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Page 1: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Author: Robert Lyons, Ph.D., 2008

License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution – Share Alike 3.0 License: http://creativecommons.org/licenses/by-sa/3.0/ We have reviewed this material in accordance with U.S. Copyright Law and have tried to maximize your ability to use, share, and adapt it. The citation key on the following slide provides information about how you may share and adapt this material.

Copyright holders of content included in this material should contact [email protected] with any questions, corrections, or clarification regarding the use of content.

For more information about how to cite these materials visit http://open.umich.edu/education/about/terms-of-use.

Any medical information in this material is intended to inform and educate and is not a tool for self-diagnosis or a replacement for medical evaluation, advice, diagnosis or treatment by a healthcare professional. Please speak to your physician if you have questions about your medical condition.

Viewer discretion is advised: Some medical content is graphic and may not be suitable for all viewers.

Page 2: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Citation Keyfor more information see: http://open.umich.edu/wiki/CitationPolicy

Use + Share + Adapt

Make Your Own Assessment

Creative Commons – Attribution License

Creative Commons – Attribution Share Alike License

Creative Commons – Attribution Noncommercial License

Creative Commons – Attribution Noncommercial Share Alike License

GNU – Free Documentation License

Creative Commons – Zero Waiver

Public Domain – Ineligible: Works that are ineligible for copyright protection in the U.S. (17 USC § 102(b)) *laws in your jurisdiction may differ

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Public Domain – Self Dedicated: Works that a copyright holder has dedicated to the public domain.

Fair Use: Use of works that is determined to be Fair consistent with the U.S. Copyright Act. (17 USC § 107) *laws in your jurisdiction may differ

Our determination DOES NOT mean that all uses of this 3rd-party content are Fair Uses and we DO NOT guarantee that your use of the content is Fair.

To use this content you should do your own independent analysis to determine whether or not your use will be Fair.

{ Content the copyright holder, author, or law permits you to use, share and adapt. }

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{ Content Open.Michigan has used under a Fair Use determination. }

Page 3: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

M1 Renal:Nitrogen Metabolism (and Related Topics)

Fall 2008

• Amino Acid Metabolism (Nitrogen metabolism)• Folate Metabolism (“One-Carbon pathways”)• Nucleotide Metabolism

Dr. Robert LyonsAssistant Professor, Biological Chemistry

Director, DNA Sequencing CoreWeb: http://seqcore.brcf.med.umich.edu/mcb500

Page 4: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Supplementary study material on the Web: http://seqcore.brcf.med.umich.edu/mcb500

R. Lyons

Page 5: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Glu, Gln,

A sp , N H 3

Amino Acid metabolismFolate metabolism

Nucleic Acid metabolism

Methylene

THF

Met

Cyc le

Purines Pyrimidines

U ric A cid

Urea

A mino acids

DNA

RN A

( energy )

TCA Cycle

f um arat e

oxa loac etat e

R. Lyons

Page 6: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Protein Degradation:

• Endogenous proteins degrade continuously- Damaged- Mis-folded- Un-needed

• Dietary protein intake - mostly degraded

Nitrogen Balance - expresses the patient’s current status - are they gaining or losing net Nitrogen?

Page 7: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Transaminases Collect Amines

Genera l reac t io n o v erv iew :

C

H

R COO

NH2

aminoacid

C

H

R COO

NH2

aminoacid

(typicall y gl utamate)

12CR COO

Oα - k e t o

a c i d( t y p i c a l l y

a l pha - k e t o g l u t a r a t e )

( - )+ +

2CR COO

O

α - k e t oa c i d

( - )

1

( - ) ( - )

Det a ils o f reac t io n m ec hanism :

C

H

R COO

NH

C

H

R COO

N

N

CH

O

CH

CH

OHOP

py r i d o x a lpho s p ha t e

a mi noa c i d

+

H O2

3

2

CH

CH

CH

OHOP

3

2

2

C

H

R COO

N

CH

CH

CH

OHOP

3

2

+

H

+

+

C

H

R COO

N

CH

CH

CH

OHOP

3

2

+

CR COO

NH

CH

O

CH

CH

OHOP

py r i do x a mi neph o s pha t e

+

3

2

2

+

H

α - k e t oa c i d

( - )( - ) ( - )

( - )

( - )

NH

NH

NH N

H

R. Lyons

Page 8: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

NH

N

CH

CH

CH

OHOP

pyridoxaminephosphate

3

2

2

H

+

H

+ CR COOO

α- ket oaci d

N

CHO

CH

CH

OHOP

pyr i doxalphosphat e

3

2

H

++ C

H

R COO

NH2

ami noaci d

( - )

Transfer the amine back to an acceptor α-keto acid

R. Lyons

Page 9: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Some amino acid + α-ketoglutarate some alpha keto acid + Glutamate

In other words, alpha-ketoglutarate is the preferredacceptor, and Glutamate is the resulting amino acid:

In peripheral tissues, transaminases tend to formGlutamate when they catabolize amino acids

Page 10: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Glutamate can donate its amines to form other amino acids as needed

Glutamate + oxaloacetate α-ketoglutarate + aspartate

A specific example - production of Aspartate in liver(described a few slides from now):

Page 11: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Getting Amines Into the Liver

O C CH CH C

H

NH

CO

2

2 2 2 2

glutamate

NAD(P)

NAD(P)H

O C CH CH C CO2 2 2 2

α- ket ogl ut ar at e

+ NH3

ammoni a

( - ) ( - ) ( - ) ( - )

O( mi t o)

C

H

OOC CH2

NH3

( +)

( - )CH

2COO

( - )

glutamate glutamine

C

H

OOC CH2

NH3

( + )

( - )CH

2C

O

NH2

NH3

ATP ADP Pi

+ +

Glutam ateDe hy drog ena se :

Glutam ine

Synthe tas e:

R. Lyons

Page 12: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

In the Liver: Precursers for Urea Cycle

Glutamine is hydro lyzed to glut amate and ammonia:

C

H

OOC CH2

NH3

(+)

(-)CH

2C

glutam ate

O

OH

glutam ine

C

H

OOC CH2

NH3

(+)

(-)CH

2C

O

NH2

H O2

NH3

Glutam ate donates its am ino group to form aspartate:

Glutamate aspartateoxaloacetate

+ +

α- ket ogl ut ar at e

OC CH CH C

H

NH

CO

2

2 2 2 2( - ) ( - ) O CCH C

H

CO2 2 2

( - ) ( - ) OC CH CH C

O

CO2 2 2 2

( - ) ( - ) OCCH C

H

NH

CO

2

2 2 2( - ) ( - )

O

Glutamate-aspartate aminotransferase:

.

.

Ammonia can also be formed by the glutamate dehydrogenase reaction and several other reactions as well.

R. Lyons

Page 13: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Liver mito chondrion

C

H

OOC CH2

NH3

( +)

( -)CH

2CH

2NH3

(+ )

O rn ithin e

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH3

( + )

O rnith ine

C

H

OOC CH2

NH3

(+ )

( - )CH

2CH

2NH C

( +)

A rg inine

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH C

O

C itru lline

C

H

OOC CH2

NH3

(+ )

(- )CH

2CH

2NH C

O

C itru lline

2ATP + HCO +3

NH 2 C

O

3OPO

( -)

C arb am o y l

p h osp hate

Pi

2ADP + Pi

O CCH C

H

2 2 2

aspartate

( - ) (- )CO

i

ATP

AMP + PP

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH C

O C CH C

H

2 2 2

(- ) ( -)CO

(+ )

A rg inin o su ccin ate

Liver cytoplasm

O C C CH

2 2(- ) (- )

COH

F um arate

H O2

C

O

U rea

NH 2

NH 2

NH 2

NH 3

NH 2

NH 2

NH 2

NH 2

NH 2NH 2

1

5

4

3

2

R. Lyons

Page 14: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

C arbam o y l pho s phat e sy nthe tas e I

HO C

O

O

ATP

ADP

P

NH

P

(- ) HO C

O

O

bicarbonatecarbonyl

phosphate i

3

HO C

O

N H2

carbamate

ATP

ADP

O C

O

NH2

P

carbamoyl

phosphate

R. Lyons

Page 15: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

O rnit h ine T rans carb am o y las e

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH3

(+ )

O rn ith in e

C

H

OOC C H2

NH3(+ )

(- )CH

2CH

2NH

2NHC

O

C itrullin e

NH2C

O

3OPO( -)

C arb am o y lp ho sp hate

P i

CH2NH3

(+ )

R. Lyons

Page 16: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

A rg in ino suc c inate s ynt he t as e

O C CH

C

H

NH2

2 2 2

aspartate

( - ) (- )CO

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH

2NHC

O

C itrulline

iATP AMP + PP

C

H

OOC CH2

NH3

( +)

( - )C H

2CH

2NH C NH

O C CH C

H

NH2

2 2 2(- ) ( - )CO

2

( +)

A rg inin o succin ate

R. Lyons

Page 17: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

A rg inino s ucc inat e lyase

C

H

OOC CH2

N H3(+ )

( -)CH

2CH

2NH NH

2C

NH2

(+ )

A rg inin e

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH C NH

O C CH C

H

NH2

2 2 2(- ) ( -)CO

2

(+ )

A rg in in osu ccin ateO C C C

H

2 2( -) ( - )C O

H

Fu m ara te

R. Lyons

Page 18: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

A rg inas e

C

H

OOC CH2

NH3( + )

( - )CH

2CH

2NH

3

( + )

O rnith ine

C

H

OOC CH2

NH3(+ )

( -)CH

2CH

2NH NH

2C

NH2

( +)

A rg inin eNH

2C

O

NH2

U rea

H2O

R. Lyons

Page 19: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Liver mito chondrion

C

H

OOC CH2

NH3

( +)

( -)CH

2CH

2NH3

(+ )

O rn ithin e

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH3

( + )

O rnith ine

C

H

OOC CH2

NH3

(+ )

( - )CH

2CH

2NH C

( +)

A rg inine

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH C

O

C itru lline

C

H

OOC CH2

NH3

(+ )

(- )CH

2CH

2NH C

O

C itru lline

2ATP + HCO +3

NH 2 C

O

3OPO

( -)

C arb am o y l

p h osp hate

Pi

2ADP + Pi

O CCH C

H

2 2 2

aspartate

( - ) (- )CO

i

ATP

AMP + PP

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH C

O C CH C

H

2 2 2

(- ) ( -)CO

(+ )

A rg inin o su ccin ate

Liver cytoplasm

O C C CH

2 2(- ) (- )

COH

F um arate

H O2

C

O

U rea

NH 2

NH 2

NH 2

NH 3

NH 2

NH 2

NH 2

NH 2

NH 2NH 2

1

5

4

3

2

R. Lyons

Page 20: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Urea Cyc le Co nnec t s t o T CA Cyc le

A rg in in e

C itru llin e

O C CH C

H

NH2

2 2 2

A spartate

( - ) ( - )CO

A rgininosuccinate

O C C CH

2 2( - ) ( - )CO

H

Fum arate

M alate

O xaloacetate

T C A C ycle

α -K etoglutarate

C itrate

U r ea

Ornithine

U r ea C ycle

R. Lyons

Page 21: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Getting Amines Into the Liver

O C CH CH C

H

NH

CO

2

2 2 2 2

glutamate

NAD(P)

NAD(P)H

O C CH CH C CO2 2 2 2

α- ket ogl ut ar at e

+ NH3

ammoni a

( - ) ( - ) ( - ) ( - )

O( mi t o)

C

H

OOC CH2

NH3

( +)

( - )CH

2COO

( - )

glutamate glutamine

C

H

OOC CH2

NH3

( + )

( - )CH

2C

O

NH2

NH3

ATP ADP Pi

+ +

Glutam ateDe hy drog ena se :

Glutam ine

Synthe tas e:

R. Lyons

Page 22: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Liver mito chondrion

C

H

OOC CH2

NH3

( +)

( -)CH

2CH

2NH3

(+ )

O rn ithin e

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH3

( + )

O rnith ine

C

H

OOC CH2

NH3

(+ )

( - )CH

2CH

2NH C

( +)

A rg inine

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH C

O

C itru lline

C

H

OOC CH2

NH3

(+ )

(- )CH

2CH

2NH C

O

C itru lline

2ATP + HCO +3

NH 2 C

O

3OPO

( -)

C arb am o y l

p h osp hate

Pi

2ADP + Pi

O CCH C

H

2 2 2

aspartate

( - ) (- )CO

i

ATP

AMP + PP

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH C

O C CH C

H

2 2 2

(- ) ( -)CO

(+ )

A rg inin o su ccin ate

Liver cytoplasm

O C C CH

2 2(- ) (- )

COH

F um arate

H O2

C

O

U rea

NH 2

NH 2

NH 2

NH 3

NH 2

NH 2

NH 2

NH 2

NH 2NH 2

1

5

4

3

2

R. Lyons

Page 23: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

C P S I is St im u lat ed by N A G

HO C

O

O

ATP

ADP

P

NH

P

( -) HO C

O

O

bicarbonatecarbonyl

phosphate i

3

H O C

O

NH2

carbamate

ATP

ADP

O C

O

NH2

P

carbamoyl

phosphate

g lu tam ate

C

H

OOC CH2

NH3

( +)

( - )

CH2C

O

OH+ CoA -

C

H

OOC CH2

NH

( - )

CH2C

O

OH

C O

CH3

C O

CH3

a cetyl C o AN -acety lg lu tam a te

(N A G )

N -acetyl

g lutam ate

synthetase

(repeating the figure from page 3 o f your han do ut)

R. Lyons

Page 24: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Muscle

Liver

Glucose Pyruvate

Alanine

Amino acids

(Amines)

α-ketoglutarate

Glutamate

Alanine

PyruvateGlucose

bloodtransport

α-ketoglutarate

Glutamate NH3

Urea

--

R. Lyons

Page 25: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Arginine

Amino acids:

Alanine Glutamate

Glutamine

Transamination Deaminationpurine

deamination:

NH4

(+)

Glutamine

Alanine NH4

(+)Citrulline

NH4

(+) Urea

Muscle:

Liver:

Intestine:

Alanine

AspartateGlu

Glutamine

NH3

Kidney:

Arginine

Citrulline

Glutamine

NH4

(+)

Complicating the picture: Other tissues may be involved

R. Lyons

Page 26: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Why is Ammonia Toxic?

Page 27: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Why is Ammonia Toxic?

• Possible neurotoxic effects on glutamate levels (and also GABA)

(due to shifting equilibria of reactions involving these compounds)

Page 28: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Why is Ammonia Toxic?

• Possible neurotoxic effects on glutamate levels (and also GABA)

(due to shifting equilibria of reactions involving these compounds)

• Possible metabolic/energetics effects:- alpha-ketoglutarate levels- glutamate levels- glutamine

Page 29: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Liver mito chondrion

C

H

OOC CH2

NH3

( +)

( -)CH

2CH

2NH3

(+ )

O rn ithin e

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH3

( + )

O rnith ine

C

H

OOC CH2

NH3

(+ )

( - )CH

2CH

2NH C

( +)

A rg inine

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH C

O

C itru lline

C

H

OOC CH2

NH3

(+ )

(- )CH

2CH

2NH C

O

C itru lline

2ATP + HCO +3

NH 2 C

O

3OPO

( -)

C arb am o y l

p h osp hate

Pi

2ADP + Pi

O CCH C

H

2 2 2

aspartate

( - ) (- )CO

i

ATP

AMP + PP

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH C

O C CH C

H

2 2 2

(- ) ( -)CO

(+ )

A rg inin o su ccin ate

Liver cytoplasm

O C C CH

2 2(- ) (- )

COH

F um arate

H O2

C

O

U rea

NH 2

NH 2

NH 2

NH 3

NH 2

NH 2

NH 2

NH 2

NH 2NH 2

1

5

4

3

2

R. Lyons

Page 30: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Defects are diagnosed based on the metabolites seen

in the blood and/or urine.

CPSD

OTCD

ASDALD

AD

No elevation except ammonia; diagnosed by elimination.

Elevated CP causes synthesis of Orotate

Elevated citrulline

Elevated argininosuccinate

Elevated arginine

Inherited Defects of Urea Cycle Enzymes: Diagnosis

Page 31: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Liver mito chondrion

C

H

OOC CH2

NH3

( +)

( -)CH

2CH

2NH3

(+ )

O rn ithin e

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH3

( + )

O rnith ine

C

H

OOC CH2

NH3

(+ )

( - )CH

2CH

2NH C

( +)

A rg inine

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH C

O

C itru lline

C

H

OOC CH2

NH3

(+ )

(- )CH

2CH

2NH C

O

C itru lline

2ATP + HCO +3

NH 2 C

O

3OPO

( -)

C arb am o y l

p h osp hate

Pi

2ADP + Pi

O CCH C

H

2 2 2

aspartate

( - ) (- )CO

i

ATP

AMP + PP

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH C

O C CH C

H

2 2 2

(- ) ( -)CO

(+ )

A rg inin o su ccin ate

Liver cytoplasm

O C C CH

2 2(- ) (- )

COH

F um arate

H O2

C

O

U rea

NH 2

NH 2

NH 2

NH 3

NH 2

NH 2

NH 2

NH 2

NH 2NH 2

1

5

4

3

2

R. Lyons

Page 32: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

C P S I is St im u lat ed by N A G

HO C

O

O

ATP

ADP

P

NH

P

( -) HO C

O

O

bicarbonatecarbonyl

phosphate i

3

H O C

O

NH2

carbamate

ATP

ADP

O C

O

NH2

P

carbamoyl

phosphate

g lu tam ate

C

H

OOC CH2

NH3

( +)

( - )

CH2C

O

OH+ CoA -

C

H

OOC CH2

NH

( - )

CH2C

O

OH

C O

CH3

C O

CH3

a cetyl C o AN -acety lg lu tam a te

(N A G )

N -acetyl

g lutam ate

synthetase

(repeating the figure from page 3 o f your han do ut)

R. Lyons

Page 33: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Liver mito chondrion

C

H

OOC CH2

NH3

( +)

( -)CH

2CH

2NH3

(+ )

O rn ithin e

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH3

( + )

O rnith ine

C

H

OOC CH2

NH3

(+ )

( - )CH

2CH

2NH C

( +)

A rg inine

C

H

OOC CH2

NH3

( + )

( - )CH

2CH

2NH C

O

C itru lline

C

H

OOC CH2

NH3

(+ )

(- )CH

2CH

2NH C

O

C itru lline

2ATP + HCO +3

NH 2 C

O

3OPO

( -)

C arb am o y l

p h osp hate

Pi

2ADP + Pi

O CCH C

H

2 2 2

aspartate

( - ) (- )CO

i

ATP

AMP + PP

C

H

OOC CH2

NH3

(+ )

( -)CH

2CH

2NH C

O C CH C

H

2 2 2

(- ) ( -)CO

(+ )

A rg inin o su ccin ate

Liver cytoplasm

O C C CH

2 2(- ) (- )

COH

F um arate

H O2

C

O

U rea

NH 2

NH 2

NH 2

NH 3

NH 2

NH 2

NH 2

NH 2

NH 2NH 2

1

5

4

3

2

R. Lyons

Page 34: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Clinical Management of Urea Cycle Defects

• Dialysis to remove ammonia• Provide the patient with alternative ways to excrete

nitrogenous compounds:

• Levulose - acidifies the gut• Low protein diet

* Intravenous sodium benzoate or phenylacetate* Supplemental arginine

Ornithine

Arginine

Citrulline

i

ATP

AMP+PP

ArgininosuccinateHO2

CO

UreaNH2NH2 Aspartate

Excreted by kidney

Excreted by kidney

XDietaryArginine

carbamoyl phosphate

X ASD

ALD

R. Lyons

Page 35: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Degrading the Amino Acid Carbon Backbone

Page 36: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Easily-degraded products after transamination:

O C CH C

H

NH3

2 2 2

aspartate

( - )C O

t ransa minat io nO C CH C

O2 2 2

( - )C O

ox a l o ac et a t e

( - ) ( - )

( +)

O C C H C

H

NH3

2 2 2

gl ut a ma t e

( - )

t ransam ina t io n

CH C

O2 2

( - )

α - ke t o gl ut ar at e

CH2

O C2

CH2

C O C O( - ) ( - )

( + )

CH C

H

NH3

3 2

a l a n i ne

( - )CO

t ra nsam ina t io n

CH C

O3 2

( - )C O

py r uva t e( +)

We also already know how to degrade Glutamine:Glutamine ----------------> glutamate + ammonia

Asparagine ---------------> aspartate + ammonia

…and by analogy, how to degrade Asparagine:

glutaminase

asparaginase

glutaminase

R. Lyons

Page 37: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Many amino acids are purely glucogenic:Glutamate, aspartate, alanine, glutamine,asparagine,…

Some amino acids are both gluco- and ketogenic:Threonine, isoleucine, phenylalanine, tyrosine, tryptophan

Amino Acids are categorized as ‘Glucogenic’or ‘ketogenic’ or both.

The only PURELY ketogenic Amino Acids: leucine, lysine

Page 38: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

C

H

OOC CH2

NH3

(+ )

( - )CH

2CH

2NH NH

2C

NH2

( +)

A rg in ine

U rea ( via

t h e u re a cy c le)

C

H

OOC CH2

NH3

( +)

( - )CH

2CH

2NH

3

( +)

Orn it hin e

α -ke t og lu t arat e

glu tam at e

C

H

OOC CH2

NH3

( +)

( - )CH

2C

glut am at e - 5 - s em iald eh yd e

O

H

NA D (P)

NA D (P)H

( + )

C

H

OOC CH2

NH3

( + )

( - )CH

2C

g lut am ate

O

OH

α - ke t o g lu t arat e

NH

( + )OOC( - )

P ro line

g lu ta min e

C

H

OOC CH2

NH3

( + )

( - )CH

2C

O

NH2

H O2

NH3

Amino acids with 5-carbon backbones tend to formαketoglutarate

R. Lyons

Page 39: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

C

H

OOC NH3

(+ )

(- )

H

Glyc in e

NAD NADH( +)

T HF N - N - me t hy l e ne THF5 10

+C O NH4

( +)

2

CH

OOC NH3

( +)

( - )

2

Gly c ineT HF N - N - met hy l ene T HF5 10S e rin e

CHOOC NH3

( +)

( - )

CH OH2

G ly c in e

Sy n th a s e :

Se rin e

H y d ro x y m e t h y l -

t ra n s f e ra s e :

S erin e

CHOOC NH3( +)

(- )

CH OH2

H O2

CO OC NH3

( +)(- )

CH2

COOC NH2

(+ )(- )

CH3

COOC( - )

CH3

H O2

NH4

( +)

OS e rin e

D e h y d ra ta s e :

Degradation and Biosynthesis of Serine and Glycine

R. Lyons

Page 40: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

C

H

COOCH2

NH3

(+)

(-)CH2

Methionine

Serine

C

H

COOCH2

NH3( +)

( - )HO

SCH3

C

H

COOCH2

NH3( +)

( - )CH2

S-Adenosyl Methionine

SCH3

ATP +H O2

PPi +Pi

( +)

CH2

O

HH H

HOH OH

Adenine

C

H

COOCH2

NH3

( +)

( - )CH2

Homocysteine

HS

C

H

COOCH2

NH3( +)

( - )CH2

S-Adenosyl Homocysteine

HS( +)

CH2

O

HH H

HOH OH

Adenine

BiosyntheticMethylation

reaction

Methyl acceptor

Methylated acceptor

* see examples

C

H

COOCH2

NH3( +)

( - )

Cysteine

HS

(remainder ofhomocysteine

degradedfor energy)

te t rah yd ro fo lat e

N5 me th ylt et rah yd ro fo la te

Methionine CycleAnd BiologicalMethyl Groups

R. Lyons

Page 41: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

P henylalan ine and T yro s ine

CH2

CH COO

NH 3

(+)

(-)

P h en ylalan in e

Tetrahydrobiopte rin + O 2

Dihydrobi opterin + H 2O

CH2

CH COO

NH 3

(+)

(-)

T yro sin e

HO

H om og entisate

En zym e:

P h en ylalan in e

h yd ro xylase

E nz ym e:

ho m o g en tisate

d ioxy g en aseCH

2C COO

(-)

P h en ylp yru vate

O

Phenylketonuria

(no phenylalanine

hydroxylase)

(N orm al path show n in black, pathological reaction show n in red)

(you don’t need to

know the rest)

Deficiency:Alkaptonuria“Ochronosis”

R. Lyons

Page 42: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

B ran c h e d C h a in A m in o A c id s

Is o le u c in e L e u c in e V a lin e

C H C O O( - )

N H3

( + )

C HC H2

C H3

C H3

C H C O O( - )

N H3

( + )

C HC H2

C H3

C H3

C H C O O( - )

N H3

( +

)

C HC H3

C H3

C C O O( - )

O

C HC H2

C H3

C H3

C C O O( - )

C HC H2

C H3

C H3

C C O O( - )

C HC H3

C H3

O O

C

O

C HC H2

C H3

C H3

CC HC H2

C H3

C H3

C S -C o AC HC H3

C H3

O O

N A D , C o A S H+

N A D H +

C O2

N A D , C o A S H+

N A D , C o A S H+

N A D H + C O2 N A D H + C O 2

S - C o AS - Co A

α −K G α −K G α −K G

G l u G lu G l u

- - - - - - - - - - - - - - - - T r a n s a m in a t io n - - - - - - - - - - - - - - - -

- - - B r a n c h e d - c h a in α - k e t o a c id d e h y d r o g e n a s e - - -

( c o n t in u e s o n t o d e g r a d a t io n p a t h s im ila r t o β - o x id a t io n o f f a t t y a c id s )

R. Lyons

Page 43: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Synthesis o f Bioact ive A mines

CH 2 CH COO

NH 3

(+)

(-)

T yrosin e

HO CH2

CH COO

NH 3

(+)

(-)HO

HO

D ih ydroxyp heny lalanin e

T yro sin e

hyd ro xy lase

(L-D O PA )

HO

HO

CH2CH NH 3

(+)

2

D op am ine

CH CH NH 3

(+)

2

N o repine phrine

OH

H

HO

HO

CH CH NH

2

Ep ineph rine

OH

H

HO

HO

CH 3

R. Lyons

Page 44: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

N

CH 2 CH COO

NH3(+)

(-) HO

N

CH2 CH COO

NH3(+)

(-)

T ryp to ph an 5 -hyd roxytryp to ph an

Tryptophan

hydroxylase

CO2

HO

N

CH2

CH NH3( +)

Sero to nin

2

PLP-dependent

decvarboxylation

NAD+

Synthesis of Bioactive Amines

R. Lyons

Page 45: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

CH 2 CH COO

NH 3(+)

(-)

CH 2COO(-)

Glut amate

Glutamate

decarboxylase

(PLP-dependent )

CH2 CH NH3( +)

CH2COO( - )

γ-amin ob ut yric ac id

(GA BA )

2

N

NH

CH2 CH COO

NH3( + )

( -

)

Hist idine

H ist id ine

de carbo xylase

( PL P-de pe nd ent )

N

NH

CH2 CH NH3( +)

Hist amine

2

Synthesis of Bioactive Amines

R. Lyons

Page 46: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Glutamate, aspartate, alanine, glutamine, asparagine,(proline), glycine, serine (cysteine, tyrosine)

NON-Essential Amino Acids:

Essential Amino Acids:

Arginine (!), phenylalanine, methionine, histidine,Isoleucine, leucine, valine, threonine, tryptophan, lysine

Page 47: Author: Robert Lyons, Ph.D., 2008 License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution

Slide 4: Robert LyonsSlide 5: Robert LyonsSlide 7: Robert LyonsSlide 8: Robert LyonsSlide 11: Robert LyonsSlide 12: Robert LyonsSlide 13: Robert LyonsSlide 14: Robert LyonsSlide 15: Robert LyonsSlide 16: Robert LyonsSlide 17: Robert Lyons Slide 18: Robert Lyons Slide 19: Robert Lyons Slide 20: Robert Lyons Slide 21: Robert Lyons Slide 22: Robert Lyons Slide 23: Robert Lyons Slide 24: Robert Lyons Slide 25: Robert Lyons Slide 29: Robert Lyons Slide 31: Robert Lyons Slide 32: Robert Lyons Slide 33: Robert Lyons Slide 34: Robert Lyons Slide 36: Robert Lyons Slide 38: Robert Lyons Slide 39: Robert Lyons Slide 40: Robert Lyons Slide 41: Robert Lyons Slide 44: Robert Lyons Slide 45: Robert Lyons

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