L16 - Introduction to Nitrogen Metabolism

Sources of Amino Acids

3 Types:

1. Intracellular proteolysis: Clears misfolded/old, and damaged proteins; Supplies essential AAs when dietary intake is insufficient; Controls cell-cycle transitions and cell disjunction

2. Digestion: Supplies both nutritionally essential and nutritionally nonessential AAs

3. de novo synthesis (Anabolic processes): Provides nutritionally nonessential AAs needed for protein synthesis; Adjusts AA pools in different tissues; Adjusts energy metabolism by controlling concentrations of central pathway metabolites, allowing cells to adapt to metabolic stress; Needed to make nucs, hemes, hormones, and neurotransmitters.

Essential AAs (Acronym); Conditional Essential AAs?

VH MILK WTF; Cannot be synthesized by mammals and must be acquired via dietary intake

R is a conditional essential AA; can be synthesized but is required in higher amounts during unimpaired growth (Childhood/pregnancy)

Y is another conditionally essential AA because it is synthesized from F

C is another conditionally essential AA because it is synthesized from M

Protein turnover; Mention the three associated mechanisms

Several processes that help maintain protein homeostasis or proteostasis

Ensures functional proteins are maintained at the correct concentration and location

Also clears cells of misfolded/aged/damaged proteins

Three proteolytic machineries:

1. Lysosome: Vessicles that engulf other vesicles filled with proteins that needs to be degraded and recycled (autophagy)

2. Ubiquitin proteasome system: Tags protein for degradation, smaller stuff (Proteins) go to the proteosome while larger stuff (Organelles) go to the lysosome

3. Autophagic pathway: Bulk delivery system to the lysosome, works for proteins up to organelles

Ubiquitination Pathway/Important Info

Post-translational modification, cellular tag of ubiquitin, three enzymes, E1, E2, and E3; Marks for proteasome but can also be used for signaling, DNA repair, or trafficking.

Attaches ubiquitin proteins to lysine residues

Proteosomes are barrel-shaped to ensure only the inner contents are digested

Enzyme roles:

1. E1: Ubiquitination-initiating enzyme: Activates the reaction by binding ubiquitin via ATP

2. E2: Ubiquitin-conjugating enzyme: Takes the activated ubiquitin and delivers it to E3

3. E3: Ubiquitin-protein ligase: Recognizes specific targets, and puts the activated ubiquitin tag on lysine residue

Monoubiquitination: Typically for protein function or localization

Polyubiquitination: For degradation

Digestion Overall Pathway/Process

Digestion: Breaking down food mechanically/enzymatically

Biopolymers must be hydrolyzed into monomeric units; Catalyzed by soluble enzymes

Protein digestion occurs in lumen of stomach and small intestine

Digestive enzymes are secreted by salivary glands, stomach and pancreas

Pancreatic enzymes and bile acids are poured into lumen of 2nd part of duodenum and the bulk of intraluminal digestion occurs distally

Digestion enzymes basics

When food enters, stomach mucosa releases gastrin, which tells stomach to release HCL and pepsinogen (zymogen) which in acidic env turns into pepsin (enzyme). When Acidic dietary contents enter duodenum, secretin is released, causing bicarb to release and neutralized acidity. At the same time Cholecystokinin makes pancreas produce zymogens for digestion.

Enzymes from pancreas

Trypsin: Cleaves carboxy of K & R

Chymotrypsin: Cleaves carboxyl of aromatic

Carboxypeptidase: Cleaves one AA at a time from C-term of a protein.

Pepsin Activation

Catalyzed by low pH, pepsinogen goes through autocatalytic activation and releases its masking sequence, turning into pepsin

Trypsin and Chymotrypsin Activation

Made and stored in pancreas; secreted into small intestines

Trypsinogen contains a trypsin inhibitor, which is removed by enteropeptidase

Chymotrypsinogen is cleaved by trypsin to active π-Chymotrypsin

π-Chymotrypsin cleaves itself into a better version of itself called α-Chymotrypsin

What absorbs the final products of digestion

Final products are absorbed by epithelial cells lining the small intestines called the Villus (Villi), which contains intestinal mucosa that absorbed the AA.

What transporter types are associated with AA absorbtion

Many types of symporters, antiporters, and uniporters take in AA

This is typically facilitated via a gradient that is produced, for example, by NA⁺/K⁺ and ATPase

Active transport takes in AA from the intestines

Gradient-based diffusion (Facilitative transporters) takes AA from epithelial cells and transfers it to bloodstream

Amino Acid Oxidation basics

AAs undergo oxidation degradation when:

1. AAs released during protein turnover are not needed for anabolism

2. Ingested AA exceeds body’s need for protein synthesis

3. Cellular proteins are used as fuel because carbs are unavailable/not properly utilized

AAs like A and N rise when intracellular proteolysis increases to meet metabolic demands, independent of dietary digestion.

Unless reused, amino groups are channeled into a single excretory end product (NH₄⁺)