Exam 3 Flashcards
1
Q
How do plants store glucose?
A
As starch: Amylose or Amylopectin
2
Q
What is the structure of amylose?
A
An unbranched polymer made up of only a1-4 linkages
3
Q
What is the structure of amylopectin?
A
A branched polymer that has a1-4 linkages along with a1-6 branch points every ~30 residues
4
Q
How do animals store glucose? What is the structure?
A
Glycogen - similar structure to amylopectin, but the branch points are every 8 to 12 residues
5
Q
What is cellulose? What is its’ structure?
A
Cellulose is the primary component of plant cell walls. B1-4 linkage.
6
Q
What is chitin? What is its’ structure?
A
Chitin is the primary component of exoskeletons. B1-4 linkage of N-acetylglucosamine.
7
Q
How do cellulose & chitin strengthen microfibrils?
A
Cellulose and chitin straight chains have extensive H-bonding that strengthen the fibrils.
8
Q
What is a N-linked protein?
A
Oligosaccharide is attached to an Asn side chain
9
Q
What is an O-linked protein?
A
Oligosaccharide is attached to a Ser or Thr side chain
10
Q
Why is the purpose of glycoproteins?
A
Since a wide variety of oligosaccharide modifications are possible, they can serve as unique identifiers for cells.
11
Q
How are ABO blood types determined?
A
ABO blood type is determined by part of an O-linked oligosaccharide on the cell surface.
12
Q
What blood types have a sugar being added and why?
A
Differences in a few active site residues of a glycosyltransferase result in a different sugar being added to the O antigen in A- and B-type individuals.
13
Q
Why don’t O type individuals have a sugar added?
A
No functional version of the glycosyltransferase
14
Q
What is connective tissue made up of?
A
Connective tissue such as cartilage, skin, and tendons include proteoglycans which are structural proteins linked to glycosaminoglycans
15
Q
Why is the structure of glycosaminoglycans useful in connective tissue?
A
The polar groups on glycosaminoglycans attract H2O to help lubricate tissue, while negative charges repel each other upon compression to act as shock absorbers.
16
Q
What is the structure of glycosaminoglycans?
A
Glycosaminoglycans are heteropolysaccharides consisting of repeating uronic acid and hexosamine residues.
17
Q
What is the structure of the peptidoglycan layer in bacterial cell walls?
A
Peptidoglycan consists of N-acetylglucosamine and N-acetylmuramic acid repeating units attached to cross-linked tetrapeptides.
18
Q
What is catablosim?
A
Breaking down larger molecules.
19
Q
What is Anabolism?
A
Building complex molecules at the expense of energy.
20
Q
How are biopolymers digested?
A
Enzymes hydrolyze biopolymers into smaller products that may be absorbed by the intestine.
21
Q
How are proteins degraded outside cells?
A
The lysosome is an organelle containing degradative enzymes that primarily breaks down extracellular or membrane proteins.
22
Q
What is the proteasome?
A
The proteasome is a multisubunit protease that targets intracellular proteins.
23
Q
How does the proteasome know which proteins to degrade?
A
Ubiquitin ligase transfers a small protein, called ubiquitin, to a Lys residue of the target protein. Once 4 ubiquitins have been added, the end cap subunits of the proteasome recognize the target protein for degradation.
24
Q
What is the role of Vitamin C in the body?
A
Vitamin C is an antioxidant and acts as a cofactor for the enzyme that hydroxylates proline residues in collagen.
25
What is the role of Vitamin B1 in the body?
Thiamine (precursor for B1) is a cofactor for the pyruvate dehydrogenase complex and a-ketoglutarate dehydrogenase.
26
What does a deficiency in Vitamin B1 do?
Leads to beriberi which is characterized by weakness and leg swelling.
27
What redox cofactors are used to conserve energy?
The phosphorylated form (NADP+/NADPH) is generally used as redox cofactor in biosynthetic pathways.
28
What is the role of Vitamin B3 in the body?
Niacin is a precursor for NAD(P)+/NAD(P)H.
29
What does a vitamin B3 deficiency lead to?
Pellagra which is characterized by diarrhea, dermatitis, dementia, and death.
30
What is Ubiquinone/ Coenzyme Q?
A lipid soluble electron carrier used as redox cofactor to conserve energy. A mobile electron carrier that often receives electrons from an FADH2 prosthetic group.
31
What are flavins?
Flavins are prosthetic groups that can carry 1 or 2 electrons.
32
What is an irreversible step in a metabolic pathway?
An irreversible step occurs early in a metabolic pathway to commit a metabolite to the pathway. (DG far from zero).
33
What types of molecules are used as energy currency by the cell?
Energy may be stored in reduced cofactors: ATP, Acetly-CoA
34
How is energy currency used?
Energy currency is used in chemical reactions to make the process favorable. (Negative DG).
35
What is the net yield of glycolysis?
Net yield = 2 ATP + 2 NADH
36
What is glycolysis?
The breakdown of glucose by enzymes releasing energy & pyruvic acid
37
What happens in glycolysis under anaerobic conditions?
2 NADH --> heat
38
What happens in glycolysis under aerobic conditions?
2 NADH --> 5 ATP
39
What happens in Step 1 of glycolysis? What are the enzymes, reactant, and products?
Step 1: Hexokinase Phosphorylates Glucose
-irreversible
-phosphorylating glucose prevents the sugars from leaving the cell and reduces intracellular [glucose] so that the gradient favors import.
- enzyme: hexokinase
- reactants: Glucose, ATP
- products: G6P, ADP, H+
40
What happens in Step 2 of glycolysis? What are the enzymes, reactants, and products?
Step 2: Phosphoglucose Isomerase
-reversible
-enzyme: Phosphoglucose Isomerase
-reactants: G6P
-products: F6P
41
What happens in Step 3 of glycolysis? What are the enzymes, reactants, and products?
Step 3: Phosphofructokinase-1 phosphorylates F6P
-enzyme: Phosphofructokinase-1
-reactants: F6P, ATP
-products: F1,6-Bisphosphate, ADP, H+
42
Draw Step 4 of glycolysis.
43
What evidence suggests aldolase uses a Schiff base mechanism in Step 4?
In alanine screening, the gene for a protein is modified to test the importance of a specific residue. Lys is essential to form the Schiff base.
44
Draw Step 5 of glycolysis.
45
Draw Step 6 of glycolysis.
46
What happens in Step 7 of glycolysis? What are the enzymes, reactants, and products?
Step 7:
-enzyme: phosphoglycerate kinase
-reactants: 1,3 BPG, ADP
-products: 3-phosphoglycerate, ATP
47
Draw Step 8 of glycolysis.
48
What happens in Step 9 of glycolysis? What are the enzymes, reactants, and products?
Step 9:
-enzyme: Enolase
-reactants: 2-phosphoglycerate
-products: Phosphoenolpyruvate, H2O
49
Draw Step 10 of glycolysis.
Pyruvate kinase generates ATP.
50
What happens to pyruvate under anaerobic conditions in animals?
Pyruvate is reduced to lactate so that NADH can be reoxidized to NAD+. NAD+ is then used in the GAPDH reaction to continue glycolysis.
51
What happens to pyruvate under anaerobic conditions in yeast?
Pyruvate is decarboxylated to acetaldehyde which is then reduced to ethanol so that NADH can be reoxidized to NAD+.
52
How do we metabolize ethanol?
convert ethanol to acetaldehyde using alcohol dehydrogenase and NAD+ and then convert that to acetate using acetaldehyde dehydrogenase, OH-, and NAD+
53
What are the other fates of pyruvate outside of glycolysis?
-Pyruvate may be converted to acetyl-CoA which is then oxidized further in the citric acid cycle or used in lipid synthesis.
-Pyruvate may be converted to oxaloacetate which can be used for amino acid or glucose biosynthesis
54
What is gluconeogenesis? What does it cost?
The synthesis of glucose which occurs primarily in the liver.
4ATP + 2GTP + 2NADH
55
How is glycolysis regulated?
High concentrations of glycolytic products such as ATP and PEP inhibit further glycolysis, while molecules that indicate low energy in the cell such as AMP and ADP activate glycolysis.
56
What does F26BP do?
F26BP is an allosteric activator of PFK-1 (glycolysis enzyme) and an inhibitor of the gluconeogenesis enzyme to ensure that the opposing pathways do not run at the same time.
57
What are the steps for glycogen synthesis?
1. Phosphoglucomutase converts G6P to G1P
2. G1P is activated by UTP to form UDP-glucose and PPi. The hydrolysis of PPi drives the reaction forward.
3. Glycogen synthase links glucose units via a1-4 and UDP functions as a leaving group.
58
How are the branch points in glycogen created?
Glycogen-branching enzyme moves 7 residues from the main chain to form a new branch.
59
How is glycogen broken down?
Glycogen phosphorylase use phosphorolysis to break a1-4 bonds and produce G1P monomers.
60
How are residues from the non-reducing ends of glycogen branches converted to an intermediate of glycolysis?
Glycogen phosphorylase makes G1P and then phosphogluco mutase makes G6P used in glycolysis
61
How does the liver increase the blood glucose concentration?
Phosphorylated sugars cannot cross the plasma membrane so G6P is converted to glucose for export.
62
What is Path 1 in creating the ribose sugar for nucleotides and/or NADPH?
Path 1: The oxidative path. Irreversible.
Produces NADPH and ribulose-5-phosphate which may be reversibly converted to ribose-5-phosphate.
63
What is Path 2 in creating the ribose sugar for nucleotides and/or NADPH?
Path 2: The carbon rearrangement.
2 F6P + 1 GAP are rearranged through a series of reversible reactions to ribulose-5-phosphate.
64
What is Path 3 in creating the ribose sugar for nucleotides and/or NADPH?
Path 3: If the cell needs NADPH but not ribose, then G6P may be converted to ribulose-5-phosphate through the oxidative path and then converted to GAP and F6P by reversing the carbon rearrangement path.
65
How can we treat cancer by targeting glucose metabolism?
Cancer cells have rates of glycolysis 10x more than normal cells so inhibiting glycolysis harms cancer cells more than regular cells.
66
What is the citric acid cycle?
Catalyzes the net oxidation of acetyl-CoA to CO2
67
What is pyruvate dehydrogenase complex?
A multienzyme that links glycolysis to the citric acid cycle
68
What are the advantages of a multienzyme?
1. The product of one active site quickly moves to the next active site
2. Easier to regulate all enzymes together
3. Minimizes side reactions
69
Where are the enzymes of the citric acid cycle located?
The mitochondrial matrix contains the pyruvate dehydrogenase complex and most of the enzymes of the citric acid cycle.
70
What does the citric acid cycle do?
The goal is to make energy for the cell using reduced cofactors.
71
How does Step 8 of the citric acid cycle proceed in the forward direction if it is very unfavorable?
The citrate synthesis reaction (Step 1) has a large enough negative free energy to pull the malate dehydrogenase reaction forward.
72
How does aconitase act stereospecifically?
Citrate is prochiral so the hydroxyl group is always moved to the carbon originating from the oxaloacetate and not the carbon from the acetyl-CoA
73
How is the citric acid cycle regulated?
1. Substrate availability of acetyl-CoA and oxaloacetate
2. Allosteric activation by Ca2+ and ADP
3. Allosteric inhibition of isocitrate dehydrogenase by ATP
4. Product inhibition (NADH, citrate, and succinyl-CoA)
5. Feedback inhibition (NADH & succinyl-CoA)
74
Why is the citric acid cycle considered to be a central metabolic pathway?
Intermediates of the citric acid cycle serve as precursors for a variety of anabolic pathways through cataplerotic reactions.
75
What happens in oxidative phosphorylation?
In oxidative phosphorylation reduced cofactors donate electrons to an electron transport chain that generates a H+ gradient. This gradient is used to generate ATP.
76
What does reduction potential tell you about where electrons will go?
Electrons flow spontaneously from the substance with the lower reduction potential to the substance with the higher reduction potential.
77
Where does oxidative phosphorylation occur?
The inner membrane of mitochondria contains all of the complexes for oxidative phosphorylation.
78
What is the difference in properties between the inner membrane and the outer membrane?
The outer membrane is very porous, while the inner membrane is impermeable to most small molecules and ions.
79
What is the Malate-Asparatate Shuttle System?
NADH produced from glycolysis is in the cytosol but needs to move into the matrix, but it is too large to be transported. The shuttle system transfers the electrons from cytosolic NADH to malate which puts it back on to matrix NADH. Malate is then converted to asparate and transferred out.
80
How are ADP and ATP moved across the mitochondrial inner membrane?
ATP is produced in the matrix, so it must be exported to the cytosol while ADP is imported into the matrix in order to make more ATP. ATP and ADP are moved using an antiporter driven by the inner membrane potential.
81
What is the net affect of the Malate-Asparatate shuttle system?
The shuttle's net effect is one fewer NADH in the cytosol and one additional NADH in the matrix.
82
How is Pi imported into the matrix?
Pi is imported into the matrix in order to make more ATP. Pi is imported along with a H+ using a symporter driven by the H+ gradient.
83
What does Complex 1 do in the electron transport chain?
Complex 1 (NADH dehydrogenase), translocates 4 H+ into the inter membrane space for every 2e- that pass through
84
How do electrons pass through Complex 1?
In complex 1, a H- ion is transferred from NADH to FMN. FMN then passes the electrons one at a time to a series of iron-sulfur clusters until they reach Q.
85
How does the cell contribute to the ubiquinol pool?
1. Succinate dehydrogenase (complex II) in the citric acid cycle
2. From fatty acid oxidation
3. From glycerol-3-phosphate
86
What happens at Complex III in the electron transport chain?
QH2 donates 2 electrons to complex III (cytochrome C) to reduce it. Cyt C can only carry 1 electron at a time. 4 H+ are translocated into the intermembrane space for every 2 e- that pass.
87
What happens in complex IV in the electron transport chain?
2 Cyt C proteins each donate 1 electron to complex 4, ultimately reducing the terminal electron acceptor O2. 2 H+ are translocated into the intermembrane space for every 2 e- that pass.
88
What is the structure of cytochromes?
Cytochromes are proteins with a heme group that are obligate single electron carriers. 'a', 'b', and 'c' denote the type of side groups on the heme.
89
What is the chemiosmotic model?
A combination of the H+ imbalance (due to e- transport), and the negative charges on the matrix side of the membrane, results in a electrochemical gradient that favors H+ moving into the matrix.
90
What is the structure of the ATP synthase?
F1 soluble portion in the matrix includes 3a and 3b subunits. Each of the B subunits has ATP synthase activity.
The F0 membrane-spanning portion includes the a subunit, where H+ enter and exit, and a c-ring. The c-ring consists of subunits that each bind an H+ to help rotate the ring.
91
How is the H+ gradient used to generate ATP?
Protons move down their gradient by passing through the ATP synthase.
92
What does the y subunit in the ATP synthase do?
The y subunit extends from F0 to F1 and rotates 120* once enough strain has built up from the c-ring rotation. 120* rotation of the y subunit forces the B subunits into one of 3 conformations, 1 full rotation of the y subunit produces 3 ATP.
93
How much ATP is generated in the electron transport chain?
1 ATP produced for every 4 H+ translocated.
94
What are the 3 conformations of the B subunit?
1. L (loose): ADP + Pi are bound
2. T (tight) : ATP is formed
3. O (open): ATP is released
95
How much energy does NADH yield from the aerobic breakdown of glucose to CO2?
NADH oxidation translocates 10 H+
10 H+ x (1 ATP/4 H+)= 2.5 ATP
96
How much energy does QH2 yield from the aerobic breakdown of glucose to CO2?
QH2 oxidation translocates 6 H+
6 H+ x (1 ATP/4 H+) = 1.5 ATP
97
How does cyanide target oxidative phosphorylation?
Cyanide blocks electron transport through Complex IV, shutting down the entire electron transport chain and preventing the formation of a H+ gradient. Without protons, the cell cannot make ATP to function.
98
How does uncoupling oxidative phosphorylation prevent ATP synthesis?
Blocking the H+ channel causes the electron transport chain to slow down as the H+ gradient gets too steep (it doesn't stop electron transport completely since some H+ can leak across the membrane).
99
How do uncouplers such as DNP work?
Uncouplers carry H+ across the mitochondrial inner membrane (down the H+ gradient) without passing through ATP synthase.
100
Where does photosynthesis occur?
Chloroplasts have an inner membrane that surrounds the stroma. Within the stroma, there are flattened vesicles called thylakoids.
101
What drives ATP synthase in the thylakoid lumen?
The thylakoid lumen has a low pH (high [H+]) and the H+ gradient drives ATP synthase.
102
How is an electron promoted to a higher state?
Absorbing a photon promotes an electron to a higher energy level.
103
What absorbs light?
Photosynthetic pigments absorb light. The pigments are bound to proteins and the differing protein environments affect the wavelength of light absorbed.
104
What are the 4 ways for an excited state to lose energy?
1. Heat
2. Light
3. Exciton transfer
4. Photooxidation
105
How are photons captured?
Photosynthetic organisms have light-harvesting complexes consisting of pigments bound to proteins.
106
How is light energy transferred?
Antenna chlorophyll surround a reaction center and pass the energy of an absorbed photon from chlorophyll to chlorophyll until the energy is trapped by the reaction center because it has a lower excited state.
107
How do plants generate ATP?
An electron transport chain generates a H+ gradient that drives ATP synthase.
108
How are electrons transferred from H2O (high E) to pheophytin (low E) in photosystem II?
Photosystem II has a P680 reaction center that is excited by photon energy, lowering the P680 reduction potential so that is can transfer an electron to pheophytin.
109
What are the steps for transferring electrons in Photosystem II?
P680 is excited by a proton and reduces pheophytin. Pheo- then passes an e- to a bound plastoguinone, PQa. PQa transfers an electron to the mobile plastoquinon, PQb.The steps repeat so that a 2nd electron fully reduces PQb- to PQbH2.
110
How is P680 restored to it's normal state.
P680+ has a high enough reduction potential that it is spontaneously reduced back to P680 by H2O.
111
What happens when PQbH2 is fully reduced?
PQbH2 carriers 2 e- away from PSII and toward cytochrome b6f
112
What happens in the Z-scheme?
the movement of 4 e- through cytochrome b6f translocates 8 H+ and reduces 4 plastocyanins (a mobile electron carrier). Plastocyanin carrys an electron to PS1. Electrons move through PS1 and reduce the mobile e- carrier ferredoxin.
113
How is free energy conserved by photosystem 1? Non cyclic vs. cyclic
Free energy can be conserved by reducing NADP+ --> NADPH (noncyclic) or in the H+ gradient by transferring the e - back to cyctochrome b6f (cyclic e- flow).
114
How does the thylakoid membrane differ from the mitchondrial intermembrane?
The thylakoid membrane is permeable to some ions so chloroplasts need a much larger pH gradient to compensate for the lack of a charge difference across the membrane.
115
When is rubisco activated?
When light reactions are occurring, the stroma pH increases to activate rubisco. Otherwise rubisco is inactive to allow the cell to conserve ATP and NADPH.
116
What happens in the Calvin cycle?
Rubisco fixes CO2 to form 3PG, which is then converted to GAP at the expense of ATP and NADPH. GAP is converted to Ru5P. Ru5P is then phosphorylated by ATP to get the Rubisco substrate RuBP.
117
How are carbons rearranged in the Calvin cycle?
For every 6 GAP produced, one is removed from the cycle to serve as a precursor for various biomolecules. The other 5 GAPs have their carbons rearranged to form 3 5-carbon ribulose sugars.
118
How are lipids transported from the intestine to the liver and adipose tissue?
Chylomicrons transport dietary triacylglycerols from the intestine to adipose tissue and transport cholesterol to the liver.
119
What do very low density lipoproteins (VLDL) do?
Transport triacylglycerols from the liver to other tissues.
120
What do intermediate density lipoproteins (IDL) do?
Form as VLDLs lose triacylglycerols
121
What do low density lipoproteins (LDL) do? What are high levels of LDL associated with?
LDL transport cholesterol to various tissues. High LDL levels are associated with an increased risk of atherosclerosis.
122
What do high density lipoproteins (HDL) do?
HDL transport excess cholesterol back to the liver.
123
What are the compositions of lipoproteins?
Lipoproteins have a highly hydrophobic core of triacylglycerols and cholesteryl esters surrounded by proteins and amphipathic lipids.
124
Draw Step 1 of glycolysis.
125
What happens in Step 4 of glycolysis? What are the enzymes, reactants, and products?
In step 4, F1,6-P is split into 2.
-enzyme: aldolase
-reactants: F1,6-P, OH-
-products: Glyceraldehyde-3-Phosphate, Dihydroxyacetone Phospohate
126
What happens in Step 5 of glycolysis? What are the enzymes, reactants, and products?
-enzyme: Triose Phosphate Isomerase
-reactants: Dihydroxyacetone Phosphate
-products: Glyceraldehyde-3-Phosphate
127
What happens in Step 6 of glycolysis? What are the enzymes, reactants, and products?
-enzyme: Glyceraldehyde-3-Phosphate Dehydrogenase
-reactants: Glyceraldehyde-3-Phosphate, NAD+, Pi
-products: 1,3-Bisphosphate, H+, NADH
128
What happens in Step 8 of glycolysis? What are the enzymes, reactants, and products?
-enzyme: phosphoglycerate mutase
-reactants: 3-phosphoglycerate
-products: 2-phosphoglycerate
129
What happens in Step 10 of glycolysis? What are the enzymes, reactants, and products?
-enzyme: Pyruvate kinase
-reactants: phosphoenol pyruvate, ADP, H+
-products: Pyruvate, ATP
130
What happens at site 1 in pyruvate dehydrogenase?
Decarboxylation of pyruvate and transfer of the acetyl group to lipoamide.
131
What happens at site 2 in pyruvate dehydrogenase?
Transfer of the acetyl group to CoA.
132
What happens at site 3 in pyruvate dehydrogenase?
Dihydrolipoamide is reoxidized using NAD+ and FAD.
133
How are fatty acids activated for catabolism?
Fatty acids are linked to CoA via a high energy thioester bond at the expense of 2 ATP equivalents
134
How does acyl-CoA generated in the cytosol produce acyl-CoA in the matrix?
Acyl-CoA is too large to move into the matrix. Instead, the acyl group is esterified to carnitine for import to the mitochondrial matrix from the cytosol.
135
How are fatty acids oxidized?
Each round of B-oxidation removes 2 carbons, and produces 1 QH2, 1 NADH, 1 Acetyl CoA. The last round produces 2 Acetyl CoA.
136
What is the energy yield for each round of B-oxidation?How does a double bond change that?
Each double bond in a fatty acid will reduce the energy yield.
137
What are the steps for fatty acid synthesis?
1. Acetyl-CoA is carboxylated in the cytosol by acetyl-CoA carboxylase (ACC) to form malonyl-CoA.
2. Acetyl-CoA is extended, 2 carbons at a time by the fatty acid synthase multifunctional enzyme
3. Fatty acid synthase uses substrate channeling: the acyl carrier protein swings intermediates between active sites
138
Where are fatty acids synthesized?
Fatty acid synthesis occurs in the cytosol.
139
What inhibits or activated fatty acid synthesis?
-Glucagon/epinephrine signaling inhibits by phosphorylating ACC
-Insulin signaling activated by dephosphorylating ACC
140
What is an elongase?
An elongase can extend palmitate (16:0) to make longer fatty acids
141
What is desaturase?
Can introduce double bonds in fatty acids
142
How is fatty acid metabolism regulated?
1. Aceteyl-CoA carboxylase (ACC) is the primary regulation point for FA metabolism
- activated by citrate
- inhibited by fatty acids
- inhibited by malonyl-CoA
143
How are ketone bodies synthesized?
Ketogenesis occurs when blood glucose is low and glycogen is depleted. The liver responds by generating glucose through gluconeogenesis and using Acetyl-CoA to make the ketone bodies which are converted back in the central nervous system for energy.
144
How is cholesterol synthesized?
Cholesterol is assembled from acetyl-CoA units.
145
How do statins lower cholesterol?
Statine mimic HMG-CoA and inhibit HMG-CoA reductase (rate limiting step of cholesterol biosynthesis). Cells that cannot make enough cholesterol compensate by increasing production of LDL receptors.
