Exam 1: Ch 2 Flashcards
water constitutes what % by weight of cells
70-80%
amphipathic
molecules with hydrophilic and hydrophobic regions
covalent bond
strongest bond
when 2 atoms share electrons
types on noncovalent interaction
ionic bonds
hydrogen bonds
van der waals forces
hydrophobic effect
most abundant elements in biological molecules
carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus
chirality
asymmetric carbon with 4 different groups around it
makes stereoisomers
biochemistry stereoisomers
different arrangement = different molecule
different biological functions b/c arrangement differences cause them to interact with the body differently
dipole moment
measure of the strength or extent of charge separation
molecular complementarity
lock and key fit of shapes, charges, or other physical properties of molecules
3 main types of biological macromolecules
protein
nucleic acids
polysacharides
phosphodiester bonds
link nucleotides together
purines
adenine
guanine
pyrimidines
cytosine
thymine
uracil
nucleoside
combination of a base/sugar without a phosphate
carbohydrate
covalently bonded combinations of carbon and water in a one to one ratio
glycogen
storage of carbohydrate in animal cells
very long highly branched polymer of glucose
10% of liver
what is starch, and its 2 forms
storage form of carbohydrate in plants
amylose - unbranched
amylopectin - branched
cullulose
major consituent of plant cell walls
peptidoglycan
polysaccharide chain cross linked by peptide bridges
rigidity and cell shape
glycosaminoglycans
major polysaccharide components of ECM
enthalpy and entropy
enthalpy: bond energy
entropy: measure of randomness or disorder
carbon fixation
ATP is hydrolyzed to provide energy for conversion of CO2 to hexoses
these sugars are food sources for the plants
oxidation of glucose rxn
C6H12O6 + 6 O2 –> 6CO2 + 6H2O
-686 kcal/mol
purpose of coenzymes NAD+ and FAD
electron carrying
electronegativity
how well an atom can attract an electron
van der waals interactions
nonspecific interactions resulting from the momentary random fluctuations in the distribution of the elections of any atom
strength of interaction decreases rapidly with distance
acetylation
most common chemical modification of a protein 80%
play an important role in controlling the life span of proteins
nonacetylated proteins are rapidly degraded
fatty acid
hydrocarbon chain attached to a carboxyl group
important energy source
esterified with phosphates to form phospholipids
microscopic reversibility
ability of a reaction to go backwards
slow at first, but speeds up as concentration of product increases
chemical equilibrium
rates of forward and reverse reactions are equal so concentrations of reactants and products stop changing
equilibrium constant
Keq is a fixed value that measures the extent to which a rxn occurs by the time it reaches equilibrium
standard biological conditions
1atm, 25 celcius
steady state
system of linked reactions where production and consumption of products is steady
helps prevent accumulation of potentially toxic intermediates
dissociation constant
the reciprocal of the equilibrium constant that describes binding reactions
when half the protein molecules are bound, the concentration of protein is equal to the Kd
what do high and low Kds mean
lower Kd means tighter binding: less protein is needed to bind half of its ligand
higher Kd is less tight binding: more protein is needed to bind half of its ligand
what is Kd measured in
molarity moles/L
pH
concentration of hydrogen ions in solution
negative log of hydrogen ion concentration
pure H2O is 7
1 unit difference in pH represents how many fold difference in proton concentration?
tenfold
zwitterion
a molecule that has an equal number of positive and negative charge
they are neutral
amino acids are zwitterions (amino end and carboxyl end cancel each other out)
Ka
equilibrium constant for acid dissociation HA –> H+ + A-
Ka = [H+][A-] / [HA]
high Ka = low pKa (stronger acid)
Henderson Hasselbach
pKa of any acid is equal to the pH when half the molecules are dissociated and half are not
pH = pKa + log [A-] / [HA]
because when [A-] = [HA], log [A-] / [HA] is 0 and then pH = pKa
buffer
a reservoir of weak acids and bases that maintain a stable pH by soaking up excess H+ or OH-
must be within 1 pH unit
buffering capacity
ability of a buffer to minimize changes in pH
depends on the concentration of the buffer and the relationship between its pKa and pH
if pH > pKa
A- dominates
disassociation occurs
if pH < pKa
HA dominates
no disassociation occurs
kinetic energy
energy of movement
potential energy
stored energy
ex. covalent bonds
thermal energy
form of kinetic energy: the energy of the motion of molecules
to perform work flows from higher temp to lower temp
radient energy
kinetic energy of photons
converted to thermal energy when light is absorbed and moves molecules
change electronic structure of a molecule by moving an electron into a higher energy orbital (photosynthesis)
mechanical energy
form of kinetic energy
can result from the conversion of chemical energy
electric energy
form of kinetic energy
energy of moving electrons
chemical potential energy
energy stored in bonds connecting atoms in molecules
harnessed to do work
ex. ATP
concentration gradient and electric potential
ex. ions of different sides of the membrane form [ ] gradient
energy of charge separation occurs on diff sides of membrane too
unit of energy
joule or calorie
1 joule = 0.239 calorie
calorie
energy required to raise temp of 1 gram of water by 1 celcius
exergonic
energy releasing rxn
products contain less energy than reactants
endergonic
energy absorbing rxn
products contain more energy than reactants
gibbs free energy
all systems change to minimize free energy
describes whether or not the products contain more or less energy than reactants
enthalpy is bond energy
entropy is a measure of disorder or randomness
units of gibbs free energy
kilocalorie/mol
delta g from standard free energy (delta g not prime)
delta g = standard delta g + RTlnKeq
delta g not prime from Keq
delta g not prime = -2.3RTlogKeq
transition state
time when system in rxn is at its highest energy level
activation energy is E needed to overcome t.s
reduction potential (E) vs. oxidation potential
reduction potential: ease an atom or molecule gains an electron
oxidation potential: ease an atom or molecule loses an electron
both measured in volts
in redox rxns electrons move spontaneously toward atoms or molecules with a more _____ reduction portential
positive
electric potential delta E
delta G = -n delta E
measured in volts
