, psi is on carbonyl carbon side
peptides are read in what direction:
amino (left) to carboxyl (right)
how are alpha helices and beta sheets stabilized?
H bonds. Alpha helices H bond between nearby residues amino acid backbones. Beta sheets stabilize parallel or antiparallel between adjacent segments (may or may not be nearby)
