Term
|
Definition
P
|
Deoxyribose-5’
|
P
|
Deoxyribose- T, G, C, A
|
P
|
Deoxyribose-3’
|
P
(continues on in this way in both/either or direction) |
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Term
Meme for remembring pyrimidines vs purines
And what matches up with what (base pairs)? |
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Definition
UCT
You see the pyrimids
All others (adenine, guanine, hypoxanthine) are purines
--
GCAT (can be pronounced G-Cat for memory)
A-T
G-C
U replaces T in RNA |
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|
Term
| What is hypoxanthine called when attached to ribose? |
|
Definition
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|
Term
What is hypoxanthine? (what two nucleotides can be made from hypoxanthine?)
What two nucleotides can be made from uracil nucleotides? |
|
Definition
A purine made first as a precursor for adenines and guanines
cytosines and thymines |
|
|
Term
| Match the base to it's corresponding nucleoside for A, G, C, T, U, I |
|
Definition
Adenine - Adenosine
Guanine - Guanosine
Cytosine - Cytidine
Thymine - Thymidine
Uracil - Uridine
Hypoxanthine (I) - Inosine |
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|
Term
|
Definition
| Nucleic Acids are polymers of nucleotides |
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Term
| Describe the numerous functions served by nucleotides, and the importance of de novo synthesis of nucleotides |
|
Definition
NAD+
FAD
CoA
ATP
GTP
ATP for SAM (a nucleoSide)
BH4
UDP-G
cAMP
cGMP
Are all nucleotides, the functions of which we have already learned.
De novo synthesis is important because we can’t absorb nucleotides very well, so it is important that we make them. |
|
|
Term
| Practice Drawing a Purine and Showing Which Parts of it came from what and donated what as a part of their structure (6) |
|
Definition
Figure 41.1 on P. 766
Glycine (+ ATP)
Formlyl-FH4 (C8)
Glutamine (N3) (+ ATP)
CO2(C6)
Aspartate (N1) (+ATP)
Formyl-FH4 (C2) |
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|
Term
How is PRPP made? (2)
And what is its function? |
|
Definition
R 5-P (ribose 5 posphate) reacts with ATP to make PRPP
R 5-P can come from glucose (via pentose phosphate pathway)
R 5-P + ATP –PRPP synthetase→ AMP + PRPP
PRPP is a good donor of R 5-P (to both purines and pyrimidines) |
|
|
Term
| Draw a schematic for PRPP |
|
Definition
P
| (position 5)
Ribose
| (position 1)
P - P |
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|
Term
| What rxn is catalyzed by Glutamine phosphoribosyl amidotransferase |
|
Definition
| Glutamine + PRPP –Glutamine phosphoribosyl amidotransferase→ 5-Phosphoribosyl 1-amine + Glutamate |
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|
Term
| Describe the conversion of hypoxanthine nucleotides into adenine and guanine nucleotides |
|
Definition
Adenine and guanine are a hypoxanthine with another N somewhere. The donor of the nitrogen is different for each.
Adenine nucleotides need aspartate; comes out as fumarate
Guanine nucleotides need glutamine; comes out as glutamate |
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|
Term
| Describe the rxn catalyzed by ribonucleotide reductase (2) |
|
Definition
| Responsible for converting any nucleotide into its deoxy version; uses thioredoxin as the reducing agent (and subsequently NADPH to reconvert thioredoxin) |
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|
Term
| What produces thymine nucleotides? |
|
Definition
Thymidylate synthase turns dUMP to TMP and requires methylene FH4. Methylene FH4 goes in and comes out as FH2 (dihydrofolate)
Thymines will always be deoxy because you find thymine instead of uracil in DNA |
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Term
|
Definition
| Orotate/orotic acid is a pyrimidine ring made from glutamine, CO2 and aspartate. It’s an intermediate in de novo synthesis of pyrimidine nucleotides. For pyrimidine synthesis we expect glutamine and aspartate to be involved. |
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|
Term
| Describe aspartate, glutamine, and CO2's specific roles in pyrimidine production |
|
Definition
Aspartate donates 3C and a nitrogen. Aspartate only has one N and 4C, so by the time this is built, one of those carbons is lost as a CO2 in a decarboxylation reaction. But other than that one carbon, all the carbons of aspartate are part of pyrimidine.
Aspartate gets involved in a different way here than in purine nucleotide synthesis: only 1 N donated, aspartate becomes fumarate
First, Carbamoyl phosphate and aspartate join together as carbamoyl aspartate which eventually becomes orotate.
– The N from glutamine and the C from CO2 don’t come independently from one another; they’re already joined together as a carbamoyl group |
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Term
| Draw the chemical structure of carbamoyl phosphate |
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Definition
| looks like an amide and a phosphate joined together |
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Term
| Give the reaction catalyzed by carbamoyl phosphate synthetase 2 (CPS-2) and compare the two carbamoyl phosphate synthetases that we have studied (CPS-2 and CPS-1) |
|
Definition
Gln + CO2 + 2 ATP + H2O --CPS-2→ carbamoyl phosphate + Glu + 2 ADP + Pi
CPSI vs CPSII
Location: mitochondria vs cytosol
Pathway: urea cycle vs pyrimidine biosynthesis
Source of N: NH4+ vs glutamine
Activator: N-acetylglutamate vs PRPP
Inhibitor: ----- vs UTP
Similarities
– Carbon source is the same: CO2/HCO3-1
– 2 ATPs are spent for each enzyme (1 ATP donates the phosphate group in carbamoyl) |
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|
Term
| Describe briefly the conversion of orotate into uracil nucleotides |
|
Definition
PRPP + Orotate --> Pyrimidine Nucleotide
Pyrimidine Nucleotide --Decaboxylation--> Uracil Nucleotide |
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|
Term
| Describe the conversion of uracil nucleotides into cytosine nucleotides |
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Definition
| UTP is converted to CTP via a reaction that involves the gain of a N from glutamine (which leaves as glutamate). |
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|
Term
| What does dihydrofolate reductase catalyze? |
|
Definition
| FH2 --Dihydrofolate Reductase--> FH4 |
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|
Term
| What does serine hydroxymethyltransferase catalyze? |
|
Definition
| FH4 + Serine --Serine Hydroxymethyltransferase--> Methylene FH4 + Glycine |
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|
Term
| Describe the rxn catalyzed by thioredoxin reductase |
|
Definition
| uses NADPH to reduce thioredoxin from its 2 S form to its 2 SH form |
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|
Term
| What is the role of 5’-nucleotidase? |
|
Definition
| cleaves the phosphate off of a nucleotide to make it a nucleoside |
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|
Term
| Describe the rxn catalyzed by phosphoribomutase |
|
Definition
| interconverts (reversible) ribose 1 and 5 |
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|
Term
| Describe the rxn catalyzed by purine nucleoside phosphorylase (PNPase; inosine phosphorylase) |
|
Definition
| metabolizes adenosine into adenine, inosine into hypoxanthine, and guanosine into guanine, in each case creating ribose 1-P |
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|
Term
| Give the reactions catalyzed by, and the cofactors required by, xanthine oxidase (2) |
|
Definition
hypoxanthine --xanthine oxidase--> Xanthine --xanthine oxidase--> Uric Acid
sometimes uses O2, sometimes uses NADPH, the use of O2 as the oxidizing agent will form H2O2; requires molybdenum in its active site, starting with a charge of +6, gains 2 e- to become +4
requires FeS where Fe3+ goes to Fe2+
requires FAD to FAD(2H)
most commonly inhibited enzyme to treat gout allopathically |
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|
Term
| Describe the methylation cycle (6) |
|
Definition
Methionine + ATP –MAT→ SAM + PPi + Pi
Which will form into 3 Pi as PPi breaks down
SAM + Precursor --methyl transferase→ SAH + CH3-product
methyl transferase (aka transmethylase) is a family of enzymes
SAH --SAH hydrolase→ Homocysteine + Adenosine
homocysteine + FH4 –methionine synthase (b-12)→ methionine + N5-Mehtyl FH4 |
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|
Term
Describe the rxn catalyzed by Tyrosine hydroxylase
~Where? |
|
Definition
a monooxygenase
tryosine + O2 + BH4 --tyrosine hydroxylase--> BH2 + H2O + dopa |
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|
Term
Describe the rxns catalyzed by dopa decarboxylase
~Where? |
|
Definition
dopa --(PLP)--> dopamine + CO2
(first catecholamine)
AND
5-HTP --(PLP)--> 5-hydroxytryptamine (serotonin) |
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|
Term
Describe the rxn catalyzed by dopamine β-hydroxylase
~Where? |
|
Definition
dopamine + vitamin C + O2 --> Norepinephrine + dehydroascorbate + H2O
(monooxygenase) |
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|
Term
Describe the rxn catalyzed by phenylethanolamine N-methyltransferase
where does this rxn happen? |
|
Definition
Norepinephrine + SAM --> Epinephrine + SAH
happens in adrenal medulla |
|
|
Term
| what is a good test for excess sympathetic nervous system activity? |
|
Definition
| checking 3-methoxy-4hydroxymandelic acid (vanillylmandelic acid, VMA) in urine, excess can possibly indicate a pheochromocytoma, since it is a product of MAO breakdown of catecholamines |
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|
Term
| Describe the rxns catalyzed by monoamine oxidase (MAO) (4) |
|
Definition
| inactivation of neurotransmitters (Serotonin, melatonin, norepinephrine, and epinephrine) |
|
|
Term
| Describe the rxns catalyzed by COMT (catechol-O-methyl transferase) |
|
Definition
| inactivation of catecholamines via SAM methylation |
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|
Term
Describe the rxn catalyzed by tryptophan hydroxylase
where might this occur? |
|
Definition
tryptophan + O2 + BH4 --> 5-hydroxytryptophan + H2O + BH2
may well be a serotonergic neuron |
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|
Term
| What two steps occur for N-acetyl serotinin production from serotonin (logical), and where might this process specificaly occur in the body? |
|
Definition
gaining an acetyl group (acetylation from acetyl-CoA) and the other step is gaining a methyl group (methylation)
cells of the pineal gland |
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|
Term
| Describe N-acetyl serotonin to MElatonin |
|
Definition
O-methylation via SAM
me for methyl |
|
|
Term
| What urine product is indicative of serotonin breakdown? |
|
Definition
| 5-hydroxyindole acetic acid; may indicate a tumor |
|
|
Term
| What does the enzyme NO synthase catalyze? |
|
Definition
Arginine + NADPH + O2 → NO + NADP+ + Citrulline
(BH4 indirectly required) |
|
|
Term
| What do neutrophils need NO for? |
|
Definition
|
|
Term
| How does NO work as a neurotransmitter? |
|
Definition
| NO is a retrograde neurotransmitter (from postsynaptic to presynaptic neurons) |
|
|
Term
| What are the three kinds of NO synthase enzymes? |
|
Definition
iNOS (inducible NO synthase)
non inducible (Ca++ activated):
neuronal NOS
nNOS
endothelial NOS
eNOS |
|
|
Term
| Why is NO considered important for memories? |
|
Definition
| Long term potentiation is believed to be the means by which memories are formed, NO is important for this process |
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|
Term
| What is cGMP important secondary messenger for? |
|
Definition
| smooth muscle vasodilation/relaxation |
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|
Term
| What does NO tell smooth muscle cells? |
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Definition
|
|
Term
Describe the fates of the carbon skeletons of amino acids in the liver (4)
Describe the fate of amino acid nitrogen in the liver |
|
Definition
can be used as fuel
used to make glucose
used to make ketone bodies
made into fat
AA nitrogen to urea |
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|
Term
| What enzyme is responsible for the oxidation of branched chain amino acids? |
|
Definition
|
|
Term
| Describe how amino acid metabolism in the liver after a high protein meal resembles amino acid metabolism in the liver in the fasting state |
|
Definition
| glucagon induces urea cycle enzymes and gluconeogenic pathway |
|
|
Term
| Draw the chemical structure of glutamine |
|
Definition
|
|
Term
| Describe the conversion of branched chain amino acids (BCAA) into glutamine |
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Definition
| They enter TCA cycle and can come out as glutamine via a-KG → Glutamate → Glutamine |
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|
Term
| Explain how (describe the route by which) the nitrogens from BCAA can become nitrogens of glutamine |
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Definition
| If two glutamates are made, one can transaminate the other making an a-KG molecule and a glutamine, in which case all N's came from BCAAs |
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|
Term
| What does histidine decarboxylase catalyze? |
|
Definition
histidine --(PLP)--> histamine
Recognize and distinguish between the chemical structures of histidine and histamine |
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|
Term
Name the rxn that creates GABA
Draw GABA |
|
Definition
| Glutamate --glutamate decarboxylase (PLP)--> GABA |
|
|
Term
| Draw the chemical structures of acetylcholine and choline |
|
Definition
|
|
Term
| What enzyme is responsible for acetylcholine production? |
|
Definition
| choline + acetyl CoA --choline acetyltransferase--> acetylcholine + CoA |
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|
Term
| What enzyme catalyzes hydrolysis of the ester bond in acetylcholine? |
|
Definition
|
|
Term
| What is the role of ubiquitin? |
|
Definition
| (protein made by cells) tags a protein making it targeted to be lysed by proteasomes |
|
|
Term
|
Definition
| Lysosomal proteases; work best in an acidic environment |
|
|
Term
| Describe how infection of cells of the uterine cervix with certain types of human papilloma virus (HPV) increases the risk of cervical cancer |
|
Definition
| some HPV (Human Papiloma Virus) viruses will infect cervical cells, and cause ubiquitin to attach to an important tumor suppressor protein called p53 |
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|
Term
| What chnages in hormonal signals lead to a net degradation of skeletal muscle protein (degradation greater than synthesis) during the fasting state? |
|
Definition
(1) a decrease in the amount of insulin as you go into the fasting state slows down protein synthesis
(2) an increase in cortisol leads to increased protein degradation. During the fasting state cortisol signals, not glucagon (glucagon doesn’t even talk to muscle cells), stimulate the ubiquitin-proteasome pathway. |
|
|
Term
| Describe how some cells use glutamine as fuel |
|
Definition
Glutamine can become a-KG and thus OAA, PEPCK turns OAA to PEP which can be made to glucose
(kidney cells can do this) |
|
|
Term
| Describe the use of glutamine by your enterocytes |
|
Definition
since enterocytes rapidly divide it requires nucleotides and thusly the N is needed
enterocytes use glutamine for purines, pyrimidines, NAD+, amino sugars, and asparagine production |
|
|
Term
| What two cells do we need to know that divide rapidly and thus require large amounts of glutamine? |
|
Definition
| intestinal mucosa use it as a fuel, for repair, and for division, and WBCs use it as fuel and for division |
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|
Term
| Why would it be beneficial for your body to break down muscle protein when you’re trying to deal with a bad infection? |
|
Definition
| The immune cells need glutamine |
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|
Term
| Describe the sources and roles of corticotropin releasing hormone (CRH) |
|
Definition
| Hypothalamus senses stress (such as sickness), anterior pituitary releases CRH, which then stimulates cortisol release, which then stimulates the ubiquitin-proteasome pathway |
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