Chapter 23: Protein Turnover and Amino Acid Catabolism

Amino acids are obtained from the diet when?

Proteins are digested

How are amino acids absorbed?

They are absorbed by the intestine and transported in the blood

What are essential amino acids?

Amino acids that cannot be synthesized and must be acquired in the diet

Why are cellular proteins degraded to amino acids?

Because of damage, misfolding, or changing metabolic demands

Can excess amino acids be stored or excreted whole?

No, they must be used as metabolic fuel

The digestion of dietary proteins begins in?

The stomach and is completed in the intestine

Protein digestion begins in the stomach where…?

The acidic environment denatures proteins into random cells

What is pepsin?

The primary proteolytic enzyme of the stomach

Pepsin is maximally active at what pH?

2

Partly digested proteins move from the stomach to the beginning of the small intestine (duodenum) which stimulates..?

The secretion of sodium bicarbonate and proteolytic enzymes from the pancrease

What enhances digestion in the plasma membrane of intestinal cells?

Aminopeptidases

The products of protein digestion are absorbed by?

The small intestine

What are transported into the intestinal cells?

Free amino acids, dipeptides, and tripeptides

How many different transporters exist, with each specific to a different group of amino acids?

7

Absorbed amino acids are released into the blood how?

By a. number of Na+ amino acid antiporters

Are cellular proteins degraded at different rates?

Yes

What is protein turnover?

The degradation and resynthesis of proteins

Does protein turnover take place constantly in cells?

Yes

What is protein turnover essential for?

Removing short-lived or damaged proteins

The half lives of proteins range over?

Several orders of magnitude

Ornithine decarboxylase catalyzes the synthesis of polyamines in about?

11 minutes

Hemoglobin is the life of

red blood cells (120 days)

What is ubiquitin?

A small (76aa) protein that tags proteins for destruction

Ubiquitin is present in..?

All eukaryotic cells

Is ubiquitin highly conserved?

Yes

Ubiquitin attaches by how?

By its carboxyl-terminal Gly residue to the ε- amino groups of 1+ Lys resides on the target protein

Ubiquitin requires?

ATP hydrolysis

How many enzymes participate in the attachment of Ubiquitin to a protein

3

What are ubiquitin activating enzyme (E1)?

Adenylates ubiquitin and transfers it to a sulfhydryl group of a Cys residues of E1

Ubiquitin activating enzyme requires?

ATP

What is ubiquitin protein ligase (E3)?

Transfers ubiquitin from E2 to an ε amino group on the target protein

What does ubiquitin protein ligase (E3) bring together?

Brings E2 and the target protein together

How can ubiquitin be transferred ?

Directly or be passed to a Cys residue of E3 first

Ubiquitin conjugation requires how many enzymes?

3 enzymes

What does E3 do after the first ubiquitin is added?

E3 may remain bound and continue adding ubiquitin molecules to form a chain

Can ubiquitin continue ifi E3 dissociates?

Yes. Another E2/E3 complex can bind and extend the ubiquitin chain.

Can multiple E2/E3 pairs build one ubiquitin chain?

Yes. Chains can be extended by different E2/E3 complexes.

Where can ubiquitin attach on another ubiquitin molecule?

Onto any of the 7 lysine (Lys) residues or the N-terminus.

How many lysines does ubiquitin contain for chain formation?

Seven lysine residues (plus N-terminus)

Which ubiquitin linkage type signals protein degradation?

Lys48-linked ubiquitin chain.

How many ubiquitins are needed to degrade a protein?

A chain of 4 or more ubiquitins.

What is the role of polyubiquitin chains?

They act as a signal for the proteasome to degrade the protein.

Does E3 always stay attached while building chains?

No. E3 may stay or be replaced by another E2/E3 complex.

What type of ubiquitin chain is most effective at targeting proteins to the proteasome?

A Lys48-linked chain of 4+ ubiquitins.

What are degrons?

A specific sequence of amino acids that indicates a protein should be degraded

For many proteins the amino terminal residue amino acid (N-degron) is an important..?

Degradation signal for E3 enzymes

N-degron may only exposed..?

After proteolytic cleavage

N-degron may be added..?

After protein synthesis

N-degron may require..?

Other modification

What happens to proteins that are not degraded?

Proteins that are not degraded because of a defective E3 may accumulate, causing a disease of protein aggregation

What is angelman syndrome?

A severe neurological disorder characterized by an unusually happy disposition, cognitive disability, absence of speech, uncoordinated movement, and hyperactivity

What is angelman syndrome caused by?

A defect in a member in the E3 family

Overexpression of an E3 causes?

Autism

Inappropriae protin turnover can lead to?

Cancer

Ubiquitination also regulates protein involved in?

• DNA repair

• Chormatin remodeling

• Innate immunity

• Membrane trafficking

• Autophagy

The proteasome digest the?

Ubiquitin tagged proteins

What is proteasome (26S proteasome)

A large, ATP driven protease complex that digests ubiquitinated proteins

The 26S proteosome is a complex of 2 components?

• 1 20S catalytic unit arranged as a barrel

• 2 19S regulatory units that control access to the interior of the 20S catalytic subunit

The 19S regulatory units contain?

Ubiquitin receptors that bind specifically to polylubiquitin chains

19S regulatory units use ATP to?

Unfold polyubiquitinated chains and direct them into the catalytic core

19S regulatory units contain an?

isopeptidase that cleaves off intact ubiquitin molecules so that they can be resused

Key components of the 19S complex are?

6 ATPases

How many active sites in the B subunits each with different specificity?

3 types

All proteolytic active sites of the 20s barrel empoy?

An N terminal Thr residue

What amino acid is found in the active site of all proteasome subunits?

N-terminal threonine (Thr).

Which functional group of threonine performs the catalytic attack?

The hydroxyl (–OH) group.

What does the threonine hydroxyl attack during proteolysis?

The carbonyl group of peptide bonds.

What intermediate is formed during proteasomal cleavage?

An acyl–enzyme intermediate.

How does the proteasome degrade substrates?

In a processive manner (without releasing intermediates).

What does “processive degradation” mean?

The protein is degraded continuously without releasing partial products.

When are peptide fragments released from the proteasome?

After being cut down to 7–9 amino acid residues.

What is the size of peptides produced by the proteasome?

Typically 7–9 residues long.

Does the proteasome release long fragments?

No, proteins are fully chopped into short peptides before release.

The first step in amino acid degredation is?

The removal of nitrogen

What happens to amino acids not needed for protein synthesis?

They are degraded to enter metabolic pathways.

What is removed first during amino acid degradation?

The amino group.

After removing the amino group, what happens to the carbon skeleton?

It is converted into a glycolytic intermediate or acetyl CoA.

What happens to the nitrogen group during amino acid breakdown?

It is removed and later excreted as urea.

Where does most amino acid degradation occur in mammals?

The live

Why is the liver the main site of amino acid breakdown?

It contains enzymes for deamination and urea synthesis.

Besides the liver, which tissue degrades amino acids?

Muscle tissue.

Which amino acids are degraded mainly by muscle?

Branched-chain amino acids (Leu, Ile, Val).

Why are branched-chain amino acids degraded in muscle?

Muscle has the necessary enzymes and uses them for energy.

Alpha-amino groups are converted into…by what?

Ammonium ions by the oxidative deamination of glutamate in the liver

What is the first step in removing amino groups from amino acids?

The α-amino group is transferred to α-ketoglutarate.

What molecule is formed when α-ketoglutarate accepts an amino group?

Glutamate.

What happens to glutamate in the liver?

It undergoes oxidative deamination.

What is produced when glutamate is oxidatively deaminated?

Ammonium ion (NH₄⁺).

In what organ does oxidative deamination mainly occur?

The liver.

What is the function of glutamate in amino acid metabolism?

It serves as the central collector of amino groups.

Why is oxidative deamination important?

It releases nitrogen for urea formation.

What is aminotransferases (transaminases)?

Catalyze the transfer of an a-amino group from an a-amino acid to an a-ketoacid

Aminotransferase reactions are… and can be used to synthesize..?

Reactions are reversible and can be used to synthesize amino acids from a-ketoacids

What is a coenzyme for aminotransferases?

Vitamin B6 derivative pyridoxal phosphate

What is aspartate aminotransferase?

Catalyzes the transfer of the amino group of aspartate to a-ketogluterate

What is alanine aminotransferase?

Catalyzes the transfer of the amino group of alanine to a-ketoglutarate

What is glutamate dehydrogenase?

A mitochondrial enzyme that converts the nitrogen atom in glutamate to a free amonnia ion by oxidative deamination

Glutamate dehydrogenase is essentially a ?

Liver specific enzyme

Glutamate dehydrogenase can use either?

NAD+ or NADP+

Glutamate dehydrogenase proceeds by?

Dehydrogenation of the C-N bond, followed by hydrolysis of the ketimine