BCHM463 Midterm 1

what are the four classes of macromolecules

proteins, nucleic acids, carbs, lipids

what are the three domains of life

bacteria, archaea, eukarya

what is the monomer of a protein

amino acid

what is the bond of a protein

peptide / amide

what are the key groups on an amino acid

NH3, COOH, R

what is the monomer of a nucleic acid

nucleotide

what is the monmer of a carbohydrate

monosaccharide

which macromolecule doesn’t form polymers

lipids

residue

individual aa within polypeptide

is a peptide bond strong/weak and covalent/noncovalent

strong, covalent

where does the peptide bond go

between C of COOH and N of NH3

what reaction joins amino acids

condensation

what reaction separates amino acids

hydrolysis

what is the bond of a carbohydrate

glycosidic

what is an alpha vs beta glycosidic bond

alpha - C6 and C1 point in diff directions

beta - C6 and C1 point in same direction

what is a nucleotide made of

sugar ribose, phosphate group, nitrogenous base

what is the bond of a nucleic acid

phosphodiester

phospholipids with two tails form

bilayer

phospholipids with one tail form

micelles

what is the bond of fats

ester

first law of thermo

E conservation

second law of thermo

entropy increasing

what is the ultimate E source

sun

autotroph

makes own food from inorganic substances (light or chem rxns)

heterotroph

consumes other organisms for food

if deltaG=0

system at equilibrium, impossible for living things

delta H neg

delta S pos

delta G always negative

delta H neg

delta S neg

delta G negative at low temps

delta H pos

delta S pos

delta G negative at high temps

delta H pos

delta S neg

delta G always positive

when you add reactions, you ADD/MULTIPLE delta G values

add

how can you make a nonspon reaction spon

coupling, increase [R], decrease [P]

what is the outcome when you take ln(fraction)

negative term

what do enzymes do

speed reaction by lowering Ea, don’t affect spontaneity

how to speed up reaction

higher temp, higher [R], lower [P], couple to fast one, lower Ea

what reaction is typically used for coupling

ATP hydrolysis

what is the monomeric unit of a lipid

fatty acid

intermolecular interactions

between molecules

intramolecular interactions

within molecule

where does the bond between nucleotides form

phosphate group and 3C OH

covalent bond

share electrons

are covalent or noncovalent bonds stronger

covalent

rank bonds from strongest to weakest

covalent, ionic, hydrogen, dipole, LDF

what are the types of van der Waals forces in order of strength

hydrogen, dipole, LDF

what EN molecules are involved in hydrogen bonding

FONS

are covalent bonds inter or intramolecular

intra

are van der Waals forces inter or intramolecular

inter

what must be true of hydrogen to hydrogen bond

connected to EN

hydrogen bond donor

EN element w/ H to donate

hydrogen bond acceptor

EN element w/ lone pair that it can share

why is ice less dense than water

H bonds become strong and rigid

rank the following from most to least H bonds: gas, liquid, solid

solid, liquid, gas

what are the two conformations of hydrogen bonds? which is stronger?

linear vs nonlinear, linear

what is water a good solvent for?

charged and polar substances

what is water a poor solvent for?

nonpolar substance

is the hydrophobic effect driven by entropy or enthalpy

entropy

define clathrate in the context of oil and water

host (water) surrounds and contains guest (oil)

explain hydrophobic effect

oil aggregates due to clathrate

entropy of oil decreases

entropy of water increases because decreased SA of oil allows for more DOF

what drives formation of micelles and bilayers

hydrophobic effect

ionization of water chemical equation

H2O → H+ + OH-

what is the concentration of water

55.5 M

Kw = 

K[H2O] = [H+][OH-] = 10^-14

ionization of water rate constant

Kw = [H+][OH-]

[H+] > 10-7

acid

[H+] < 10-7

base

[H+]=[OH-]=?

10^-7

define buffer

solution that resists changes in pH upon addition of acid or base

acid dissociation chemical equation

HA + H2O → H3O+ + A-

acid dissociation constant

Ka = [H3O+][A-]/[HA]

henderson hasselbalch

pH = pKa + log[A-]/[HA]

if pH < pKa

protonated

if pH > pKa

deprotonated

is a low or high pKa more acidic

low

is a low or high Ka more acidic

high

what is the typical charge of a protein at low pH

positive

what is the typical charge of a protein at high pH

negative

define pI

point at which overall charge of protein = 0

what is true of the ½ equivalence point

pH = pKa

define equivalence point

mol added titrant = mol initial analyte

weak vs strong acid

strong fully dissociates

what is the buffering range

pKa ± 1

what is a buffer made of

WA and its salt or WB and its salt

what is the ratio of [A-]/[HA] for a buffer

0.1 to 10

completely deprotonated functional group

pH and pKa at least 2 apart

partially deprotonated functional group

pH and pKa less than 2 apart

charged proteins are soluble/insoluble

soluble

neutral proteins are soluble/insoluble

insoluble

when is buffering capacity greatest

pH = pKa

what is the only achiral aa

glycine

what does R/S correspond to D/L

*exception

all S are L

all R are D

cysteine (R & L)

is D or L more stable or common

L

what wavelength do proteins absorb at

280 nm

which amino acids are phosphorylated

serine and threonine

what is the function of proline in the alpha helix

kinks reduce flexibility

which amino acids forms disulfide bonds

cysteine

what is special about histidine

only charged aa that is neutral at physiologic pH

are all amino acids polar or nonpolar

polar

what is the molecular geometry of the alpha carbon in an aa

tetrahedral

what is the order of priority in labelling substituents for R vs S

S, O, N, C, H

what do you need to double check before confirming R or S

4 group pointing back