Phase 4 Flashcards
(288 cards)
1
Q
Which organs are responsible for destroying excess amino acids?
A
Kidney and Liver
2
Q
What is the half life of the longest living protein and where is it located?
A
10 days and it is in the muscle
3
Q
What are the two sources of protein?
A
Intracellular and dietary
4
Q
What is NH4 removed by?
A
Aminotransferase
5
Q
What are uricotelic animals?
A
Example: birds
Do not produce urea; produce uric acid
6
Q
What are ammonotelic animals?
A
Example: fish
Dispose ammonia directly
7
Q
What do we need to produce urea?
A
Water
8
Q
What are urotelic animals?
A
Example: mammals
Produce urea
9
Q
What is the main transporter of ammonia from the muscles?
A
Alanine
10
Q
What is the main transporter of ammonia from tissues?
A
Glutamine
11
Q
What do mosquitoes depend on?
A
The consumption of sugar
12
Q
What is the water we ingest used for?
A
For producing urea
13
Q
What do we not need to ingest?
A
Fat
14
Q
What is the difference between enzymes?
A
Their selectivity
15
Q
What cofactor and enzyme does alpha ketoglutarate use to get converted to L-glutamate?
A
PLP (pyridoxal phosphate) is the cofactor and aminotransferase is the enzyme
16
Q
What happens if you take excess vitamins?
A
Schiff bases are created everywhere and they are very reactive
17
Q
What does pyridoxal phosphate have that allows it to be converted?
A
It has an aldehyde which the aminotransferase changes to a Schiff base (pyridoxamine phosphate)
18
Q
What does the conversion of glutamate to alpha ketoglutarate release?
A
NH4 which can be converted to urea or uric acid or can stay as NH4
19
Q
Where does glutamate in the liver come from?
A
Amino acids turn into alpha ketone acids (alpha ketoglutarate) which gets converted to glutamate via PLP or glutamine can enter directly from muscles and other tissues and be converted to glutamate. Alpha ketoglutarate can also come from the krebs cycle. Alanine can also be converted into glutamate
20
Q
What happens when pyridoxal combines with the aminotransferase?
A
It attacks the epsilon lysine to form a schiff base
21
Q
What does glutamate dehydrogenase use?
A
It can use NAD+ or NADP+
22
Q
What happens via glutamate dehydrogenase?
A
A reduction occurs to form an intermediate between glutamate and alpha ketoglutarate
23
Q
What is NADH used for generally?
A
Catabolism
24
Q
What is NADPH used for generally?
A
Anabolism
Can be used for synthesis of fatty acids but not a very important source
25
What is NH4 in tissues converted to and how?
Glutamine by reacting with glutamate and getting transported to the liver through the bloodstream to regenerate glutamate
26
What happens to the fumarate generated in the Urea Cycle?
It can move to the Krebs Cycle. Remember it is converted to malate in the cytosol so it can move back into the mitochondria
27
Where does the Krebs Cycle occur?
Mitochondria
28
Where does the Urea Cycle occur?
Partially in the mitochondria but mostly in the cytosol
29
Where is urea from the urea cycle released?
Cytosol
30
How is aspartate converted to oxaloacetate or backwards?
Alpha ketoglutarate goes to glutamate or reverse
31
How is oxaloacetate converted to malate and back?
By using NADH to NAD+ or reverse
32
What is urea production regulated by?
By the amount of amino acids present and allosteric intervention of N-acetylglutamate
33
What does the ingestion of more protein mean?
More urea produced
34
What does a large amount of aminotransferases in urine mean?
We have too many amino acids and are ingesting too much protein
35
Which aa specifically is affected by ingesting more protein?
More glutamate produced
36
How does glutamate go to carbamoyl phosphate?
Glutamate to N-Acetylglutamate via N-Acetylglutamate synthase and releasing Co-A
N-Acetylglutamate to carbamoyl phosphate via carbamoyl phosphate synthetase I and 2ATP going to A ADP + Pi
37
What do ketogenic amino acids produce?
Ketone bodies via acetyl coA
38
What do glucogenic amino acids produce?
Glucose
39
What amino acids are solely ketogenic?
Leucine and Lysine
40
What are all of the ketogenic amino acids?
```
Lysine
Leucine
Tyrptophan
Tyrosine
Phenylalanine
Isoleucine
Threonine
```
41
What are the glucogenic amino acids?
All aa except lysine and leucine
42
Why do we have low pH in the stomach?
Due to hydrochloric acid
43
How do we ingest material?
Pepsinogen goes to pepsin (a Ser protease)
44
What are the 3 main degradative proteases?
Trypsin, pepsin, and chymotrypsin
45
What does pepsin do?
Breaks down proteins to polypeptides
46
What happens after pepsin acts?
The polypeptides move through the intestine where zymogens (active proteases) break down the rest of the material
47
What does the small intestinal wall do?
Absorbs amino acids
48
What does the movement of substances from the intestine to the intestinal epithelial require?
A glucose sodium symporter
49
What does the movement of substances from the intestinal epithelial to the blood require?
A 3Na+(out)/2K+(in) antiporter and a glucose uniporter (out)
50
Why is alanine used in the muscle more than glutamate?
Since pyruvate is produced in the muscle and does not go to krebs in the muscle
51
What happens to excess pyruvate?
Goes to lactic acid or it is converted to alanine via aminotransferase
52
Why does the heart not need alanine?
It uses different energy sources
53
What does every aminotransferase use as a cofactor?
PLP
54
Why do we need 2 units of ATP to go from glutamate to carbamoyl phosphate?
Bicarbonate requires one unit along with carbamoyl phosphate synthetase and the other phosphorylates carbamate
55
Where does glutamate for the urea cycle come from?
1) Extrahepatic tissues
2) Synthesis from alanine or other amino acids thru alpha ketoglutarate
3) Conversion of oxaloacetate to aspartate via aminotransferase and uses alpha ketoglutarate to move NH4 around
56
How does oxaloacetate enter and leave the mitochondria?
Leaves by being converted to aspartate and enters by being converted to malate
57
What is the most abundant aminotransferase?
ALS (alanine aminotransferase)
58
What happens if you consume too much water?
You lose electrolytes and pass out because they dissolve in the water
59
What happens to the Schiff base that is created by the reaction of PLP with epsilon lysine?
It becomes an electrophile that can be attacked by another amino acid such as alanine (attacks at the carbon)
60
What happens to the tetrahedral intermediate that is formed by the reaction of alanine with the Schiff base that is formed by the reaction of PLP and epsilon lysine?
It can form pyruvate by reacting with water or it can form pyridoxamine
61
What is an amino acid?
Any compound that contains a amino and acid group
62
Where is beta alanine used?
Coenzyme A
63
Where is carnosine found?
The muscle
64
What is carnosine composed of?
Beta alanine histidine
65
What is the function of carnosine?
Histidine has a pKa of 6.1 but carnosine has a pKa of 6.8 so it is used as a buffer in blood
66
What is an advantage of using beta alanine as opposed to alpha alanine?
It is not coded so you are not limited in the amount that you can make
67
What are the various functions of glutamate?
```
Part of glutathione
Processing of Ammonia
Used as starting material for aa
Glycolysis
Serves in proteins as acid/base catalyst and nucleophile
```
68
How many essential amino acids are there?
9
69
What vitamin is used as an antioxidant and what group does it have?
Vitamin E
| Has a phenol
70
What amino acids can move in and out of the cytosol freely into the mitochondria?
Orinthine and Citrulline
71
What is the first step of the urea cycle?
Formation of carbamoyl phosphate
72
What enzyme forms alpha ketoglutarate in the urea cycle?
Glutamate dehydrogenase
73
What enzyme forms carbamoyl phosphate from NH4 and what is used in that conversion?
Carbamoyl phosphate synthetase
| HCO3 and 2 ATP to form 2 ADP + Pi
74
What does oxaloacetate get converted into to leave the mitochondria?
To enter?
Leave: Aspartate
Enter: Malate
75
Where are protons in relation to the mitochondria?
More protons in the intermembrane space than outside
76
What does ATP synthase allow for?
Facilitated diffusion because it is not a proton pump
77
What is the general purpose of the 4 complexes/proton pumps in the chemioosmotic theory?
To reduce the energy of the electrons to the proper amount so that they can form O2
78
In the chemioosmotic theory, what is energy from electron flow stored as?
Electrochemical potential
79
What happens when a proton enters ATP synthase?
It forces the synthase to move and brings ADP and Pi close together so that they have to react to form ATP
80
What is the process of the chemioosmotic theory in the mitochondria?
1) Reduced substrate donates electrons
2) Electron pumps H+ as electrons flows to O2
3) Energy of electron flow stored as electrochemical potential
4) ATP synthase uses electrochemical potential to synthesize ATP
81
What is the process of the chemioosmotic theory in the chloroplast?
1) Light converts H2O to good electron donor
2) electron carriers pump protons in as electrons flow to NADP+
3) Energy of electron flow stored as electrochemical potential
4) ATP synthase uses electrochemical potential to synthesize ATP
82
What is complex 1 known as and what is its shape?
NADH dehydrogenase
| L-Shaped
83
Where are the electrons from complex 1 transferred to and how?
Transferred to complex 3 by CoQ
84
How many protons does complex 1 pump out?
4
85
How does complex 1 allow the protons out?
When NADH comes in, the conformation of complex 1 changes and allows the pores to open to let the protons out
86
What are the prosthetic groups of complex 1?
FMN and Fe-S
87
Why is FMN used in complex 1?
Fe-S can only take 1 electron at a time so NADH cannot transfer electrons directly to it
88
What is complex 2 known as and where do its electrons go?
Succinate dehydrogenase
| Electrons go to CoQ
89
How many protons does complex 2 pump?
0
90
What are the prosthetic groups of complex 2?
FAD and Fe-S
91
How does FADH2 enter complex 2?
Via the reaction of succinate to fumarate
92
What are the characteristicsof CoQ?
Lipophilic
Benzoquinone linked to 10 isoprene units
Can transfer 2 electrons in one step via stable semiquinone intermediate
93
What is complex 3 known as and where do its electrons go?
Cytochrome C oxidoreductase
| Electrons go to cytochrome C
94
What prosthetic groups does complex 3 have?
Hemes, Fe-S
95
What are the coppers of complex 3 held in place by?
Histidines
96
What should all cytochromes be associated with?
Heme proteins
97
How many protons does complex 3 pump?
4
98
What is complex 4 known as and how many protons does it pump?
Cytochrome oxidase
| 2
99
What are the prosthetic groups of complex 4?
CuA, CuB, Hemes
100
When you lower the energy of the electrons by moving through the complexes, what can be said about the oxidation state?
You are moving from low to high oxidation state
101
Through the whole respiratory system, how many protons does one NADH pump?
10
102
Through the whole respiratory system, how many protons does 1 FADH2 pump?
6
103
What happens in the chemioosmotic theory when there is too much oxygen?
It will react in CoQ to form superoxide which will react with proton to form hydroxyl radical that is highly unstable
104
What will the hydroxyl radical in the chemioosmotic theory do?
React with any hydrogen to make water
105
What does superoxide dismutase make?
H2O2 from superoxide
106
What does glutathione reductase aid in in the chemioosmotic theory?
It converts NADPH to NADH+
107
How do you increase the amount of superoxide dismutase?
Breathing (increasing amount of oxygen in the body)
108
How do you decrease your heart rate?
By dilating the arteries through exercise
109
Why are you warmer when you exercise?
You use the protons that are pumped to produce thermogenin
110
What type protein is ATP synthase and how can it be removed?
Integral protein that can be removed by detergent
111
What are the subunits of ATP synthase F1?
3 alpha and 3 beta
112
What are the two portions of ATP synthase?
F0 attached to membrane
| F1 in the mitochondria
113
Where is the ATP present in ATP synthase?
In the beta subunits of F1
114
How many total protons are required to make APT synthase work?
9
115
How do you move electrons as NADH from outside to inside the mitochondria?
Convert oxaloacetate to malate using 1 NADH and malate dehydrogenase
116
How do you move electrons as NADH from inside to outside the mitochondria?
Convert oxaloacetate to aspartate via aspartate aminotransferase
117
How does CO inhibit the respiratory chain?
Interferes in complex 4 by binding in place of oxygen and in hemoglobin
118
How does CN inhibit the respiratory chain?
Binding in place of oxygen
119
Where do barbiturates inhibit the respiratory chain?
Complex 1
120
Why will a small amount of cyanide kill you immediately but a large amount will not?
Large amount overwhelms the system so it won't reach the complex immediately
121
What does the respiratory chain do overall?
Catalyzes the flow of electrons from low reduction potential carriers to high reduction potential carriers
122
What are the electron carriers in the respiratory chain?
Flavoproteins contain FMN or FAD (I and II)
Iron sulfur proteins contain non-heme iron clusters like F-S or Fe4S4 (I, II, III)
Coenzyme Q
Cytochromes contain hemes (a, b, c)
2 and 3 contain 3 b-type
3 has c
4 has a and a3
123
What is used to produce heme?
Succinate
124
Why does the conversion of NADH to O2 have to be stepwise?
The energy changes are specific
125
What are the energy changes in the conversion of NADH to O2?
NADH -> FMN -69.5 kJ/mol
CoQ -> cytB -36.7 kJ/mol
Cyta -> O2 -112 kJ/mol
126
How do elevators work?
Via the photoelectric effect
127
Why does FADH2 transfer one electron to Fe-S at a time?
CoQ functions best when it takes 1 electron at a time
128
What is the reduction potential equation?
ΔG = -nFΔEº
129
What enzymes in the krebs cycle produce NADH?
α-ketoglutarate dehydrogenase complex
isocitrate dehydrogenase
malate dehydrogenase
130
What are the direct products of glycolysis and what is the ATP yield from these?
2 NADH -> 3 or 5 ATP
| 2 ATP -> 2 ATP
131
What are the direct products of pyruvate oxidation and what is the ATP yield from these?
2 NADH -> 5
132
What are the direct products of acetyl CoA oxidation in Krebs cycle and what is the ATP yield from these?
6 NADH -> 15
2 FADH2 -> 3
2 ATP or GTP -> 2
133
Why does the complete oxidation of glucose yield 30 or 32 ATP?
30 if we do not go through complex 1
134
What happens when glycerol dehydrogenase phosphate 1 is high?
The body makes more fat because you have high sugar
135
What basic reactions occur in the light reactions?
H2O to O2
| NADP+ to NADPH
136
What basic reactions occur in the dark reactions?
ADP + Pi to ATP
| Carbohydrates to CO2
137
Where do the light reactions occur?
Thylakoids
138
Where do the dark reactions occur?
Stroma
139
What are grana?
Stacks of thylakoid membranes
140
What happens when light hits the leaves?
Light hits the antenna chlorophyll or carotenoids and it is absorbed and transferred between them until it reaches the reaction center
141
What happens in the reaction center?
Photochemical reaction converts the energy of a photon into a separation of charge, initiating electron flow
142
What residues are present in F0 of ATP synthase?
Asp
143
Compare chlorophyll and hemoglobin
Structured the same except chlorophyll uses Mg2+ because Mg2+ has great light absorbing abilities
144
What do X-Rays do to bonds?
Break them completely
145
What do UV do to bonds?
Break most bonds
146
What does IR do to bonds?
Vibrates the bonds which is how we get the IR spectrum
147
What do microwaves do to bonds?
Causes the molecule to spin and hit surrounding molecules
148
What are the most abundant in plants?
Chlorophyll A and B which will be destroyed fast so they're the first to go and that's why leaves turn orange and yellow
149
What occurs in photosystem 2?
1) Light excites an antenna molecule which raises the electron to a higher energy level
2) Excited antenna passes electron to another antenna
3) Energy transferred to reaction center chlorophyll
4) Excited chlorophyll passes electron to electron acceptor
5) Electron hole in reaction center is filled by electron from electron donor
150
How does an electron travel in PSII?
Pheo -> PQA -> PQB -> Cytbf6 complex -> plastocyananin -> PSI
151
How does an electron travel through PSI?
e- gets excited -> A0 -> A1 -> Fe-S then iron sulfur protein transfers electron to NADP+ to make NADPH
152
What activates ATP synthase in photosynthesis?
Proton gradient activates ATP Synthase
153
What are the dark reactions also known as?
Carbon assimilation reactions
154
Where does chlorophyll B have the highest absorbance?
450 nm
155
Where does chlorophyll A have the highest absorbance?
At 410 nm and also high at 670 nm
156
Where is the highest absorbance of beta carotene?
450 nm
157
Where is the highest absorbance of phycocyanin?
620 nm
158
Where is the highest absorbance of phycoerythrin?
580 nm
159
What does PSI use?
Ferredoxin and plastocyanin
160
What is used in CO2 reduction?
NADPH an ATP produced through light reactions
161
What do CO2 reduction reactions induce?
The movement of protons from the stroma into the thylakoid and Mg2+ from the thylakoid to the stroma
162
What conditions favor enzyme activity?
Alkaline conditions and high Mg2+ concentration
163
What cycle is critical in seeds?
Glyoxylate cycle; produces succinate from acetyl CoA
164
Why do plants also need to produce NADH?
For energy for catabolic processes
165
What percentage of CO2 is in the body and outside? Compare to air
5% in the body, lower outside the body. CO2 more dense than air
166
What protects from mosquitoes and how?
Mosquitoes smell CO2 and can sense the concentration and know to attack. Applying antiperspirant closes the pores so CO2 can't come out
167
What are the stages of the Calvin cycle?
1) Carbon fixation
2) Reduction
3) Regeneration of acceptor
168
What is the enzyme responsible in plants for conversion of CO2 into an organic form and how present is it in plants?
RUBISCO
| Makes up 50% of soluble proteins in plants because it has turnover rate of 3CO2/second
169
When is rubisco inactive?
When ribulose 1,5-bisphosphate alone occupies its active site blocking a critical Lys residue.
170
What do rubisco activase + ATP do?
Displace the ribulose-1,5-bisphosphate allowing the carbamoylation of the Lys residue by CO2. Mg2+ binds, polarizes and orients the reactants for nucleophilic attack on CO2 by a ribulose intermediate
171
What fixates Mg2+ in the calvin cycle?
Asp and Glu
172
What amino acids do you need for the calvin cycle to proceed?
Lys, Arg, Glu, and His
173
What is the intermediate formed from ribulose-1,5-bisphosphate?
Enediolate by reacting with His and His extracts a proton
174
What does a transketolase do?
Uses TPP prosthetic group and Mg2+ and moves 2 carbon ketol group to an aldose acceptor
175
What does the synthesis of large carbohydrates start with?What is it converted into?
Glyceraldehyde-3-PO4
| Starch for storage and sucrose for transport
176
Where is sucrose made? Starch?
Cytosol
| Stroma
177
What does the pi-triose phosphate antiporter do and how?
Facilitates movement of ATP and electrons from stroma to cytosol
As dihydroxyacetone PO4 moves from stroma to cytosol, Pi moves in opposite.
As 3-phosphoglycerate moves form stroma to cytosol, Pi moves other way
178
What is UDP and what does it do?
Activated form of glucose most often used in carbohydrate synthesis and cellulose synthesis
Sucrose produced from it
179
Where does the glucose needed for the synthesis of cellulose come from?
Derives from sucrose, the normal transport system for glucose in plants
180
What does sucrose synthase do?
Generates UDP glucose after it is bound to sitosterol
181
What does fatty acid biosynthesis require?
Acetate which is shuttled out of the mitochondria as citrate
182
What is the main fatty acid we produce?
Palmitic acid
183
What occurs in the cytosol in animal cells?
NADPH production
Isoprenoid and sterol synthesis (early stages)
Fatty acid synthesis
184
What occurs in the ER in animal cells?
Phospholipid synthesis
Sterol synthesis (late stages)
Fatty acid elongation
Fatty acid desaturation
185
What occurs in the mitochondria in animal cells?
Fatty acid oxidation
Acetyl CoA production
Ketone body synthesis
Fatty acid elongation
186
What occurs in the mitochondria of animal cells?
No fatty acid oxidation
187
What occurs in the chloroplasts of plant cells?
NADPH and ATP Production
| Fatty acid synthesis
188
What occurs in the peroxisomes of plant cells?
Fatty acid oxidation
| Catalase, peroxidase
189
What does the biosynthesis of fatty acids require and what is it made by?
Requires malonyl-CoA which is made by 3 functional regions of acetyl CoA carboxylase
1) Biotin Carboxylase
2) Biotin Carrier Protein
3) Transcarboxylase
190
What does Malonyl-CoA do in fatty acid synthase and how?
Adds 2 carbons in a 4 step sequence. First 2 steps introduce acetyl group and remove CO2. Second 2dehydrate and convert initial acetyl to a saturated ethyl group.
1) Condensation (removes CO2)
2) Reduction (NADPH->NADP+)
3) Dehydration (Removes Water)
4) Reduction (NADPH-> NADP+)
191
What is the precursor of other long chain fatty acids?
Palmitate
192
What can't mammals do?
Convert oleate to linoleate
193
What is desaturation performed by?
A mixed-function oxidase using NADPH and O2 as electron acceptor
194
What does desaturation of palmitate 16:0 produce?
Palmitoleate 16:1 (Δ9)
195
What does elongation of palmitate produce?
Stearate 18:0
196
What does elongation of stearate 18:0 produce?
Longer saturated fatty acids
197
What does desaturation of stearate 18:0 produce?
Oleate 18:1 (Δ9)
198
What does desaturation of oleate 18:1 (Δ9) produce?
Linoleate 18:2 (Δ9,12)
199
What does desaturation of Linoleate 18:2 (Δ9,12) produce?
α-linolenate 18:3 (Δ9,12,15)
| γ-linolenate 18:3 (Δ6,9,12)
200
What does elongation of γ-linolenate 18:3 (Δ6,9,12) produce?
Eicosatrienoate 20:3 (Δ8,11,14)
201
What does saturation of Eicosatrienoate 20:3 (Δ8,11,14) produce?
Arachidonate 20:4 (Δ5,8,11,14)
202
Where does destauration take place and what does it use?
In the smooth ER and uses mixed-function oxidases
203
What are oxidases?
Use O2 as electron acceptor but O2 is not incorporated in the molecyle
204
What are oxygenases?
Use O2 and incorporate one O (monooxygenases) or 2 (disoxygenases) in the molecule
205
what are the two main routes for NADPH production?
Malic Enzyme
| Pentose Phosphate Pathway
206
What are eicosanoids formed from and where is what they're formed from stored?
Arachidonate
| Stored in middle carbon of glycerol in membrane phospholipids
207
What does cyclooxygenase COX do?
Comes from smooth ER and converts arachidonate to prostaglandin H2, precursor of other prostaglandins and thromboxanes
208
What type of addition does COX perform?
3+2
209
How does COX affect inflammation?
Aspirin and Ibuprofen block COX which reduced inflammation
210
What type of hormones are Eicosanoids?
Paracrine
211
What does leukotriene synthesis use?
Lipooxygenases found in leukocytes, heart, brain, lung, and spleen
212
To what family do lipoxygenases belong?
P-450 family, not inhibited by NSAIDs
213
What are TAGs and glycerophospholipids made from?
Fatty acyl CoA
| L-glycerol-3-PO4 (derived mostly from glycolysis
214
What does L-glycerol 3-
| PO4 make and how?
Phosphatidic acid via 2 acyl transferases which can be converted to TAGs or glycerophospholipids
215
What does glyceroneogenesis use?
Glycerol 3 PO4 made by adipose tissue and has a link to type 2 diabetes, and controls the rate of fatty acids released in the blood
216
What does glyceroneogenesis account for during fasting?
65% of fatty acids reesterified to TAGs
217
Synthesis of cholesterol?
1) Condensation of 3 acetate units make mevalonate
2) Mevalonate is converted to activated 5-carbon isoprene
3) Six units of isporene polymerize to form squalene (from sharks)
4) Cyclization of squalene to form, after some oxidation and methyl shifts, the 4 rings of cholesterol
218
What is cholesterol converted to?
Hormones, bile acids, or hydrophobic esters for storage and transport as lipoproteins
219
Describe trends going from Chlyomicron to VLDL to IDL to LDL to HDL?
Protein increases
TAGs decreases
Cholesterol Esters increase
Phospholipids increase
220
How do we transport fats?
Through lipoproteins
221
What is lipoprotein lipase?
A member of the serine esterase family (like trypsin) with active site Ser, His, and Asp
222
What does the liver orchestrate?
Lipoprotein transport pathways to redistribute fat and cholesterol
223
How do fats enter the liver?
Fats -> Chylomicron -> remnants of chylomicron and cholesterol go into liver and leave as VLDL
VLDL goes through capillaries and remnants produced are IDL which can go into liver or get converted to LDL which enters the liver
LDL has receptor and can make HDL which can go to liver or to produce steroids
224
What is atmospheric N2 fixed by?
Some bacteria and archaea in the nitrogenase complex
225
Where does NH4+ in plants come from?
NO3- reduced to NO3- reductase and NO2 reductase
226
What is NH4+ in plants converted to?
Glutamine by reaction with glutamate catalyzed by glutamine synthetase then glutamine is converted to glutamate by glutamate synthase
227
Where are all aminoacids derived from?
Intermediated of glycolysis, citric acid cycle, or pentose phosphate pathway
228
How does nitrogen enter various pathways?
By glutamate and glutamine
229
Where does ribose-5-PO4 make?
Histidine
230
Where does serine come from and what does it make?
3-phosphoglycerate and it makes glycine and cysteine
231
What aa does phosphoenolpyruvate make?
Tryptophan
Phenylalanine
Tyrosine
232
What aa does pyruvate make?
Alanine
Valine
Leucine
Isoleucine
233
What aa does oxaloacetate make?
Aspartate which makes asparagine, methionine, threonine, and lysine
234
What aa does alpha ketoglutarate make?
Glutamate which makes glutamine, proline, and arginine
235
What are the essential aa?
```
Val
Ile
Leu
Met
Thr
Lys
His
Phe
Trp
```
236
What is phosphocreatine made by?
Glycine
Arginine
Methionine
237
What composes glutathione
γ-Glu-Cys-Gly via the usage of 2 ATP and the use of γ-glutamyl cysteine synthetase and glythathione synthetase
238
What are derivatives of tyrosine?
Epinephrine, norepinephrine, and Dopamine. Norepinephrine involves Vit C
239
What is produced from glutamate?
GABA and it involves removal CO2
240
What is produced from histadine?
Histamine and it involves removal of CO2
241
Where does seratonin come from?
Tryptophan
242
How is nitric oxide made?
From arginine via NADPH+O2 and a hydroxyarginine intermediate that will react to form citrulline and NO
243
How does DNA get converted to a polypeptide?
DNA (double strand) to mRNA (single strand) to polypeptide
244
What is the function of the centromere?
A link to the mitotic spindle
245
What are telomeres?
Repeated sequences that help stabilize the chromosome
246
How is cellular DNA compact and compare it to the cellular environment?
It is compact by supercoiling but still is underwound in the cellular environment
247
What does underwiring promote?
Cruciform formation and topoisomerases catalyze the extent of underwinding
248
What do Topo I and II do?
I breaks one strand (Lk=1)
| II breaks both both strands (Lk=2)
249
Steps of topoisomerase
1) Active Site Tyr attacks phosphodiester bond in one DNA strand and creates covalent linkage
2) Enzyme changes to open conformation
3) Unbroken DNA strand passes through break in the first strand
4) Enzyme in closed conformation; liberated OH attacks protein linkage to religate the strand
250
What does chromatin contain?
Basic histone proteins that have 1/4 Arg and Lys residues
251
What does packagine of the final chromosome start with?
Nucleosome
252
What is DNA replication and where does it start and proceed?
Semiconservative, semidiscontinuous
| Starts at an origin and proceeds 5'->3'
253
What is DNa made by and degraded by?
Made by DNA polymerase
| Degraded by nucleases
254
What are endo and exonucleases?
Exonuxleases degrade at ends
| Endonucleases at internal sites reducing it to smaller and smaller fragments
255
What does DNA polymerase contain?
2 Asp
| 2 Mg2+
256
What serves as a template and primer strand and what does it provide?
Single unpaired strand
| Provides the free 3'OH to which the new nucleotide is added. Migration occurs after to make room for next addition
257
What are many primers?
Oligonucleotides of RNA made by dedicated enzymes when needed. The number of nucleotides added before polymerase dissociations is processivity
258
Comparison of DNA polymerases
I, II, & III all move 3' to 5'
Only I moves 5' to 3'
III does the synthesis of DNA
Processivity increases from I to II to III
259
What happens if an addition error occurs?
Translocon is inhibited. A 3'-> 5' exonuclease removed the mispaired nucleoride and the polymerase begins again
260
What are the components of the replisome?
Primosome and 2 poly III for each strand
| Primosome has primase, helicase, and accessory proteins
261
Role of Helicase
Unwinds double helix
262
Role of primase
Synthesizes RNA primers
263
Role of Single-strand binding proteins
Stabilizes single stranded regions
264
Role of DNA gyrase
Relives torque
265
Role of DNA polymerase III
Synthesizes DNA
266
Role of DNA polymerase I
Erases primer and fills gaps
267
Role of DNA ligase
Joins the ends of DNA segments; DNA repair
268
What must happen to chromatin?
Must be dismantled prior to the replication fork in eukaryotic replication
269
How does helicase unwind the material?
Uses ATP
270
What is Topoisomerase I attached to?
Tyrosine
271
Function of mRNA
Encodes aa specified by a gene or set of genes
272
Function of rRNA
Part of ribsomes, the makers of proteins
273
Function of tRNA
Reads mRNA and transfers the given aa to a polypeptide chain
274
Lagging strand synthesis
Primers made by primase are removed by Poly I via its 5'->3' exonuclease. Nick between fragments is sealed by DNA ligase
275
What is the synthesis of RNA done by?
A DNA dependent RNA polymerase in a way chemically equivalent to DNA replication
276
Why does RNA not require primer or proof reading?
DNA is more important
277
Where does RNA synthesis begin?
Specific DNA sequences called promoters. The RNA transcript is identical to the nontemplate strand but T is replaced by U
278
Where are most RNAs made and what do they serve?
They are outside classical mRNAs tRNAs and rRNAs. They serve special functions such as regulation. Syntehsis in 5' to 3'
279
What is the initial RNA made?
Primary transcript and contains introns which are spliced to join the exons into a unit that specifies a functional polypeptide
280
How can a gene give rise to multiple products?
Differential processing generating two isozymes, for example
281
What does the cdentral dogma include?
RNA dependent synthesis of DNA y reverse transcriptases and RNA. RNA viruses provide the most characterized RNA polymerases
282
DNA replication
DNA template directed duplication of he genome prior to cell division
283
Transcription
DNA template-directed biosynthesis of RNA
284
Reverse Transcription
RNA template-directed biosynthesis of DNA
285
Translation
mRNA template-directed biosynthesis of proteins
286
Where does synthesis of proteins take place?
In the ribosomes that are attached externally to the ER
287
What does the anticodon loop contain?
A trinucleotide sequence called the anticodon that is complementary to the appropriate trinucleotide codon in the mRNA.
288
What are the stop codons
UAA
UAG
UGA
