MCP Flashcards
(319 cards)
1
Q
What are the five most common aldoses?
A
glyceraldehyde, ribose, glucose, mannose, galactose.
2
Q
What are the three most common ketoses?
A
dihydroxyacetone, ribulose, fructose.
3
Q
What are enantiomers? How do they get their designation?
A
mirror image molecules. The D sugar has the -OH group on the 5th C on the RIGHT and the L sugar on the LEFT.
4
Q
Which enantiomer is more common? (D or L)
A
D is more biologically abundant
5
Q
What is the name of the 1st carbon in the ring structure?
A
anomeric carbon
6
Q
How do a and B anomers differ?
A
a anomer has the -OH and the -CH2OH group pointed in opposite direction (with the -OH group down) and the B anomer has the groups pointing in the same direction.
7
Q
What type of bond connects two monosaccharides?
A
glycosidic bond
8
Q
What are the naming criteria for a glycosidic bond?
A
a/B configuration of the anomeric carbon and the numbers of the connecting carbons (e.g. B-1, 4)
9
Q
What are the two “starch” molecules we ingest?
A
amylose and amylopectin
10
Q
What is “milk sugar?”
A
lactose
11
Q
What is table sugar?
A
sucrose
12
Q
Describe the bonds in amylose.
A
linear glucose polysaccharide with a-1,4 linkages
13
Q
Describe the bonds in amylopectin.
A
branched glucose polysaccharide with both a-1,4 and a-1,6 linkages
14
Q
Describe the bonds in lactose.
A
disaccharide with glucose and galactose with a B-1, 4 linkage
15
Q
Describe the bonds in sucrose.
A
disaccharide with fructose and glucose with a a-1,2 linkage.
16
Q
How do amylopectin and glycogen differ?
A
glycogen is more branched than amylopectin.
17
Q
What is dietary fiber?
A
cellulose
18
Q
Describe the bonds in cellulose.
A
linear glucose polysaccharide with B-1,4 linkages.
19
Q
Can we digest cellulose?
A
No, humans do not have an enzyme that breaks this type of bond
20
Q
What type of enzyme breaks down carbohydrates?
A
glycosidases
21
Q
What is the enzyme that breaks internal glycosidic bonds?
A
endoglycosidases
22
Q
What is the enzyme that breaks terminal glycosidic bonds?
A
exoglycosidases
23
Q
What is the enzyme that breaks down disaccharides?
A
disaccharidases
24
Q
What are the defining characteristics of the specificity of glycosidases? (3)
A
structure of the bond (e.g. B 1,4), types of sugar in the bond, and position (internal or terminal)
25
What are the criteria for a-amylase activity?
a-1,4 linkages, glucose, internal bonds
26
What are the types of a-amylase?
pancreatic and salivary
27
Are the products of a-amylase activity monosaccharides?
no. a-amylase only creates smaller polysaccharides and oligosaccharides.
28
What has to happen before carbohydrates can be absorbed into the blood stream?
they need to be broken down by glycosidases at the intestinal brush border into monosaccharides.
29
What are the main intestinal glycosidases? (5)
glucoamylase, maltase, isomaltase, sucrase, and lactase.
30
What are the criteria for glucoamylase activity?
a-1,4 linkages, glucose, terminal bonds
31
What two products does glucoamylase activity produce?
glucose and isomaltose
32
What are the criteria for maltase activity?
a-1,4 linkages, glucose-glucose bonds in maltose (disaccharide)
33
What are the criteria for isomaltase activity?
a-1,6 linkages, glucose, internal bonds
34
What are the criteria for sucrase activity?
a-1,2 linkages, glucose-fructose bonds in sucrose (disaccharide)
35
What are the criteria for lactase activity?
B-1,4 linkages, glucose-galactose bonds in lactose (disaccharide)
36
Deficiency in what enzyme causes lactose intolerance?
lactase
37
The process of oxidating glucose to make ATP and pyruvate is known as...
glycolysis
38
The storage polymer of glucose is?
glycogen
39
The process of oxidating glucose to a pentose sugar and NADPH is known as...
pentose phosphate pathway
40
What two processes does the liver use to regulate blood glucose levels?
gluconeogenesis and glycogenolysis
41
Does skeletal muscle play a role in maintaining blood glucose levels?
no. glycogen breakdown in muscle only serves to meet the glucose needs of the fatiguing muscle.
42
What is the normal range for blood glucose levels?
80-100 mg/dL
43
Decrease in blood glucose triggers release of what? What does it do?
glucagon. mobilizes fluels - increases gluconeogensesis, glycogen breakdown, lipolysis.
44
Increase in blood glucose triggers release of what? What does it do?
insulin. stores fuels - increases glycogen synthesis, fatty acid synthesis, triglyceride synthesis
45
What kind of energy do autotrophs convert? What are their substrates?
solar energy to chemical energy. they convert CO2 and H2O to glucose and O2 using pigments and a photon.
46
Heterotrophs convert what type of energy?
chemical energy to heat (IR)
47
Describe the second law of thermodynamics?
entropy never decreases and systems evolve towards maximum entropy (including spontaneous reactions).
48
How do organisms apply to the second law of thermodynamics?
organisms disorder their environment by releasing IR heat more than they order themselves. S(universe) = S(system) + S(surroundings)
49
What types of bonds does ATP contain?
phosphodiester bond (between a-phosphate and suar) and 2 phonsphoanhydride bonds (high energy)
50
What are the three reasons the phosphoanhydride bond releases so much energy?
1. charge repulsion is relieved
2. resonance stabilization of products
3. favorable interactions with water
51
How quickly is the ATP pool turned over?
1/2 of the pool every hour!
52
What are the three necessary work functions?
mechanical, transport, and biosynthetic work.
53
How does ATP meet our energy requirements at all times?
ATP immediately, carbohydrates intermediately, fats and lipids in the long term.
54
What two ATP functions are humans incapable of doing?
gas expansion (bombardier beetle) and bioluminesence (fireflies)
55
Why is ATP the primary energy carrier? (4 reasons)
1. 2 phosphyanhidride bonds to break (high energy)
2. soluable and mobile (readily diffusible)
3. high affinity binding to enzymes (structure)
4. recognizable by adenosine base (can compartmentalize energy stores)
56
What determines the rate of a chemical reaction?
the activation energy
57
Is the reaction for ATP hydrolysis (uncatalyzed) spontaneous?
No. the activation energy cannot be overcome.
58
How do enzymes change the rate of reactions? What other ability do they have?
They lower the activation energy height (while preserving the deltaG). The enzyme also has control over the expression of the products of the reaction.
59
Can ATP act as an energy donor or acceptor?
Both! it has an intermediate thermodynamic value - meaning it has higher energy phosphate compounds and low energy phosphate compounds.
60
What does the common intermediate principle state?
exergonic reactions are obligatorily coupled to endergonic reactions by virtue that they have a common intermediate (ATP)
61
How does the enzyme involved in ATP hydrolysis change the overall energy requirements of the reaction?
The extra energy (compared to the uncatalyzed reaction) is stored in the high energy bond between the enzyme and product (E-P).
62
Can ATP readily be converted to other NTPs?
Yes! Exergonic reversible reactions can take place to convert ATP to other NTPs. The net energy is 0 because it is as simple as breaking and forming the same type of bond.
63
What enzyme is responsible for NTP conversion?
nucleoside diphosphate kinase (NDK)
64
How does the cell use ATP hydrolysis levels to monitor the energy state of the cell?
ATP generating pathways are inhibited by ATP and stimulated by ADP & AMP. ATP utilizing pathways are the opposite.
65
How does the cell decipher between ATP generating pathways and ATP utilizing pathways?
Enzymes have feedback inhibition due to allosteric binding of end products at the regulatory site (changing the catalytic site's affinity for substrate).
66
What enzyme do muscles and nerves use to generate ATP? What are its substrates?
creatine kinase - phosphocreatine + ADP
67
What enzyme catalyzes the formation of ATP from two ADP?
adenylate kinase
68
What enzyme catalyzes the reaction of H2O and AMP to drive the reaction of adenylate kinase forward?
adenylate deaminase
69
In the first step of glycolysis, glucose is converted to what, by using what enzyme?
G6P, by hexokinase (glucokinase in liver)
70
In the second step of glycolysis, G6P is converted to what, by using what enzyme?
F6P, by phosphoglucose isomerase.
71
In the third step of glycolysis, F6P is converted to what, by using what enzyme?
FBP, by phosphofructose kinase.
72
In the fourth step of glycolysis, FBP is converted to what two products, by what enzyme?
DHAP (ketose) and GAP (aldose), by aldolase.
73
In the fifth step of glycolysis, DHAP is converted to what, and by what enzyme?
GAP, by triose-P isomerase.
74
In what steps of glycolysis is ATP necessary?
Step 1 (conversion of glucose to G6P), and step 3 (conversion of F6P to FBP)
75
In the sixth step of glycolysis, GAP in converted to what, by using what enzyme?
1,3 BPG by GAPDH
76
What kind of intermediate is formed in the GAPDH reaction?
Thioester intermediate
77
In the seventh step of glycolysis, 1,3 BPG is converted to what, by what enzyme?
3PG by phosphoglycerate kinase.
78
In the eighth step of glycolysis, 3PG is converted to what, using what enzyme?
2PG by phosphoglycerate mutase.
79
What kind of intermediate is formed in the phosphoglycerate reaction?
Phosphohistidyl intermediate.
80
In the ninth step of glycolysis, 2PG is converted to what, by what enzyme?
PEP by enolase
81
In the final step of glycolysis, PEP is converted to what, by using what enzyme?
Pyruvate by pyruvate kinase
82
In what step of glycolysis is NAD+ necessary?
Step 6 (GAP to 1, 3, BPG)
83
In what two steps of glycolysis is ATP produced?
Step 7 (1,3 BPG to 3PG) and step 10 (PEP to pyruvate).
84
How many net ATP does glycolysis produce?
2, 4 total, but 2 are used in the investment phase.
85
What are three ways that NAD+ in regenerated?
Lactic acid fermentation, alcohol fermentation, and the citric acid cycle.
86
At what intermediates doe fructose enter glycolysis as? How does it differ between muscle and liver?
In the muscle, fructose is phosyphorylated and enters as F6P. In the liver, it is first phosphorylated, then fructose-1-phosphate aldolase converts it to GAP.
87
Deficiency in what enzyme causes fructose intolerance characterized by liver damage and hypoglycemia?
Fructose-1 phosphate aldolase (aldolase B in Kaplan)
88
At what intermediate does mannose enter glycolysis? What 2 enzymes are necessary?
F6P using hexokinase and phosphomannose isomerase.
89
At what intermediate does galactose enter glycolysis?
G6P
90
Deficiency in what enzyme causes formation of galactitol, and causes cataracts?
Galactokinase
91
Deficiency in what enzyme causes mental retardation and liver failure due to buildup of UDP-glucose?
UMP transferase
92
What enzyme catalyzes the reaction of UTP and glucose-1 phosphate to form UDP-glucose in glycogen synthesis?
UDP-glucose phosphorylase
93
What enzyme pieces together UDP-glucoses together? What is the side product?
Glycogen synthase, and UDP is the side product.
94
What enzyme condenses glycogen by forming a1,6-linkages?
Branching enzyme
95
What is the goal of branching glycogen for storage?
Creating a storage molecule that is compact, but still has room for enzymes to react. It branches every 10 glucose residues
96
During glycogen breakdown, what enzyme phosphorylates glycogen to create glucose-1 phosphate?
Glycogen phosphorylase
97
Once glucose-1 phosphate is released, how does it enter glycolysis? Does it require energy?
It is converted to glucose-6 phosphate by phosphoglucomutase and doesn't require energy.
98
What enzyme breaks the a1,6-linkage left by glycogen phosphorylase? Why is this reaction less favorable?
Debranching enzyme breaks the bond and the products are a glucose-1 phosphate (easily enter glycolysis) and glucose (which needs to be converted using hexokinase, and thus requiring ATP).
99
What is the energetic cost (in terms of ATP) to release G6P for glycolysis?
1 ATP (UTP) to use glycogen phosphorylase, and then an extra 0.1 ATP for every glucose that needs to be broken from an a1,6-linkage. 1.1ATP/1G6P
100
Von Gierke disease is a defect in what enzyme? What are the consequences?
G6P phosphatase, increased glycogen causing hepatomegaly, and failure to thrive
101
Anderson disease is a defect in what enzyme? What are the consequences?
Branching enzyme. Severe cirrhosis and death by age 2. Glycogen has very few branches.
102
McArdle disease is a defect in what enzyme? What are the consequences?
Glycogen phosphorylase. limited exercise tolerance due to muscle cramping, usually normal glycogen levels and structure.
103
The most high energy needy cells are found where?
Heart muscle, kidney for transport, and liver for biosynthesis.
104
Where within the mitochondrion does the citric acid cycle take place?
Mitochondrial matrix
105
Where within the mitochondrion does oxidative phosphorylation happen?
Inner mitochondrial membrane
106
How does pyruvate enter the mitochondria for the TCA cycle?
Through a transport protein.
107
Does NADH directly cross the mitochondrial membrane?
No, it is indirectly carried by a H transporter in the XH form then recombines with NAD+ in the matrix.
108
How does ATP cross the mitochondrial membrane?
An ADP/ATP antiporter.
109
Step 1 of the pyruvate dehydrogenase complex involves what enzyme? What prosthetic group is involved?
E1 pyruvate dehydrogenase, TPP (thiamine)
110
Thiamine deficiency is known as?
Beriberi or Wernicke's encephalopathy (Wernicke-Korsakoff syndrome)
111
Step 2 of the pyruvate dehydrogenase complex involves what enzyme? What prosthetic group is involved?
Dihydrolipolyl transacetylase, lipoamide
112
Step 3 of the pyruvate dehydrogenase complex involves what enzyme? What prosthetic group is involved?
Dihydrolipoyl dehydrogenase, FAD
113
What product in the pyruvate dehydrogenase complex is the target in arsenic poisoning?
Dihydrolipoamide
114
What is the advantage of having the pyruvate dehydrogenase complex (swinging arm model)?
The rate of reactions are not limited by diffusion as all the necessary enzymes are attached.
115
Step 1 of the TCA cycle combines what with acetyl CoA to make citrate? What enzyme is used?
Citrate synthetase combines oxaloacetate with acetyl CoA with make citrate. It is a condensation reaction.
116
Step 2 of the TCA cycle converts citrate to what? Using what enzyme? Is there an intermediate? What kind of reaction is this? What is the cofactor?
Aconitase converts citrate to cis-aconitase (intermediate), then eventually to isocitrate using a hydration and dehydration reaction. The cofactor is FeS center.
117
Step 3 of the TCA cycle converts isocitrate to what? Using what enzyme?
Isocitrate is converted to a-ketoglutarate by isocitrate dehydrogenase via oxidative decarboxylation. NADH and CO2 is a byproduct of the reaction.
118
Step 4 of the TCA cycle converts a-ketoglutarate to what? Using what enzyme? What type of reaction? What are the cofactors?
A-ketoglutarate is converted to succinyl CoA by a-ketoglutarate dehydrogenase via oxidative decarboxylation. NADH and CO2 is a byproduct of the reaction. TPP, lipoic acid, and FAD are cofactors.
119
Step 5 of the TCA cycle converts succinyl CoA to what? Using what enzyme? What type of reaction? What are the byproducts?
Succinyl CoA is converted to succinate using succinyl CoA synthetase via substrate level phosphorylation and the common intermediate principle. GTP is a byproduct.
120
Step 6 of the TCA cycle converts succinate to what? Using what enzyme? What are the byproducts?
Succinate is converted to fumarate by succinate dehydrogenase via oxidation. FADH2 is a byproduct.
121
Step 7 of the TCA cycle converts fumarate to what? Using what enzyme?
Fumarate is converted to malate using fumarase via decarboxylation.
122
Step 8 of the TCA cycle converts malate to what? Using what enzyme? What is the byproduct?
Malate is converted to oxaloacetate using malate dehydrogenase via oxidation. NADH is a byproduct.
123
In one turn of the TCA cycle (1 pyruvate) how many electron carriers are produced? ATP? CO2?
3 NADH and 1 FADH2, 1 GTP, and 2 CO2
124
In what step of the TCA cycle is ATP produced?
Succinyl CoA synthetase converting succinyl CoA to succinate.
125
What are the overall functions of the TCA cycle? (4)
1. converts products to common fuel (NADH/FADH2)
2. makes ATP and NADH while converting glucose to pyruvate
3. serves as a meeting place for all oxidizable substrates
4. provides intermediates for biosynthesis
126
Where are the pentose phosphate pathway enzymes found?
Cytosol.
127
What are the important products of the pentose phosphate pathway?
ribose-5-phosphate and NADPH.
128
What are the first three steps of the pentose phosphate pathway known as? Are they reversible?
Oxidative phase, it is not reversible.
129
What are the starting and ending products of the oxidative phase of the pentose phosphate pathway?
G6P (hexose) begins, 2 NADPH, Ru5P (pentose), and CO2 are end-products.
130
What types of enzymes are involved in the oxidative phase of the pentose phosphate pathway?
2 dehydrogenases, and a lactonase
131
What are steps 4-8 of the pentose phosphate pathway known as? Are they reversible?
Non-oxidative phase, they are reversible.
132
What are the starting and "end-products" of the non-oxidative phase of the pentose phosphate pathway?
Ru-5P starts, and ends as intermediates of glycolysis (F6P and GAP). Step 4 is where ribose-5-phosphate is produced.
133
What types of enzymes are inolved in the non-oxidative phase of the pentose phosphate pathway?
isomerse, epimerase, transketolase, transaldolase.
134
What enzyme in the pentose phosphate pathway uses TPP (thiamine) as a prosthetic group?
transketolase (transfers C groups).
135
If we start with one glucose, what are the end products of the pentose phosphate pathway?
2 NADPH, 1 CO2, 1 R5P.
136
Ru5P is converted into what 2 products? In what proportion?
If you begin with 3 Ru5P, 2 will become Xu5P and 1 will become R5P.
137
The intermediates of non-oxidative phase of the pentose phosphate pathway (R5P and Xu5P) are converted to what? What is substituted in this reaction?
They are converted to two F6P (4 GAP), and 1 GAP. One GAP (normally 6 produced from glucose) is substituted for the 6 NADPH.
138
Which form (NADP+ or NAD+) is found in higher abundance in its oxidized state?
NAD+
139
Does NADPH or NADH typically act as a reductant?
NADPH
140
What is the function of NADPH in the liver?
To detoxify xenophobic substances using cytochrome P450.
141
What is the function of NADPH in red blood cells?
To detoxify ROS.
142
How does NADPH interact with glutathione to have an antioxidant effect?
Glutathione becomes oxidized to glutathione disulfide when it interacts with reactive species. NADPH donates its H to reduce glutathione back to its original form.
143
What is the role of G6PDH in the pentose phosphate pathway?
It is the first enzyme, and responsible for creating NADPH by removing the H from G6P and putting it on NADP+.
144
How does G6PDH deficiency clinically manifest itself?
Hemolytic anemia and selective advantage against malaria.
145
If R5P is needed, and NADPH isn't, how do you generate R5P?
Non-oxidative phase of the pentose phosphate pathway is run in reverse and R5P is created from F6P and GAP.
146
What are the biosynthetic uses of ribose?
RNA, ATP, NADH, CoA - information storage, energy transfer, redox reactions, and enzyme catalysis.
147
Why can glycolysis not be run in reverse to create glucose?
Three of the four kinase reactions in glycolysis are irreversible and need to be bypassed using alternative pathways.
148
In gluconeogenesis, pyruvate is first converted to what? By what enzyme?
Oxaloacetate by pyruvate carboxylase.
149
Pyruvate oxidase catalyzes what reaction? What is its prosthetic group? Is energy necessary?
Conversion of pyruvate to oxaloacetate in gluconeogenesis. The prosthetic group is biotin (B7) and energy is needed to activate bicarbonate.
150
In the second step of gluconeogenesis, oxaloacetate is converted to what? By what enzyme? Is energy required?
Oxaloacetate is converted to PEP by PEPCK. Energy is required.
151
Where does gluconeogenesis begin?
Mitochondria, pyruvate carboxylase is there.
152
Do triglycerides contribute to gluconeogenesis?
Yes (but barely...). Fatty acids cannot directly produce glucose, but glycerol backbone can.
153
How does oxaloacetate cross the mitochondrial membrane?
It is first converted to malate or aspartate and then a transport protein shuttle can move it.
154
How does PEP get converted back to F6P?
All these steps are reversible steps of glycolysis.
155
In the second bypass of gluconeogenesis, FBP is converted to what? Using what enzyme?
FBP is converted to F6P by fuctose bis-phosphatase.
156
What is the third bypass in gluconeogenesis?
G6P is converted to glucose. It happens specifically in the liver because that's where glucose-6-phosphatase is.
157
How many ATP are consumed in gluconeogenesis?
6 - 1 ATP at pyruvate carboxylase, 1 at PEPCK, and 1 at phosphoglycerate kinase. (all x2 because 2 pyruvate are used to make 1 glucose)
158
When is lactate produced?
When ATP demands exceed those capable of oxidative phosphorylation.
159
What are the mobile components of the electron transport chain?
cytochrome c, Q
160
What is the advantage of a membrane-bound electron transport chain?
No mobile carriers are needed and there is no rate limit by diffusion. Also, to have an electrical-chemical gradient two compartments are necessary and the membrane serves as a boundary.
161
What are the five classes of redox centers in the electron transport chain?
Flavins, iron-sulfur centers, ubiquinone, heme, and copper centers.
162
What kind of electron donor/acceptor are flavin centers?
2-electron donor/acceptors.
163
What are some examples of flavins? Which is the small and which is the large form?
FMN (small form), FAD (large form).
164
Which electron transport chain complexes utilize flavin redox centers?
Complex I (NADH dehydrogenase) and complex II (succinyl dehydrogenase).
165
What kind of electron donor/acceptor are iron-sulfur centers?
1-electron donor/acceptors.
166
What kind of iron-sulfur complex does Complex III use?
2-iron, 2-sulfur planar complex stabilized by cystine and histidine residues.
167
What kind of iron-sulfur complex does Complex II use?
4-iron, 4-sulfur cube shaped complex stabilized by 4 cystine residues.
168
Where do iron-sulfur complexes accept electrons from?
Flavins and Q.
169
What kind of electron donor/acceptor is Ubiquinone? What are some other important features of it?
2-electron donor/acceptor. It is extremely hydrophobic allowing it to move within membrane lipids and it acts as a cofactor that is an electron buffer.
170
What kind of electron donor/acceptor is heme?
1-electron donor/acceptor.
171
In cytochromes c and c1, what redox center is used? How is it attached to the protein?
Cytochrome c and c1 use a heme center and it is covlaently bound by two cystine residues.
172
In cytochrome c, the heme group coordinates with what amino acid residues? What does this mean for its electron affinities?
It coordinates with methionine and histidine. Becuase it can have a close or far confirmation, the iron binding has a wide array of electron affinities.
173
What kind of electron donor/acceptor are copper centers?
1-electron donor/acceptor.
174
How many coppers does the redox center of copper center A have?
2 coppers
175
Describe the redox center in copper center B...
Copper center B has a single copper covalently bounded by 2 histidine residues. It interacts with the heme from heme a3 and makes a sandwich where oxygen can bind.
176
What are the components of Complex IV (cytochrome oxidase)?
Cytochrome a, Copper a, copper b, cytochrome a3.
177
What is the function of cytochrome oxidase?
To quickly transfer four electrons to oxygen so that the production of H2O2 and superoxide radical can be avoided (decreasing oxidative damage).
178
Why are genetic defects in cytochrome oxidase detrimental?
They cause slower transfer of electrons to oxygen so cells are more likely to get oxidative damage and thus age faster.
179
How are the components of the electron transport chain arranged?
They increase in their affinity for electrons, allowing efficient flow.
180
What do the large gaps in energy flow in the ETC mean? How is this energy used?
The large gaps represent exergonic reactions. The energy released in these steps is used to couple the endergonic reaction of transferring a H across the membrane against its concentration gradient, thus establishing an electrochemical gradient.
181
What are the parts of ATP synthase?
F1 is the catalytic end with three sites for ATP synthesis. It is connected to Fo, the membrane portion that is hydrophobic and allows for hydrogen ions to pass through down their concentration gradient.
182
What is respiratory control?
The endergonic synthesis of ATP is obligatorily coupled to exergonic redox reactions, but it goes both ways. The redox reactions cannot happen without ATP synthesis. The oxygen consumption by the redox reactions is dependent on the concentration of ADP (ATP precursors)
183
What is the overall reaction for ATP synthesis?
NADH + H + 1/2 O2 + 3 ADP + 3P = NAD+ + 3 ATP + 4 H2O.
184
How is the establishment of the H+ gradient linked to ATP synthesis?
If ATP synthase doesn't move H+ down its concentration gradient, H+ will cause back pressure and repel electrons from crossing at the redox reaction sites, thus further coupling ATP synthesis and redox reactions.
185
What is complex I known as?
NADH dehydrogenase
186
What is complex III known as?
Cytochrome b/c1 (Fe heme protein)
187
What is complex IV known as?
Cytochrome oxidase (Cu heme protein cytochrome a/a3)
188
Complex I, complex II, and glycerol-P shuttle all donate their electrons to what?
Coenzyme Q
189
In the ETC, coenzyme Q donates its electron to?
Complex III (cytochrome b/c1)
190
In the ETC, complex III donates its electron to?
Cytochrome C (mobile carrier on the cytosolic side of inner membrane)
191
In the ETC, cytochrome C donates its electrons to?
Complex IV (cytochrom oxidase).
192
Cytochrome oxidase donates its electrons to what? Why is this important?
Oxygen, because oxidative phosphorylation cannot happen without the presence of oxygen as the final electron acceptor.
193
On what side of the inner mitochondrial membrane is the proton concentration higher (lower pH)?
Cytoplasm side, the matrix has less H+ concentration.
194
Where is the final ATP product released into?
Mitochondrial matrix
195
What component of the ETC is effected by cyanide and carbon monoxide poisoning?
Complex 4 (cyrochrome oxidase/cytochrome a/a3) and it prevents electron transfer to oxygen. Carbon monoxide may also competitively bind against oxygen in hemoglobin, further increasing hypoxemia.
196
What is the net effect of an uncoupler? What does it uncouple?
It uncouples oxidation and phosphorylation. It stimulates oxygen consumption in the absence of ADP.
197
What happens to ATP synthase in the absence of the proton gradient?
It runs in reverse, hydrolyzing ATP.
198
What are the properties of uncouplers?
Weak acids, hydrophobic, delocalized charge.
199
What is an example of an uncoupler?
Dinitrophenol.
200
Where is a natural uncoupler protein found? What is it used for?
Brown fat, it is used for non-shivering thermogenesis.
201
What hormone controls the natural uncoupler? What pathway does it utilize?
Norepinephrine. It increases PKA which then phosphorylates triglycerol lipase which can then make free fatty acids from triglycerides. These activate uncoupling protein in the membrane, creating a reduction of the H+ gradient, uncoupling oxidation and phosphorylation.
202
How do phosphorylation inhibitors effect the ETC? What is an example?
The prevent H+ movement down ATP synthase, preventing ATP synthesis. Oligomycin is an example of a phosphorylation inhibitor.
203
Is there a natural phosphorylation inhibitor? Where is it abundant?
Yes, the inhibitor protein. It is very abundant in heart muscle, as it protects against rapid ATP hydrolysis during ischemia.
204
Hoe does the inhibitor protein work?
As the pH of the matrix space increases, the inhibitor is protonated (changes conformation) and then binds ATP synthase. Once the normal pH is established, it becomes deprotonated and is released from ATP synthase allowing normal phosphorylation.
205
What does Mitchell's chemiosmotic theory state?
It states that ATP synthesis comes from the electrochemical gradient that is established from electron carriers such as NADH and FADH2 that are the result of breakdown of glucose.
206
Describe how ATP synthase works, including the alpha, beta, gamma, a, b, and c subunits...
The c subunits allow H+ to bind and then cause rotation of the wheel like structure. This also rotates the y subunit that is inside the three alpha/beta units. The alpha/beta units bind ATP and its substrates for synthesis. The rotation of the y subunit changes the conformation of the alpha/beta, and thus the affinities for ATP and its substrates. the a and b subunits act as a membrane anchor for the alpha/beta subunits, allowing them to remain stationary.
207
How was it established that ATP synthase was actually rotating?
A fluorescent actin filament was attached to the y subunit and observed under microscope! The filament was the equivalent of 2 football fields long, if the y subunit was the size of a person.
208
Where has another H+ driven rotary motor been discovered?
Bacterial flagella. The use lactose/H+ symporter to maintain the H+ gradient used to drive it.
209
What are other alternatives of donating electrons to the ETC? (2)
Glycerol phosphate shuttle and malate/aspartate shuttle.
210
From which side of the membrane does the glycerol phosphate shunt enter ETC?
It enters from the cytosolic side, because that's where the enzyme is.
211
What are the three regulatory steps in gluconeogenesis?
Conversion of pyruvate to PEP, conversion of FBP to F6P, and conversion of G6P to glucose.These are also the regulatory steps in glycolysis.
212
What product participates in feedback inhibition of PFK?
ATP, AMP also competes for the allosteric site, but promotes its activity rather than decreases it.
213
What enzymes catalyze the conversion of pyruvate to PEP? What shuttle is necessary? Are there cofactors?
Pyruvate decarboxylase converts pyruvate to OAA, which is then converted to malate and transported through the malate shuttle and converted back to OAA. OAA is converted to PEP by PEPCK. Both steps requite ATP and biotin is a necessary cofactor for pyruvate decarboxylase.
214
What enzyme catalyzes the conversion of FBP to F6P?
F6 phosphatase.
215
What enzyme catalyzes the conversion of G6P to glucose?
G6 phosphatase.
216
Describe the role of F2,6BP in glycolysis and gluconeogenesis...What kind of things control its expression?
F2,6BP is produced from F6P by PFK2 (normally F1,6BP is produced by PFK 1 in glycolysis). F2,6BP then acts as a modulator for PFK1. PFK2 is controlled by insulin and glucagon, insulin stimulated PFK2 activity, increasing F2,6BP, and increasing PFK1 activity. The opposite happens for glucagon. The opposite is true for F2,6BPs activity on FBPase. F2,6BP inhibits FBPase. So, indirectly insulin inhibits gluconeogenesis and glucagon stimulates gluconeogenesis through the levels of F2,6BP via PFK2.
217
Besides F2,6BP, what is the major regulator of F6Pase activity?
ATP/AMP. High AMP levels inhibit F6Pase activity.
218
How is pyruvate kinase activity regulated? Does it participate in feed-forward regulation? Feedback inhibition?
Pyruvate kinse is involved in feed-forward regulation by being stimulated by high levels of FBP. Its feedback inhibitors are ATP, Acetyl CoA, and cAMP phosphorylation.
219
What are the overall effects of glucagon on the glycolytic enzymes and gluconeogenic enzymes?
Glucagon supresses glycolytic enzymes and increases activity of gluconeogenic enzymes.
220
How does glucagon effect the levels of cAMP in the cell? What does this mean for the regulation of enzymes?
Glucagon increases levels of cAMP in the cell. Glucokinase, PFK1, and pyruvate kinase are all inhibited by cAMP. G6Pase, FBPase and pyruvate decarboxylase are stimulated by cAMP.
221
How is glycogen synthesis/glycogenolysis mainly regulated?
Reversible protein phosphorylation.
222
Describe the 2 enzyme pathway to increase activity of glycogen phosphorylase...
Glucagon increases cAMP, which activates PKA. PKA then phosphorylates (activates) phosphorylase kinase. Phosphorylase kinase then can phosphorylate (activate) glycogen phosphorylase.
223
How are the effects of the glucagon stimulated kinases reversed? What is responsible for this?
The kinases are turned off by phosphoprotein phosphorylase which is stimulated by insulin.
224
What effects do glucagon and insulin have on muscle cells? What else effects the synthesis of ATP?
Glucagon has no effect because muscle has no role in maintianing blood glucose levels. Insulin increases the amount of GLUT4 channels in the membrane, thus increasing glucose uptake for glycogen synthesis in liver and triglyceride synthesis in adipose tissue. Epinephrine also increases cAMP which frees G6P from glycogen to make ATP.
225
What is the second regulator of glycogen storage?
Allosteric regulation (the first is reversible protein phosphorylation).
226
What is the allosteric modulator of activating phosphorylase? Why is this necessary?
AMP is the allosteric modulator. It is important because phosphorylase needs to be activated if AMP levels are high, regardless of the blood glucose status. (meet the needs of the metabolic liver)
227
How is the pyruvate dehydrogenase complex regulated?
It has its own regulators, E4 and E5 (a kinase and phosphorylase). The kinase inactivates E1 and is stimulated by NADH, Acetyl CoA, and inhibited by pyruvate and ADP. The phosphorylase activates E1 and is stimulated by calcium (from adrenergic stimulation).
228
How are E2 and E3 of the pyruvate dehydrogense complex regulated?
Endproduct inhibition (NADH inhibits E3 and Acetyl CoA inhibits E2).
229
When blood sugar increases, insulin is released. This leads to (blank) of enzymes. When it decreases (blank) is released and leads to (blank) of enzymes.
Dephosphorylation, glucagon, phosphorylation.
230
In what ways is the CAC regulated? (3)
Product inhibition, feedback inhibition, and allosteric regulation.
231
What can deltaG predict about chemical reactions?
Spontaneity. If it is negative, the reaction is spontaneous, if positive, non-spontaneous, and if 0 the reaction is in equillibrium.
232
What is the equation for a chemical reaction? What portion corrects for varying concentrations of S and P compared to standard conditions?
deltaG = deltaG + RTln(P/S). RTln = 1.36log
233
Why is the deltaG equation useful?
It can predict the changed deltaG under non-standard conditions if the original deltaG is known.
234
What are the three advantages of storing energy as fat?
1. carbons in TGs have lower oxidations state than carbs and protein.
2. TGs are stores in anhydrous state - not bound by water.
3. Fats don't participate in osmotic balance (lots can be stored without disturbing water balance)
235
What are the most abundant length fatty acids?
16 or 18 chain fatty acids.
236
In polyunsaturated fatty acids, how are the double bonds arranged?
Neither adjacent or conjugated. They are usually separated by a methylene group.
237
How are fatty acids typically bound?
They are typically bound to proteins and can be esterified to compounds like glycerol. Very few free fatty acids are found biologically.
238
What is the normal conformation of fatty acid double bonds, trans or cis?
cis conformation.
239
Can the brain use non-esterified fatty acids as fuel? What cells prefer to?
No the brain cannot, the heart prefers to use fatty acids.
240
14 carbon fatty acids are called?
Myristic
241
The 2 16 carbon fatty acids are...
Palimitic acid, and palmitoleic (1 DB)
242
The 4 18 carbon fatty acids are...
Stearic acid, oleic acid, linoleic acid, linolenic acid. (DB go 0, 1, 2, 3)
243
The 20 carbon fatty acid is?
Arachadonic acid (4 DB)
244
What is responsible for fat emulsification? What else does it release?
Bile, it also releases fat soluable vitamins A, D, E, K.
245
What type of bond is in fatty acids? What enzyme breaks these bonds?
Ester bonds, lipases break them.
246
Where does fat digestion begin? How is in continued?
Salivary lipase, pancreatic lipase, then bile salts in the small intestine.
247
What is the main digestor of long chain fatty acids? What else is necessary? What are the products?
Long chain fatty acids are mostly degraded by pancreatic lipase. It needs colipase to gain access (activated by trypsin). It makes NEFA and monoacylglycerol (MAG).
248
The addition of bile salts creates? What are the components?
The addition of bile salts creates mixed micelles. They contain bile salts, cholesterol, and phosphatidylcholine.
249
How are lipids absorbed?
A transporter (fatty acid transport protein) takes up lipids into enterocytes. AQP3 mediates glycerol transport.
250
What is steatorrhea? What can cause this?
Excessively fatty stools. Blockage of bile flow, pancreas dysfunction, or lack of uptake into enterocytes.
251
Once absorbed into the cell, MAGs and LCFAs are synthesized into what? What enzymes are necessary?
LCFAs and MAGs are re-synthesized into triglycerides and then they are stored in cholymicrons. Acyltransferases can make MAGs from LCFAs.
252
How are TGs transported in the the lymph and blood?
In lipoproteins, more specifically cholymicrons. These have a protein and lipids with the hydrophobic portion on the interior and hydrophilic portion at the exterior.
253
What releases fatty acids from cholymicrons? What are the products of this? What protein does it recognize?
Lipoprotein lipase. Lipoprotein lipase cleaves all the bonds in TGs so the products are NEFA and glycerol. It recognizes cholymicrons by ApoCII.
254
What is the most prominent protein in cholymicrons?
ApoB48
255
What enzyme preferentially cleaves FA from DG and MG?
Hormone sensitive lipase. It creates NEFA and glycerol.
256
What enzyme preferentially cleaves FA from TG? Why is this step important?
Adipose triglyceride lipase. It is the rate limiting step in the lipolysis.
257
Where is HSL active?
Adipocytes.
258
Where is adipose triglyceride lipase active?
Mostly adipose tissue, but any tissue that can accumulate TGs.
259
What activates HSL? How is it activated?
Glucagon activates HSL, it increases cAMP which activates PKA, which can then phosphorylate it to activate it.
260
What inactivates HSL?
Insulin activates a phosphatase that cleaves the phosphate off the active HSL.
261
How are released NEFA transported to other tissues like muscle, liver, kidney?
They are transported while bound to albumin in the serum.
262
What other thing (besides HSL) does PKA phosphorylate that is important in lipolysis?
Perilipins. They are proteins on the surface of lipid droplets within the cell, mostly concentrated on the smaller surface ones. When phosphorylated, they change conformation allowing access by HSL to release the NEFA.
263
What does glycerol kinase do? Where is it active?
It catalyzes the formation of G3P from glycerol. It is only active in liver and kidney cells, and rarely adipose tissue.
264
How is the delta naming system of fatty acids used? How is this different from the omega system?
It shows the number of bonds, and their placement from the carbonyl carbon. The omega system names the double bonds starting from the position away from the last carbon.
265
What are the essential fatty acids?
Linoleic and linolenic (omega 6 and 3 respectively).
266
What are the three other pathways of FA oxidation besides beta-oxidation?
B oxidation of very long chain FAs in peroxisomes, alpha oxidation of branches FAs, and omega oxidation in the ER.
267
What is the first enzyme in beta oxidation of fatty acids? What is the energetic cost?
Thiokinase (acyl co-A synthetase). It costs 2 high energy bond (2 ATP equivalent).
268
What are the substrates and products of thiokinase?
Fatty acid and ATP make fatty acyl Co-A and AMP
269
How does fatty acyl Co-A get into the mitochondria for beta oxidation?
It is combined with carnitine from CPTI, shuttled across the membrane, then released from carnitine with CPTII. (Note: short, medium, and long chain fatty acids all have their respective transporters across the IMM).
270
How is beta oxidation inhibited?
CPTI is inhibited by malonyl C-A (the first product in fatty acid synthesis) meaning that fatty acid synthesis and oxidation can't happen at the same time.
271
Once the acyl Co-A is in the mitochondria, what enzyme acts on it? What is necessary for this reaction?
Acyl Co-A dehydrogenase. FAD is necessary. This reaction produces an enoyl Co-A.
272
What enzyme acts on the Enoyl Co-A? What is needed for this reaction?
Enoyl Co-A hydratase. Water is necessary. It produces a hydroxy acyl co-A.
273
What enzyme acts on the hydroxyl Co-A? What is necessary for this step?
Hydroxy acyl co-a dehydrogenase makes B-keto acyl Co-A. NAD is necessary for this step.
274
What enzyme acts on the B-keto acyl co-A?
Thiolase. It produces the acetyl co-A and another acyl co-A that is 2 carbons shorter than the previous one.
275
How are steps 2-4 of beta oxidation accomplished? What type of enzyme?
A single trifunctional enzyme.
276
What pathology is associated with medium chain oxidation? How is it treated?
Medium chain acyl co-A dehydrogenase deficiency. Avoiding fasting and high carb, low fat diet.
277
What type of double bonds cannot be oxidized in beta oxidation of fatty acids?
beta-gamma bonds. enoyl co-A isomerase must first switch the bond.
278
What other configuration cannot be oxidized in beta oxidation of fatty acids?
a delta4 and delta2 double bond at the same time. This requires NADPH.
279
What are the energy costs of breaking these types of bonds?
the By reduces the energy yield by 1 FADH2 so 2 ATP are lost. In the delta4/delta2 1 NADPH is used so you are missing 1 NADH so 3 ATP equivalent.
280
What is the end fat of odd chain fatty acids? What vitamins are necessary for their breakdown?
They enter TCA at succinyl co-A. It requires biotin and cobalamin.
281
Where are ketone bodies formed?
Liver
282
What are the three ketones produced? Are they all metabolically viable?
Acetoacetone, B-hydroxybuturate, and acetone. Acetone is considered the metabolic dead end because it is just secreted.
283
Under what conditions are ketone bodies formed?
Fasting, alcohol consumption, high fat-low carb diets, and uncontrolled diabetes.
284
What enzymes are used in ketone body generation?
HMG Co-A lyase, synthase, and Bketothiolase.
285
What is the clinical consequence of ketone body release in uncontrolled diabetes?
Diabetic ketoacidosis.
286
What are the most common amino acids in the serum?
Glutamine and alanine
287
What are the essential amino acids?
phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine, arginine, leucine, lysine.
288
How are amino acids absorbe in thr sm. intestine and secreted in the urine?
Na+ or H+ transporters. They have a high degree of redundancy.
289
What is Hartnup's disease? What vitamin deficiency is associated?
It is a defect in neutral amino acid transporter. It results in over secretion of tryptophan in the urine. It is similar to pellagra, or niacin deficiency.
290
What is cyntinuria?
It is a defect in cystine amino acid transporter. It results in cystine crystals that can contribute to kidney store formation.
291
Describe nitrogen balance.
The total daily nitrogen loss in urine, skin, and feces is equal to the nitrogen intake.
292
What does it mean to have positive nitrogen balance? Who typically has this?
It means the nitrogen loss is less than the intake. Growing children, body builders, or people recovering from significant injury have this.
293
What does it mean to have negative nitrogen balance? Who typically has this?
It means the nitrogen loss is greater than the intake. Wasting or malnourished individuals have this.
294
What are the three ways the body can remove free ammonia?
1. glutamate dehydrogenase
2. glutamine synthase (reversible by glutaminase)
3. carbomoyl phosphate synthases
295
Transamination involved what cofactor?
Pyridoxal phosphate (B6)
296
What kind of enzymes does transamination use? What does alanine turn into? What does aspartate turn into?
transaminases or aminotransferases. Alanine becomes pyruvate, aspartate becomes oxaloacetate.
297
Describe the dual role of glutamate dehydrogenase... What is its cofactor?
When the cell is energy rich, GD can make glutamate from a-ketoglutarate. If the cell needs energy it can make a-ketoglutarate from glutamate to enter the TCA cycle. GD needs NAD or NADP to function.
298
In the first step of the urea cycle, what is formed from NH4+ and CO2? What enzyme is used? Is energy necessary?
Carbamoylphosphate is formed by carbamoylphosphate synthease. 2 ATP are required.
299
Carbamoylphosphate is added to what to make citrulline? What enzyme is necessary?
Carbamoylphosphate is added to ornithine to make citrulline. OTC makes it, and it is a common genetic defect.
300
Citrulline is added to what to make what? What enzyme? Is energy necessary?
Citrulline is added to aspartate to make argininosuccinate. Argininosuccinate synthetase is the enzyme. 1 ATP is hydrolyzed.
301
Argininosuccinate is cleaved to make arginine and fumurate. What enzyme is used?
argininosuccinate lyase. fumurate can enter the TCA cycle.
302
Arginine is further cleaved to form? What enzyme?
Urea and ornithine. arginase is used.
303
Overall the energy requirements for the urea cycle? What is consumed? What is produced?
3 ATP. A consumed, fumurate is produced.
304
The balancing activity of pyruvate dehydrogenase and pyruvate carboxylase are dependent on levels of what?
Acetyl Co-A
305
Can acetyl Co-A cross the mitochondrial membrane?
No, it must be transported via the citrate shuttle and using citrate lyase.
306
What is necessary for the synthesis of fatty acids? Where does this come from (2 places)?
NADPH. It can come from recycling of OAA by malic enzyme, or the pentose phosphate pathway.
307
What are the two enzymes necessary for fatty acid synthesis?
Acetyl Co-A carboxylase (ACC) and fatty acid synthase.
308
What is the rate limiting enzyme in fatty acid synthesis?
ACC.
309
ACC catalyzes what reaction? What is the necessary cofactor? Why is this step so important?
ACC adds a carboxyl group to acetyl Co-A to make malonyl Co-A. Biotin with ATP is the necessary cofactor. It is the rate-controlling step and highly regulated.
310
What are the regulators of ACC activity?
High levels of citrate (alloteric regulation increases activity), insulin (de-phosphorylates to active form), and caloric intake which increases gene transcription. Glucagon/epinephrine decrease activity by phosphorylating. palmitoyl co-A causes end-product feed back inhibition, and low energy (AMP) downregulated.
311
Are carbons from malonyl Co-A ever incorporated into the fatty acid?
No, the CO2 group that was added is removed with fatty acid synthase.
312
What is the only fatty acid that humas are able to synthesize de novo?
Palmitate.
313
What vitamin is needed in the ACP portion of fatty acid synthetase?
Pantothenic acid (B5).
314
What are the five general steps in fatty acid synthesis?
1. activation
2. condensation
3. reduction
4. dehydration
5. reduction
315
How are mono-unsaturated fats created? How many types of these enzymes?
Desaturases insert a double bond. There are 3: delta9, 6, and 5.
316
What kind of polyunsaturated fats are needed for ecosanoid synthesis?
Omega-3 and omega-6. These have to be obtained from the diet.
317
What three things are synthesized from arachadonic acid?
Prostaglandins, thromboxanes, and leukotrienes.
318
What are the three arachadonic acid pathways? What do they make?
1. cyclooxygenase - prostaglandins, cyclins, and thromboxanes
2. lipoxygenase - leukotrienes and HETEs
3. cytochrome P450 - epoxides
319
NSAIDs inhibit what arachadonic pathway enzyme?
COX.
