exam 1 Flashcards
1
Q
enthalpy
A
total heat content
2
Q
entropy
A
level of disorder
3
Q
exothermic
A
(-), release of heat, 1 structure breaking into multiple parts, spontaneous, exergonic
4
Q
endothermic
A
(+), multiple parts joining into 1 structure, non-spontaneous, endergonic
5
Q
ONLY animals cells have
A
lysosomes
6
Q
ONLY plant cells have
A
chloroplasts
7
Q
ONLY bacterial cells have
A
zero membrane-bound organelles
8
Q
plant and bacterial cells have
A
cell walls
9
Q
animal and bacterial cells have
A
flagella
10
Q
animal and plants cells have
A
golgi, rough/smooth ER, mitochondria, nucleus, similar in size + both eukaryotic
11
Q
animal, plant and bacterial cells have
A
cell membrane, ribosomes, DNA, cytoplasm
12
Q
prokaryotic cells don’t have a
A
nucleus
13
Q
cell membrane
A
barrier that protects cell; semipermeable, in pro and euk cells
14
Q
ribosomes function
A
protein synthesis; in euk and pro cells
15
Q
mitochondria
A
responsible for cell respiration that creates ATP; in euk cells only
16
Q
nucleus
A
encloses genetic info and site of replication; euk cells only
17
Q
DNA
A
contains instructions for reporduction/proteins; in both euk and pro cells
18
Q
cell wall
A
controls water intake and prevents osmotic lysis
in both euk (PLANT ONLY) and pro cells
19
Q
rough ER
A
has ribosomes, makes proteins that leave the cell
20
Q
smooth ER
A
no ribosomes, produces lipids
21
Q
chloroplasts
A
IN PLANTS ONLY; site of photosynthesis in euk plant cells only
22
Q
golgi apparatus
A
“shipping” center for materials; modifies, pack/ships and transports proteins/lipids/etc in euk cells
23
Q
functional groups in proteins
A
amine group and carboxylic acids
24
Q
functional group containing phosphate found in DNA
A
phosphoric acid ester
25
symbol for change in enthalpy
delta H
26
change in entropy
delta S
27
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
28
does human beings/organisms violate the second law of thermodynamics?
no--we exchange energy with our environment, staying in compliance with the second law
29
difference between exothermic and exergonic?
exothermic: releases HEAT
exergonic: releases ENERGY
30
equation for pH of any aqueous solution
[H+] [OH-] = 1.0 x 10^-14 M
31
equation for H+ and pH
pH = -log10 [H+]
32
Ka represents
acid disassociation constant which describes the strength of an acid
33
Ka =
[H+] [A-] / HA
where HA is the weak acid and A- is the conjugate base
34
pka is used for
strong acids mainly
35
pka =
-log(Ka)
36
Henderson-Hasselbach equation is used to calculate
the pH of a buffering system
37
native conformation
major conformation of proteins considered protein's "native conformation"
38
levels of protein structure
primary, 2ndary, tertiary, quarternary
39
primary structure is the...
sequence of amino acids in a polypeptide chain, read from N terminus to C terminus
40
tertiary structure is the...
3D arrangement of all atoms
41
changes in one AA in the primary sequence can...
alter biological function
42
secondary structure is the
H-bonded arrangement of protein's backbones
includes alpha helix and beta pleated sheet
43
each AA residue has 2 bonds with reasonably free rotation
alpha carbon and amino nitrogen
alpha-carbon and carboxyl carbon
44
alpha helix has peptide bonds and each are
trans and planar
45
carboxyl and amino H bonds are parallel..
to helical axis which allows stability of H bond
46
all R groups point
outward from the helix
47
direction of alpha helix coil?
clockwise or right handed
48
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)
49
each peptide bond in beta pleated sheets is...
trans and planar
may be parallel or antiparallel
50
polypeptide chains lie
adjacent to one another
51
beta-pleated sheet's R groups
alternate (first above and then below plane)
52
carboxyl and amino H bonds are b/w adjacent sheets and...
perpendicular to the direction of the sheet
53
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
54
forces stabilizing tertiary structure
noncovalent interactions and covalent interactions
55
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 -)
56
covalent interactions
disulfide bonds between side chains of cysteines
57
quarternary structure is the association of...
polypeptide monomers into multisubunit proteins (dimers, trimers, tetramers)
58
hydrophobic interactions are major factors in
protein folding
59
hydrophobic interactions help proteins
fold so that nonpolar side chains are on inside away from water
hydrophobic interactions are spontaneous
60
protein folding chaperones
aid in correct and timely folding of many proteins; exist in organisms from prokaryotes and humans
61
denaturation is the
loss of structure order that controls assignment of biological activity of each protein structure
62
causes of denaturation
heat, changes in pH, detergents (disrupts hydrophobic interactions), urea (disrupts H bonding), mercaptoethanol (reduces disulfide bonds)
63
what atoms does carboxyl group give up in a hydrolysis rxn?
Oxygen
64
what atoms are lost from the amino group in a hydrolysis
2 hydrogen
65
direction of peptides?
N-terminus (amino group) to C-terminus (carboxylic acid)
66
what bonds stabilize the alpha-helix?
h bonds + alpha-helix is part of 2ndary structure
67
h bonds direction...
parallel to helix axis
68
which way do R groups point?
outwards from helix b/c they are too big to fit in the coil of the helix
69
what bonds stabilize the beta sheet?
h bonds
70
h bonds in a beta sheet are between the carboxyl of...
one AA to amine group of another AA
71
h bonds in a beta sheet lie...
perpendicular to the beta pleated sheet
72
r groups point above or below plane of the sheet?
alternate above and below plane
73
in antiparallel beta-sheets, chain runs..
in alternating directions (N--C and C---N)
74
in parallel sheets..
N===C N===C
75
why does proline disrupt alpha-helix and beta sheet?
proline's R group is bonded to the backbone amine group
76
where is proline found in either alpha-helices and beta-pleated sheets?
beginning
77
which 'small' AA might accommodate the tight turns of reverse turns observed in beta-pleated sheets?
glycine (R group is just H)
78
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
79
R groups are involved in..
nonpolar/hydrophobic interactions b/c they're hydrophobic
80
what interactions among subunit R group help stabilize tertiary and quarternary structures?
h bonds
hydrophobic interactions
electrostatic attraction
electrostatic repulsion
disulfide bonds
81
how can pH denature proteins?
could affect h bonds or electrostatic attraction/repulsion
can deprotonate/protonate molecules
82
how can detergents denature proteins?
they disrupt hydrophobic interactions
83
how can urea denature proteins?
disrupts h bonds and electrostatic interactions
84
mercaptoethanol: how can it denature proteins?
disrupts S-S bonds (disulfide bridge)
85
how can heat denature proteins?
usually can disrupt all bonds seen in secondary, tertiary and quarternary structures
extreme heat will disrupt primary (covalent bonds)
