Exam 1: M1&2 Flashcards
(229 cards)
1
Q
T/F: cells are densely packed w macromolecules
A
T
2
Q
Do bacteria have nucleosomes
A
no
3
Q
what are the 4 classes of biological polymers
A
Proteins
polysaccharides/carbohydrates
lipids
nucleic acids
4
Q
what is the largest/most diverse biological polymer class
A
proteins
4
Q
are lipids true biological polymers
A
no
4
Q
polysaccharides can be ___ or ____
A
linear, branched
4
Q
nucleic acids consist of ___ and ___
A
DNA, RNA
5
Q
what are the characteristics of CHNOPS
A
small, stable, 4 val e-
5
Q
3 main molecular forces in macromolecules
A
covalent, noncovalent, hydrophobic
5
Q
Noncovalent bonds in order of inc strength
A
van der waals, H bonds, ionic
5
Q
strongest molecular force
A
covalent
5
Q
ion pairs are highly susceptible to …
A
pH bc pH affects charge state
5
Q
dipole-dipole interactions are between ___ molecules
A
neutral
5
Q
what causes a dipole-dipole interaction
A
e- cloud not very distributed, dependent of separation of charges
5
Q
what do H bonding need
A
electron acceptor and donor; direction is important
6
Q
distance for ion pair bonding
A
3-10 angstrom
7
Q
dipole-dipole distance
A
3-10 angstrom
8
Q
H bonding distance
A
1.5-2 angstrom
9
Q
T/F: Van der waals is in all macromolecules/atoms
A
T
10
Q
distance of van der waals
A
3-5 angstrom
11
Q
T/F: van der waals can be strong collectively
A
T
12
Q
what drives hydrophobic interactions
A
entropy of water
13
Q
entropically, more organized arrangement of water molecules around surface of hydrophobic molecules is ____
A
unfavorable
14
Q
more organized water around surface of hydrophobic molecules is unfavorable so…
A
hphobic molecules come together and reduce overall surface area of hydrophobic molecules which lets water molecules be more random in soln
15
hphobic interactions are an ____ effect
exclusion
16
how is entropy a driving factor of hphobic interactions
entropic cost of arrangement of water molecules; they have to be very ordered on hphobic molecules surface. interactions will give less surface area
17
examples of how hphobic interactions are important
membranes and amphipathic molecules, diff macromolecules interacting for protein folding and formation of diff types of membranes
18
Features of biological polymers
directional, informational, structured in 3D
19
how do we build biopolymers
condensation reaction
20
T/F: not all chemical reactions happen in equil
F
21
properties of water
polar, non-linear, bent, H bond donor and acceptor, can form 4 H bonds
22
what makes water a good solvent
irregular network of H bonded molecules, soluble for ionic and other polar molecules
23
T/F: strength of an acid is specificed by its dissociation constant
T
24
pK is the -log of the ___?
dissociation constant
25
when pH
protonated form
26
when pH>pKA...
deprotonated form
27
pH=pK when
half the molecules are protonated and other half is deprotonated
28
pK depends on ___?
molecular structure
29
acid next to a positive charge will inc or dec pk?
dec
30
base close to hydrophobic pathc will inc or dec pk?
inc
31
acid close to hydrophobic patch will inc or dec pk?
dec
32
blood ph
7.35-7.45
33
how to pick a buffer for a rxn if we want to mimic the cellular env?
pk of buffer must be close to pH rxn occuring in
34
first law of thermodynamics
energy is conserved and is primarily concerned w enthalpy
35
second law of thermodynamics
entropy inc toward a state of disorder
36
T/F: rxns don't have to be spontaneous to occur
F
37
gibbs free energy is a measure of...
spontaneity
38
spontaneity doesn't predict anything about
kinetics/rate/speed of rxn
39
At equil, delta G =
0
40
delta G is independent of
rxn mechanism
41
delta G is influenced by ?
changes in free energy of products and reactants
42
endergonic
nonspont.
43
exergonic
spont.
44
+deltaH, +deltaS
spont when T> deltaH/deltaS
45
+deltaH, -deltaS
nonspont at all temps
46
-deltaH, -deltaS
spont when T < deltaH/deltaS
47
-deltaH, +deltaS
spont at all temps
48
delta g is ___ ____?
rxn specific
49
delta g depends on...
conc of reactants of products
50
free energy changes depends on ___ and on ___ of reactants and products
rxn taking place; concentration
51
free energy is a function of change in ___?
entropy
52
proteins are polymers of ?
aa
53
4 key components of aa
alpha carbon, amine group. carboxyl group, R group
54
pk of amino group of aa
9.4
55
pk of carboxylic acid of aa
2.2
56
all aa in proteins are in ____
L
57
at physiological pH, aa are ___
charged
58
peptide bonds are ___ and ___ than typical C-C bonds
shorter; stronger
59
backbone is ___, _____, and _____
hydrophilic; soluble; polar
60
what determines folding and chemical properties?
side chains
61
acidic aa
aspartic acid, glutamic acid
62
basic aa
histidine, arginine, lysine
63
nonpolar/hydrophobic aa
phenylalanine, alanine, leucine, methionine, isoleucine, tryptophan, proline, valine
64
polar/uncharged aa
cysteine, glycine, glutamine, asparagine, serine, tyrosine, threonine
65
structurally important aa
proline (5 mem ring)
glycine (no R group)
both have small R groups
66
sulfur-containing aa
methionine and cysteine
67
which sulfur containing aa can't form disulfide bridge
methionine
68
which sulfur-containing aa can form disulfide bridge
can form disulfides
69
which bonding interactions do disulfide bridges have
covalent linkages betwn 2 sulfhydryl groups
70
disulfide bridge is the ___ form of sulfhydryl
reduced
71
why can't methionine form disulfide bridges
it doesn't have sulfhydryl group
72
alcoholic aa
serine, threonine, tyrosine
73
which aa are targets of phosphorylation
alcohols
74
aromatic aa
phenylalanine, tyrosine, tryptophan
75
where are aromatic aa usually found
protein interior bc they are hydrophobic from bulky sidechains
76
pk of aspartic acid
4
77
pk of glutamic acid
4
78
pk of lysine
10.5
79
pk of arginine
12.5
80
pk of histidine
6
81
what can acidic and basic aa do
can grab or donate a proton or make salt bridges and ion pairs
82
ion pairs are common btwn ___ and ____
acids; bases
83
at cellular pH, which side chains are + charged?
?
84
at cellular pH, which side chains are - charged
?
85
histidine pk
6.04
86
at physiological pH, histidine can be ___ or ___
protonated; deprotonated
87
pK values depend on ____ ______
chemical surroundings
88
why is histidine special
pk is close to physiological ph
89
N terminus pK
9-10
90
C terminus pk
2-3
91
what is the pI
pH nat which a molecule carries no net electric charge
92
how to calculate pI
(pki + pkj) / 2
93
Pi of polypeptide must be determined experimentally bc ______ dictates what the pk is
env of every side chain
94
protein w low PI is ___
acidic
95
protein w high pI is ____
basic
96
which aa is neither hydrophobic or hydrophilic
glycine
97
which aa undergo phosphorylation
serine, threonine, tyrosine
98
which group gets replaced by what other group during phosphorylation
phosphate group replaces hydroxyl
99
what does phosphorylation do to the side chains
changes charge from neutral to -2
100
which aa gets hydroxylated
lysine and proline
101
what group replaces what group during hydroxlation
OH replaces H
102
what does hydroxylating a side chain do
controls activity of proteins and stabilizes certain structures
103
which aa gets methylated
lysine, arginine, histidine
104
what does methylating a side chain do
cell "markers"
ex. histones in chromatin controls epigenetics
105
which aa gets ubiquinated
lysine
106
how is ubiquitin linked to lysine
covalent bond
107
how does the sanger sequencing work
1) start w protein purified in soln (can be one or multiple polypeptide chains linked)
2)a reducing agent is used to reduce the disulfide bonds and separate the chains
3)use proteases to get smaller pieces by fragmenting chains (use 2 diff proteases to get 2 diff sets of fragments we can overlap later)
4) sequence 1 aa at a time from N terminus of each fragment and end up w series of smaller peprides we nkow the sequence of
5) use computers to overlap diff fragments to read out overall seq
108
why is protein sequencing important
can figure out where specific modifications are in a given chain
109
define primary strucutre
linear sequence of aa
110
define secondary structure
regularly repeating folding patterns (alpha helices or beta sheets)
111
in secondary structure, what do patterns depend on
position of atoms in peptide bond
112
define tertiary structure
overall 3D fold of a given protein, includes both atoms in backbone and R groups
113
define quarternary structure
assembly of units
114
what are restrictions to peptide bonds
rigid and planar bc of db character from resonance
115
all a but proline are in the ____ conformation
trans
116
which atoms is the psi angle between
alpha carbon to next carbon
117
which atoms is the theta angle between
alpha carbon to N
118
what determines/defines secondary structures
dihedral angles
119
how do we know what psi and theta angles are allowable for given aa sequences
ramachandran plots
120
121
allowable theta angles
-60 to -150
122
___ is the most flexible/least sterically hindered aa bc it lacks typical R group
glycine
123
___ is the most restricted/most sterically hindered aa bc it has a cyclical ring
proline
124
extensive ___ bonding along peptide backbone
H
125
n and n+? residue pattern for alpha helix
4
126
distance btwn residues (up and down) for helix
1.5A
127
which atoms in the aa are h bonded
H on amide N to O from carbonyl
128
how many resides per turn
3.6
129
distance for one full turn of helix (pitch)
5.4A
130
sidechains project out and ___
down
131
what interactions stable core of helix
van der waals
132
how do r groups give rise to structure
r groups not physcially interacting through H bonding or any other force w the atoms in the backbone so not contributing the helix physically but do dictate allowable theta and psi angles which determine if a given pepride can fold into helix or sheet
133
distance btwn residues for sheets
3.5A
133
beta sheets have theta and psi angles much cloesr to ___
180 degrees bc more extended structure
133
In sheets, H bonding occurs between
neighboring chains
134
in beta sheets, every successive aa faces ___ _____
in opposite directions
135
every ___ aa forms same face of beta sheet
other
136
in antiparallel beta sheet, H bonding occurs btwn
H of amide and O of carbonyl
137
parallel beta sheets aren't as stable bc
H bonding isn't in perfect register like they are in antiparallel sheets
138
secondary structure is stabilized primarily by ___
H bonding
139
secondary structure doesn't usually involve
side chains
140
alpha helices and beta sheets are connected to each other by tight ___ or flexible ___
turns;loops
141
other secondary structures include
reverse turns (not a true secondary structure) and polyproline helix (true secondary structure)
142
reverse turns are often found on
protein surface
143
what defines reverse turns
n and n+3
144
T/F: alpha helices are tighter than reverse turns
F
145
reverse turns usually have ___ at residue 2 in type 1
proline
146
reverse turns usually have ___ at residue 2 in type 2
glycine (to avoid steric clash)
147
polyproline helix has ____ H bonding
unusual
148
what is polyproline helix found in
collagen
149
what is the aa composition of a polyproline helix
33% glycine, 15-30% proline, and Hyp
150
what define a polyproline helix
repeating sequences of gly-Pro-Hyp
151
what interactions are involved w polyproline helices
van der waals, H bonding
152
what is Hyp
modified version of proline
153
the enzyme necessary to modify prline to make Hyp requires __?
vitamin c
154
T/F: polyproline helices are v diff than alpha helices
T
155
each indiv polyproline helix is
left handed
156
collagen triple helix is
right handed
157
1 polyproline helix
left handed
3 residues per turn
van der waals stabilized
proline prevetns formation of alpha helix
158
collagen
3 polyproline helices
right handed
H bonding btwn H of amide group of glycine to carbon of carbonly of proline
159
what dictates secondary structure
protein sequence
160
acidic residues are what color
red
161
basic residues are what color
blue
162
hydrophobic/ nonpolar is what color
white
163
a very basic patch will be (?) charged and will want to bind to (?)
(+); (-)
164
define tertiary structure
overall 3D shape of protein and fold
165
what determines tertiary structure
linear sequence of aa
166
T/F: hard to predict overall 3D shape of protein based on primary aa sequence
T
167
3 classifications of proteins
1. globular
2. fibrous
3. membrane
168
characteristics of globular proteins
soluble, compact
ex: myoglobin, hemoglobin
169
for globular proteins, where are hydrophobic residues
protein interior
170
for globular proteins, where are hydrophilic residues
protein surface
171
characteristics of fibrous proteins
regular repeating elements
makes elongated structures
172
fibrous proteins form...
protective connective structures like keratin or collagen
173
membrane proteins are very
hydrophobic
174
for membrane proteins, hydrophobic residues are on
surface
175
for membrane proteins, hydrophilic residues are on
protein interior
176
tertiary structures (globular) stabilize by
hydrophobic effect
177
densely packed core of globular protein is stabilized by
van der waals
178
the 7 supersecondary structures
1. BaB
2. B hairpin
3. aa motif (coiled coil, helix bundles)
4. greek key motif
5. helix loop helix
6. helix turn helix
7. zinc finger domain
179
BaB supersecondary structure
parallel B sheets that are connected by alpha helix;
important in Rosmann fold
180
B hairpin supersecondary structure
antiparallel B sheets connected by tight turns; beta barrels
181
aa motif supersecondary structure
2 alpha helices tilted but connected by loop or turn
182
Greek key motif supersecondary structure
mutliple antiparallel beta sheets aligned w one another; ex beta cliftolin
183
helix loop helix
one helix connected to another by a loop;
can be oriented diff;
interact w IMF
184
helix turn helix
one helix connected to another by a reverse turn
185
loops vs. turns
loops are longer and more flexible (10-20aa) turns are tight and not flexible (3-4 aa)
186
zing finger domain
25-60 aa arranged around 1 or 2 zinc ions; Zn tetrahedrally coordinated to 4 aa side chains;
involved w genome editing
187
define a domain
w/in a polypeptide chain, indiv folded units structurally independent
188
T/F: each domain has discrete functions
T
189
many proteins have multiple folded domains connected by flexible ____
linkers
190
domains vs subunits
w/in one subunit can have multiple domains; 1 polypeptide chain = subunit which can have multiple domains
191
define quaternary structure
arrangement of indiv subunits wrt one another
192
T/F: diff subunits are often covalently linked together
mostly F; use noncovalent forces (hphobic, salt bridges, VDW, H bonding) but sometimes covalently linked via disulfide bonds
193
T/F: proteins are in equilibrium w folded and unfolded state
T
194
T/F: equilibrium favors unfolded state
F
195
which side chains are most mobile
lysine, arginine
196
intrinsically disordered proteins are rich in ___
polar/charged aa--> glutamine, serine, glutamate, llysine, glycine, alanine
197
proteins are sensitive to:
heat, pH, detergetns, chaotropic agetns, reducing agetns
198
what are the chaotropic agents
urea, guanodidium
199
reducing agents break apart
disulfide bonds
200
a protein is only ____ KJ/mol more stable in folded state relative to unfolded state
40
201
a. single H bond is __ KJ/mol
20
202
small free energy difference allows proteins to be ___
dynamic
203
protein folding is a ____ process
reversible
204
what did Anfinfsen's experiment show with RNaseA
all the info you need to fold a protein is encoded in primary sequence
205
describe the RNase A experimental steps
add urea and mercaptoethanol to denature protein and break disulfide bonds
dialyze away urea + mercaptoethanol which renatures the re-forms the disulfide bonds in presence of O2
206
what drives proteins folding
hydrophobic collapse
207
T/F: proteins fold randomly
F
208
Levinthal's paradox
10^n conformations (n=# residues)
209
T/F: proteins fold in seconds
T
210
protein folding order
1. formation of local segments of secondary structure during tsln right away
2. hphobic collapse drives molten globule formation
3. secondary structures are stabilized through long range interactions, driving tertiary structure formation
4. rearrangements occur until final tertiary structure is acheived thorugh packing of internal side chains and formation of H bonds
211
competetion btwn native state and ____
aggregation
212
chaperones help proteins fold into
native state
213
what does PDI do
mediates correct disulfide bridge formation via nuc attacks (PDI has own cysteine residues that initiate attack)
214
molecular chaperones often recognize and bind ____ surfaces to block aggregation
hphobic
215
T/F: most molecular chaperones do not require ATP hydrolysis for energy
F
216
what happens with GroEL
1) unfolded protein is delivered to GroEL by HSP70 via ATP; hydrophobic patches bind unfolded substrates
2)ATP binds to GroEL and recruits GroES
3) cap binding causes conf. change that exposes the hydrophilic patches
4) protein can now re-fold in polar env
5) ATP is hydrolyzed and the cap and protein gets released
217
protein misfolding can drive
alzheimer's and prion disease
