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Biochemistry Exam 3 > Chapter 31: Amino Acid Synthesis > Flashcards

Chapter 31: Amino Acid Synthesis Flashcards

1
Q

Why is nitrogen important?

A
  • it is an essential component of DNA, RNA, proteins
  • all organisms require it to live and grow
  • majority of Earth’s atmosphere is N2
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2
Q

How much of the atmosphere is made up of nitrogen?

A

78%

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3
Q

Why is most of the nitrogen in the atmosphere unavailable for use by organisms?

A

Because the strong triple bond between the N atoms in N2 molecules make it inert.

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4
Q

What form does nitrogen take in the atmosphere?

A

N2

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5
Q

What is the Nitrogen Cycle?

A

The process of converting nitrogen into compounds that can be used by plants and animals.

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6
Q

What are the four processes of the Nitrogen Cycle?

A
  1. Nitrogen Fixation
  2. Ammonification
  3. Nitrification
  4. Denitrification (converting back to N2)
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7
Q

What is nitrogen fixation?

A

The process in which N2 in the atmosphere breaks and combines with other compounds.

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8
Q

What must nitrogen be combined with to become ‘fixed’ and what is the product of the fixation?

A

Combined with Hydrogen to make Ammonia (NH3)
OR
Combined with Oxygen to make Nitrous Oxide (N2O)

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9
Q

What are the 3 ways to ‘fix’ nitrogen?

A
  1. Bacteria convert nitrogen gas (N2) to ammonia (NH3) to be used by legume plants (peas, beans)
  2. Lightning strikes convert N2 to N2O or NO3
  3. Industrial production where chemical manipulation turns N2 into NH3 (fertilizer)
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10
Q

Which of the 3 ways to ‘fix’ nitrogen is the main process?

A

Bacteria converting N2 into NH3

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11
Q

Why is industrial processing of nitrogen difficult?

A

Because it requires lots of energy (must be mixed with H2 over iron catalyst at 500C and 300atm pressure).

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12
Q

What enzyme do bacteria use to convert N2 to NH3?

A

Nitrogenase

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13
Q

What are the 2 types of bacteria that fix nitrogen?

A
  1. Rhizobium
  2. Azobacter
  3. Cyanobacteria
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14
Q

Where do Rhizobium bacteria live?

A

In the root nodules of leguminous plants

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15
Q

What are Azobacter bacteria associated with?

A

The rooting zone of plants in grasslands

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16
Q

What is unique about Cyanobacteria?

A

They are nitrogen and carbon fixers (are photosynthetic).

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17
Q

About how much N2 is fixed per year by bacteria?

A

10^11 kg per year

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18
Q

How do bacteria use the nitrogenase enzyme to convert N2 to NH3?

A

Reaction involves splitting N2 and adding hydrogen to make ammonia.
N2 + 8H + 16 ATP -> 2NH3 + H2 + 16 ADP + 1 Pi

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19
Q

How much ATP do bacteria use to convert N2 to NH3?

A

16 ATP

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20
Q

What are the components of the nitrogenase enzyme complex?

A
  1. Reductase= provides high energy electrons for reducing power
  2. Nitrogenase= uses electrons to reduce N2 to NH3
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21
Q

What form do electrons provided by the reductase part of the nitrogenase complex take?

A

The form of ferredoxin

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22
Q

What is the process of ammonification?

A

After living organisms use organic nitrogen and die, decomposer bacteria convert the nitrogen to ammonia.

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23
Q

What is the process of nitrification?

A

The process that converts ammonia (NH3) to nitrites (NO2) and nitrates (NO3).
*ammonia comes from both nitrogen fixation and ammonification

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24
Q

How is the process of nitrification performed?

A

Performed by bacteria

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25
Q

What is the process of denitrification?

A

Process where nitrogen compounds convert back into atmospheric nitrogen (N2 or N2O).

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26
Q

Why is the process of denitrification necessary?

A

In order to prevent depletion of nitrogen from the atmosphere.

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27
Q

How is denitrification performed?

A

Mainly by bacteria, also by burning fossil fuels.

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28
Q

What organism is required in every step of the nitrogen cycle?

A

Bacteria!

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29
Q

What organisms can synthesize all 20 amino acids?

A

Most bacteria and plants. Not mammals.

30
Q

What are amino acids that mammals cannot synthesize called?

A

Essential amino acids (because must be gotten from the diet).

31
Q

How are essential versus nonessential amino acids derived?

A

Nonessential- from glycolysis and the citric acid cycle

Essential- from diet (carbon skeleton can’t be synthesized)

32
Q

What are two more differences between essential and nonessential amino acids?

A
  1. nonessential synthesis doesn’t require as much energy while essential has greater energy investmet
  2. nonessential- very simple reactions, essential- more complicated reactions
33
Q

Examples of nonessential amino acids.

A

alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine

34
Q

What makes cysteine and tyrosine different than other nonessential amino acids?

A

Cysteine- gets its sulfur from methionine (essential a.a.)

Tyrosine- is a hydroxylated PHE

35
Q

Examples of essential amino acids.

A

arginine, methionine, histidine, phenylalanine, isoleucine, threonine, leucine, tryptophan, lysine, valine

36
Q

What is unique about arginine?

A

it is essential in infants but not adults.

37
Q

The pathways for the biosynthesis of amino acids are ______.

A

diverse

38
Q

Some amino acids can be made by simple _________ reactions.

A

Transamination reactions

39
Q

What does a transamination reaction involve?

A

The transfer of an amino group from an alpha-amino acid to an alpha-keto acid.

40
Q

What enzyme performs transamination reactions and what cofactor does it require?

A

Enzyme: transaminase

It requires the cofactor pyridoxine (comes from vitamin B6)

41
Q

How do you synthesize glutamine?

A
  1. change alpha-ketoglutarate to glutamate
    - enzyme: glutamate dehydrogenase
  2. change glutamate to glutamine
    - enzyme: glutamine synthetase
    * can go back to glutamate from glutamine using glutaminase
42
Q

Where do the carbon skeletons for amino acid synthesis come from?

A

Provided by intermediates of the glycolytic pathway, the citric acid cycle, and the pentose phosphate pathway

43
Q

What are the 5 families for the biosynthesis of amino acids?

A
  1. oxaloacetate family 2. phosphoenolpyruvate family 3. ribose 5-phosphate family 4. pyruvate family 5. alpha-ketoglutarate family 6. 3-phosphoglycerate
44
Q

What amino acids come from the intermediate oxaloacetate?

A

aspartate, asparagine, methionine, threonine, lysine, isoleucine

45
Q

What amino acids come from the intermediate phosphoenolpyruvate?

A

phenylalanine, tyrosine, tryptophan

46
Q

What amino acids come from the intermediate ribose 5-phosphate?

A

histidine

47
Q

What amino acids come from the intermediate pyruvate?

A

alanine, valine, leucine

48
Q

What amino acids come from the intermediate alpha-ketoglutarate?

A

glutamate, glutamine, proline, arginine

49
Q

What amino acids come from the intermediate 3-phosphoglycerate?

A

serine, cysteine, glycine

50
Q

How is 3-phosphoglycerate made into serine?

A
  1. 3-phosphoglycerate -> 3-phosphohydroxypyruvate by 3-phosphoglycerate dehydrogenase
  2. 3-phosphohydroxypyruvate -> 3-phosphoserine by amino transferase
  3. 3-phosphoserine to serine by phosphoserine phosphatase
51
Q

What two amino acids can serine be changed into?

A

cysteine and glycine

52
Q

What are the two ways glycine can be made?

A
  1. direct conversion of serine to glycine by hydroxymethyltransferase
  2. condensation of N5,N10 methylene-THF with CO2 and NH4
53
Q

Where does THF come from?

A

Folic acid is reduced to THF by dihydrofolate reductase- must get folic acid from diet

54
Q

Why is THF important?

A

It’s essential for synthesis of many amino acids and nucleotides, important for embryonic development of the nervous system.

55
Q

Insufficient amount of THF can lead to ____ or ____.

A

spina bifida or anencephaly

56
Q

How does serine get changed into cysteine?

A
  1. serine -> O-acetylserine by serine acetyltransferase

2. O-acetylserine -> cysteine by O-acetylserine (thiol) lyase

57
Q

Where does the sulfur for cysteine synthesis come from?

A

methionine

58
Q

The condensation of ATP and methionine yields ______ and is catalyzed by ________.

A

yields S-adenosylmethionine (SAM) and is catalyzed by methionine adenosyltransferase

59
Q

What is SAM used for?

A

A precursor for numerous methyl transfer reactions

60
Q

What are the steps in the utilization of methionine in the synthesis of cysteine?

A
  1. conversion of SAM to homocysteine
  2. condensation of homocysteine with serine to cystathione
  3. cystathione is cleaved to cysteine
61
Q

What is homocystinuria?

A
  • Deficiency in cystathionine synthetase (part of cysteine synthesis pathway).
  • Effects: increase in Met, S-AdMet, S-AdHomocystine, Homocysteine
  • Clinical Effects: mental retardation, dislocation of the eye lens
62
Q

What is phenylketonuria?

A
  • Caused by defect in Phenylalanine hydroxylase.
  • Tyrosine not made and phenylalanine accumulates.
  • Causes mental retardation.
63
Q

How is amino acid biosynthesis regulated?

A

Feedback inhibition- the final product in a pathway inhibits the enzyme catalyzing the committed step.

64
Q

The committed step in serine synthesis is catalyzed by ____ , which is inhibited by ____.

A

Catalyzed by 3-phosphoglyercate dehydrogenase, which is inhibited by serine.

65
Q

The three methods of regulating branched pathways are:

A
  1. feedback inhibition and activation
  2. enzyme multiplicity
  3. cumulative feedback inhibition
66
Q

How does feedback inhibition/activation work in branched pathways?

A

If 2 pathways have initial common step, 1 pathway inhibited by its own products and stimulated by product of other pathway. (Ex: valine and isoleucine synthesis - if you need valine, isoleucine prod. is blocked and vice versa)

67
Q

How does enzyme multiplicity work?

A

Each end product inhibits both the 1st individual committed step and 1 of the enzymes performing the 1st common committed step (Ex: 3 aspartate kinases control the synthesis of threonine, met, lys)

68
Q

How does cumulative feedback inhibition work?

A

Ex: full inhibition of glutamine synthetase needs Trp, His, AMP to block its activity)
*All end products required to cumulatively block activity

69
Q

How does the pesticide Roundup kill plants?

A

By inhibiting synthesis of aromatic amino acids

70
Q

What causes albinism?

A

A hereditable defect in tyrosinase.

Biochemistry Exam 3 (10 decks)

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