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Biochemistry II > Chapter 22 > Flashcards

Chapter 22 Flashcards

1
Q

Nitrogen conservation

A

most organisms are very conservative in how they use their nitrogen

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2
Q

Free amino acids and nucleotides

A

often salvaged and reused

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3
Q

Main source of nitrogen

A

the air, 80% N2

*we can’t use, bacteria can

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4
Q

Nitrogen cycle

A
  1. fixation
  2. nitrification
  3. denitrification
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5
Q

Fixation Overview

A
  • in some bacteria

- fixes atmospheric N2 to yield ammonia

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6
Q

Nitrification

A
  • in bacteria

- ammonia from soil converted to nitrate

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7
Q

Plant nitrification

A

some plants take up and reduce nitrate in the soil and produce ammonia for their own use in amino acids and nucleotides

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8
Q

Animal nitrogen sources

A

often plants

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9
Q

Denitrification

A
  • some bacteria

- convert nitrates back to N2

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10
Q

Nitrogen Fixation

A
  • exergonic
  • high activation energy because of stable triple N-N bond
  • facilitated by ATP
  • requires other things
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11
Q

Nitrogen Fixation Requirements

A
  • 8 electrons
  • 6 for reduction of N2
  • 2 to make H2
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12
Q

Ammonia incorporation

A

assimilated into amino acids then other molecules

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13
Q

Glutamate

A

main source of amino groups thru a.a. oxidation via transamination

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14
Q

Glutamine

A

main source of amino groups for biosynthetic processes

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15
Q

Glutamine synthetase

A

-catalyzes ammonia and glutamate to make glutamine

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16
Q

Glutamine transfer in mammals

A

ammonia must be transferred by glutamine because glutamate has a large negative charge

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17
Q

Glutamine in the liver

A

liberated to form glutamate to feed the urea cycle or is reused for amino acid biosynthesis

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18
Q

Allosteric regulation of glutamine synthetase

A
  • primary point of entry for reduced N2
  • primary point of regulation
  • > 6 products of glutamine metabolism, glycine and alanine inhibit
  • effect is “more than additive”
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19
Q

“more than additive” inhibition

A

multiple allosteric binding sites for multiple effectors

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20
Q

Amidotransferase mechanism

A
  • glutamine amidotransferase

- Cys acts as a nucleophile and cleaves the amide bond and channels it to the other substrate

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21
Q

Glutamine amidotransferase

A

catalyzes the transfer of amine from one substrate to another

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22
Q

Amino acid derived intermediates

A

all a.a’s are derived from intermediates in glycolysis, citric acid cycle or the pentose phosphate pathway

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23
Q

Nonessential amino acids

A
  • 11

- we make

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24
Q

Essential amino acids

A
  • 9
  • mostly non polar
  • obtained from the diet
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25
Q

From glycolysis

A
  • 3 phosphoglycerate
  • phosphoenolpyruvate
  • pyruvate
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26
Q

From pentose phosphate pathway

A
  • ribose 5-phosphate

- erythrose 4-phosphate

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27
Q

From citric acid

A
  • alpha ketoglutograte

- oxaloacetate

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28
Q

alpha ketoglutarate in E coli

A
  • P, E, R, Q
  • makes E by transamination
  • E can be converted to Q
  • E can be cyclized to form P using 3 enzymes and 2 reductions
  • E can be converted to R via ornithine and the urea cycle in bacteria
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29
Q

3-phosphoglycerate in humans

A
  • 3-PG is oxidized and gets an amino group from E, then is hydrolyzed to make S
  • methylene group transferred to THF to make G
  • use S and get sulfur from Met
30
Q

Oxaloacetate

A
  • T from transamination from glutamate

- N amidation of Asp using NH4+ from Q

31
Q

Branching point between Lys and either Met or Thr

A

Aspartate beta-semialdehyde

32
Q

Branching point between Met and Thr

A

Homoserine

33
Q

Interconnected biosynthesis in oxaloacetate

A

Lys, Met, Thr, Iso, Val and Leu are all interconnected

34
Q

Pyruvate

A
  • A from pyruvate and transamination from E
  • I and V share 4 common enzymes
  • L is made from an intermediate in the V pathway
35
Q

Interconnected biosynthesis in pyruvate

A

K, M, T, V, L, and I are interconnected

36
Q

PEP and Erythrose 4-phosphate

A
  • condense to form shikimate in 4 steps
  • shikimate condensed into chorismate with another PEP and phosphate hydrolysis
  • chorismate is branch point for Trp and Phe/Tyr
37
Q

Chorismate to W

A
  • gets amino group, loses pyruvate -> anthranilate -> condenses with PRPP ->cyclized to form indole ring
  • tryptophan synthase
38
Q

Tryptophan synthase

A

-releases glyceraldehyde 3-phosphate -> indole + serine -> Trp

39
Q

Chromate to Y and F

A
  • pyruvate group moved by a mutate to form prephenate
  • prephenate dehydrogenase/dehydratase accepts prephenate branching into Tyr and Phe
  • then transamination with E
  • done in E coli
40
Q

Ribose 5-phosphate

A
  • > PRPP by ribose phosphate pyrophosphokinase
  • His from:
    • PRP, 5 carbons
    • ATP, N and C
    • E, 2nd nitrogen ring
  • not made in humans
41
Q

Inhibition of amino acid biosynthesis

A
  • 1st reaction
  • end products
  • most responsive mechanism
42
Q

1st reaction in each pathway

A

usually irreversible and catalyzed by an allosteric enzyme

43
Q

End products of each pathway

A

negatively allosterically regulate to prevent formation of more product

44
Q

Sequential feedback inhibition

A
  • not common
  • isozymes of protein are independently allosterically regulated
  • prevents one product from stopping the synthesis of intermediates which are used for the production of a different product
45
Q

Glycine in porphyrins

A
  • common precursor
  • in mammals glycine and succinyl-CoA make delta-aminolevulinate
  • glutamate in plants not glycine
  • 2 delta-alv condense and make porphobilnogen
  • 4 porphobilnogen condense to make protoporphyrin
  • chelates Fe2+ and makes heme
46
Q

Porphyrins

A
  • nucleus of 4 cyclic amines

- in heme proteins like hemoglobin and cytochromes

47
Q

Heme precursor to bile pigments

A

-damage/death of RBC’s release heme ->degraded by heme oxygenase -> biliverdin -> bilirubin

48
Q

Bilirubin

A
  • bruises -> black/purple -> green (biliverdin) -> yellow (bilirubin) -> urobilin (yellow in urine) or stercobilin (red/brown in feces)
  • impared liver fun or blocked bile secretion can cause leakage into blood -> jaundice
  • newborns don’t have enough of the enzyme to degrade -> jaundice
49
Q

Aromatic amino acids are precursors o plant compounds

A
  • Phe and Tyr are key components of plant polymer lignin
  • Trp is precursor to plant growth hormone auxin
  • Phe and Tyr give rise to alkaloids and flavorings (morphine, vanilla)
50
Q

De Novo pathways

A
  • synthesize nucleotides

- uses amino acids, ribose 5-phosphate, CO2 and NH3 are precursors

51
Q

Salvage pathways

A
  • synthesize nucleotides

- uses recycled free bases and nucleosides released from nucleic acid breakdown

52
Q

Purines

A

G and A

53
Q

De novo purine synthesis

A
  • PRPP provides the ribose and phosphate
  • amine transferred from glutamine
  • 3 atoms from glycine
  • formyl group from THF
  • amine from glutamine
  • ring closure to form imidazole ring
  • C from bicarbonate
  • N from aspartate
  • formyl group from THF
  • condensation closes 2nd ring forming inosinate
  • takes a lot of ATP
54
Q

Inosinate precursor to adenylate snd guanylate

A
  • inosinate converted to adenylate (AMP) by addition of amino group from aspartate and loose of fumarate
  • inosinate converted to guanylate (GMP) by NAD dependent oxidation to xanthanylate followed by addition of an amino group from glutamine
55
Q

Feedback inhibition of purine synthesis

A
  • end products; IMP, AMP, GMP inhibit run catalyzed by glutamine-PRPP amidotransferase
  • AMO and GMP act synergistically
  • AMP and GMP inhibit synthesis of branch point products of IMP
56
Q

Pyrimidine

A

T and C

57
Q

De novo pyrimidine synthesis

A
  • transfer of carbamoyl group from carboxyl phosphate to the amine of apsartate followed by dehydration, cyclization and oxidation to form orotate.
  • orotate + ribose 5-phosphate = uridylate (UMP)
  • UMP phosphorylated to UTP
  • CTO formed from UTP with glutamine as amine donor
58
Q

Pyrimidine vs Purine synthesis

A

-in pyrimidine, pyrimidine ring is synthesized first then attached to ribose 5-phosphate in the form of PRPP

59
Q

Thymidylate

A

(part of UTP)

  • made when ribose is reduced to deoxyribose
  • keeps thymine from being incorporated into RNA
60
Q

Feedback inhibition of pyrimidine synthesis

A
  • primary regulatory step is aspartate to N-carbamoylaspartate using aspartate transcarbamoylase
  • end product CTP inhibits aspartate transcarbamoylase shutting down its own synthesis
61
Q

Nucleoside monophosphate to nucleoside triphosphates

A

-adenylate kinase phosphorylates AMP to ADP
-ADP to ATP via glycolytic enzymes or by oxidative phosphorylation
-nucleoside monophosphate kinases
nucleoside diphosphate kinases

62
Q

Nucleoside monophosphate kinases

A
  • base specific

- use ATP to phosphorylate

63
Q

Nucleoside diphosphate kinases

A
  • single enzyme
  • not specific
  • uses ATP to convert NDP to NTP
64
Q

Ribonucleotide reductase

A
  • catalyzes the reduction of the 2’-carbon of D-ribose to 2’-deoxyribose using ribonucleoside diphosphate substrates
  • e- for this reduction come from NADPH either via glutathione and glutaredoxin or thioredoxin
65
Q

Ribonucleotide reductase mechanism

A
  • nucleoside diphosphate reduced by ribonucleotide reductase to form dNDPs via an active site radical which is stabilized by a binocular Fe3+ cofactor
  • radical stabilize the cation after water loss
  • 2 1-e- transfers with the oxidation of the dithiol reduces the radical cation
66
Q

Regulation of ribonucleotide reductase

A
  • primary regulation binding site
  • substrate specificity site
  • complex regulation
  • just know that they are interconnected and keep a constant pool of all 4 deoxy and all 4 ribonucleotides
67
Q

Primary regulation binding site

A

ATP binds and activates, dATP binds and inactivates

68
Q

Substrate specificity site

A

ATP/dATP bind and favor reduction of UDP/CDP; dTTP binds and favors reduction of GDP; dGTP binds and favors reduction of ADP

69
Q

Thymidylate (dTMP) derived from dCDP/dUMP

A
  • de novo pathway of thymine only involves deoxyribonucleotides
  • dUMP is the immediate precursor of dTMO and is catalyzed by thymidylate synthase which uses the cofactor THF to provide a methyl C at C5 of the uridine base
70
Q

Purine and Pyrimidine degradation

A
  • purines hydrolyzed to form free bases -> uric acid (allantoin in us)
  • pyrimidines leads to ammonia production and urea synthesis
  • carbon skeleton of thymine converted to succinyl-CoA
71
Q

Gout

A

trouble breaking down nucleotides

-uric acid build up in the joints

72
Q

Purine and Pyrimidine salvage pathways

A
  • free purine bases are released in cells during metabolic degradation and are salvaged by phosphoribosyltransferases which transfer the free purine base to PRPP
  • simliar for pyrimidines have been identified in microorganisms, not identified in mammals

Biochemistry II (8 decks)

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