Exam 3 Flashcards
(167 cards)
1
Q
How are dietary proteins broken down?
A
Proteases hydrolyze them into free amino acids, dipeptides, and tripeptides
2
Q
What are essential amino acids? Which ones are they?
A
Essential amino acids are those that must be acquired from the diet because an organism is unable to synthesize them.
TV FILM HW(R*)K
3
Q
What is the primary protease of the stomach?
A
Pepsin; it is a nonspecific protease
4
Q
Where are MOST digestive enzymes synthesized, and how are they released?
A
Most digestive enzymes are synthesized in the pancreas, and they are secreted into the intestine as zymogens
5
Q
What is aminopeptidase?
A
It is a nonspecific protease that hydrolyzes proteins from the amino terminal end
6
Q
The half life of proteins varies. How is the half life of proteins determined?
A
The N-terminal sequence determines the half life
7
Q
Which amino acids on the N terminal favor ubiquitination (fast destruction)?
A
Arginine and Leucine
8
Q
Which amino acids on the N terminal disfavor ubiquitination (slow destruction)?
A
Methionine and Proline; these amino acids signal a long half life
9
Q
How are proteins marked for degradation?
A
Polyubiquitination; ubiquitin (Ub) forms polymers; it is the “mark of death” for proteins
10
Q
How is ubiquitin covalently attached to proteins marked for destruction?
A
The C terminal glycine of Ub is attached to the epsilon amino group of lysine; all proteins have at least 1 lysine residue on their surface
11
Q
Which 3 enzymes are involved in the attachment of Ub to proteins?
A
E1 or Ubiquitin-activating enzyme
E2 or Ubiquitin-conjugating enzyme
E3 or Ubiquitin-protein ligase
12
Q
What does Ubiquitin-activating enzyme do?
A
It activates Ub by adenylation; it attaches the C terminal carboxylate of the activated Ub to itself via a thioester bond
13
Q
What does Ubiquitin-conjugating enzyme do?
A
It transfers the activated Ub from a sulfhydryl of E1 to E2 (itself)
14
Q
What does Ubiquitin-protein ligase do?
A
It transfers Ub from E2 to the target protein
15
Q
What is the largest gene family in humans?
A
Ubiquitination enzymes
16
Q
Which 3 diseases are linked to improper functioning of E3?
A
Some forms of Parkinson’s disease, Angelman syndrome, and HPV
17
Q
Describe the structure of proteasomes
A
2 19S alpha caps
1 20S beta catalytic core
Has a total of 28 subunits
18
Q
On which subunit of the proteasome is the active site located?
A
On the beta subunits within the 20S core; threonine residue acts as a nucleophile
19
Q
What do proteasomes do?
A
Proteasomes hydrolyze ubiquitinated proteins
20
Q
What is Bortezomib (Velcade)
A
It inhibits proteasomes; used as therapy for multiple myeloma
21
Q
What are the primary and secondary sites of amino acid degradation?
A
The liver is primary; muscle is secondary, and degrades branches chain aa’s (L,I, V)
22
Q
What are the 2 steps involved in amino acid degradation?
A
- Removal of a-amino group (it is transferred to a-KG)
2. Conversion of C-N to C=O (by glutamate DH)
23
Q
What do aminotransferases use as their prosthetic group?
A
PLP from vitamin B6 (pyridoxine); they transfer a-amino groups from amino acids to a-KG to form glutamate
24
Q
What does glutamate dehydrogenase do, and what is special about it?
A
Glutamate dehydrogenase converts nitrogen of glutamate to ketoacid and free ammonium ion; it can use EITHER NAD+ or NADP+
25
How are Schiff bases formed during amino acid degradation?
Pyridoxal phosphate forms the Schiff base; it can accept/ donate protons
26
Which two amino acids can be directly deaminated? And what are the products of these reactions?
Serine and threonine; they do not have to go through glutamate
Serine --> pyruvate + NH4+
Threonine --> a-ketobutyrate + NH4+
27
Which enzymes deaminate serine and threonine respectively, and how?
Serine dehydratase and threonine dehydratase;
Both enzymes dehydrate their substrates, and then re-hydrates them w/ the loss of the amino group
28
What is the alanine cycle? And where does it occur?
The alanine cycle occurs between muscle tissue and liver;
Branched chain amino acids are degraded and converted to alanine in muscle tissue
Alanine leaves the muscle and travels to the liver, where it is converted to pyruvate and glutamate.
Pyruvate can then be used in GN
29
What are ureotelic organisms?
Ones that excrete excess nitrogen in the form of urea; includes terrestrial vertebrates, like humans
30
Organisms that excrete excess nitrogen as uric acid are called?
Uricotelic; includes birds and reptiles
31
Aquatic organisms excrete excess nitrogen in the form of what?
Ammonium; they're called ammonotelic
32
What is the urea cycle?
The synthesis of urea from carbamoyl phosphate and ornithine
33
Where do the atoms of urea come from?
1 nitrogen comes from ammonium
1 nitrogen comes from aspartate
1 Carbon comes from bicarbonate (dissolved CO2)
34
What enzyme synthesizes carbamoyl phosphate, and from what substrates?
Carbamoyl phosphate synthetase I; it is located in the mitochondrial matrix
It uses ammonia and bicarbonate
35
How many ATP are used in the synthesis of carbamoyl phosphate?
2 ATP/ 1 carbamoyl phosphate synthesized
36
What 3 sites are located on carbamoyl phosphate synthetase I?
Glutamine hydrolysis site (source of NH4+)
Bicarbonate phosphorylation site
Carbamic acid phosphorylation site
37
What is substrate channeling, and which 2 enzymes use this?
Substrates pass from one active site to another through a channel; not released by enzyme.
Used by carbamoyl phosphate synthetase 1 and in the synthesis of tryptophan (protects the indole group)
38
Name the 4 enzymes used in the urea cycle
Ornithine transcarbamoylase
Argininosuccinate synthetase
Argininosuccinate
Arginase
39
This enzyme catalyzes the synthesis of citrulline. What are its substrates?
Ornithine transcarbamoylase; it uses ornithine and carbamoyl phosphate
40
This enzyme condenses citrulline and aspartate to argininosuccinate
Argininosuccinate synthetase
41
This enzyme cleaves argininosuccinate into arginine and fumarate
Argininosuccinase
42
What does arginase do in the urea cycle?
It hydrolyzes arginine into ornithine and urea
43
What two intermediates link the urea cycle to gluconeogenesis?
Aspartate (can come from OAA) and fumarate (can be converted to malate, and then OAA)
44
What are hyperammonemias, and what can cause them?
Elevated level of ammonia in the blood; can be caused by lack/ reduced synthesis of carbamoyl phosphate or by lack/ reduced activity if one of the four enzymes of the urea cycle
45
Which amino acids are essential?
TV FILM HWK
46
Threonine can be degraded into pyruvate. What is the intermediate in this pathway?
2-amino-3-ketobutyrate (we just oxidized C3 from an alcohol to a carbonyl group)
47
What is the sulfur atom of cysteine converted to during catabolism?
It can be converted to H2S, SCN-, or SO32-
48
Branched chain amino acids, and aromatic amino acids can be broken down into what products?
Acetyl CoA and acetoacetyl CoA; note that HMG is an intermediate as well
49
What are oxygenases? They are required for the catabolism of which amino acids?
Oxygenases are enzymes involved in redox reactions; they're required for the breakdown of aromatic amino acids (F, W, Y)
50
What is a monooxygenase? Give example
An enzyme capable of splitting a molecule of oxygen, in which each oxygen atom ends up in two different products;
Phenylalanine hydroxylase is a monooxygenase; oxygen ends up in Tyrosine and water
51
Which two pathways is phenylalanine hydroxylase involved in?
Conversion of Phe to Tyr
And the synthesis of Tetrahydrobiopterin (BH4) from phenylalanine
52
Which two other enzymes are involved in the synthesis of BH4, and what are their substrates?
What are their coenzymes?
Dihydrofolate reductase reduces dihydrobiopterin to BH4
Dihydropteridine reductase reduces quinoid dihydropterin to BH4
Both enzymes use NADPH
53
What are the two dioxygenases uses in the catabolism of Phe/ Tyr?
p-hydroxyphenylpyruvate hydroxylase AND homogentisate oxidase
Phe/ Tyr can be both glucogenic and ketogenic
54
What two products can tryptophan be broken down into?
Alanine and acetoacetate via both mono and dioxygenases
55
What is the product of destination of glutamate?
a-Ketoglutarate
56
What enzyme hydrolyzes the nitrogen of glutamine to glutamate?
Glutaminase
57
Which 2 amino acids from a glutamate gamma- semialdehyde intermediate during their catabolism?
Proline and arginine
58
A 4-imidazole-5-propionate intermediate is involved in the catabolism of which amino acid?
Histidine
59
The catabolism of some amino acids involve intermediates common to the oxidation of odd numbered fatty acids. What are they?
Propuinyl CoA
Methylmalonyl CoA
Succinyl CoA
60
The catabolism of methionine involves this intermediate, that acts as a methyl donor:
S-adenosylmethionine (SAM)
61
Serine and homocysteine combine to form:
Crystathionine, which is converted to a-ketobutyrate by removing cysteine
62
Which 4 enzymes are directly deaminated (amino group not transferred to glutamate)?
Serine, threonine, aspartate, and asparagine
63
Aspartate is directly deaminated to what?
OAA
64
What enzyme converts asparagine to aspartate by removing ammonium (side chain)
Asparaginase
65
What was the first description of an inborn error of metabolism?
Which amino acids aren't degraded properly?
What intermediate accumulates as a result?
Alcaptonuria
Defective degradation of Phe/ Tyr
Homogentisate accumulates = black urine
66
What defect leads to maple syrup urine disease MSUD?
Defect in the degradation of branched-chain amino acids (muscle tissue) (Val, Ile, and Leu)
67
In MSUD, a-ketoacids in urine react with this molecule for detection:
2,4-dinitrophenylhydrazine
68
What enzyme is defective/ missing in patients with phenylketonuria?
Phenylalanine hydroxylase; Phe accumulates (causing reactions) and Tyr isn't synthesized
Phenylpyruvate in urine reacts w/ FeCl3, turning urine olive green
69
What is the source of nitrogen for the synthesis of amino acids and nucleotides?
Nitrogen gas (N2), which is fixed/ reduced to ammonia mostly by diazotrophic microorganisms
70
What does the Haber process require?
500 degrees Celsius, 300 atm pressure, and an iron catalyst. 25% of nitrogen fixation
71
What two components make up the nitrogenase complex, and what do they do?
Reductase: transfers electrons (8) from reduced ferredoxin to nitrogenase complex
Nitrogenase: uses electrons from reductase to reduce nitrogen gas to ammonia
72
Describe reductase (aka Fe protein) of the nitrogenase complex
Reductase has 4Fe-4S cluster; it is a dimer, and each subunit binds ATP (2/e- transferred), so they have P loops (NTPase family)
73
What does reductase use to transfer electrons to nitrogenase?
The hydrolysis of ATP; 2 ATP are hydrolyzes per electron transferred
74
Describe nitrogenase (aka MoFe protein) of the nitrogenase complex
MoFe = molybdenum iron cofactor
A2B2 tetramer
P cluster (stores electrons before transfer)
Has 2 unique iron sulfur clusters:
M-3Fe-3S, in which M = Mo in one cluster, and M= Fe in the other cluster
75
Which orientation are the amino acids in our bodies?
In the L orientation
76
What reaction does glutamate dehydrogenase catalyze in the catabolism and the anabolism of amino acids?
Anabolism: the synthesis of glutamate from ammonium and a-KG and NADPH
Catabolism: converts a-amino group of glutamate to C=O; NH4+ is a byproduct
Glutamate dehydrogenase can use either form of NAD+/ NADP+ in its reactions
77
What are the common features of amino acid synthesis?
There is some activated intermediated;
A Schiff base is formed, followed by protonation, and reduction
78
When is the stereochemistry of all chiral amino acids established?
In the second step of glutamate dehydrogenase mechanism, in which the protonated Schiff base accepts a hydride from NADPH
79
What enzyme synthesizes glutamine, and how is the precursor activated?
Glutamine synthetase; it uses ATP to phosphorylate glutamate. Then the phosphate group is displaced by ammonia
80
Synthesis of aspartate:
| Enzyme and precursor
Aspartate transaminase transfers ammonium from glutamate to OAA to make aspartate
81
Alanine synthesis enzyme and precursor?
Alanine transaminase transfer ammonium from glutamate to pyruvate to make alanine
82
Synthesis of asparagine: enzyme and precursor. What is special about the precursor?
Asparagine synthetase uses glutamine ** (NH4+ donor) and aspartate to make asparagine
83
Asparagine synthetase and glutamine synthetase both use ATP, but how are they different?
Asparagine synthetase uses ATP to activate aspartate by adenylation
Glutamine synthetase uses ATP to activate glutamate by phosphorylation
84
What serves as the precursor for the synthesis of proline, arginine, and ornithine? What happens?
Glutamate; glutamate is phosphorylated by ATP, then the carboxylate is reduced, forming an aldehyde (glutamic gamma-semialdehyde)
85
Which intermediate is common in both the synthesis and degradation of the amino acids arginine and proline?
Glutamic gamma-semialdehyde
86
What are the two precursors/ ways serine can be synthesized from?
3-phosphoglycerate (glycolytic intermediate) or glycine
87
How is serine synthesized from 3-PG
First, the alpha hydroxyl group of 3-PG is oxidized to a carbonyl, forming 3-phosphohydroxy pyruvate
Then glutamate provides a-amino group, making 3-phosphoserine, which is then dephosphorylated to make serine
88
Which two amino acids are in equilibrium in every cell? What does this mean?
Glycine and serine; it means they can be synthesized from each other
89
In what 2 ways can glycine be synthesized?
1. Serine hydroxymethyl transferase
| 2. Serine synthase (aka glycine cleavage enzyme)
90
How is glycine made using serine hydroxymethyl transferase?
Serine HMT uses serine and THF to make glycine and methyl-THF
91
How is glycine made using serine synthase?
Serine synthase uses ammonium, carbon dioxide, and N5N10-methylene-THF (cofactor) to make glycine and THF
92
What is tetrahydrofolate?
THF is a cofactors that carries activated one carbon units, which may be attached to N5, N10, or both
Humans are not able to synthesize it (vitamin B9)
93
Which enzymes use some form of THF?
Serine hydroxymethyl transferase Serine synthase
| Dihydrofolate reductase
94
What is SAM synthesized from? How many phosphate groups are retained?
Methionine and ATP
None
95
What is the purpose of the activated methyl cycle?
To regenerate methionine from homocysteine
96
How is homocysteine converted to methionine?
It is methylated
97
What enzyme synthesizes methionine, and what does it require?
Methionine synthase (aka homocysteine methyltransferase)
It requires methyl cobalamin (B12)
98
What are the two ways to get rid of homocysteine?
Synthesize methionine
```
Synthesize cysteine (serine + homocysteine)
* cystathionine is an intermediate
```
99
What 2 enzymes are used to synthesize cysteine from homocysteine?
What does 1 use?
What are the substrates?
Cystathionine B- synthase (uses PLP, B6)
Cystathionase
Homocysteine + serine
* Sulfur comes from homocysteine; carbon backbone comes from serine
100
What is the most common cause of high homocysteine levels, and what does elevated levels cause?
A mutation in the cystathionine B-synthase enzyme
High levels lead to coronary heart disease
101
How is high levels of serum homocysteine treated?
Vitamins:
B12 and THF required for methionine synthase
B6 required for cystathionine B-synthase
102
How is tyrosine synthesized?
From Phe via phenylalanine hydroxylase (a monooxygenase that requires BH4- an electron carrier)
103
Phenylalanine, tyrosine, and tryptophan are synthesized in bacteria. Which intermediates are used, and what pathways do they come from?
PEP (from glycolysis)
Erythrose-4P (from PPP)
104
What are two intermediates in the synthesis of the aromatic amino acids? Which one is the last common intermediate?
Shikimate and Chorismate
Chorismate is the last common intermediate
105
What is the chemical name for Roundup, and what pathway does it inhibit?
Glyphosate
It inhibits synthesis of aromatic amino acids
106
From Chorismate, how are phenylalanine and tyrosine synthesized?
Chorismate --> phenylpyruvate --> phenylalanine
Chorismate --> p-hydroxyphenylpyruvate --> tyrosine
107
How is the indole group of tryptophan incorporated? Where does tryptophan's amino group come from?
The indole group is combined with serine, which provides tryptophan w/ an amino group
108
Which two amino acids do NOT get their a-amino group from glutamate?
Arginine (from glutamine)
Tryptophan (from serine)
109
What is PRPP involved in?
PRPP = activated ribose
The synthesis of the amino acid tryptophan and the synthesis of nucleotides
110
When is substrate channeling used?
In the synthesis of tryptophan and the synthesis of carbamoyl phosphate
111
What is negative nitrogen balance?
More proteins are broken down than synthesized.
Occurs when there is an amino acid deficiency
112
All aminotransferases contain which 2 conserved amino acids? What do they do?
Lysine (forms Schiff base w/ PLP)
Arginine (interacts w/ alpha carbonyl of ketoacid)
113
Nitric acid (NO) is synthesized from what amino acid?
Arginine
114
What are the precursor amino acids for glutathione?
Glutamate
Cysteine
Glycine
(ECG)
115
Porphyrins are used to synthesize what molecule? And what are the precursors of porphyrins?
Heme;
Glycine and succinyl CoA
116
What does glutathione reductase do?
Reduces GSSG to GSH; used NADPH and FAD
117
What does glutathione peroxidase do?
It reduces hydrogen peroxide to water; a selenium ion replaces the sulfur of a cysteine residue in the active site
118
What enzyme catalyzes the synthesis of nitric oxide? What are the substrates?
Nitric oxide synthase; it uses arginine, NADPH and molecular oxygen (O2)
119
What does nitric oxide do?
It functions as a smooth muscle dilator and as a messenger in signal transduction pathways
120
What are porphyrins?
Which one is heme?
Porphyrins are cyclic compounds that readily bind metal ions
Protoporphyrin IX = Heme
121
Where in the cell is heme synthesized? Which tissues/ cells carry out heme synthesis?
Heme synthesis occurs in the mitochondria and the cytoplasm
Erythrocyte-producing cells of bone marrow and hepatic cells carry out heme synthesis
122
What is ferrochelatase?
An enzyme that enhances the rate of addition of iron
123
What is ferritin?
An iron storage protein
124
What is transferrin?
Iron transport protein
125
What are porphyrias?
Autosomal dominant disorders caused by deficiency of enzymes in the heme biosynthetic pathway
126
How is bilirubin made? What enzyme? Where is bilirubin broken down?
The enzyme bilirubin reductase synthesizes bilirubin from the reduction of biliverdin (a linear tetrapyrrole)
Bilirubin is broken down in the liver
127
What are the two sources of nucleotide synthesis?
Salvage pathways (bases are recovered and attached to PRPP)
De novo synthesis
128
What is the difference between pyrimidine synthesis and purine synthesis?
Pyrimidines are synthesized FIRST, and then attached to ribose
Purines are synthesized WHILE attached to ribose
129
What is the final step in the synthesis of thymine?
Methylation of uracil
130
What are deoxyribonucleotides synthesized from?
Ribonucleotides
131
What kind of base are xanthine and inosine?
They are purines
132
What are the sources of the atoms of the pyrimidine ring?
Carbamoyl phosphate (N3, and C2)
Aspartate (N1, C4,5,6)
133
Carbamoyl phosphate synthetase synthesizes carbamoyl phosphate. What is the difference in CPS I and CPS II?
CPS I is used for the urea cycle, and thus is only found in the liver
CPS II is used in nucleotide biosynthesis, and this is found in all cells
134
What reaction does dihydrorotase catalyze?
The synthesis of dihydroorotate through hydrolytic cyclization
135
What does pyrimidine phosphoribosyl do in nucleotide biosynthesis?
It attaches orotate (pyrimidine) to ribose (PRPP)
136
What does dihydroorotate dehydrogenase do?
It catalyzes oxidation of the ring, converting dihydroorotate to orotate
137
What does orotidylate decarboxylase do?
Converts orotidylate (OMP) to uridylate (UMP)
138
What is the reaction of nucleotide diphosphate kinase?
NDP + XTP --> NTP + XDP
139
What enzyme catalyzes the synthesis of CTP? From what? How?
CTP synthetase (uses ATP)
From UTP
By animation of the keto group on C4; the amino group comes from the R group of Glutamine
140
What enzyme catalyzes the synthesis of TMP? From what? How?
Thymidylate synthase
From dUMP !! Produces dUMP
The prosthetic group of thymidylate synthase (N5,N10-methylene-THF) donates one carbon and two hydrogens
During the reaction, THF is converted to DHF
141
What molecule inhibits thymidylate synthase? How?
Fluorouracil; it is a nucleotide analog; competes for active site; suicide inhibitor
142
What enzyme catalyzes the reduction of DHF to THF? What drugs inhibit it? How?
Dihydrofolate reductase
Inhibited by aminoptrin and methotrexate; both are competitive inhibitors
143
What is methotrexate?
A competitive inhibitor; will INDIRECTLY inhibit ANY drug that uses THF as a prosthetic group, because it prevents the synthesis of THF from DHF
144
PRPP is used in the synthesis of what molecules?
Nucleotides and histidine
145
What is the last common intermediate of purine synthesis?
Inosine (IMP)
146
In purine synthesis, the activation of a carbonyl by phosphorylation is common. Which molecules are activated like this?
Glycine and bicarbonate
147
Purine synthesis: Glutamine phosphoribosyl amidotransferase
The snide group of glutamine replaces the pyrophosphate group on C1 of ribose
(PRPP + NH4+ --> phosphoribosyl amine
148
What enzyme does IMP inhibit?
Glutamine phosphoribosyl amidotransferase
149
What does pyrophosphorylase do?
Hydrolyze pyrophosphate to provide energy
150
Phosphoribosyl amine combines with this amino acid to form ?
It combines w/ glycine
They form glycinamide ribonucleotide
151
Formyl transferase enzymes appear twice in purine synthesis. What is its prosthetic group, and what does it carry?
THF is the PG, and it adds formal groups (aldehyde) to nitrogen atoms
152
What type of enzyme catalyzes the formation of an amidine group? Where does the amino group come from?
A synthetase is used
The amino group comes from glutamine
Glutamine donates an amino group to convert the carbonyl into an amidine group
153
There are 2 ring closing reactions in purine synthesis. Which enzymes catalyze them?
Which ring is synthesized first?
A synthetase first closes the imidazole ring
Then a cyclohydrolase closes the pyrimidine ring through (dehydration)
154
In purine synthesis, this step is not catalyzes by an enzyme. How does it happen?
The carbon dioxide (from bicarbonate) jumps from N3 to C5, becoming C6
This reaction is under equilibrium control; no enzyme used
155
Purine synthesis: when step is fumarate lost in?
8. Adenylsuccinate lyase, in which a C-N bond is cleaved
156
Which enzyme catalyzes the formation of the last common intermediate (IMP) of purine synthesis?
Cyclohydrolase
157
What enzyme synthesis AMP from IMP? Where does the amino group come from?
Adenylosuccinats synthetase; amino group comes from aspartate
158
What enzyme catalyzes the synthesis of GMP from IMP? How?
GMP synthetase
Inosinate is oxidized to xanthylate (using NAD+)
The keto group of Xanthylate is then aminated (NH4+ from Glu) to form Guanylate (GMP)
159
What enzyme converts ribonucleotides into deoxribonucleotides? How?
Ribonucleotide reductase reduces the 2' hydroxyl to a hydrogen
It uses NADPH
160
What order are dNTPs synthesized in?
First, nucleotide monophosphates are made
Then, they are phosphorylated to nucleotide diphosphates
Lastly, ribonucleotide reductase is used to convert rNDPs into dNDPs
dNTPs are made by further synthesis from nucleoside diphosphate kinase
161
How are purines catabolized? What is the final product?
Both AMP and GMP are converted into xanthine
Xanthine is converted to urate, which is excreted in the urine
Hydrogen peroxide is formed in this catabolism, and must be degraded
162
What is urate?
Product of purine catabolism; it is a powerful scavenger of ROS
163
Which amino acid is the precursor of sphingosine?
Serine
164
Which amino acid is the precursor of histamine? How?
Histidine
Decarboxylation
165
Which amino acid is the precursor of of epinephrine, melanin, and thyroxine?
Tyrosine
166
Which amino acid is the precursor of serotonin?
Tryptophan
167
Which amino acid is the nicotine mode ring of NAD+ synthesized from?
Tryptophan
