Exam 1 Flashcards
(281 cards)
1
Q
What are the two functional groups of amino acids?
A
amino (NH2)
carboxyl (COOH)
2
Q
What does an amino acid backbone look like?
A
NH2–C(alpha)–COOH
3
Q
Amino acids contain a central __________ carbon atom
A
tetrahedral
4
Q
Only ____-amino acids are found in eukaryotes
A
L
5
Q
What is the only amino acid in eukaryotes that isn’t in the L conformation and why?
A
glycine
its R group is just an H
6
Q
Are water molecules charged are neutral?
A
neutral
7
Q
Are water molecules polar or non-polar?
A
polar
8
Q
What is the strongest bond?
A
covalent
9
Q
Why does NaCl dissolve easily in water?
A
its very positive so it makes bonds with water easily
10
Q
Are polar or non polar molecules insoluble?
A
nonpolar
11
Q
What makes aspartic acid and glutamic acid polar negative?
A
carbonyl R groups
12
Q
What makes lysine, arginine, and histidine polar positive?
A
amine R groups
13
Q
What makes asparagine and glutamine polar uncharged?
A
Amine R group
14
Q
What makes serine, threonine, and tyrosine polar uncharged?
A
OH R groups
15
Q
What makes glycine, alanine, valine, leucine, and isoleucine nonpolar?
A
carbonyl R groups
16
Q
What rare amino acid is considered the 21st amino acid and is used as a stop codon?
A
Selenocysteine (SEC, U)
17
Q
Where is the rare amino acid hydroxylysine and hydroxproline usually found?
A
connective tissue (collagen)
18
Q
Where is the rare amino acid carboxyglutamic acid usually found?
A
clotting factors
19
Q
What rare amino acid is found in bacteria?
A
PCA (pyroglutamic acid)
20
Q
What is the role of amino acid that do not occur in proteins?
A
neurotransmitters and hormones
21
Q
What are essential amino acids?
A
received through the diet (humans cannot synthesize)
22
Q
What are conditionally essential amino acids?
A
made under times of stress
23
Q
What are dispensable amino acids?
A
easily made all the time
24
Q
Amino acids are amphoteric, what does this mean?
A
they can either accept a proton or donate a proton
25
What does the cationic form an amino acid look like?
NH3+
COOH
26
What does the zwitterion form an amino acid look like?
NH3+
COO-
27
What does the anionic form an amino acid look like?
NH2
COO-
28
How do you calculate isoelectric point of a molecule?
PI = pK1 + pK2 / 2
29
What is the isoelectric point?
the pH at which a molecule is electrically neutral
30
How many pKa does a charged amino acid have?
3
31
Does formation of a peptide bond cause dehydration and rehydration?
dehydration
32
How does a peptide bond come together?
COO- bonds with NH2
33
What enzyme catalyzes peptide bond formation?
peptidyl transferase
34
What conformation are peptide bonds in?
trans
35
Is the peptide bond fully or partial double bonded?
partial
36
What is the length of a peptide bond?
0.133 nm
37
Due to the double bond characteristics, the peptide bond is on a ________ plane
amide
38
What direction is the protein read in?
N to C terminus
39
What level of protein structure is primarily determined by hydrophobic/phillic interactions?
tertiary
40
What are 2 ways proteins can be sequenced?
1. real amino acid sequencing
2. sequencing the corresponding DNA in the gene
41
What are 2 examples of real amino acid sequencing?
Sanger method
Mass spec
42
Protein function depends on _________
structure
43
Protein structure depends on sequence and ___________ forces
non-covalent
44
Is the number of protein folding patterns infinite or finite?
finite
45
Marginal stability facilitates ________
motion
46
Motion enables ___________
function
47
What bond is Phi and Psi inbetween?
Phi: C(a)--N
Psi: C(a)--C(o)
48
What are the possible phi and psi angles?
anything but 0
49
Secondary, tertiary, and quaternary structure of protein is formed and stabilized by ___________
non-covalent forces
50
Where do ionic interactions usually occur on a protein?
surface
51
Hydrogen bonding between ____ and ____ on peptide backbone is common
C=O
NH
52
Secondary protein structure is primarily stabilized by ___________
hydrogen bonds
53
What are 4 examples of secondary protein structure?
alpha helix
other helix
beta sheets
beta turns
54
What are alpha helices stabilized by?
hydrogen bonds
55
What is a dipole moment?
arrangment of NH groups are pointed one way and C=O groups are pointed in same the other making one end positive and one end negative (alpha helix)
56
What is helical capping?
Formation of H bonds with other nearby donors at the end of helicies
57
What is a anphiphilic helix?
hydrophobic lines up on one side and hydrophilic on the other
58
What holds beta pleated sheets together?
hydrogen bonds
59
How many residues are required for a beta turn?
4
60
What 2 amino acids are common in beta turns?
proline
glycine
61
What amino acid is never found in the middle of an alpha helix or beta sheet because it causes a kink/turn in peptide chain?
proline (has a large ring)
62
What is Type I beta turn?
proline in position 3
63
What is Type II beta turn?
proline in position 2
glycine in position 3
64
What is the cause of Sickle Cell Anemia?
Glu to Val (single base change)
65
Why do protein secondary structures form whenever possible?
hydrogen bonding
66
What two ways do proteins fold to be more stable?
formation of intramolecular bonds
reduction in the surface area
67
What is the only covalent bonding in protein folding?
disulfide bonds
68
Globular or fibrous? Create maximum internal bonds (intramolecular) and minimize solvent contact
globular
69
Globular or fibrous? Create maximum intermolecular bonds and maximize molecule to molecule contact
fibrous
70
Do all proteins have quaternary structure?
No (but they all have 1, 2, 3)
71
Covalent or non-covalent association for globular proteins?
non-covalent
72
Covalent or non-covalent association for fibrous proteins?
Covalent
73
What are the 5 advantages of quaternary structure?
1. stability
2. efficiency
3. assembly
4. cooperativity/allostery
5. regulation
74
How do quaternary proteins have stability?
minimize surface area
75
How do quaternary proteins have efficiency?
synthesize large protein in small subunits
76
How do quaternary proteins have assembly?
combination of 2 proteins to make a catalytic site
77
How do quaternary proteins have cooperativity/allostery?
binding of one substrate increases affinity for other substrates
78
What is the simplest kind of symmetry?
rotational
79
Can quaternary structures polymerize?
yes
80
What are 3 examples of quaternary structures that can polymerize?
Tubulin
TMV
flagella
81
What are the 4 classes of globular proteins?
alpha
beta
alpha/beta (combined)
alpha+beta (seperate)
82
Are globular or fibrous proteins more common?
globular
83
In fibrous proteins, polypeptide chain is organized _______ to a single axis
parallel
84
What is alpha keratin made of?
What is beta keratin made of?
alpha keratin: alpha helix
beta keratin: beta sheets
85
Are fibrous proteins soluble or insoluble?
insoluble
85
What are 3 examples of fibrous proteins?
alpha keratin
beta keratin
collagen
86
What is the amino acids sequence for beta keratin?
Gly-----Ala/Ser----Gly-------Ala/Ser.........
every other amino acid is a glycine
87
What is beneficial about all the glycine's in beta keratin pointed the same way?
allows for tight packing of sheets
88
alpha keratin is what shape?
coiled coil
89
What is a coiled coil?
dimers line up to form a antiparallel tetramer
90
Alpha keratin is 2 _____ alpha helices super coiled in a _____handed manner
2 right handed ---> left handed
91
What is the defect in Osteogenesis imperfecta?
collagen
92
What is the defect in Creutzfeldt-Jacob disease?
prions (misfolded proteins)
93
What is the defect in Sickle Cell anemia (protein wise)?
polymerization of hemoglobin
94
What is the most abundant protein in animals?
collagen
95
What is the most common collagen type?
Type I
96
What is the amino acids sequence for collagen?
Gly------X-------Y
X = proline
Y = hydroxyproline
97
What are the 2 modified amino acids found in collagen?
hydroxyproline
hydroxylysine
98
What is required for the hydroxylation of proline in collagen?
Proline
oxygen
alpha-ketogluterate
ascorbic acid (Vit C)
99
What are the products of hydroxylation of proline in collagen?
hydroxyproline
succinate
dehydroascrobate
100
How is scurvy caused?
deficiency in vitamin C causes no hydroxylation of proline affecting collagen
101
What is required for the hydroxylation of lysine in collagen?
lysine
oxygen
alpha ketogluterate
ascorbic acid (Vit C)
102
Attaching glucose to _____________ creates bone mineralization
5-hydroxylysine
103
What is the enzyme involved in hydroxylation of proline?
Prolyl hydroxlyase
104
What is the enzyme involved in hydroxylation of lysine?
lysyl hydroxylase
105
Collagen has high levels of glycine, proline, and hydroxyproline. How does this affect collagen's secondary structure?
CANNOT form traditional alpha helices and beta sheets
-forms left handed helicies
106
What is the tertiary structure of collagen?
3 left handed helices intertwine to form a right handed **triple helix**
107
In the tertiary structure of collagen, every third residue is _________ which points inside the helix
Gly
108
What is tropocollagen?
basic structural unit of collagen (before individual collagen cross link together)
109
What occurs in the holes present when collagen cross links?
bone mineralization when glucose is added to hydroxylysine
110
What is Type I collagen called?
fiber forming
111
Where is most of the iron and heme in our bodies located?
RBC
112
As young cells differentiate into RBC, _____ continent increases
hemoglobin
113
Gamma globin is is fetal or adult?
fetal
114
Beta globin is fetal or adult?
adult
115
Does gamma globin increase or decrease with age?
decrease (its fetal globin)
116
Cooley's anemia is caused by the absence of ___________ chains
beta globin
117
Myoglobin is a monomeric oxygen ______ protein
storage
118
Hemoglobin is a tetrameric oxygen __________ protein
transport
119
Hemoglobin is an allosteric _________
regulator
120
_______ iron interacts with 6 ligands in Hb and Mb
heme
121
When Mb or Hb bind oxygen, the O2 molecule binds to ____________
heme iron
122
What happens when O2 binds to the heme iron as the last ligand?
the heme plane is tilted (conformational change) rupturing the salt bridges
123
How many binding ligands does Hb or Mb?
6
124
DeoxyHb is the tense or relaxed state?
and is O2 bound?
tense
O2 not bound
125
OxyHb is the tense or relaxed state?
and is O2 bound?
relaxed
O2 bound
126
The oxygen binding curve for Mb and Hb is what shape?
Mb:hyperbolic
Hb: sigmoidal
127
what is the effect of the oxygen binding curve for Hb being sigmoidal shaped?
positive cooperativity
128
What is the positive cooperativity effect on the oxygen binding curve?
When the first oxygen binds it easier for the other oxygens to bind
129
What is the P50 on an oxygen binding curve?
partial pressure of oxygen when Hb is 50% saturated
130
P50 is ________ proportional to the oxygen affinity
inversely
131
Does Hb or Mb have a greater affinity for oxygen at all presures?
Mb
132
Hb binds to oxygen in the _______ and releases it in the capillaries
lungs
133
What is 2,3-bisphosphoglycerate?
allosteric effector of hemoglobin
134
The sigmodial binding curve shape is only observed in the presence of _____________
2,3-bisphosphoglycerate
135
_____________ binds at a site distant from Fe where oxygen binds, which makes it an allosteric effector
2,3-bisphosphoglycerate
136
Why does 2,3-bisphosphoglycerate bind easily to Hb?
its very negative and Hb is very positive
137
What is the purpose of 2,3-bisphosphoglycerate?
stabilizes deoxyHb (tense form;no oxygen bound)
- allows the hemoglobin to act as an effective oxygen carrier delivering oxygen to muscles
138
Fetal hemoglobin has a higher affinity for O2, why?
because it has a lower affinity for 2,3-bisphosphoglycerate (2,3-BPG stabilizes oxygen off loading)
139
Where is the fetal Hb located on the oxygen saturation curve?
to the left because it has high oxygen affinity because it doesn't bind well to 2,3-bisphosphoglycerate
140
What is the mechanism of sickle cell anemia involving hemoglobin?
when Hb goes deoxy (no O2 bound), a pocket is exposed causing Hb to polymerize and distort shape
141
What is the new CRISPR study for Sickle Cell Anemia?
decrease BCL11A which suppresses fetal hemoglobin
142
Water has ________ specific heat
high
143
Water has __________ fusion and vapor heat
high
144
Water has ___________ surface tension
high
145
Is water polar or non-polar?
polar
146
How many H bonds can water form?
4
147
Why does water have a dipole moment?
The O makes one side negative and Hs make the other side positive
148
How many hydrogen bonds does water and ice make?
ice: 4
water: 2.3
149
Is water or ice more stable half life?
ice
150
Is ice or water less dense?
ice
151
What is capillary action of water?
water rises in narrow tubes against gravity
152
Why is ice less dense than water?
it forms a lattice shape where the molecules are more spread out
153
What is important about water having a high dielectric constant?
dissolve ions easily
154
What is a hydration shell?
water surrounds ions (positive ions have oxygen pointing towards them)
155
What are colligative properties?
physical changes that occur when a solute is added to a solvent (water)
156
What are the 4 colligative properties of water?
1. vapor pressure lowering
2. boiling point elevation
3. freezing point depression
4. increased osmotic pressure
157
Explain water having increased osmotic pressure when a solute is added
when solute is added to water it rises in semipermeable tube and 1 atm needs to be added to lower the level to before
158
How do nonpolar solutes organize water?
The H bonds reorganize water
159
Does non-polar solutes increase or decrease entropy?
decrease (less chaos)
160
What is an amphiphilic molecule?
attracted to both polar and nonpolar environments
161
What is an amphipathic molecule?
contain both polar and nonpolar group
162
What is an example of an amphipathic molecule?
fatty acids
163
What does ionized water form?
hydronium ions (H3O or H+)
164
What is the equation for Ka?
Ka = [H+][A-]/[HA]
165
Ka = [H+][A-]/[HA]
What is the HA?
weak acid
166
Ka = [H+][A-]/[HA]
What is the A-?
conjugate base
167
What is pKa?
When weak acid is 50% acid and 50% base
168
On a titration curve, what happens when the pH is close to the pKa?
the pH barley changes
169
When pKa is 0.5 then its equal to the ____
pH
170
How do you determine how many humps are there on a titration curve?
how many hydrogens the molecules have
171
What are buffers?
solutions that resist changes in pH as acids or bases are added
172
Buffers can only be used reliably within a pH of ____ from thier pKa
1
173
What is Gibbs free energy (G)?
amount of usable energy in that system to do work
174
What is the equation for Gibbs free energy?
G=H-TS
175
What is H?
What is S?
in Gibbs free energy
H = enthalpy (heat)
S = entropy (disorder)
176
Is a positive delta G an endergonic or exergonic reaction?
endergonic
177
Is a positive delta G a spontaneous or non-spontaneous reaction?
non-spontaneous
178
endergonic = spontaneous or non-spontaneous reaction?
non-spontaneous
179
Is a negative delta G an endergonic or exergonic reaction?
exergonic
180
Is a negative delta G a spontaneous or non-spontaneous reaction?
spontaneous
181
exergonic = spontaneous or non-spontaneous reaction?
spontaneous
182
Which direction does the arrow go for endergonic reactions?
backwards
183
Which direction does the arrow go for exergonic reactions?
forward
184
For endergonic reaction, Does the initial G or final G higher energy?
G final (goes from lower to higher energy)
185
For exergonic reaction, Does the initial G or final G higher energy?
G initial (goes from higher to lower energy)
186
Do exergonic or endergonic reactions release energy?
exergonic
187
Do exergonic or endergonic reactions require energy?
endergonic
188
Endergonic reactions are usually what kind of reactions?
synthesis
189
Exergonic reactions are usually what type of reactions?
break down
190
What does the little circle next to the delta G mean?
standard gibbs free energy (same constants)
191
How are endergonic reactions possible in the body even though they are not favored because they require energy?
energy coupling (ex ATP)
192
What are the 3 chemical groups of ATP?
three phosphates
adenine
ribose
193
What is the order of the three phosphates on ATP?
gamma (business end)
beta (middle)
alpha (next to ribose)
194
Is ATP hydrolysis spontaneous or non-spontaneous?
spontaneous
195
What is the non-native structure of proteins?
unfolded (primary structure)
196
What is a native structure of a protein?
folded conformation
197
Is protein folding spontaneous or non-spontaneous?
spontaneous
198
If protein folding is spontaneous, what is the gibbs free energy and is the starting energy higher or lower?
negative G
starting E is higher
199
When G is negative, what is H and S?
H < 0 (releasing heat)
S > 0 (environment around protein is now disordered)
200
Electrostatic interactions occur between _______ and ________
cation and anion
201
What 3 things are needed for an H bond?
1. acceptor
2. donor
3. hydrogen
202
What is the most common acceptor and donor in H-bonds?
acceptor: oxygen
donor: nitrogen
203
What happens in van der Waal interactions if the molecules atomic volumes get too close?
they aren't attracted anymore and are repulsed from each other
204
Hydrophobic effect is not an attractive force, its a ______________ driven process
thermodynamically driven
205
What is the value of water being able to shield?
weaken interactions between molecules
206
What are the 4 trivial enzyme names?
kinase
phosphate
dehydrogenase
reductase
207
What are zymogen enzymes?
inactive precursor of an enzyme that has little or no enzymatic activity
but once proceed post-translationally it become active
208
What are coenzymes?
non-peptidic molecules that bind to enzyme and are needed for reaction to take place
209
____ are not refereed to as coenzymes
ions
210
What are cofactors?
same as coenzymes but are substrates of low abundance (ex NAD+)
-typically a chemical group
- not required
211
What are prosthetic groups?
cofactors that are tightly/covalently bound to enzyme
212
What are apoenzymes?
(typically inactive) coenzyme-dependent enzyme that doesn't have the co-enzyme bound to it
213
What is a holoenzyme?
when the Apoenzyme has the coenzyme bound to it (active)
214
What are isoenzymes?
enzymes that catalyze the same reaction yet differ in thier amino acid sequence (hexokinase)
215
Isoenzyme catalyze the same reactions but have different ______ and ____
Vmax
Km
216
Why don't spontaneous reactions just occur all the time in a cell?
it must get past the activation energy barrier
217
What helps a reaction get over the activation energy by lowering it?
enzymes
218
Enzymes only affect the reaction path not the ______ and _______
products and reactants
219
Most enzymes in a cell are proteinaceous, what does proteinaceous mean?
built by amino acids and cofactors
220
What is the worlds oldest and most abundant enzyme?
ribozyme (RNA)
221
What is enzyme specificity?
an enzyme has an active site SPECIFIC for a given substrate
222
What is the Lock and Key theory?
substrate fits into enzyme like a key in a lock
223
Why is the lock and key theory not completely correct?
enzymes can change to fit their substate
224
What is the Induced fit theory?
enzymes can change to fit their substate
225
What is the catalytic constant (kcat)?
the rate of ES --> E + P (cannot be reversed)
slowest step of reaction
226
kcat is also known as the turnover number, what does that mean?
maximal number of catalytic cycles an enzymes performs in one second (similar to RPM)
227
How do you calculate the turnover number (kcat)?
1/duration of catalytic cycle
228
What is the unit of measurement of kcat?
s-1
229
According to Michaelis-Menten kinetics...
The [E] is much _________ than [S]
smaller
230
According to Michaelis-Menten kinetics...
[E] and [S] binding is ________ and defined by k1 and k-1
reversible
231
According to Michaelis-Menten kinetics...
formation of product is _____________
irreversible
232
According to Michaelis-Menten kinetics...
What is the steady state assumption?
the [ES] is constant during the initial peroid of enzyme reaction
as the [ES] forms = slowing of [ES] formation rate
* number of people entering and exiting the room is the same
233
What is the Michaelis-Menten kinetics equasion for v/Vmax?
v/Vmax = [S] / Km+[S]
234
0
0
235
Why is the v/Vmax and [S] curve hyperbolic for affinity?
as the [S] starts increasing the rate us very fast but as more S is added the enzymes slows down
236
How do you find Km on graph?
go to 0.5 on the Y axis and go down
237
What does Km indicate?
how well the enzyme interacts with the substrate (AFFINITY)
238
Is a higher or lower Km mean a stronger affinity for substrate?
lower Km (more left on curve)
239
When [S] > Km the v/Vmax = ?
1 ( aka v=Vmax)
-cannot go any faster
240
As Km increases, [S] __________
increases
241
How do you make an enzyme reach Vmax?
add more substrate
242
Michaelis-Menten kinetics only applies to what kind of enzymes?
ones with 1 active site
243
What is cooperativity?
when first substrate binds enhances the binding of other substrates
244
What is the shape of cooperativity enzymes on a graph?
sigmoidal (S-shaped)
245
How do you tell on a graph which enzyme has more cooperativity?
at concentrations below K0.5, the most cooperative line has low activity
at concentrations above K0.5, the most cooperative line has high activity
246
When an enzyme has high cooperativity, its activity below Km (S 0.5) is very ______, but _________ after the [S] exceeds S 0.5
low
increases
247
What is an allosteric site?
used by small molecules to bind to enzyme not at active site and inhibits or activates
248
How does allosteric activators affect V max?
increases (enzyme can go faster)
249
How does allosteric activators affect Km?
decrease
(much sharper curve increase)
250
Where do competitive inhibitors bind?
active site
251
non-competitive inhibitors are the same as _________ inhibitors
allosteric
252
Who do you get rid of competitive inhibitors?
increase [S] and it will kick inhibitor out
253
What are irreversible inhibitors?
bind covalently to active site
ex: aspirin
254
What is inhibition of the activity of an enzyme by a downstream product?
feedback inhibition
255
What is inhibition of an enzyme by its own product?
product inhibition
256
What is downstream activation of an enzyme by a compound upstream in a pathway
feedforward activation
257
Enzyme that catalyze __________ reactions are usually very regulated
irreversible
258
What is flux in steady state?
concentration of reactants and products doesnt change (waterfall)
259
If an enzyme is blocked (deficient) what happens
upstream...
downstream...
first irreversible reaction...
upstream - increased [ ]
downstream - decreased [ ]
first irreversible reaction - nothing
260
What is the 2 equations for pH?
pH = -log[H+]
pH = pKa + log [A-]/[HA]
261
How do you find the moles of a solute?
How do you find the concentration from that?
grams X 1 mol/grams
mol/volume
262
How do you find the [H+] if found the [OH]?
10e-14 -- [H+]
263
If a enzyme has a small Km what does that mean for affinity?
the smaller the Km the stronger the affinity
264
If an enzyme is slower at low concentrations then faster at higher concentrations, what does that say about the cooperativity?
it has high cooperativity because it is able to easily bind more substrate once some is bound
265
What shape curve does cooperativity have? What shape does affintiy have?
cooperativity: sigmoidal
affinity: hyperbolic
266
Are proteins more or less soluble at thier isoelectric point?
least soluble (neutrally charged)
267
Does increasing Hb cooperativity promote unloading of O2?
No, increased Hb cooperativity helps O2 bind better to Hb
268
Does increasing [CO2] promote unloading of O2?
yes
269
Does increasing [2,3-BPG] promote unloading of O2?
yes
270
Does fetal Hb have a higher or lower affinity for O2 and why?
high
because it has a low affinity for 2,3-BPG
271
Dissolved solutes alter colligative properties of water because they change...
the concentration of water
272
What must a buffer consist of?
weak acid and strong conjugate base
273
What is the optimal van der Waal distance?
3.4 A
274
At which point in an enzymatic reaction will the Michaelis constant (Km) equal substrate concentration?
V = 1/2Vmax
275
How does a competitive inhibitor affect Vmax?
no effect
- as more S is added the inhibitor will just get kicked out so it wont affect speed at high [S]
276
How does a competitive inhibitor affect Km?
increases Km
- since some of the active sites are occupied by the inhibitor, more S is needed to achieve the same level of activity
277
How does a competitive inhibitor affect kcat?
no effect
- doesn't affect Vmax so it does effect kcat
278
How does a non-competitive inhibitor affect Vmax?
decrease Vmax
- inhibitor is always present since its not in the active site so it wont be kicked out
279
How does a non-competitive inhibitor affect Km?
no effect
- The substrate can bind regardless of the inhibitor because its not bound to the active site, so substrate can easily bind as if the inhibitor isnt there
280
How does a non-competitive inhibitor affect kcat?
decreases kcat
- decreases Vmax so it decreases kcat
