Chapters 18 , 22 - Biochemistry 18 : Amino acid oxidation and production of urea 22: nitrogen Assimilation

1. 18|
Amino
Acid
Oxida/on
Produc/on
of
Urea
© 2013 W. H. Freeman and Company
22|
Nitrogen
Assimila/on,
Biosynthe/c
Use,
and
Excre/on

2. The
use
of
amino
acids
as
fuel
varies
greatly
by
organism
• About
90%
of
energy
needs
of
carnivores
can
be
met
by
amino
acids
immediately
a*er
a
meal
• Microorganisms
scavenge
amino
acids
from
their
environment
for
fuel
when
needed
• Only
a
very
small
frac3on
of
energy
needs
of
herbivores
are
met
by
amino
acids
• Plants
do
not
use
amino
acids
as
a
fuel
source,
but
can
degrade
amino
acids
to
form
other
metabolites

3. Metabolic
Circumstances
of
Amino
Acid
Oxida/on
• Le?over
amino
acids
from
normal
protein
turnover
• Dietary
amino
acids
that
exceed
body’s
protein
synthesis
needs
• Proteins
in
the
body
can
be
broken
down
to
supply
amino
acids
for
energy
when
carbohydrates
are
scarce
(starvaFon,
diabetes
mellitus)

4. Dietary
proteins
are
enzyma/cally
hydrolyzed
into
amino
acids
• Pepsin
cuts
protein
into
pepFdes
in
the
stomach
• Trypsin
and
chymotrypsin
cut
proteins
and
larger
pepFdes
into
smaller
pepFdes
in
the
small
intesFne
• AminopepFdase
and
carboxypepFdases
A
and
B
degrade
pepFdes
into
amino
acids
in
the
small
intesFne

5. Dietary
protein
is
enzyma/cally
degraded
through
the
diges/ve
tract

6. Overview
of
Amino
Acid
Catabolism
The amino groups and the carbon
skeleton take separate but
interconnected pathways.

7. Removal
of
the
Amino
Group
The
first
step
of
degradaFon
for
all
amino
acids

8. Fates
of
Nitrogen
in
Organisms
• Plants
conserve
almost
all
the
nitrogen
• Many
aquaFc
vertebrates
release
ammonia
to
their
environment
– Passive
diffusion
from
epithelial
cells
– AcFve
transport
via
gills
• Many
terrestrial
vertebrates
and
sharks
excrete
nitrogen
in
the
form
of
urea
– Urea
is
far
less
toxic
that
ammonia
– Urea
has
very
high
solubility
• Some
animals
such
as
birds
and
repFles
excrete
nitrogen
as
uric
acid
– Uric
acid
is
rather
insoluble
– ExcreFon
as
paste
allows
the
animals
to
conserve
water
• Humans
and
great
apes
excrete
both
urea
(from
amino
acids)
and
uric
acid
(from
purines)

9. Excretory
Forms
of
Nitrogen
Notice that the carbon atoms of
urea and uric acid are highly
oxidized; the organism discards
carbon only after extracting most of
its available energy of oxidation.

10. Enzyma/c
Transamina/on
• Catalyzed
by
aminotransferases
• Uses
the
pyridoxal
phosphate
cofactor
• Typically,
α-­‐ketoglutarate
accepts
amino
groups
• L-­‐Glutamine
acts
as
a
temporary
storage
of
nitrogen
• L-­‐Glutamine
can
donate
the
amino
group
when
needed
for
amino
acid
biosynthesis

11. Enzyma/c
Transamina/on
readily reversible

12. Structure
of
Pyridoxal
Phosphate
and
Pyridoxamine
Phosphate
• Intermediate,
enzyme-­‐bound
carrier
of
amino
groups
• Aldehyde
form
can
react
reversibly
with
amino
groups
• Aminated
form
can
react
reversibly
with
carbonyl
groups

13. Pyridoxal
phosphate
is
covalently
linked
to
the
enzyme
in
the
res/ng
enzyme
• By
an
internal
aldimine
• The
linkage
is
made
via
a
nucleophilic
aVack
of
the
amino
group
of
an
acFve-­‐site
lysine

14. Chemistry
of
the
Amino
Group
Removal
by
the
Internal
Aldimine
The
external
aldimine
of
PLP
is
a
good
electron
sink,
avoiding
formaFon
of
an
unstable
carbanion
on
the
α
C
allowing
removal
of
α-­‐hydrogen
3 alternative fates
for the external
aldimine
transamination
decarboxylation
racemization

15. • OxidaFve
deaminaFon
occurs
within
mitochondrial
matrix
• Can
use
either
NAD+
or
NADP+
as
electron
acceptor
• Ammonia
is
processed
into
urea
for
excreFon
• Pathway
for
ammonia
excreFon;
transdeaminaFon
=
transaminaFon
+
oxidaFve
deaminaFon
Ammonia
collected
in
glutamate
is
removed
by
glutamate
dehydrogenase

16. Ammonia
is
safely
transported
in
the
bloodstream
as
glutamine
• Excess
ammonia
in
Fssues
is
added
to
glutamate
to
form
glutamine
(by
glutamine
synthetase).
• Excess
glutamine
is
processed
in
intesFnes,
kidneys,
and
liver
(by
glutaminase)
liberaFng
NH4
+
in
mitochondria.

17. Glutamate
can
donate
ammonia
to
pyruvate
to
make
alanine
• Vigorously
working
muscles
operate
nearly
anaerobically
and
rely
on
glycolysis
for
energy
• Glycolysis
yields
pyruvate
–
if
not
eliminated
lacFc
acid
will
build
up
• This
pyruvate
can
be
converted
to
alanine
for
transport
into
liver

18. The
Glucose-­‐Alanine
Cycle
Alanine serves as a
carrier of ammonia and
of the carbon skeleton
of pyruvate from
skeletal muscle to liver.

20. Excess
glutamate
is
metabolized
in
the
mitochondria
of
hepatocytes

21. Ammonia
is
highly
toxic
and
must
be
u/lized
or
excreted
• Free
ammonia
released
from
glutamate
is
converted
to
urea
for
excreFon.
• Carbamoyl
phosphate
synthetase
I
captures
free
ammonia
in
the
mitochondrial
matrix
• First
step
of
the
urea
cycle
• Regulated

22. Ammonia
is
recaptured
via
synthesis
of
carbamoyl
phosphate
• The
first
nitrogen-­‐acquiring
reacFon
of
the
urea
cycle

23. Nitrogen
from
carbamoyl
phosphate
enters
the
urea
cycle

24. The
Reac/ons
in
the
Urea
Cycle

25. Entry
of
Aspartate
into
the
Urea
Cycle
This
is
the
second
nitrogen-­‐acquiring
reacFon.

26. Aspartate
–arginosuccinate
shunt
links
urea
cycle
and
citric
acid
cycle

27. Regula/on
of
the
Urea
Cycle
• Carbamoyl
phosphate
synthetase
I
is
acFvated
by
N-­‐acetylglutamate
• Formed
by
N-­‐acetylglutamate
synthase
– When
glutamate
and
acetyl-­‐CoA
concentraFons
are
high
– AcFvated
by
arginine
• Expression
of
urea
cycle
enzymes
increases
when
needed
– High
protein
diet
– StarvaFon,
when
protein
is
being
broken
down
for
energy

28. Not
all
amino
acids
can
be
synthesized
in
humans
• EssenFal
amino
acids
must
be
obtained
as
dietary
protein
• ConsumpFon
of
a
variety
of
foods
supplies
all
the
essenFal
amino
acids
– including
vegetarian-­‐
only
diets

29. End
products
of
Amino
Acid
Degrada/on
• Intermediates
of
the
Central
Metabolic
Pathway
• Some
amino
acids
result
in
more
than
one
intermediate
• Ketogenic
amino
acids
can
be
converted
to
ketone
bodies
• Glucogenic
amino
acids
can
be
converted
to
glucose
Six to pyruvate Ala, Cys, Gly, Ser, Thr, Trp
Five to α-ketoglutarate Arg, Glu, Gln, His, Pro
Four to succinyl-CoA Ile, Met, Thr, Val
Two to fumarate Phe, Tyr
Two to oxaloacetate Asp, Asn
Seven to Acetyl-CoA Leu, Ile, Thr, Lys, Phe, Tyr, Trp

30. Summary
of
Amino
Acid
Catabolism
Only two amino acids, leucine and lysine,
are exclusively ketogenic.

31. Several
cofactors
are
involved
in
amino
acid
catabolism
• Important
in
one-­‐carbon
transfer
reacFons
– Tetrahydrafolate
(THF)
– S-­‐adenosylmethionine
(adoMet)
– BioFn
• BioFn,
as
we
saw
in
Chapter
16,
transfers
CO2

32. THF
is
a
versa/le
cofactor
• Tetrahydrofolate
is
formed
from
folate
– an
essenFal
vitamin
(B9)
• THF
can
transfer
1-­‐carbon
in
different
oxidaFon
states
– CH3,
CH2OH,
and
CHO
• Used
in
a
wide
variety
of
metabolic
reacFons
• Carbon
generally
comes
from
serine
• Forms
interconverted
on
THF
before
use

33. THF
is
a
versa/le
cofactor

34. adoMet
is
beTer
at
transferring
CH3
• S-­‐adenosylmethionine
is
the
prefered
cofactor
for
methyl
transfer
in
biological
reacFons
– Methyl
is
1000
Fmes
more
reacFve
than
THF
methyl
group
• Synthesized
from
ATP
and
methionine

35. Ac/vated
Methyl
Cycle

36. Degrada/on
of
ketogenic
amino
acids

37. Degrada/on
intermediates
of
tryptophan
are
to
synthesize
other
molecules

38. Gene/c
defects
in
many
steps
of
Phe
degrada/on
lead
to
disease

39. Phenylketonuria
is
caused
by
a
defect
in
the
first
step
of
Phe
degrada/on
• A
buildup
of
phenylalanine
and
phenylpyruvate
• Impairs
neurological
development
leading
to
intellectual
deficits
• Controlled
by
limiFng
dietary
intake
of
Phe

40. Degrada/on
of
Glycine
• Pathway
#1:
hydroxylaFon
to
serine
à
pyruvate
• Pathway
#2:
Glycine
cleavage
enzyme
– Apparently
major
pathway
in
mammals
– SeparaFon
of
three
central
atoms
– Releases
CO2
and
NH3
– Methylene
group
is
transferred
to
THF
• Pathway
#3:
D-­‐amino
oxidase
– RelaFvely
minor
pathway
– UlFmately
oxidized
to
oxalate
– Major
component
of
kidney
stones

41. Degrada/on
of
Amino
Acids
to
α-­‐Ketoglutarate

42. Degrada/on
of
branched
chain
amino
acids
does
not
occur
in
the
liver
• Leucine,
Isoleucine,
and
Valine
are
oxidized
for
fuel
– In
muscle,
adipose
Fssue,
kidney,
and
brain

43. Degrada/on
of
Asn
and
Asp
to
Oxaloacetate

46. Importance
of
Nitrogen
in
Biochemistry
• Nitrogen
(with
H,
O,
and
C)
is
a
major
elemental
consFtuent
of
living
organisms
• Mostly
in
nucleic
acids
and
proteins
• But
also
found
in:
– several
cofactors
(NAD,
FAD,
bioFn
…
)
– many
small
hormones
(epinephrine)
– many
neurotransmiVers
(serotonin)
– many
pigments
(chlorophyll)
– many
defense
chemicals
(amaniFn)

47. Biochemistry
of
Molecular
Nitrogen
• Atmosphere
is
80%
N2
but
non-­‐useful
form
– N2
chemically
inert
– Need
N2
+
3
H2
à
2
NH3
– Even
though
ΔGʹ′°=
–33.5
kJ/mol…breaking
triple
bond
has
high
ac4va4on
energy

48. A
few
non-­‐biological
processes
can
convert
N2
to
biologically
useful
forms
• N2
and
O2
à
NO
via
lightning
• N2
and
H2
à
NH3
via
the
industrial
Haber
process
• Requires
T>400°C,
P>200
atm

49. Some
bacteria
can
“fix”
N2
to
useful
forms
• Most
are
single-­‐celled
prokaryotes
(archaea)
• Some
live
in
symbiosis
with
plants
-­‐
(e.g.,
proteobacteria
with
legumes
such
as
peanuts,
beans)
• A
few
live
in
symbiosis
with
animals
-­‐ (e.g.,
spirochaete
with
termites)
They
have
enzymes
that
overcome
the
high
ac3va3on
energy
by
binding
and
hydrolyzing
ATP.

50. Review:
Oxida/on
States
of
Nitrogen
Compounds
• N+5
O3
–
à
N+3
O2
–
• Nitrate
àNitrite
• “ate” is
the
higher
oxidaFon
state
• (Memory
trick:
I
ate
too
much)
• NH3:
N
has
oxidaFon
state
of
–3

51. The
Nitrogen
Cycle
Chemical
transforma4ons
maintain
a
balance
between
N2
and
biologically
useful
forms
of
nitrogen.
1. Fixa4on.
Bacteria
reduce
N2
to
NH3/NH4
+
2. Nitrifica4on.
Bacteria
oxidize
ammonia
into
nitrite
(NO2
–)
and
nitrate
(NO3
–).
3. Assimila4on.
Plants
and
microorganisms
reduce
NO2
–
and
NO3
–
to
NH3
via
nitrite
reductases
and
nitrate
reductases.
NH3
is
incorporated
into
amino
acids,
etc.
Organisms
die,
returning
NH3
to
soil.
Nitrifying
bacteria
again
convert
NH3
to
nitrite
and
nitrate.
4. Denitrifica4on.
Nitrate
is
reduced
to
N2
under
anaerobic
condiFons.
NO3
–
is
the
ulFmate
electron
acceptor
instead
of
O2.

52. The
Nitrogen
Cycle

53. Two
Important
Enzymes
in
Nitrate
Assimila/on
Nitrate
AssimilaFon:
(step
3)
process
by
which
plants
and
microorganisms
convert
NO3
–
to
NH3
1. Nitrate
reductase
NO3
–
+
2
e–
à
NO2
–
-­‐
large,
soluble
protein,
contains
novel
Mo
cofactor,
e–
from
NADH
2. Nitrite
reductase
NO2
–
+
6
e–
à
NH4
+
-­‐ Found
in
chloroplasts
in
plants,
e–
comes
from
ferredoxin
-­‐
In
nonphotosyntheFc
microbes,
e–
comes
from
NADPH

54. Nitrate
Assimila/on
by
Nitrate
Reductase

55. Nitrate
Assimila/on
by
Nitrite
Reductase

56. Nitrate
Assimila/on
(step
3)
vs.
Nitrogen
Fixa/on
(step
1)
• Both
are
electron-­‐transfer
processes
• Both
use
Mo
cofactor
– Nitrate
reductase
has
an
Mo
cofactor
– The
nitrogenase
complex
has
an
Fe-­‐Mo
cofactor
• Both
processes
involve
electron
transfer
through
groups
such
as
Fe-­‐S
complexes,
cytochromes,
SH
groups,
NADH,
NADPH,
etc.

57. Nitrogen
fixa/on
is
carried
out
by
the
nitrogenase
complex
• N2
+
3
H2
=
2
NH3
– Exergonic
(ΔG°
=
–33.5
kJ/mol)
but
very
slow
due
to
the
triple
bond’s
high
acFvaFon
energy
• The
nitrogenase
complex
can
accelerate
this
rx
– Has
two
subunits:
• Dinitrogenase
reductase
• Dinitrogenase
• Passes
electrons
to
N2
and
catalyzes
a
step-­‐wise
reducFon
of
N2
to
NH3
N2
+
8
H+
+
8
e–
+
nATP
=
2
NH3
+
H2
+
nADP
+
nPi
2
NH3
+
2
H+
=
2
NH4
+
About
16
ADP
molecules
are
consumed
per
one
N2.

58. Features
of
the
Nitrogenase
Complex
• Source
of
e–
varies
between
organisms
– O?en
pyruvate
àferredoxin
• ATP
hydrolysis
and
ATP
binding
help
overcome
the
high
acFvaFon
energy
• Has
regions
homologous
to
GTP-­‐binding
proteins
used
in
signaling
• Has
novel
FeMo
cofactor
(or
V
in
some
organisms)

59. Enzymes
and
Cofactors
in
the
Nitrogenase
Complex

60. The
Fe-­‐Mo
Cofactor
in
the
Dinitrogenase
Subunit
• Consists
of:
– 7
Fe
atoms
– 9
S
atoms
– 1
Mo
atom
– 1
bound
homocitrate
• The
nitrogen
binds
to
the
center
of
the
Mo-­‐FeS
cage
and
is
coordinated
to
the
molybdenum
atom
• Electrons
are
passed
to
the
molybdenum-­‐bound
nitrogen
via
the
iron-­‐sulfur
complex

61. The
Electron-­‐Transfer
Cofactors

62. Oxida/on
of
pyruvate
provides
electrons
to
nitrogenase
• Pyruvate
passes
e–
to
ferredoxin
or
flavodoxin
• Ferredoxin
or
flavodoxin
pass
e–
to
dinitrogenase
reductase
• The
reductase
passes
e–
to
dinitrogenase
• Dinitrogenase
passes
e–
to
nitrogen
(or
to
protons)
to
make
NH3
• FormaFon
of
H2
appears
an
obligatory
side-­‐reacFon

63. Nitrogen
Fixa/on
by
the
Nitrogenase
Complex

64. Redox
Reac/ons
in
Dinitrogenase
• The
net
rx
of
the
nitrogenase
complex:
N2
+
8
H+
+
8
e–
+
16
ATP
=
2
NH3
+
H2
+
16
ADP
+
16
Pi
• Dinitrogenase
reductase
catalyzes:
– transfer
of
8
e–
to
dinitrogenase
– hydrolysis
of
ATP
with
release
of
protons
• Dinitrogenase
catalyzes:
– transfer
of
6
e–
to
nitrogen:
formaFon
of
NH3
– transfer
of
2
e–
to
protons:
formaFon
of
H2

65. The
mechanism
of
dinitrogenase
remains
poorly
understood
• Extremely
complex
redox
reacFon
that
involves
several
metal
atoms
as
cofactors
and/or
electron
transporters
• Two
mechanisms
are
plausible
that
involve
the
Fe-­‐Mo
cofactor
binding
directly
to
N

66. Two
Hypotheses
for
the
Intermediates
of
N2
Reduc/on

67. The
nitrogenase
complex
is
very
unstable
in
O2
– Some
bacteria
live
in
anaerobic
environments
– Some
bacteria
uncouple
electron
transfer
and
ATP
synthesis―so
that
O2
is
removed
quickly
from
the
cell.
– Many
bacteria
live
in
root
nodules
coated
with
O2-­‐binding
heme
leghemoglobin.

68. Broader
Impact
of
Understanding
the
Nitrogen
Fixa/on
• Industrial
synthesis
of
NH3
via
the
Haber
process
is
one
of
mankind’s
most
significant
chemical
processes
– Made
chemical
ferFlizer
possible!
– Yields
over
100
million
tons
of
ferFlizer
annually
– sustains
life
of
over
one-­‐third
of
human
populaFon
on
Earth
– Consumes
non-­‐renewable
energy
(1–2%
of
total
annual
energy)
• Mimicking
biological
nitrogen
fixaFon
(biomimeFc
nitrogen
fixaFon)
may
yield
significant
energy
savings,
or
allow
use
of
renewable
energy
sources.

69. Nitrogen-­‐Fixing
Bacteria
in
Root
Nodules
of
Legumes
• Takes
care
of
energy
requirement
and
O2
lability
• Bacteria
have
access
to
plant’s
carbohydrate
and
CAC
intermediates
for
energy
• Bacteria
are
covered
with
leghemoglobin
to
bind
O2
• Can
produce
more
NH3
than
plant
needs;
excess
released
to
soil

70. Nitrogen-­‐Fixing
Nodules

71. The
Anammox
Reac/ons
• Anaerobic
ammonia
oxidaFon
• Newly
discovered
ability
of
some
bacteria
to
oxidize
NH3
and
NO2
–
into
N2
• “short-­‐circuits”
the
nitrogen
cycle
(no
denitrificaFon)
• Used
in
waste
treatment
for
cheaper
ammonia
removal

72. Surprising
Features
of
the
Anammox
Reac/ons
• Bacteria
are
of
unusual
phylum
Planctomycetes
– Have
DNA
enclosed
in
membrane
– Use
hydrazine
(N2H4)
à
(rocket
fuel),
toxic,
reacFve,
nonpolar
and
diffuses
across
membranes
• Phospholipids
made
of
ladderanes
– FaVy
acid
chains
contain
cyclobutane
rings
that
stack
Fghtly,
slow
the
diffusion
of
N2H2

73. Anammox
Reac/ons

74. Ladderane
Lipids

75. Ammonia
is
incorporated
into
biomolecules
through
Glu
and
Gln
• Glutamine
is
made
from
Glu
by
glutamine
synthetase
in
a
two-­‐
step
process:
Glu
+
ATP
à
γ-­‐glutamyl
+
NH4
+
à
Gln
+
Pi
phosphate
• PhosphorylaFon
of
Glu
creates
a
good
leaving
group
that
can
be
easily
displaced
by
ammonia
H3
N
NH2
O
COOH3
N
O
O
COO H3
N
O
O
COO
P
O
O
O
OH
P
O
O
O
+ -+ -
ATP
+ -
NH3 +

76. Structure
of
Gln
Synthetase

77. Regula/on
of
Glutamine
Synthetase
by
Allosteric
Inhibitors
• Endpoints
of
Gln
metabolism
provide
feedback
inhibiFon
– Ala,
Gly,
Trp,
carbamoyl
phosphate,
AMP,
CTP,
His,
glucosamine
6-­‐phosphate
• Effects
are
addiFve

78. Regula/on
of
Gln
Synthetase―by
Six
Endpoints
of
Gln
Metabolism

79. Gln
synthetase
is
also
inhibited
by
adenylyla/on
Adenylyla4on
(aVachment
of
AMP)
to
Tyr-­‐397
assists
in
inhibiFon.
– Increases
sensiFvity
to
inhibiFtors
– AdenylaFon
via
adenylyltransferase
– Part
of
complex
cascade
that
is
dependent
on
[Glu],
[α-­‐ketoglutarate],
[ATP],
and
[Pi]
– AcFvity
of
adenylyltransferase
regulated
by
binding
to
regulatory
protein
PII

80. PII
is
regulated
by
uridylyla/on
(Remember
that
PII
regulates
adenylyltransferase,
which
helps
inhibit
Gln
synthetase.)
• When
PII
is
uridylylated,
adenylyltransferase
sFmulates
deadenylylaFon
of
Gln
synthetase
(increasing
the
laVer’s
acFvity)
• ALSO,
uridylylated
PII
upregulates
transcripFon
of
Gln
synthetase

81. End
Result
of
Mul/ple
Levels
of
Control
of
Gln
Synthetase
• When
Gln
is
high,
Gln
synthetase
is
less
acFve
– Need
less
NH4
+
conversion
to
Gln
• When
Gln
is
low
and
substrates
α-­‐
ketoglutarate
and
ATP
are
available,
Gln
synthetase
is
more
acFve
– To
convert
more
NH4
+
to
Gln

82. Covalent
Modifica/on
of
Gln
Synthetase

83. Biosynthesis
of
Amino
Acids
and
Nucleo/des―Three
Types
of
Reac/ons
1. TransaminaFons
and
rearrangements
using
pyridoxal
phosphate
(PLP)
– PLP
is
acFve
form
of
Vit
B6
– Catalyzed
by
amidotransferases
– PLP
has
aldehyde
group
that
forms
Schiff
base
with
Lys
of
aminotransferase

84. 2. Transfer
of
1-­‐C
groups
using
tetrahydrofolate
(H4
folate)
or
S-­‐
adenosylmethionine
(adoMet)
– Both
can
act
as
carbon
donors
H4
folate
adotMet

85. 3. Transfer
of
amino
groups
derived
from
amide
of
Glu
All
three
of
these
categories
of
reacFons
use
glutamine
amidotransferases.

86. Glutamine
Amidotransferases
Catalyze
Bisubstrate
Reac/ons
• Two
domains
– One
binds
Gln
– Other
is
amino
group
acceptor
and
binds
substrate
• Cys
acts
as
nucleophile
to
cleave
amide
bond
of
Gln
– àForms
glutamyl-­‐enz
intermediate
• Then
second
substrate
binds
to
accept
amino
group
from
enzyme

87. Proposed
Mechanism
for
Glutamine
Amidotransferases

88. Amino
Acid
Biosynthesis―Overview
• Source
of
N
is
Glu
or
Gln
• Derive
from
intermediates
of
– Glycolysis
– Citric
acid
cycle
– Pentose
phosphate
pathway
• Bacteria
can
synthesize
all
20
• Mammals
require
some
in
diet

89. Amino
Acid
Synthesis
Overview

90. All
amino
acids
derive
from
one
of
seven
precursors
(See
Table
22-­‐1
and
Figure
22-­‐11)
• CAC:
– α-­‐ketoglutarate,
oxaloacetate
• Glycolysis
– Pyruvate,
3-­‐phosphoglycerate,
phosphoenolpyruvate,
erythrose
4-­‐phosphate
• Pentose
phosphate
pathway
– Ribose
5-­‐phosphate

91. Several
pathways
share
5-­‐phosphoribosyl-­‐1-­‐
pyrophosphate
(PRPP)
as
an
intermediate
• Synthesized
from
ribose
5-­‐phosphate
of
PPP
via
ribose
phosphate
pyrophosphokinase
– A
highly
regulated
allosteric
enzyme

95. Proline
and
arginine
derive
from
glutamate
• (Glu
derives
from
α-­‐ketoglutarate)
• Proline
is
a
cyclized
reduced
derivaFve
of
Glu
– ATP
reacts
w/
γ-­‐carboxyl
group
à
acyl
phosphate
– NADPH
or
NADH
reduces
the
acyl
phosphate
to
a
semialdehyde
that
rapidly
cyclizes
– Final
reducFon
step
yields
proline
– Pathway
operates
in
animals
AND
bacteria
– See
Fig.
22-­‐12

96. Biosynthesis
of
Pro
and
Arg
from
Glu
in
Bacteria

97. Arginine
is
synthesized
from
Glu
via
ornithine
in
animals
• Ornithine
comes
from
the
urea
cycle
• In
bacteria,
ornithine
has
special
synthesis
pathway
– Fig.
22-­‐12
shows
ornithine-­‐derived
synthesis
of
arginine
in
bacteria

98. In
animals,
proline
can
ALSO
be
synthesized
from
arginine
• Arginase
converts
Arg
to
ornithine
• Ornithine
δ-­‐aminotransferase
converts
ornithine
to
glutamate
γ-­‐semialdehyde
that
cyclizes
and
converts
to
Pro
• See
Fig
22-­‐13

99. Mammalian
Conversion
of
Ornithine
(from
Arg)
to
Cyclized
Precursor
to
Pro

100. Serine
derives
from
3-­‐
phosphoglycerate
of
glycolysis
• Same
pathway
in
~all
organisms
so
far
• Requires
Glu
as
source
of
NH2
group
• OxidaFon
àtransaminaFon
à
dephosphorylaFon
to
yield
serine
• See
Fig.
22-­‐14

101. Glycine
derives
from
serine
• Carbon
removed
using
tetrahydrofolate
(H4
folate)
to
accept
the
C
atom
and
pyridoxal
phosphate
(PLP).
• Rx
uses
serine
hydroxymethyltransferase
• See
Fig.
22-­‐14.
• In
the
liver,
Gly
can
be
made
by
another
pathway

102. Biosynthesis
of
Ser
and
Gly
from
3-­‐
Phosphoglycerate

103. Cysteine
also
derives
from
serine
• In
bacteria
and
plants,
sulfates
are
the
source
of
S
– See
Fig.
22-­‐15
• In
animals,
Met
is
the
source
of
S
– Met
à
S-­‐adenosylmethionine
– Loses
CH3,
is
hydrolyzed
to
homocysteine,
which
reacts
with
Ser
– Yields
cystathionine
then
rx
w/PLP
and
a
cleavage
step
to
yield
cysteine
– See
Fig.
22-­‐16

104. Biosynthesis
of
Cys
from
Ser
in
Plants
and
Bacteria

105. Biosynthesis
of
Cys
from
Homocysteine
and
Ser
in
Mammals

106. Oxaloacetate
yields
Asp,
which
yields
Asn,
Met,
Lys,
and
Thr
Thr
can
be
converted
to
Ile
(or
Ile
can
be
made
from
pyruvate)
Lots
of
complicated
chemistry!
• See
Fig.
22-­‐17
in
text

107. Pyruvate
yields
Ala,
Val,
Leu
and
Ile
• Again,
see
Fig.
22-­‐17
in
text
(too
big
to
show
here)

108. Reminder
of
Essen/al
Amino
Acids
• Humans
cannot
synthesize
Met,
Thr,
Lys,
Val,
Leu,
Ile

109. The
bacteria-­‐derived
enzyme
asparaginase
is
a
chemotherapy
agent
• Childhood
acute
lymphoblasFc
leukemia
(ALL)
dependent
on
serum
Asn
• Asparaginase
removes
Asn
• Has
side-­‐effects
• Being
used
in
conjuncFon
with
inhibitor
of
human
Asn
synthetase

110. Aroma/c
amino
acids
derive
from
phosphoenolpyruvate
and
erythrose
4-­‐
phosphate
• Very
complicated
chemistry!
• Rings
must
be
synthesized
and
closed
then
oxidized
to
create
double
bonds
• Chorismate
is
a
common
intermediate
See
Figs.
22-­‐18
through
22-­‐21
in
text.

111. His
derives
from
PPP
metabolite
ribose
5-­‐phosphate
• Also
involves
the
purine
ring
of
ATP,
PRPP
(5-­‐phosphoribosyl-­‐1-­‐pyrophosphate,
which
is
also
derived
from
the
Pentose
Phosphate
Pathway)
and
of
course
Gln
(source
of
N)
– See
Fig.
22-­‐22
in
text.

112. There
are
many
layers
of
regula/on
in
amino
acid
synthesis
• First
enzyme
in
a
sequence
is
o?en
most
highly
regulated
• Feedback
inhibiFon
can
be
coupled
with
allosteric
regulaFon
– Example:
Ile
synthesis
from
Thr
• Threonine
dehydratase
is
inhibited
by
Ile
• See
next
slide
(Fig.
22-­‐23)

113. Feedback
Inhibi/on
in
Ile
Synthesis
from
Thr

114. Use
of
isozymes
is
another
important
means
of
regula/on
Example:
Asp
can
lead
to
Lys,
Met,
Thr,
and
Ile.
Use
of
isozymes,
all
regulated
by
different
effectors,
allows
E.
coli
to
produce
the
amino
acids
when
needed.
– Example:
At
step
1,
isozyme
A1
is
inhibited
if
Ile
is
high
but
not
if
Met
or
Thr
are
high
– Only
the
A1
isozyme
is
inhibited
by
Ile
at
this
step

115. Regula/on
of
Aspartate-­‐Derived
Pathways

116. Glycine
or
glutamate
is
the
precursor
to
porphyrins
• Porphyrin
makes
up
the
heme
of
hemoglobin,
cytochromes,
myoglobin
• In
higher
animals,
porphyrin
arises
from
rx
of
glycine
with
succinyl-­‐CoA
• In
plants
and
bacteria,
glutamate
is
the
precursor
• Pathway
generates
two
molecules
of
the
important
intermediate
δ-­‐aminolevulinate
• Porphobilinogen
is
another
important
intermediate

117. Synthesis
of
δ-­‐Aminolevulinate
in
Higher
Eukaryotes

118. Synthesis
of
δ-­‐Aminolevulinate
in
Plants
and
Bacteria

119. Synthesis
of
Heme
from
δ-­‐Aminolevulinate
• Two
molecules
of
δ-­‐aminolevulinate
condense
to
form
porphobilinogen
• Four
molecules
of
porphobilinogen
combine
to
form
protoporphyrin
• Fe
ion
is
inserted
into
protoporphyrin
with
the
enzyme
ferrochelatase

120. Synthesis
of
Heme
from
δ-­‐Aminolevulinate

121. Defects
in
Heme
Biosynthesis
• Most
animals
synthesize
their
own
heme
• MutaFons
or
misregulaton
of
enzymes
in
heme
biosynthesis
pathway
lead
to
porphyrias
– Precursors
accumulate
in
red
blood
cells,
body
fluids,
and
liver.
– Homozygous
individuals
also
suffer
intermiVent
neurological
impairment,
abdominal
pain
– King
George
III
may
have
been
affected

122. Other
Types
of
Porphyrias
• AccumulaFon
of
precursor
uroporphyrinogen
I
– Urine
becomes
discolored
(pink
to
dark
purplish
depending
on
light,
heat
exposure)
– Teeth
may
show
red
fluorescence
under
UV
light
– Skin
is
sensiFve
to
UV
light
– Craving
for
heme
• Explored
as
possible
biochemical
basis
for
vampire
myths
as
well
as
neurological
condiFons
of
famous
individuals
(King
George
III,
etc.)
but
all
speculaFve

123. Enzymes
Inhibited
in
Heme
Synthesis
Defects

124. Heme
is
the
source
of
bile
pigments
• Heme
from
dying
erythrocytes
is
degraded
to
bilirubin
in
two
steps:
1. Heme
oxygenase
linearizes
heme
to
create
biliverdin,
a
green
compound
(seen
in
a
bruise)
2. Biliverdin
reductase
converts
biliverdin
to
bilirubin,
a
yellow
compound
that
travels
bound
to
serum
albumin
in
the
bloodstream

125. • In
liver,
bilirubin
diglucouronide
is
made
from
bilirubin
– Secreted
with
rest
of
bile
into
small
intesFne
– Microbial
enzymes
break
it
down
to
urobilinogen
and
other
compounds
– Some
urobilinogen
is
transported
to
the
kidney
and
converted
to
urobilin
• Gives
urine
its
yellow
color
• Remaining
intesFnal
urobilinogen
is
microbially
digested
to
stercobilin
of
feces

126. Forma/on
and
Breakdown
of
Bilirubin

127. Jaundice
is
caused
by
bilirubin
accumula/on
• Jaundice
(yellowish
pigmentaFon
of
skin,
whites
of
eyes,
etc.)
can
result
from:
– Impaired
liver
(in
liver
cancer,
hepaFFs)
– Blocked
bile
secreFon
(due
to
gallstones,
pancreaFc
cancer)
– Insufficient
glucouronyl
bilirubin
transferase
to
process
bilirubin
(occurs
in
infants)
• Treated
with
UV
to
cause
photochemical
breakdown
of
bilirubin

128. Gly
and
Arg
are
precursors
of
crea/ne
and
phosphocrea/ne
• PhosphocreaFne
is
hydrolyzed
for
energy
in
muscle
• Gly
and
Arg
combine,
then
Adomet
acts
as
a
methyl
donor

129. Biosynthesis
of
Crea/ne
and
Phosphocrea/ne

130. Glutathione
(GSH)
derives
from
Glu,
Cys,
and
Gly
• GSH
is
present
in
most
cells
at
high
amounts
• Reducing
agent/anFoxidant
– Keeps
proteins,
metal
caFons
reduced
– Keeps
redox
enzymes
in
reduced
state
– Removes
toxic
peroxides
• Oxidized
to
a
dimer
(GSSG)

131. Biosynthesis
and
Oxida/on
of
Glutathione

132. D-­‐amino
acids
in
bacteria
arise
from
racemases
• Bacterial
pepFdoglycans
contain
D-­‐Al
and
D-­‐Glu
• Racemases
act
on
D-­‐amino
acids,
use
PLP
as
cofactor
• Racemase
inhibitors
are
used/studied
as
anFbioFc
targets

133. Aroma/c
amino
acids
are
precursors
to
plant
lignins,
hormones,
and
natural
products
• Lignin
(rigid
polymer
in
plants)
from
Phe
and
Tyr
• Auxin
(growth
hormone
indole-­‐3-­‐acetate)
from
Trp
• Other
extracts:
spices
(nutmeg,
vanilla),
alkaloids
(morphine),
etc.

134. Biosynthesis
of
Auxin
from
Trp
and
Cinnamate
from
Phe

135. Amino
acid
decarboxyla/on
yields
neurotransmiTers,
inhibitors
• DecarboxylaFons
o?en
require
PLP
• Trp
yields
catecholamines
such
as
dopamine,
norepinephrine,
and
epinephrine
• Glu
yields
neurotransmiVers
γ-­‐aminobutyrate
(GABA)
and
serotonin
• His
yields
the
vasodilator
and
stomach
acid
secreFon
sFmulant
Histamine

136. Biosynthesis
of
Some
NeurotransmiTers

137. Arg
is
precursor
for
nitric
oxide
(NO)
• Mid-­‐80’s
discovery
that
pollutant
NO
played
important
role
in
blood
pressure
regulaFon,
blood
clo{ng,
etc.
• Synthesized
from
Arg
via
nitric
oxide
synthase
using
NADPH
– Enz
similar
to
cyt
P450
reductase
– SFmulated
by
interacFon
with
Ca2+
and
calmodulin

138. Biosynthesis
of
Nitric
Oxide

139. Nucleo/de
Biosynthesis
• NucleoFdes
can
be
synthesized
de
novo
from
amino
acids,
ribose-­‐5-­‐phosphate,
CO2,
and
NH3
• NucleoFdes
can
be
salvaged
from
nucleobases
• Many
parasites
(e.g.,
malaria)
lack
de
novo
biosynthesis
pathways
and
rely
exclusively
on
salvage
– Compounds
that
inhibit
salvage
pathways
are
promising
anF-­‐parasite
drugs

140. De
Novo
Biosynthesis
of
Nucleo/des
• Approximately
the
same
in
all
organisms
studied
• Bases
synthesized
while
aVached
to
ribose
• Glu
provides
most
amino
groups
• Gly
is
precursor
for
purines
• Asp
is
precursor
for
pyrimidines
• NucleoFde
pools
are
kept
low,
so
cells
must
conFnually
synthesize
them
– This
synthesis
may
actually
limit
rates
of
transcripFon
and
replicaFon

141. Origin
of
Ring
Atoms
in
Purines

142. De
novo
biosynthesis
of
purines
begins
with
PRPP
• Adenine
and
guanine
are
synthesized
as
AMP
and
GMP
• Synthesis
begins
with
rx
of
5-­‐phosphoribosyl
1-­‐
pyrophosphate
(PRPP)
with
Glu
• Purine
ring
builds
up
following
addiFon
of
three
carbons
from
glycine
• The
first
intermediate
with
full
purine
ring
is
inosinate
(IMP)

143. Construc/on
of
IMP

147. Synthesis
of
AMP
and
GMP
from
IMP

148. Regula/on
of
purine
biosynthesis
in
E.
coli
is
largely
feedback
inhibi/on
Four
major
mechanisms
1. Glutamine-­‐PRPP
amidotransferase
is
feedback
inhibited
by
end-­‐products
IMP,
AMP,
and
GMP
2. Excess
GMP
inhibits
formaFon
of
xanthylate
from
inosinate
by
IMP
dehydrogenase
(or
excess
adenylate
inhibits
formaFon
of
adenylosuccinate
by
adenylosuccinate
synthetase)

149. 3. GTP
limits
conversion
of
IMP
to
AMP,
and
ATP
limits
conversion
of
IMP
to
GMP
4. PRPP
synthesis
is
inhibited
by
ADP
and
GDP

150. Regula/on
of
Adenine
and
Guanine
Biosynthesis
in
E.
coli

151. Pyrimidines
are
made
from
Asp,
PRPP,
and
carbamoyl
phosphate
• Unlike
purine
synthesis,
pyrimidine
synthesis
proceeds
by
first
making
the
pyrimidine
ring
and
then
aVaching
it
to
ribose
5-­‐phosphate
• First
commiVed
step
is
rx
between
Asp
and
N-­‐carbamoylphosphate,
catalyzed
by
aspartate
transcarbamoylase
(ATCase)

152. De
novo
Synthesis
of
Pyrimidine
Nucleo/des

153. ATCase
channels
substrates
from
one
site
to
another

154. Regula/on
of
pyrimidine
biosynthesis
is
also
via
feedback
inhibi/on
• ATCase
is
inhibited
by
end-­‐product
CTP
and
is
accelerated
by
ATP

155. Allosteric
Regula/on
of
ATCase
by
CTP
and
ATP

156. Ribonucleo/des
are
precursors
to
deoxyribonucleo/des
• 2’C-­‐OH
bond
is
directly
reduced
to
2’-­‐H
bond…without
acFvaFng
the
carbon!
– Catalyzed
by
ribonucleo3de
reductase
• Mechanism:
Two
H
atoms
are
donated
by
NADPH
and
carried
by
proteins
thioredoxin
or
glutaredoxin

157. Reduc/on
of
Ribonucleo/des
to
Deoxyribonucleo/des
by
Ribonucleo/de
Reductase

158. Structure
of
Ribonucleo/de
Reductase

159. Proposed
ribonucleo/de
reductase
mechanism
involves
free
radicals
• Most
forms
of
enzyme
have
two
catalyFc/
regulatory
subunits
and
two
radical-­‐generaFng
subunits
– Contain
Fe3+
and
dithiol
groups
– Enz
creates
stable
Tyr
radical
to
abstract
H•
from
sugar
• A
3’-­‐ribonucleoFde
radical
forms
• 2’-­‐OH
is
protonated
to
help
eliminate
H2O
and
form
a
radical-­‐stabilized
carbocaFon
• Electrons
are
transferred
to
the
2’-­‐C

160. Proposed
mechanism
for
ribonucleo/de
reductase

161. Ribonucleo/de
reductase
has
two
types
of
regulatory
sites
• One
type
affects
ac3vity
– ATP
acFvates,
dATP
inhibits
• Other
type
affects
substrate
specificity
in
order
to
maintain
balanced
pools
of
nucleoFdes
– If
ATP
or
dATP
high
à
less
specificity
for
adenine
and
MORE
specificity
for
UDP
and
CDP,
etc.
– Enzyme
oligomerizes
to
accomplish
this
change.

162. Regula/on
of
Ribonucleo/de
Reductase
by
dNTPs

163. Oligomeriza/on
of
Ribonucleo/de
Reductase
when
dATP
Binds

164. dTMP
is
made
from
dUTP
• Roundabout
pathway…
1. dUTP
is
made
(via
deaminaFon
of
dCTP
or
by
phosphorylaton
of
dUDP)
2. dUTP
à
to
dUMP
by
dUTPase
3. dUMP
à
dTMP
by
thymidylate
synthase
-­‐
adds
a
methyl
group
from
tetrahydrofolate
Thymidylate
synthase
is
a
target
for
some
anFcancer
drugs.

165. Biosynthesis
of
dTMP

166. Conversion
of
dUMP
to
dTMP
by
Thymidylate
Synthase

167. Folic
acid
deficiency
leads
to
reduced
thymidylate
synthesis
• Folic
acid
deficiency
is
widespread,
especially
in
nutriFonally
poor
populaFons
• Reduced
thymidylate
synthesis
causes
uracil
to
be
incorporated
into
DNA
• Repair
mechanisms
remove
the
uracil
by
creaFng
strand
breaks
that
affect
the
structure
and
funcFon
of
DNA
– Associated
with
cancer,
heart
disease,
neurological
impairment

168. Catabolism
of
Purines:
Forma/on
of
Uric
Acid
• DegradaFon
of
purines
proceeds
through
dephosphorylaFon
(via
5’-­‐nucleo3dase)
• Adenosine
is
deaminated
to
inosine
and
then
hydrolyzed
to
hypoxanthine
and
ribose
• Guanosine
yields
xanthine
via
these
hydrolysis
and
deaminaFon
reacFons
• Hypoxanthine
and
xanthine
are
then
oxidized
into
uric
acid
by
xanthine
oxidase
• Spiders
and
other
arachnids
lack
xanthine
oxidase

169. Catabolism
of
Purines

170. Conversion
of
Uric
Acid
to
Allantoin,
Allantoate,
and
Urea

171. Catabolism
of
Purines:
Degrada/on
of
Urate
to
Allantoin
• Urate
is
oxidized
into
a
5-­‐hydroxy-­‐
isourate
by
urate
oxidase
• Hydrolysis
and
the
subsequent
decarboxylaFon
of
5-­‐hydroxy-­‐
isourate
yields
allantoin
• Most
mammals
excrete
nitrogen
from
purines
as
allantoin
• Urate
oxidase
is
inacFve
in
humans
and
other
great
apes;
we
excrete
urate
• Birds,
most
repFles,
some
amphibians,
and
most
insects
also
excrete
urate
NH
N N
H
N
H
O
O
O
NH
N N
N
H
O
O
O OH
NH2
N
H
N
H
N
H
O
O
O
H
H
+
-
-
O2 + H2O
H2O2
CO2
H2O
urate oxidase
spontaneous
or
catalyzed
urate
5-hydroxyisourate
allantoin

172. Catabolism
of
Purines:
Degrada/on
of
Allantoin
• Most
mammals
do
not
degrade
allantoin
• Amphibians
and
fishes
hydrolyze
allantoin
into
allantoate;
bony
fishes
excrete
allantoate
• Amphibians
and
carFlaginous
fishes
hydrolyze
allantoate
into
glyoxylate
and
urea;
many
excrete
urea
• Some
marine
invertebrates
break
urea
down
into
ammonia
NH2
N
H
N
H
N
H
O
O
O
H
NH2
N
H
N
H
NH2
O O
O
H
O
H
+
OH
OO
NH2
NH2
ONH2
NH2
O
NH4+
H2O
H2O
2 H2O + 4 H+
2 CO2
4
allantoinase
allantoicase
urease
allantoin
allantoate
urea
ammonium cation

173. Catabolism
of
Pyrimidines
• Leads
to
NH4
+
then
urea
• Can
produce
intermediates
of
CAC
– Example:
Thymine
is
degraded
to
succinyl-­‐CoA

174. Catabolism
of
Thymine,
a
Pyrimdine

175. Purine
and
pyrimidine
bases
are
recycled
by
salvage
pathways
• Free
bases,
released
in
metabolism,
are
reused
– Example:
Adenine
reacts
with
PRPP
to
form
the
adenine
nucleoFde
AMP
• Catalyzed
by
adenosine
phosphoribosyltransferase
• Brain
is
especially
dependent
on
salvage
pathways
• Lack
of
hypoxanthine-­‐guanine
phosphoribosyltransferase
leads
to
Lesch-­‐Nyhan
Syndrome
with
neurological
impairment,
finger-­‐
and-­‐toe-­‐biFng
behavior

176. Excess
uric
acid
seen
in
gout
• Painful
joints
(o?en
in
toes)
due
to
deposits
of
sodium
urate
crystals
• Primarily
affects
males
• May
involve
geneFc
under-­‐excreFon
of
urate
and/or
may
involve
over-­‐consumpFon
of
fructose
• Treated
with
avoidance
of
purine-­‐rich
foods
(seafood,
liver)
or
avoidance
of
fructose.
• Also
treated
with
xanthine
oxidase
inhibitor
allopurinol

177. Allopurinol
inhibits
xanthine
oxidase

178. Many
chemotherapeu/c
agents
target
nucleo/de
biosynthesis
• Glutamine
analogs:
azaserine,
acivicin
– Inhibit
glutamine
amidotransferases
• Fluorouracil
– Converted
by
salvage
pathway
into
FdUMP,
which
inhibits
thymidylate
synthase
• Methotrexate
and
aminopterin
– Inhibit
dihydrofolate
reductase
(compeFFve
inhibitors)

179. An/bio/cs
also
target
nucleo/de
biosynthesis
• Allopurinol,
etc.
– Studied
against
African
sleeping
sickness
(trypanosomiasis)
because
the
trypanosomes
lack
enzymes
for
de
novo
nucleoFde
synthesis
• Trimethoprim
–
– Inhibits
bacterial
dihydrofolate
reductase
but
binds
human
enzyme
several
orders
of
magnitude
less
strongly

180. Azaserine
and
Acivicin,
Inhibitors
of
Glutamine
Amidotransferases

181. Chemotherapy
Targets―Thymidylate
Synthesis
and
Folate
Metabolism

182. fdUMP
Inhibi/on
of
dUMPàdTMP
Conversion