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Biochemistry > Biosynthesis of Amino Acids L7 > Flashcards

Biosynthesis of Amino Acids L7 Flashcards

(109 cards)

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1
Q

what happens in the nitrogen cycle

A

Nitrogen assimilation
Nitrogen in atmosphere fixed in soil
Some plants have special root nodules that fix nitrogen
Nitrogen transferred to several compounds in plant
Animals eat plant and receive nitrogen
Plants and animals die, nitrogen returned to soil
Bacterias in soil break apart nitrogen compounds and release into atmosphere

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2
Q

what is NH4+

A

ammonium salt

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3
Q

what is NO2-

A

nitrite

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4
Q

what is NO3-

A

nitrate

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5
Q

what happens in the global nitrogen cycle - terrestrial biotic community

A

Nitrogen in atmosphere fixed by bacteria attached to plants in nodules
Transform nitrogen into ammonium salt
Ammonium salt oxidised to nitrite
Nitrite oxidised to nitrate
Nitrate used by plants (plants die and return nitrogen)
Denitrifying bacteria convert nitrate to nitrogen gas

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6
Q

what happens in global nitrogen cycle - aquatic biotic community

A

Some nitrate into seas – runoff
Cyanobacteria fixing nitrogen in ocean convert nitrogen gas to ammonium salt
Ammonium salt to nitrate which feeds phytoplankton
phytoplankton feed fish
fish decompose free ammonium
Denitrifying bacteria convert nitrate to nitrogen gas

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7
Q

how can plants visibly show nitrogen deficiency

A

Yellow older leaves beneath green ones on top – nitrogen deficient

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8
Q

what is the incorporation of nitrogen into living organisms

A

biochemically difficult in terms of energy and complexity

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9
Q

what is the percentage of carbon in living dry matter

A

50%

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10
Q

what is the percentage of oxygen in living dry matter

A

30%

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11
Q

what is the percentage of hydrogen in living dry matter

A

3%

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12
Q

what is the percentage of nitrogen in living dry matter

A

9%

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13
Q

what happens in the industrial nitrogen fixation

A

ammonia –> nitrites –> nitrates

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14
Q

what happens in biotic nitrogen fixation

A

protein (plants and microbes) decay and animal protein –> ammonia –> nitrites –> nitrates

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15
Q

how is nitrogen fixed into naturally

A

Lightning can fix nitrogen gas – deposition of nitrates into soil

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16
Q

why is nitrogen hard to assimilate

A

Nitrogen triple bond is extremely stable, so very difficult to break

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17
Q

what is nitrogen gas like

A

inert and difficult to incorporate into living organisms

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18
Q

what are the main producers / procedures to fix nitrogen of ammonia and ammonium salts

A

microorganisms 67%
lightning 10%
industry 23%

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19
Q

how does industry make ammonia

A

haber process

N2 + H2 –> NH3

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20
Q

what does the Haber process require

A

High pressure 300 atm
High temperature 500°C
Fe catalyst

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21
Q

what happens in industrial fixation

A

nitrogen from air distillation and hydrogen from methane + steam
N2+H2 form ammonia (NH3)
NH3 forms nitric acid which forms nitrates

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22
Q

what are the nitrate products of industrial fixation

A

plastics
explosives
fertiliser

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23
Q

how does nitrogen fixation occur

A

symbiotic bacteria live in root nodules of plants (legumes) and exchange NH4+ for carbohydrate precursors and a supply of leghaemoglobin maintains anaerobic conditions, as O2 inactivates nitrogenase

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24
Q

what does nitrogenase do

A

catalyses a redox reaction

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25
how is nitrogen reduced to ammonia
Electrons flow from ferredoxin to reductase (iron protein) to nitrogenase
26
what drives conformational change
ATP hydrolysis within reductase
27
how do microorganisms fix nitrogen
eight high-potential electrons come from reduced ferredoxin, generated by photosynthesis or oxidative processes Two molecules of ATP are hydrolyzed for each electron transferred at least 16 molecules of ATP are hydrolyzed for each molecule of N2 reduced
28
what is nitrogenase
heterotetramer made of two α subunits and two β subunits
29
what is the nitrogen-reduction site
FeMo cofactor contains an open centre that is likely site of nitrogen binding and reduction
30
what are microbial nitrogenases for
complex enzymes that reduce N2 to NH4+
31
what is needed in the inversion process of nitrates to nitrites
nitrate reductase
32
what is needed in the inversion process of nitrites to ammonia
nitrite reductase
33
what are the main goals of nitrogen fixation
transfer nitrogen fixing genes to non-leguminous plants
34
ammonium salt examples
sulphide and chloride
35
what happens in conversion of ammonium salt to amino acids
Use ammonium salt, alpha-ketoglutarate and lots of energy | Need to form glutamate
36
what is alpha-ketoglutarate used in
krebs cycle
37
how is glutamate synthesised
Glutamate is synthesized from NH4+ and alpha-ketoglutarate
38
what aids ammonium salts to amino acids
glutamate dehydrogenase
39
what happens in glycolysis
glucose is broken down into pyruvate
40
what happens in krebs cycle
Pyruvate forms acetyl-CoA, CO2 and NADH molecule Acetyl-CoA enters Krebs cycle (in mitochondrion) Acetyl-CoA transferred to a 4 carbon molecule to 6 carbon compound CoA molecule released CO2 released forming a 5 carbon compound (NAD+ --> NADH) 4 carbon molecule made as NADH, CO2 and ATP made Original 4 carbon molecule regenerated as NADH and FADH2 are formed
41
how many times does the krebs cycle happen to remove glycolysis products
Krebs cycle happens twice to break down the two pyruvate molecules made in glycolysis
42
where are most of intermediate products are derived from
krebs cycle
43
what do alpha-ketoglutarate and ammonium salt form
intermediate compound
44
where does the ammonium salt bind to when forming amino acids
bind to C=O, remove O
45
what does glutamate dehydrogenase do
protonated Schiff base is reduced by transfer of a hydride ion from NADPH to form glutamate
46
what does Glutamate dehydrogenase do
puts first nitrogen on
47
what does Glutamine synthetase do
puts second nitrogen on
48
where are glutamate dehydrogenase and glutamine synthetase found
present in all organisms | most prokaryotes also contain an evolutionarily unrelated enzyme, glutamate synthase
49
what drives amidation
hydrolysis of ATP
50
what happens to the second ammonium ion in biosynthesis of amino acids
incorporated into glutamate to form glutamine by action of glutamine synthetase
51
how is glutamine formed
ATP phosphorylates side chain of glutamate, form an acyl-phosphate intermediate, reacts with ammonia to form glutamine
52
what is an allosteric enzyme
Glutamine synthetase is a highly regulated ‘allosteric’ enzyme in bacteria
53
what dictates rate of reaction
rate of reaction of ‘ordinary’ enzymes is largely dictated by concentration of substrate
54
what do allosteric enzymes respond to
levels of activators and inhibitors
55
why is glutamine important
nitrogen source to form many things such as histidine purines, pyrimidines and tryptophan
56
what happens if end products e.g. histidine purines, pyrimidines and tryptophan made excessively
act as allosteric inhibitors - conformational change which will stop enzyme producing more glutamine inhibit reaction to make glutamine Pathway shut down when is not needed as has enough – feedback inhibitors
57
what enzymes are necessary for initial steps of ammonium salts --> amino acids
Glutamate dehydrogenase and Glutamine Synthase
58
what is the problem with ammonium salts
toxic
59
what drives the formation of asparagine from aspartate
ATP hydrolysis
60
what drives the formation of glutamine from glutamate
ATP hydrolysis
61
what is the nitrogen donor for asparagine
glutamine
62
what is glutamate a precursor of
glutamine, proline, arginine and main ‘N’ donor for other amino acids
63
what is serine important for
can lead to production of many different molecules
64
how are different amino acids formed
Depending on what ‘starting material’ you have can form different amino acids
65
what can pyruvate form
alanine valine leucine
66
what is the production of amino acids like
multi step biosynthetic system | Metabolic precursor will instruct the Biosynthetic family
67
what is a co-factor
Enzyme is not functional unless something else is attached to it
68
what do tranaminases require
co-factor PYRIDOXAL PHOSPHATE
69
what is formed when an amino group added to oxaloacetate and pyruvate
Aspartate and alanine
70
what is pyridoxal phosphate
a temporary ‘holder’ of nitrogen | Conveys nitrogen to other molecules
71
what is PMP
pyridoxamine phosphate
72
what happens when a carbon is added to molecule - S-Adenosylmethionine
SAM donates methyl group When SAM donates a methyl group forms homocysteine Reforms a methyl again Repeats in a cycle
73
what happens when a carbon is added to molecule - Tetrahydrofolate
Mammals synthesise pteridine ring, unable to conjugate it to the other two units. They obtain tetrahydrofolate from their diets or from microorganisms in their intestinal tracts
74
How does deoxyribose monophosphate (dUMP) and deoxyribose monophosphate (dTMP) differ
deoxyribose monophosphate dtMP has a methyl group
75
how can some synthesis reactions still occur even if enzyme is mutated
various cascades to reach same end product, therefore more than one enzyme can do job If there is a mutation in an enzyme the other enzyme can still produce the product
76
what is amino acid catabolism
degradation too much amino acids does not frequently happen as require a lot of energy to make amino acids Highly regulated as when start to make too much – allosteric inhibition
77
examples of specific protein degradation
ubiquitin system
78
what is most of the cellular energy consumed in
95% of cellular ‘energy’ in animals is consumed by protein biosynthesis
79
what energy is recovered from protein breakdown
very little ‘energy’ is recovered by protein breakdown
80
what is gluconeogenesis
generation of glucose from non-carbohydrate carbon substrates such as lactate
81
what happens in amino acid catabolism
amino acid broken to form useful carbon skeletons and unwanted NH4
82
what is the major site of amino acid degradation in mammals
liver
83
are amino acids part of the krebs cycle
Certain amino acids broken and get into krebs cycle
84
how does the krebs cycle make glucose
Krebs cycle assimilate broken down carbon skeleton and make glucose
85
what is the strategy of amino acid degradation
transform carbon skeletons into major metabolic intermediates that can be converted into glucose or oxidized by krebs cycle
86
what ate ketogenic amino acids
Amino acids that are degraded to acetyl CoA or acetoacetyl CoA
87
what do ketogenic amino acids make
they can give rise to ketone bodies or fatty acids
88
what are glucogenic amino acids
amino acids that are degraded to pyruvate, alpa-ketoglutarate, succinyl CoA, fumarate, or oxaloacetate
89
what is the first step of amino acid catabolism
removal of unwanted NH4
90
what catalyses the removal of NH4
aminotransferases and glutamate dehydrogenase
91
what is ammonotelic
ammonium as final product
92
what is Uricotelic
uric acid as final product
93
what is Ureotelic
urea as final product
94
how is excess nitrogen removed
excreted as urea | integration of nitrogen metabolic and Urea cycle
95
what is the second step in amino acid catabolism
the urea cycle
96
what is some of the NH4+ formed in the breakdown of amino acids used in
consumed in the biosynthesis of nitrogen compounds
97
where does the urea cycle occur
cytoplasm and inside mitochondria
98
what processes are Metabolic Integration of Nitrogen Metabolism
urea cycle | krebs cycle
99
how are the urea and krebs cycle linked
transamination of oxaloacetate are linked by fumarate and aspartate
100
what percent of amino acids are reused
About 75% of liberated AA are reutilised
101
what percentage os body proteins do humans turn over
each day 1-2%
102
what happens to amino acids that are not immediately incorporated into new proteins
rapidly degraded
103
where is urea mainly excreted
through kidney in urine | some transported to intestine
104
where is ammonia released, how is it removed
Ammonia release at intestine goes back to liver for reconversion to urea
105
when is lactate formed
made in muscles when ATP demand exceeds capacity of oxidative phosphorylation
106
what happens when lactate is formed
Lactate is then circulated through blood to liver where lactate is converted to glucose Glucose feeds the muscle
107
does all amino acids degradation occur in liver
no | muscles lack urea cycle
108
what are amino acids used in
Feedback into the Krebs cycle+ glycolysis Backbone of many other important biomolecules Nitric Oxide biosynthesis
109
why are amino acids important
precursors of many important Biomolecules

Biochemistry (13 decks)

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