Lecture 4: Introduction to Nitrogen Metabolism

Overall idea

When proteins are degraded, they release nitrogen in the form of ammonia which can be toxic and must go to the urea cycle for discarding from the body

List the three sources of amino acids

Intracellular proteolysis, digestion of dietary proteins, de novo synthesis

Intracellular proteolysis

Removes misfolded, old, and damaged proteins. Supplies essential amino acids when dietary intake is insufficient. Controls cell cycle transitions and cell disjunction

Digestion of dietary proteins

Supplies both nutritionally essential and non-essential amino acids

De novo synthesis

Provides nutritionally nonessential amino acids that are needed for protein synthesis. Adjust protein pools in different tissues. Adjusts energy metabolism by controlling concentrations of central pathway metabolites which allows cells to adapt to metabolic stress

Essential amino acids

Amino acids that we cannot produce and we must obtain from our diet includes tryptophan, valine, phenylalanine, methionine, threonine, leucine, histidine, isoleucine, lysine (Valerie trwpped, face mutilated, to hospital, I know! Loser!)

Conditionally essential amino acids

We can produce them but not in large enough quantities so we must obtain some from our diet includes arginine, tyrosine, cysteine, glutamine, glycine, proline (R Y Coming? Quick? Green Pepper)

Selenocysteine

Considered the 21st amino acid

is unique in that it requires the essential dietary micronutrient selenium

when a UGA stop codon appears:

-if no selenium is present = stop

-if selenium is present equals selenocysteine.

Plays an important role in redox reactions, homeostasis and antioxidant defense

Intracellular protein turnover

Regulated by tightly controlled processes that help facilitate protein homeostasis (Proteostasis)

Ensures that the functional proteins are maintained at their correct concentrations and in the proper locations, also helps to remove misfolded, old, or damaged proteins. Occurs via three proteolytic machineries (proteasome, autophagy, lysosomal)

Ubiquitin proteasome proteolysis

Selective degradation of misfolded, old, damaged regulatory proteins, highly selective requires (ubiquitin tagging), located in the cytosol and nucleus, ATP dependent, generates free amino acids for deamination

Autophagy

bulk degradation of cytoplasmic components, can be selective or not, sometimes uses tagging, located in lysosome, requires energy for vesicle formation and trafficking, generates amino acids during starvation to fuel metabolism

Lysosomal

degradation of endocytose proteins, membrane proteins, and long lived intracellular proteins, less selective, no tagging, passive once in lysosome, located in lysosome, contributes to amino acid pool especially from extracellular sources

Ubiquitination

form of post-translational modification where ubiquitin polypeptide is attached to a protein

three enzymes: ubiquitination initiating enzyme (E1), ubiquitination conjugating enzyme (E2), and ubiquitin protein enzyme (E3)

uses ATP

Ubiquitin tagged protein can then enter the proteasome for degradation (acidic barrel like structure that breaks down the protein but doesn’t damage the rest of the cell)

Protein digestion

Dietary proteins are immunogenic and may hurt our bodies

Proteins are degraded via sequential proteolysis

enzymes are released as zymogens that need to be activate, this helps to prevent the self-digestion of tissues

Zymogens

Prevent self digestion, must be activated

stomach zymogens (initiation)

At low pH: pepsinogen → pepsin

activation is autocatalytic (active pepsins activated other pepsins like a cascade)

perform the initial protein cleavage

small intestine zymogens

trypsinogen → trypsin (activated in the intestinal lumen)

activated trypsin activates other proteases

break down proteins into single amino acids and di/tripeptides

absorption

Amino acids and di/tripeptides are absorbed, occurs mostly in the small intestine across intestinal epithelial cells (Enterocytes)

transport into Enterocytes :

amino acids → transporters

di/tripeptides → peptide transporters

once inside the cell, peptides get fully broken down into amino acids where they can enter the portal system and be transported to the liver

Amino acid transporter

Into cell: Na+/AA symporter (secondary active transport)

Into blood: facilitated diffusion

(Na+/K+ pump is required to create Na+ gradient for transport)

Amino acid oxidation

Amino acids undergo oxidative degradation when:

-amino acid released during protein turnover are not needed for new protein synthesis

-ingested amino acids exceed the body’s need for protein synthesis

-cellular proteins are used as fuel because carbohydrates are either unavailable or not properly utilized

unless reused, amino groups are channeled into a singular excretory end product (urea)