exam 1 Flashcards
enthalpy
total heat content
entropy
level of disorder
exothermic
(-), release of heat, 1 structure breaking into multiple parts, spontaneous, exergonic
endothermic
(+), multiple parts joining into 1 structure, non-spontaneous, endergonic
ONLY animals cells have
lysosomes
ONLY plant cells have
chloroplasts
ONLY bacterial cells have
zero membrane-bound organelles
plant and bacterial cells have
cell walls
animal and bacterial cells have
flagella
animal and plants cells have
golgi, rough/smooth ER, mitochondria, nucleus, similar in size + both eukaryotic
animal, plant and bacterial cells have
cell membrane, ribosomes, DNA, cytoplasm
prokaryotic cells don’t have a
nucleus
cell membrane
barrier that protects cell; semipermeable, in pro and euk cells
ribosomes function
protein synthesis; in euk and pro cells
mitochondria
responsible for cell respiration that creates ATP; in euk cells only
nucleus
encloses genetic info and site of replication; euk cells only
DNA
contains instructions for reporduction/proteins; in both euk and pro cells
cell wall
controls water intake and prevents osmotic lysis
in both euk (PLANT ONLY) and pro cells
rough ER
has ribosomes, makes proteins that leave the cell
smooth ER
no ribosomes, produces lipids
chloroplasts
IN PLANTS ONLY; site of photosynthesis in euk plant cells only
golgi apparatus
“shipping” center for materials; modifies, pack/ships and transports proteins/lipids/etc in euk cells
functional groups in proteins
amine group and carboxylic acids
functional group containing phosphate found in DNA
phosphoric acid ester
symbol for change in enthalpy
delta H
change in entropy
delta S
correlation between level of organization in molecules and change in entropy
exothermic enthalpy: increase in entropy means MORE randomness in product
endothermic enthalpy: decrease in entropy means MORE disorder
does human beings/organisms violate the second law of thermodynamics?
no–we exchange energy with our environment, staying in compliance with the second law
difference between exothermic and exergonic?
exothermic: releases HEAT
exergonic: releases ENERGY
equation for pH of any aqueous solution
[H+] [OH-] = 1.0 x 10^-14 M
equation for H+ and pH
pH = -log10 [H+]
Ka represents
acid disassociation constant which describes the strength of an acid
Ka =
[H+] [A-] / HA
where HA is the weak acid and A- is the conjugate base
pka is used for
strong acids mainly
pka =
-log(Ka)
Henderson-Hasselbach equation is used to calculate
the pH of a buffering system
native conformation
major conformation of proteins considered protein’s “native conformation”
levels of protein structure
primary, 2ndary, tertiary, quarternary
primary structure is the…
sequence of amino acids in a polypeptide chain, read from N terminus to C terminus
tertiary structure is the…
3D arrangement of all atoms
changes in one AA in the primary sequence can…
alter biological function
secondary structure is the
H-bonded arrangement of protein’s backbones
includes alpha helix and beta pleated sheet
each AA residue has 2 bonds with reasonably free rotation
alpha carbon and amino nitrogen
alpha-carbon and carboxyl carbon
alpha helix has peptide bonds and each are
trans and planar
carboxyl and amino H bonds are parallel..
to helical axis which allows stability of H bond
all R groups point
outward from the helix
direction of alpha helix coil?
clockwise or right handed
what can disrupt an alpha-helix?
proline created a bend
electrostatic repulsion caused by proximity of side chains of like charge (Lys +, Arg +, Glu -, Asp -)
steric crowding caused by proximity of bulky side chains (Val, Ile, Thr)
each peptide bond in beta pleated sheets is…
trans and planar
may be parallel or antiparallel
polypeptide chains lie
adjacent to one another
beta-pleated sheet’s R groups
alternate (first above and then below plane)
carboxyl and amino H bonds are b/w adjacent sheets and…
perpendicular to the direction of the sheet
structures of reverse turns involves…
protein folding that needs polypeptide changes in direction
spatial/steric reasons - glycine common in reverse turns
proline also encountered in reverse turns
forces stabilizing tertiary structure
noncovalent interactions and covalent interactions
noncovalent interactions
H bonds b/w polar side chains (Ser and Thr)
hydrophobic interaction of non-polar (Val, Ile)
electrostatic attraction of charge (Lys +, Glu -)
electrostatic repulsion (Lys/Arg +, Glu/Asp -)
covalent interactions
disulfide bonds between side chains of cysteines
quarternary structure is the association of…
polypeptide monomers into multisubunit proteins (dimers, trimers, tetramers)
hydrophobic interactions are major factors in
protein folding
hydrophobic interactions help proteins
fold so that nonpolar side chains are on inside away from water
hydrophobic interactions are spontaneous
protein folding chaperones
aid in correct and timely folding of many proteins; exist in organisms from prokaryotes and humans
denaturation is the
loss of structure order that controls assignment of biological activity of each protein structure
causes of denaturation
heat, changes in pH, detergents (disrupts hydrophobic interactions), urea (disrupts H bonding), mercaptoethanol (reduces disulfide bonds)
what atoms does carboxyl group give up in a hydrolysis rxn?
Oxygen
what atoms are lost from the amino group in a hydrolysis
2 hydrogen
direction of peptides?
N-terminus (amino group) to C-terminus (carboxylic acid)
what bonds stabilize the alpha-helix?
h bonds + alpha-helix is part of 2ndary structure
h bonds direction…
parallel to helix axis
which way do R groups point?
outwards from helix b/c they are too big to fit in the coil of the helix
what bonds stabilize the beta sheet?
h bonds
h bonds in a beta sheet are between the carboxyl of…
one AA to amine group of another AA
h bonds in a beta sheet lie…
perpendicular to the beta pleated sheet
r groups point above or below plane of the sheet?
alternate above and below plane
in antiparallel beta-sheets, chain runs..
in alternating directions (N–C and C—N)
in parallel sheets..
N===C N===C
why does proline disrupt alpha-helix and beta sheet?
proline’s R group is bonded to the backbone amine group
where is proline found in either alpha-helices and beta-pleated sheets?
beginning
which ‘small’ AA might accommodate the tight turns of reverse turns observed in beta-pleated sheets?
glycine (R group is just H)
why do hydrophobic interactions among subunit R groups take place?
b/c of aqueous outside environment, R groups that are nonpolar orient towards inside, away from water
R groups are involved in..
nonpolar/hydrophobic interactions b/c they’re hydrophobic
what interactions among subunit R group help stabilize tertiary and quarternary structures?
h bonds
hydrophobic interactions
electrostatic attraction
electrostatic repulsion
disulfide bonds
how can pH denature proteins?
could affect h bonds or electrostatic attraction/repulsion
can deprotonate/protonate molecules
how can detergents denature proteins?
they disrupt hydrophobic interactions
how can urea denature proteins?
disrupts h bonds and electrostatic interactions
mercaptoethanol: how can it denature proteins?
disrupts S-S bonds (disulfide bridge)
how can heat denature proteins?
usually can disrupt all bonds seen in secondary, tertiary and quarternary structures
extreme heat will disrupt primary (covalent bonds)
