amino acid metabolism student edition 6/3/13 version pharm. 304 biochemistry fall 2014 dr. brad...

Amino Acid Metabolism Student Edition 6/3/13 version

Pharm. 304 Biochemistry

Fall 2014

Dr. Brad Chazotte 213 Maddox Hall

chazotte@campbell.eduWeb Site:

http://www.campbell.edu/faculty/chazotte

Original material only ©2004-14 B. Chazotte

Goals

• Understand the relationship of nitrogen to carbon intermediary metabolism.

• Learn the Urea Cycle sequence, reactions, and products.• Have an understanding of an overview of amino acid

catabolism resulting in 7 basic products and the difference between ketogenic and glucogenic catabolism.

• Have an understanding of an overview of amino acid anabolism from basic precursors.

• Understand the concept of essential and nonessential amino acids in the diet of humans.

• Understand that many diseases can arise from errors in amino acid metabolism.

Do NOT memorize any of the specific amino acid catabolic or anabolic pathways. They are for informational purposes only.

Nitrogen Pathways in

Intermediary Metabolism

Matthews et al 2000 Figure 20.1

Plants

Dietary Amino Acids in Metabolism

“Excess dietary amino acids are not simply excreted but are converted to common metabolites that are precursors of glucose, fatty acids, ketone bodies – and are therefore metabolic fuels”

Voet, Voet & Pratt 2008 p.732

Protein Synthesis & Degradation

1. Nutrient storage as protein; break proteins down in times of metabolic need (muscle a prime source)

2. Eliminate accumulation of abnormal proteins that would harm the cell

3. Permit the regulation of cellular metabolism by the elimination of unneeded enzymes and regulatory proteins.

Voet, Voet & Pratt 2008 p.733

Catabolism

Cellular Protein Degradative Routes Lysosomal - a cellular compartment at ~pH 5 containing hydrolytic enzymes (cathepsins). Degrade substances taken up by endocytosis. Recycle intracellular constituents enclosed within vacuoles. In “well nourished cells” protein degradation is nonselective. In starving cells a selective pathway is activated that imports and degrades proteins that contain the pentapeptide (Lys-Phe-Glu-Arg-Gln; KFERQ) e.g., in muscle and liver, but not brain.

Ubiquitin-Based – ATP-based process independent of lysosomes. Proteins are marked for degradation by linking to ubiquitin.

Rx Involved in Protein Ubiquination

Voet, Voet & Pratt 2013 Fig 21.2 Matthews et al 2000 Figure 20.11

Matthews et al 2000 Figure 20.10

Proteasome

Voet, Voet & Pratt 2013 Fig 21.4

Distinguishing Protein Lifetimes

The N-end Rule:

N-terminal residues Asp, Arg, Leu, Lys & Phe

half-life ~ 2-3 minutes

Ala, Gly, Met, Ser Thr, & Val

half-life > 20 hrs in eukaryotes

(>10 prokaryotes)

PEST proteins Proteins with segments rich in Pro, Glu, Ser, & Thr are rapidily degraded- these AA have sites that can be phosphorylated – thus targeting them for ubiquitination.

Voet, Voet & Pratt 2013 Table 21.1

Some Cellular Processes Regulated by Protein Degradation

e.g,NF-κB –I κB system

Berg, Tymoczko, & Stryer 2012 Table 23.3

Protein (“Macro”)

Digestion in the Human

Gastrointestinal Tract

Lehninger 2000 Figure 18.3Berg, Tymoczko, & Stryer 2012 Figure 23.1

Amino Acid Catabolism: Overview

Voet, Voet & Pratt 2013 Fig 21.6Lehninger 2004 Figure 18.1

Amino acid degradation includes a key step of separating the amino group from the carbon skeleton.

Amino Acid Deamination Transamination - most amino acids are deaminated by this process carried out by transaminases (aminotransferases). Amino group of amino acid is transferred (predominately) to -ketoglutarate

Oxidative Deamination – of glutamate by glutamate dehydrogenase yields ammonia and -ketoglutarate

Voet, Voet & Pratt 2013 Chap. 21 page 722

Voet, Voet & Pratt 2013 Chap. 21 page 719

Forms of Pyridoxal-5’-Phosphate

Voet, Voet & Pratt 2013 Fig 21.7

Needed by aminotransferases as a coenzyme.

PLP-Dependent Enzyme Catalyzed Transamination Mechanism

Voet, Voet & Pratt 2013 Fig 21.8

Oxidative Degradation of Amino Acids

Occurs under three different circumstances in animals:

1) During normal homeostasis

2) Protein-rich diet

3) Starvation or uncontrolled diabetes mellitus

Lehninger 2000 Chapter 18

Glutamate Dehydrogenase (Oxidative Deamination)

A mitochondrial enzyme yielding ammonia and -ketoglutarate

It is the only enzyme that can accept either NAD+ or NADP+ as a coenzyme

G° = ~30 kJ mol-1

Due to the high toxicity of ammonia – it is important that under physiological conditions G ≈ 0, i.e. at equilibrium.

Lehninger 2000 Figure 18.7

mammalian liver

Ammonia Transport to Liver for Urea Synthesis

Matthews et al 2000 Figure 20.14 Lehninger 2000 Figure 18.8

Urea Cycle

Urea Cycle Enzymes

(1) Carbamoyl Phosphate synthetase (mitochondrion)

(2) Ornithine transcarbamoylase (mitochondrion)

(3) Argininosuccinate synthetase (cell cytosol)

(4) Argininosuccinase (cell cytosol)

(5) Arginase (cell cytosol)

Overall Urea Cycle Reaction

Voet, Voet & Pratt 2013 Chap 21 p 723

Urea Cycle & Feeder Reactions

Voet, Voet & Pratt 2013 Fig 21.9

Lehninger 2000 Figure 18.9

Urea Cycle Diagram

Lehninger 2000 Figure 18.9

Nitrogen-acquiring reactions in Urea Synthesis

Lehninger 2004 Figure 18.11

Linking the Urea & Citric Acid Cycles“ Krebs ‘Bicycle’ ”

Lehninger 2004 Figure 18.12

AA Degradation to 1 of 7 Common Intermediates

Voet, Voet & Pratt 2013 Fig 21.13

Glucogenic vs Ketogenic Amino Acid Degradation

• Glucogenic - degradation lead to glucose precusors: pyruvate, α-ketoglutarate, succinyl-CoA, fumarate or oxaloacetate

• Ketogenic – degradation leads to fatty acids or ketone body precursors: acetyl-CoA or acetoacetate

• Some amino acids are gluco- and keto-genic

Examples of a Few Disorders of Human Amino Acid Catabolism

Lehninger 2000 Table 18.2

PKU

Tyrosimenia I, II, or III Rx 5, 2, or 4- respectively {side 35}

Anabolism

Human Essential & Non-Essential Amino Acid

Voet, Voet & Pratt 2013 Table 21.3

Amino Acid Biosynthetic Families

Lehninger 2000 Table 22.1

CAC

CAC

Glycolysis

Glycolysis

PP

PP

Metabolic Relationships Among Amino Acids Derived from Citric Acid Cycle

Intermediates

Matthews et al 2000 Figure 21.1

Essential Human amino acid

THOSE AA HIGHLIGTED BY AN ORANGE BOX ARE ESSENTIAL AMINO ACIDS FOR HUMANS.

Biosynthesis of Non-Essential Amino Acids

With the exception of tyrosine, all the nonessential amino acids come from one these four metabolic intermediates: pyruvate, oxaloacetate, α-ketoglutarate, and 3-phosphoglycerate.

End of Lecture Materials

Supplementary Material on Amino Acid Catabolism

• This material will NOT be on any test and is for informational purposes only.

Pathways for Ala, Cys, Gly, Ser & Thr to Pyruvate

Voet, Voet & Pratt 2008 Fig 21.14

Serine Dehydratase

Voet, Voet & Pratt 2008 Fig 21.15

Pathways for Arginine,

Glutamate, Glutamine, Histidine & Proline to -

ketoglutarate

Voet, Voet & Pratt 2008 Fig 21.17

Methionine Degradation

Voet, Voet & Pratt 2008 Fig 21.18

TetraHydroFolate

Voet, Voet & Pratt 2008 Table 21.2, Fig 21.19

2-State Reduction of Folate to THF

Branched-Chain AA Degradation

Voet, Voet & Pratt 2008 Fig 21.21

Mammalian Liver Lysine Degradation

Voet, Voet & Pratt 2008 Fig 21.22

Saccharopine dehydrogenase

Saccharopine dehydrogenase

aminoadipate semialdehyde dehydrogenase

Sminoadipate amino- transferase

Α-keto acid dehydrogenase

Glutaryl-CoA dehyd.

decarboxylaseEnoyl-CoA dehydratase

Β-hydrozyacylCoA dehydrogenase

HMG-CoA synthase

HMG-CoA lyase

1

Tryptophan Degradation

Voet, Voet & Pratt 2008 Fig 21.23

Tryptophan-2,3- dioxygenase

formamidase

Kynureninase-3- monooxygenase

Kynureninase

Phenylalanine Degradation

Voet, Voet & Pratt 2008 Fig 21.24

Phenylalanine hydroxylase

Tyrosine aminotransferase

p-hydroxyphenyl pyruvate dioxygenase

Homogentisate dioxygenase

fumarylacetoacetase

Supplementary Information of Amino Acid Anabolism

• The information in the slides hereafter is for informational purposes only, if you are interested, and will NOT be part of any test.

• Amino acid degradative and biosynthetic pathways are sites for a significant number of illnesses and/or genetic defects.

Alanine, Aspartate, Glutamate, Asparagine

& Glutamine Syntheses (Non-essential)

Voet, Voet & Pratt 2008 Fig 21.27

Glutamate “Family” Syntheses:Arginine, Ornithine & Proline

Voet, Voet & Pratt 2008 Fig 21.30

γ-glutamyl kinase

Glutamate dehydrogenase

Pyrroline carboxylate reductase

Path in mammals

3-Phosphoglycerate Serine Conversion

Voet, Voet & Pratt 2008 Figure 21.31

3-phosphoglycerate dehydrogenase

Phosphoserine aminotransferase

Phosphoserine phosphotase

Biosynthesis of Essential Amino Acids

Biosyntheses of Aspartate “Family”:

Lysine, Methionine, & Threonine

Voet, Voet & Pratt 2008 Fig 21.32

Biosyntheses of the

Pyruvate “Family”: Isoleucine, leucine &

Valine

Voet, Voet & Pratt 2008 Figure 21.33

Biosyntheses of

Phenylalanine, Tryptophan, & Tyrosine

Voet, Voet & Pratt 2008 Fig 21.34

Biosynthesis of Histidine

Voet, Voet & Pratt 2008 Fig 21.36

Heme Biosynthesis

Voet, Voet & Pratt 2008 Fig 21.38

Summary: Glucogenic

& Ketogenic Amino Acids

Lehninger 2000 Figure 18.29

Amino Acid Biosynthesis: Overview I

Lehninger 2000 Figure 22.9a

Amino Acid Biosynthesis: Overview II

Lehninger 2000 Figure 22.9b

Amino Acid Biosynthesis: Overview III

Lehninger 2000 Figure 22.9c

End of Supplementary Material