Biochemistry Final - AA and Nucleotide Metabolism

Under what 3 circumstances do amino acids undergo oxidative degradation

1. Provide energy when carbohydrates are unavailable

2. Get rid of harmful proteins and prevent accumulation

3. Regulate metabolic processes

2 mechanisms of protein turnover

1. Lysosomal degradation

2. Proteosomal degradation via ubiquitination

Role of chaperone-mediated autophagy (CMA) during times of starvation

Provides amino acids to continue protein synthesis and gluconeogenesis

How are proteins selected for CMA?

Chaperone proteins look for KFERQ amino acid sequences

Chaperones transport these proteins to the lysosome for degradation

Role of Lamp2A in CMA

Binding site and protein complexes on the surface of lysosomes that KFERQ proteins bind to and move through to get into the lysosome

What is the main role of proteosomal degradation

Degrades misfolded/damaged proteins and regulatory proteins with short lifespans

Role of ubiquitin in proteosomal degradation

Serves as a “tag” on proteins that need to be degraded

Role of ATP hydrolysis in proteosomal degradation

Hydrolysis by ATPases unfold the protein so it can enter the proteosome

Role of the 19S component of the proteosome

Binds the ubiquitin-tagged protein and activates ATPases for unfolding

Role of the 20S component of the proteosome

Barrel-shaped protein containing proteases that cleaves the protein to degrade it

2 general products of amino acid breakdown

1. Nitrogen is removed and incorporated into urea → excreted

2. Oxidation of carbon skeleton creates glucose, acetyl CoA, or ketones

What happens in transdeamination

1. Aminotransferase transfers amino acids to L-glutamate

2. L-glutamate dehydrogenase removes the amino group from L-glutamate

Goal of the urea cycle

Converts toxic ammonia into urea for excretion

Where does the urea cycle occur

Liver

How does NH3 enter the urea cycle

As carbamoyl phosphate and aspartate

Role of carbamoyl phosphate synthase 1

Combines bicarb (HCO3-) and NH3 to make carbamoyl phosphate

Energy cost to synthesize carbamoyl phosphate

2 ATP

Role of aspartate aminotransferase

Transfers an amino group from glutamate to aspartate

Where in the cell does the urea cycle occur

1st step is in the mitochondria

Cytosol everywhere else

What happens to nitrogen in cells other than liver cells?

Detoxifies it by attaching it to glutamine, then transports it to the liver

Role of glutaminase

Removes the nitrogen from glutamine → converts it to glutamate and goes towards the urea cycle

Role of the glucose-alanine cycle in muscle cells

Transports nitrogen from muscles to the liver for the urea cycle

Muscle cells do not utilize glutamine

What happens in the glucose-alanine cycle

1. Amino groups are attached to alanine and transported to the liver for urea cycle

2. leftover carbon skeleton is used for gluconeogenesis

Long-term regulation of urea cycle

Occurs during periods of starvation or consumption of high-protein diet

Increased transcription of urea cycle enzymes

Short term regulation of urea cycle

N-acetylglutamate allosterically activates carbamoyl phosphate synthase 1 to:

1. Increase amino acid breakdown

2. Increased intracellular concentrations of glutamate (due to increased transamination)

3. Increased intracellular concentrations of N-acetylglutamate

General sources of carbon skeleton for AA synthesis

Intermediates of glycolysis, CAC and PPP

Sources of amino groups for AA synthesis

Glutamine and glutamate

2 general pathways for nucleotide synthesis

1. de novo synthesis: creating from scratch using amino acids, CO2, and formate

2. salvage pathways: creating from recycling other nucleic acids

What components contribute to purine nitrogen rings

1. Aspartate

2. Formate

3. Glutamine

4. Glycine

5. CO2

Role of PRPP in purine biosynthesis

Precursor molecule that provides the pentose sugar backbone

1st committed step of the pathway

When is PRPP added in purine synthesis

It is made from Ribose 5-phosphate and is made to create IMP

Role of glutamine-PRPP amidotransferase

Converts PRPP to IMP

Role of IMP

Precursor to AMP and GMP

Energy molecule needed to produce AMP

GTP

Energy molecule needed to produce GMP

ATP

Regulation of PRPP

Inhibited by ADP (low energy state)

Regulation of 1st committed step of purine synthesis

Inhibited by AMP, GMP, IMP (products)

Regulation of AMP production

Inhibited by high AMP

Activated by high PRPP

Regulation of GMP production

Inhibited by high GMP

Activated by high PRPP

Components of pyrimidine rings

1. Glutamine

2. Aspartate

3. Bicarbonate

Role of carbamoyl phosphate synthetase II in pyrimidine synthesis

First step of synthesis by creating carbamoyl phosphate from bicarb and ammonia

Role of PRPP in pyrimidine synthesis

Provides pentose sugar backbone for UMP

When is PRPP added in pyrimidine synthesis

After the creation of carbamoyl phosphate

Direct nucleotide product of pyrimidine synthesis

UTP

How is UTP related to CTP

UTP is needed to make CTP - precursor molecule

Regulation of pyrimidine synthesis

UDP and UTP inhibits carbamoyl phosphate synthetase II

Role of ribonucleotide reductase

Reduces ribonucleotides to deoxyribonucleotides

Why is regulation of ribonucleotide reductase important

It is the only enzyme that can make deoxynucleotides for DNA synthesis

Controls the rate of DNA synthesis

What reaction does thymidylate synthase catalyze?

Conversion of dUMP to dTMP (thymine)

Role of N5,N10 methylene tetrahydrofolate in thymidylate (thymine) synthesis

Provides carbon needed to convert dUMP to dTMP

How does fluorouracil function as a chemotherapy agent?

Binds to and inhibits thymidylate synthase (suicide inhibitor) preventing dTMP production

Excreted end produce of purine catabolism

Uric acid

Process of purine catabolism

1. Nucleotides broken down to nucleosides

2. Nucleosides are eventually broken down to Xanthine

3. Xanthine is broken down into uric acid

Role of uric acid in gout

Uric acid accumulates in joints due to overproduction or impaired excretion

Crystallizes causing pain

How does allopurinol work as a treatment for gout

Inhibits xanthine oxidase preventing the breakdown of hypoxanthine and xanthine to uric acid

More soluble → less likely to form uric acid crystals

What products does the Purine salvage pathway release

1. Adenine

2. Guanine

3. Hypoxathine

Role of APRT in purine salvage pathway

breaks down AMP into adenine and PRPP

Role of HGPRT in purine salvage pathway

breaks down IMP into hypoxanthine and PRPP

breaks down GMP into guanine and PRPP

3 products of pyrimidine catabolism

1. Ammonia/urea

2. Malonyl CoA (for FA synthesis)

3. Succinyl CoA (for CAC)