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Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire Lecture 10 - Protein Turnover and Amino Acid Catabolism
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Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

Jun 01, 2020

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Page 1: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

Chem 454: Regulatory Mechanisms in BiochemistryUniversity of Wisconsin-Eau Claire

Lecture 10 - Protein Turnover and Amino Acid Catabolism

Page 2: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextProteins are degraded into amino acids.Protein turnover is tightly regulated.First step in protein degradation is the removal of the nitrogenAmmonium ion is converted to urea in most mammals.Carbon atoms are converted to other major metabolic intermediates.Inborn errors in metabolism

Introduction

Page 3: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextAmino acids used for synthesizing proteins are obtained by degrading other proteins

Proteins destined for degradation are labeled with ubiquitin.

Polyubiquinated proteins are degraded by proteosomes.

Amino acids are also a source of nitrogen for other biomolecules.

Introduction

Page 4: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextExcess amino acids cannot be stored.Surplus amino acids are used for fuel.

Carbon skeleton is converted toAcetyl–CoAAcetoacetyl–CoAPyruvateCitric acid cycle intermediate

The amino group nitrogen is converted to urea and excreted.

Glucose, fatty acids and ketone bodies can be formed from amino acids.

Introduction

Page 5: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextDietary proteins are a vital source of amino acids.

Discarded cellular proteins are another source of amino acids.

1. Protein Degradation

Page 6: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextDietary proteins are hydrolyzed to amino acids and absorbed into the bloodstream.

1.1 Dietary Protein Degradation

Page 7: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextCellular proteins are degraded at different rates.

Ornithine decarboxylase has a half-life of 11 minutes.

Hemoglobin lasts as long as a red blood cell.

Υ-Crystallin (eye lens protein) lasts as long as the organism does.

1.2 Cellular Protein Degradation

Page 8: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextThe protein ubiquitin is used to mark cellular proteins for destruction.

2. Regulation of Protein Turnover

Page 9: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextUbiquitin is activated and attached to proteins using a group of three enzymes

E1 - Ubiquitin activating enzymeE2 - Ubiquitin-conjugating enyzmeE3 - Ubiquitin-protein ligase

2.1 Ubiquitin

Page 10: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextThe N-terminal amino acid residue in proteins influences when a protein will be unbiquinated.

2.1 Ubiquitin

Page 11: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextPolyubiquination increases the rate of destruction for a protein

Ubiquitin is activated and attached to the lysine residues on other ubquitin molecules to form the polyubiquitin.

2.1 Ubiquitin

Page 12: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextProteosomes are large multisubunit complex (26S)

The 20S proteosome complex is the catalytic portion.

Four rings of seven subunits each (28 subunits)

The 19S proteosome complex is the regulatory complex

2.2 Proteosomes

Page 13: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextProtein degradation can be used to regulate biological function

2.3 Regulation of Biological Functions

Page 14: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextThe first step in amino acid degradation is the removal of the nitrogen.

The liver is the major site of protein degradation in mammals.

Deamination produces α-keto acids, which are degraded to other metabolic intermediates.

3. Removal of Nitrogen

Page 15: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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Textα–Amino groups are converted to ammonium ions by the oxidative deamination of glutamate

3.1 Conversion to Ammonium Ions

Page 16: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextGenerally these enzyme funnel amino groups to α–ketoglutarate.

Aspartate transaminase

Alanine transaminase

3.1 Transamination

Page 17: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextGlutamate dehydrogenase

3.1 Deamination

Page 18: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextIn most terrestrial vertebrates the ammonium ion is converted to urea.

3.1 Deamination

Page 19: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextPyridoxal phosphate forms a Schiff-base intermediates in aminotransferase reactions.

3.2 Pyridoxal Phosphate

Page 20: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextPyridoxyl phosphate can under go acid/base tautomerization.

3.2 Pyridoxyl Phosphate

Page 21: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextThe aldehyde forms a Schiff–base with an ε–amino group on the enzyme.

This Schiff-bases can be exchanged for one with the α–amino group of an amino acid

3.2 Pyridoxyl Phosphate

Page 22: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextTransamination mechanism:

The second half of the reaction reverses these steps with a different α–keto acid.

3.2 Pyridoxyl Phosphate

Page 23: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextPyridoxyl phosphate is is a very versatile cofactor

used to make bonds to Cα susceptible to cleavage.

3.2 Pyridoxyl Phosphate

Page 24: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextThe β–hydroxy amino acids, serine and threonine, can be directly deaminated

3.4 Serine and Threonine

Serine Pyruvate + NH4+

Threonine a-Ketobutarte + NH4+

Page 25: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextUrea is produced in theThe alanine cycle is used to transport nitrogen to the liver

3.5 Transporting Nitrogen to Liver

Page 26: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextAmmonium ion is converted into urea in most terrestrial vertebrates

4. Ammonium Ion

NH4+

H2NCO

NH2

Urea

Page 27: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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Text

4. The Urea Cycle

Page 28: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextCarbamoyl synthetase

Free NH4 reacts with HCO3 to form carbamoyl phosophate.Reaction is driven by the hydrolysis of two molecules of ATP

4.1 Formation of Carbamoyl Phosphate

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TextOrnithine transcarbamoylase

Citrulline is formed from transfer of the carbamoyl group to the γ-amino group of ornithine.

4.1 Formation of Citrulline

Page 30: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextCondensation of citrulline with aspartate to form arginosuccinate

Two equivalent of ATP are required.

4.1 Formation of Arginosuccinate

Page 31: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextArginosuccinase

Cleaves arginosuccinate to form arginine and fumarate

4.1 Formation of Arginine and Fumarate

Page 32: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextArginase

The arginine is hydrolyzed to produce the urea and to reform the ornithine.The ornithine reenters the mitochondrial matrix.

4.1 Formation of Urea

Page 33: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextThe urea cycle is linked to the citric acid cycle:

4.2 Linked to Citric Acid Cycle

Page 34: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextSection 23.4.3

4.3 Evolution of Urea Cycle (skip)

Page 35: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextSection 23.4.4

4.4 Inherited Defects in Nitrogen Metabolism (skip)

Page 36: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextThe carbon atoms of degraded amino acids emerge as major metabolic intermediates.

Degradation of the 20 amino acids funnel into 7 metabolic intermediates

Acetyl–CoAAcetoacetyl–CoAPyruvate

α-KetoglutarateSuccinyl–CoAFumarateOxaoloacetate

5. Carbon Atoms

Ketogenic

Glucogenic

Page 37: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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Text

5. Carbon Atoms

Ketogenicleucinelysine

Glucogenicserine

threonineaspartic acidglutamic acid

asparagineglutamine

glycinealaninevalineproline

histidinearginine

methioninecysteine

Bothisoleucine

phenylalaninetryptophan

tyrosine

Page 38: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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Text

5. Carbon Atoms

Page 39: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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Text

5.1 Pyruvate Entry Point

Page 40: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextAspartate

Transamination to oxaloacetateAsparagine

Hydrolysis to Aspartate + NH4+

Transmination to oxaloacetate

5.2 Oxaloacetate Entry Point

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TextFive carbon amino acids

5.3 α–Ketoglutarate Entry Point

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TextHistidine

5.3 α–Ketoglutarate Entry Point

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TextProline and Arginine

5.3 α–Ketoglutarate Entry Point

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TextMethionine, Valine & Isoleucine

5.4 Succinyl–CoA Entry Point

Page 45: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextMethionine

Forms S-Adenosylmethionine

5.4 Succinyl–CoA Entry Point

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Text

5.6 Branched-chained Amino Acids

Page 47: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextPhenylalanine

5.7 Aromatic Amino Acids

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TextTetrahydrobiopterin - electron carrier

5.7 Aromatic Amino Acids

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TextPhenylalanine & Tyrosine

5.7 Aromatic Amino Acids

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TextTryptophan

5.7 Aromatic Amino Acids

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TextAlcaptonuria

Absence of homogentisate oxidase activity

6. Inborn Errors in Metabolism

Page 52: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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TextMaple syrup urine disease

Lack of branch-chain dehydrogenase activityLeads to elevation of α–keto banched-chain acids (branched-chain keto aciduria)

6. Inborn Errors in Metabolism

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TextPhenylketonuria

Absence of phenylalanine hydroxylase activity

6. Inborn Errors in Metabolism

Page 54: Lecture 10 - Protein Turnover and Amino Acid Catabolism · Excess amino acids cannot be stored. Surplus amino acids are used for fuel. Carbon skeleton is converted to Acetyl–CoA

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Text

6. Inborn Errors in Metabolism