Exam 4 Flashcards
(272 cards)
1
Q
Amino acids contain a central _________ carbon
A
tetrahedral
2
Q
Is water lost or gain in peptide bind formation?
A
loose water
3
Q
What kind of bond is a peptide bond?
A
covalent
4
Q
What enzyme catalyzes peptide bond formation?
A
Peptidyl transferase
5
Q
What does a peptide bond join?
A
amino acids
6
Q
What are the 4 types of amino acids?
A
- nonpolar/hydrophobic
- polar/hydrophilic
- acidic
- basic
7
Q
Selenocysteine (SEC, U) is a rare amino acid, what does it look like?
A
cysteine with selenium replacing the sulfur
8
Q
What are proteins that depend on Selenocysteines catalytic activity?
A
selenoenzymes
9
Q
Pyrrolysine (Pyl, O) is a rare amino acid, what synthesized it?
A
synthesized from 2 L-lysine
10
Q
Is the rare amino acid, Pyrrolysine (Pyl, O), positive or negative?
A
positive
11
Q
The rare amino acids, Hydroxylysine (Hyl) and Hydroxyproline (Hyp) are post-translationally modified and are found in _____________
A
connective tissue (collagen)
12
Q
The rare amino acid, Carboxyglutamic acid, is post-transcriptionally modified how?
A
glutamic acid undergoes carboxylation
13
Q
The rare amino acid, Carboxyglutamic acid, is important for _____________
A
clotting factors
14
Q
The rare amino acid, Pyroglutamic acid (PCA), is a cyclic form of __________
A
glutamic acid (glutamine)
15
Q
Amino acids that do not occur in proteins are know to be responsible for __________ and ____________
A
hormones and neurotransmitters
16
Q
What are essential amino acids?
A
cannot be synthesized from scratch by humans
17
Q
What are conditionally essential amino acids?
A
obtained from diet
18
Q
What are dispensable amino acids?
A
can be synthesized by humans
19
Q
How many possible triplets (codons) are possible?
A
64
(63 without stop codon)
20
Q
Why are there 64 possible triplets but only 20 amino acids?
Give 2 reasons
A
- If you increased the number of amino acids beyond 20 then it would be difficult to create suitable tRNA molecules that could be distinguished between one another by the aminoacyl-tRNA synthetase so that the correct amino acid could be added
- these 20 amino acids are fairly stable
21
Q
What is known as the 21st amino acid and why is it not present anymore in organisms?
A
it was apart of the anaerobic world before there was oxygen present, but now there is lots of oxygen so its not useful
SELENOCYSTEINE
22
Q
What is the cationic form of amino acids?
A
NH3+
COOH
23
Q
What is the anionic form of amino acids?
A
NH2
COO-
24
Q
What is the Zwitterion form of amino acids?
A
NH3+
COO-
25
amino acids are weakly _________ acids
polyprotic
26
What is a polyprotic acid?
has more than one acidic H+ so it can donate for than one H+
27
The degree of dissociation of amino acids depends on the ______ of the medium
pH
28
For amino acids that don't have a dissociable side chain, the first thing to dissociate is _______________ and the second thing is _________
alpha carbonyl group
alpha amino group
29
What is the pKa of alpha carboxyl group?
2 (acidic)
30
What is the pKa of alpha amino group?
9 (basic)
31
What are optically active molecules?
can rotate the plane of polarized light
32
Optically active molecules are __________
chiral
33
What amino acid does not have a chiral carbon?
glycine
34
Chiral centers of amino acids allow for _____________(mirror images but not superimposable)
stereoisomerism (mirror images but not superimposable)
35
What are the mirror images of chiral amino acids called?
enantiomers
36
____-amino acids are the most common
L-amino acids
37
All amino acids absorb __________ wavelengths
infrared
38
What 3 amino acids absorb UV?
Phe
Tyr
Trp
39
_______ spectra are characteristic for each amino acid residue in proteins
NMR
40
What can NMR spectra tell you about a protein?
its 3D structure
41
Proteins are ______ polymers of amino acids
unbranched
42
amino acids join head-to-tail through formation of ____________ bonds (peptide)
covalent
43
The peptide backbone of a protein consists of the repeated sequence ___________
--N--C(alpha)--C(o)
44
In the peptide backbone sequence, --N--C(alpha)--C(o), what does the N stand for?
amide nitrogen (NH3)
45
In the peptide backbone sequence, --N--C(alpha)--C(o), what does the C(alpha) stand for?
alpha carbon
46
In the peptide backbone sequence, --N--C(alpha)--C(o), what does the C(o) stand for?
carbonyl carbon (COOH)
47
What conformation is the peptide bond usually found in?
trans
48
What is positive and negative in the peptide bond?
positive: N
negative: O
49
The peptide bond is ______ than single bonds but ______ than double bonds
shorter
longer
50
Due to the double bond character of the peptide bond, the size atoms of the bond define a ________ plane
amide plane
51
Is the double bond in peptide bonds usually on the O or N?
neither; it moves between both
52
What is each amino acid unit called?
residue
53
What is 2 residues called?
dipeptide
54
What is 3 residues called?
tripeptide
55
What is 12-20 residues called?
oligopeptide
56
What is 20+ (many) residues called?
polypeptide
57
What is one polypeptide chain called?
monomeric protein
58
What is more than one polypeptide chain called?
multimeric protein
59
What is a protein with one kind of chain called?
homomultimeric
60
What is a protein with two or more kinds of chains called?
heteromultimer
61
What is an example of a heteromultimer protein?
beta globin has 2 alpha nd 2 beta chains
62
Is the sequence if amino acids in a protein considered genetic information?
yes
63
What direction is the amino acid sequence read in?
amino to carboxyl terminus
64
What 2 groups interact to form a peptide bond?
alpha COOH and alpha NH3+
65
Peptide formation is the creation of an _________ bond between the carboxyl and amino group
amide bond
66
Peptide bonds are ___-planar
co-planar
67
What is the 2 planes (angles) on either side of the alpha carbon formed when a peptide bond occurs?
phi and psi
68
What are the 2 shapes of proteins?
fibrous
globular
69
What is the primary structure of proteins?
sequence
70
What are 3 example of secondary structures of proteins?
helix
sheet
loop/turns
71
What is the tertiary structure of proteins?
3D shapes (domains)
72
Are fibrous proteins water soluble or insoluble?
insoluble
73
What bridges are formed in primary structures of proteins?
disulfide bridges
74
Disulfide bonds occur in the primary structure of proteins between what amino acid and itself?
Cys
75
Can multiple secondary structures come together to form a unit?
yes
76
What is an example of a tetramer (quaternary structure)?
hemoglobin
77
What is the difference between configuration and conformation?
configuration: breaking bonds
conformation: no bond breaking
78
Proteins tend to be least soluble at thier ____________ point
isoelectric point
79
During protein purification, what happens first salting in or out?
salting in
80
Does salting in or our increase solubility?
salting in
81
What is the protein purification, Ion exchange?
separates proteins based on their net charge
82
What is the protein purification, Size exclusion?
separates proteins based on their size
83
During protein purification, what dramatically increases as the protein is purified?
specific activity
84
What is specific activity of a protein?
activity of the enzyme per mg of protein
85
What are 3 methods estimating protein concentrations?
Bradford assay
Lowry assay
BCA (purple complex)
86
Several methods of estimating protein concentration rely on the reduction of ______ to ______
Cu2+
Cu+
87
Determination of protein concentration by UV absorption depends on the presence of ____________
aromatic amino acids in proteins
88
__________ and ________ absorb UV light at 280nm (the very end of spectrum)
tyrosine
tryptophan
89
What 2 ways can proteins be sequenced?
1. real amino acid sequencing
2. sequencing the corresponding DNA in the gene
90
What are the 2 methods of amino acid sequencing that are used together ?
Sanger Method (one at a time)
Mass Spec (cleaves into fragments)
91
What are the steps of determining protein sequence?
1. separate polypeptide chains
2. remove S-S (disulfide bonds)
3. identify N and C end residues
4. cleave each polypeptide into smaller pieces and sequence (Edman and Mass Spec)
5. repeat step 4 with different cleavage procedures to make different overlapping fragments
6. using overlapping fragments to reconstruct the protein sequence
92
What end of the residue is susceptible to cleavage by Trypsin, Chymotrypsin, Clostripaon, Staph, and Cyanogen bromide in protein sequencing?
C
93
What part of the residue is susceptible to cleavage by pH 2.5?
Asp-Pro bonds
94
What are some uses of amino acid sequences?
1. function of protein
2. domain structure
3. mosaicism in primary structure
4. facilitate predications on higher order of structures
5. facilitate construction of proves for genes
6. evaluation of relationships between proteins (in a species of between species)
95
What are some biological function of proteins?
1. enzymes
2. control metabolism and gene expression
3. transport proteins
4. storage proteins
5. movement
6. structure
96
What are 3 structural methods to characterize proteins at atomic resolution?
1. X-ray crystallography
2. NMR
3. Cryo-electron microscopy
97
Protein function depends on _________ and _______forces
structure
weak, non-covalent forces
98
The number of protein folding patterns is large but _________
finite
99
Structures of globular proteins are marginally __________
stable
100
marginal stability facilitates ________
motion
101
__________ enables function
motion
102
What are 4 examples of non-protein amino acids? (neurotransmitteres and hormones)
GABA
epinepherine
histamine
serotonin
103
Why do polar and non polar amino acids only have 2 pKa values?
one from the carboxyl and one from the amino group
104
Why do basic and acidic amino acids have 3 pKa values?
one for COOH
one for NH3
one for side chain
105
What wavelength do amino acids absorb at?
280
106
What is the length of peptide bonds?
0.133nm
107
What are the possible phi and psi angles?
nothing with a 0
180 and 180
-60 and 180
108
Secondary, tertiary, and quaternary structures of proteins are formed and stabilized by ________ forces
weak forces
109
____________ bonds are formed whenever possible
H bonds
110
___________ interactions drive protein folding
hydrophobic
111
__________ interaction usually occur on the surface of a protein
ionic
112
__________ interactions are ubiquitous
Van der waals
113
Phi is the angle between what 2 atoms?
C(alpha) -- N
114
Psi is the angle between what 2 atoms?
C(alpha) -- C
115
What does a Ramachandran Map show?
Sterically favored Phi and Psi angles (shaded)
116
Alpha helices are stabilized by ________
hydrogen bonds
117
When defining a helix, what is p?
pitch
118
When defining a helix, what is the number of repeating units?
n
119
Right handed helix have positive or negative "n"?
positive
120
Left handed helix have positive or negative "n"?
negative
121
In a helix hydrogen bonds all point in one direction causing...
dipole moment
122
in a helix hydrogen bonds form with near by donors and acceptor groups called .....
helix capping
123
What is a helical wheel?
when 2 helices interact with each other making a circle shape
124
What are 3 examples of "other" helices?
3(10) helix
pi-helix
left handed helix
125
What is the peptide unit for left and right handed helices?
left: 3.3
right: 3.6
126
What is the pitch of left and right handed helices?
left: 9.8
right: 5.4
127
Beta pleated sheets are made of...
beta strands
128
Why are antiparallel beta sheets more stable?
the H bonding is more optimum
129
What do beta turns allow?
peptide chain to reverse directions
130
How many residues are required for beta turns?
4
131
How are the atoms bonded in beta turns?
the carbonyl C on residue 1 is H bonded with the amide proton of residue 3
132
What amino acid is common in beta turns and why?
proline; restricts movement
133
What is type I beta turns?
proline in position 3
134
What is type II beta turns?
proline in position 2 and glycine at position 3
135
________ proteins create maximum internal bonds and minimize solvent contact
globular
136
___________ proteins create maximum intermolecular bonds and maximize molecule to molecule contact
fibrous
137
Helices and sheets are often packed ________
closely
138
Peptide segments between secondary structures tend to be ________ and direct
short
139
What are 2 ways stability arises in proteins?
1. hydrogen bonding
2. reduction of surface area (folding)
140
T/F?? Proteins are usually a mix between hydrophobic and philic?
true
141
T/F?? most of the polypeptide chain is organized approximately parallel to a single axis
true
142
fibrous proteins are usually strong/weak and soluble/insoluble?
strong
insoluble
143
Fibrous proteins usually play a ___________ role in nature
structural
144
What are 3 examples of fibrous proteins?
keratin
fibrin
collagen
145
Two right handed alpha helices intertwine to form a ______________ superhelix
left-handed
146
Left handed twists in coiled coils reduces what?
reduces the number of residues per turns
147
What does keratin look like?
2 dimers combine to make a antiparallel tetramer
148
What fibrous protein is a triple helix?
collagen
149
What is the most abundant protein in vertebrates?
collagen
150
Ramachandran and Kartha published the first ________________
triple helix
151
Three left handed helices intertwine to form a _____________ superhelix
right handed
152
What protein shape is the most diverse functionally?
globular
153
Are there more fibrous or globular proteins?
globular
154
What are the 4 classes of globular proteins?
1. alpha proteins
2. beta proteins
3. alpha/beta
4. alpha+beta
155
What are random coils?
segments of proteins that are not helices or sheets
don't conform to recurring patterns
156
Why do secondary structures form whenever possible?
Hydrogen bonding
157
Are two adjacent helices usually parallel or antiparallel?
antiparallel
158
Up-and-down barrels have similar __________
topology
159
What are jelly role barrels made of?
beta sheets
160
How are beta helices made?
stacking of parallel beta sheets
161
____ strand and _____ strand beta sheets exist
2 and 3
162
Where is the active site in a/b barrels?
in the hole
163
Where is the active site in twisted a/b domains?
crevice outside the carboxyl end
164
non-covalent association is usually for ___________ proteins
globular
165
covalent association is usually for ____________ proteins
fibrous
166
Can proteins with one polypeptide chain have a quaternary structure?
no
167
What is 2 protein subunits called?
dimer
168
What is 3 protein subunits called?
trimer
169
What is 4 protein subunits called?
tetramer
170
What are identical protein subunits called?
homo---
171
What are non-identical protein subunits called?
hetero-----
172
What are the 5 advantages of quaternary structure?
1. stability
2. efficiency
3. assembly
4. cooperatively
5. regulation
173
How are quaternary structures efficient?
small polymerizing units are synthesized more accurately than a single large protein
174
Quaternary structures assembles _________ sites
catalytic
175
What is simplest kind of symmetry?
rotational
176
How do you tell the fold of symmetry?
360/2 = 180
so the fold is 2
177
Multimeric proteins are symmetric arrangements of _____________ objects
asymmetric
178
What is isologous?
the same interface (rotational symmetry)
179
What is heterologous?
two different interfaces (translational symmetry)
180
Many proteins form tetramers by means of two sets of ______________ interactions
isologous
181
What is an example of an isologous interaction?
antibody
182
What are 3 examples of a polymerizing quaternary structure?
tubulin
Hep E
TMV (virus)
183
What is an example of a protein than can self assemble?
E. coli flagellar motor
184
What is the cause of flagella spinning so fas?
ions flowing in and out quickly
185
What is the rpm of flagella?
22,000
186
What is the cause of Osteogenesis imperfecta?
defect in collagen caused by malformation of protein structure
187
What is Creutzfeldt-Jacob disease caused by?
prions
188
What are prions?
misfolded proteins that are infectious to other proteins
189
What are 6 examples of diseases of protein folding?
1. Alzheimer
2. FAP
3. Cancer
4. Creutzfeldt-Jacob
5. HE
6. Cystic Fibrosis
190
What are post translational modifcations?
covalent changes to proteins after their biosynthesis
191
In PTM, functional groups serve as ___________
nucleophiles
192
Where do PTM occur?
amino acid side chains
N and C terminus
193
What are the 4 amino acid side chains that contain PTM?
hydroxyl
amine
thiol
carboxylate
194
What is the most common PTM?
phosphorylation
195
What amino acids are affected by phosphorylation?
Ser
Thr
Tyr
196
What functional group is affected by phosphorylation?
-OH
hydroxyl
197
What mediates phosphorylation?
protein kinase
198
Is phosphorylation reversible?
yes
199
What is the consequence of phosphorylation?
increased negative charge changing protein conformation and affecting positively charged ligands
200
What mediates dephosphorylation?
phosphatase
201
membrane bound receptor tyrosine kinases are activated by _________
dimerization
202
When receptor tyrosine kinases are unbound what do they look like?
monomer
203
proximity of kinase domains promotes ______________
tran-auto-phosphorylation
204
What does receptor tyrosine kinases activation cause?
downstream signaling
205
What is Src?
first discovered protein tyrosine kinases
206
What are the steps of Scr (protein tyrosine kinase)
1. De-phosphorylation of C-terminal tyrosine frees SH2 domain
2. SH3 dissociates from internal peptide and binds activating ligand
3. kinase activation promotes autophosphorylation of tyrosine
4. downstream signaling
207
What is the inactive state of Scr (protein tyrosine kinase) look like for SH2 and SH3?
SH2 bound to C-terminal phosphotyrosine
SH3 bound to internal peptide
208
High intracellular calcium activates and binds calineurin (phosphatase), how does this affect transcription?
- dephosphorylation of NFAT
- calineurin blocks nuclear export signal
- protein can enter nucleus =
YES transcription
209
Low intracellular calcium inactivated and removes calineurin (phosphatase), how does this affect transcription?
- nuclear export signal is exposed
- kinase phosphorylates and blocks nuclear import signal
NO transcription
210
o
o
211
What are the 3 types of lipidation?
1. Myristoylation
2. Palmitoylation
3. Prenylation
212
In Myristoylation (lipidation), a myristol group is added where?
N terminal glycine
213
In Palmitoylation (lipidation), a palmitoyl group is added where?
cysteine
214
in Prenylation (lipidation), a farnesyl group is added where?
cysteine near C terminus
215
What facilitates the lipidation, Myristoylation (lipidation)?
N-myristol transferase
216
What facilitates the lipidation, Palmitoylation (lipidation)?
palmitoyltransferase
217
What facilitates the lipidation, Prenylation (lipidation)?
farnesyltransferase
218
Methylation is transfer of a methyl group from ________________ to other proteins
SAM
219
What 2 side chains are most common for methylation?
arginine
lysine
220
What mediates methylation?
methytransferase
221
What reverses methylation?
demethylases
222
What 2 places can acetylation be done?
lysine residue
N terminus
223
What mediates acetylation?
acetyltransferase
224
What reverses acetylation?
deacetylase
225
What is the most important role of acetylation?
regulating histones
226
Can methylation and acetylation occur on the same side chain?
no
227
Can multiple PTMs occur on a histone tail?
yes
228
Where does N-linked glycosylation start?
ER
229
What amino acid does N-linked glycosylation happen on?
N terminus of asparagine
230
What does N-linked glycosylation?
oligosaccharyl transferase
231
Oligosaccharyl transferase is a type of ___________
glycotransferase
232
Where does N-linked glycosylation continue?
golgi
233
Where does O-linked glycosylation occur?
golgi
234
In the Golgi sugars are added in chunks or one by one?
one by one
235
What amino acids does O-linked glycosylation happen on?
hydroxyl group of serine and threonine
236
What mediates O-linked glycosylation?
GalNac transferase
237
What does monoubiquitination regulate?
histones
238
What does multiubiquitination regulate?
endocytosis
239
which ubiquitination is most common?
polyubiquitination
240
What is the steps of ubiquitination?
1. E1 attaches to ubiquitin
2. E2 interacts with E1+ubiquitin
3. E2 attaches E3 and E1+ubiquitin to target protein
241
What is E1 in ubiquitination?
activating enyzme
242
What is E2 in ubiquitination?
conjugating enzyme
243
What is E3 in ubiquitination?
ligase
244
What is Proteolysis?
cleaving protein bonds
245
Is Proteolysis reversible?
no
246
What are 2 exopeptidases (Proteolysis)?
aminopeptidase
carboxypeptidase
247
What ends of proteins does aminopeptidase
and carboxypeptidase target (Proteolysis)?
aminopeptidase : N
carboxypeptidase: C
248
What are 2 endopeptidases (Proteolysis)?
Trypsin
chymotrypsin
249
Where does the endopeptidase, Trypsin, target (Proteolysis)?
C terminus of Lys and Arg
250
Where does the endopeptidase, chymotrypsin, target (Proteolysis)?
C terminus of Phe, Tyr, and Trp
251
What are the 4 proteases that target functional groups?
Cysteine protease
Serine protease
Aspartic acid protease
Zinc metalloprotease
252
What amino acid does disulfide bonds occur between?
cystine
253
What does disulfide bonds promote?
protein folding
254
What is an example of a disulfide bond regulating protein folding?
protein disulfide isomerase
255
Folding of pro-insulin is stabilized by __________
disulfide bonds
256
_____________ of connecting peptides makes mature insulin
proteolysis
257
What are primary antibodies and secondary antibodies?
primary: specific for protein of interest
secondary: same as primary but has a tag that sends a signal
258
Western blot separates proteins by ________ and __________
size/charge
259
What is the advantage of immunohistochemistry?
can look cell to cell (different cell types)
260
Does western blot or immunohistochemistry use tissue samples?
immunohistochemistry
261
Does western blot or immunohistochemistry use fluorescence?
immunohistochemistry
262
Western blot can detect cleavage?
yes
263
What is the advantage of Tandem Mass Spec?
you don't have to know the protein or the modification
264
How does Tandem Mass Spec work?
by measuring the changes in mass of the peptide sequences (controlled v. modified) you can tell where the changes are
265
What are the 2 methods of Tandem Mass Spec?
1. Peptide Analysis MS
2. Peptide Sequencing MS
266
How does the method Peptide Analysis MS work in Tandem Mass Spec?
you figure out the mass to charge ratio
267
How does the method Peptide Sequence MS work in Tandem Mass Spec?
fragment the pieces and look for slight shifts in mass from the control to see where and what modification is present
268
What is the activating step of Scr kinase?
dephosphorylation of SH2 domain
269
What PTM are not reversible?
lipidation
proteolysis
270
What functional group is subject to phosphate addition?
Hydroxyl
271
A protein undergoing proteolysis undergoes a __________ reaction and will have severed bonds between ___________ and __________ functional groups
hydrolysis
carboxyl and amino group
272
What amino acid does ubiquitantion occur on?
Lys
