1404- Biochem- nitrogen metabolism- protein turnover

Essential amino acids importance

Cannot be synthesized by the body and must be obtained from the diet. They are crucial for protein synthesis, tissue repair, and metabolic functions.

Ubiquitin-proteasome system (UPS)

The UPS is the main pathway for targeted protein degradation in eukaryotic cells. It involves tagging proteins with ubiquitin and degrading them in the proteasome to regulate protein turnover and remove damaged proteins.

Role of ubiquitin in protein degradation

Ubiquitin serves as a molecular tag that marks proteins for degradation. At least four ubiquitin molecules must attach to a lysine residue on a target protein to signal its destruction in the proteasome.

Autophagy vs. UPS

Autophagy degrades bulk cytoplasmic material and organelles through lysosomes, while the UPS selectively degrades short-lived proteins via proteasomes. Autophagy is more involved in cellular stress responses.

Chaperone-mediated autophagy (CMA) and key proteins

CMA selectively degrades proteins with a KFERQ-like motif. Key proteins: HSC70 (binds target proteins) and LAMP2A (lysosomal receptor for protein translocation).

Nitrogen balance and its significance

Nitrogen balance reflects the difference between nitrogen intake and nitrogen excretion. Positive balance (intake > output) occurs in growth and pregnancy, while negative balance (output > intake) indicates muscle wasting or malnutrition.

Estimating nitrogen balance

Estimated by dividing daily protein intake (g) by 6.25. Primary nitrogen output component: Urinary urea nitrogen (UUN), measured in 24-hour urine samples.

Three factors affecting nitrogen balance

1. Dietary intake (protein/energy availability), 2. Physiological states (growth, pregnancy, illness), 3. Disease/trauma (catabolic states increase nitrogen loss).

Marasmus vs. Kwashiorkor

Marasmus: Total calorie deficiency → muscle and fat wasting. Kwashiorkor: Protein deficiency with sufficient calories → edema and fatty liver.

Disease linked to UPS dysfunction

Angelman syndrome: Caused by mutations in the E6-AP ubiquitin ligase (UBE3A), leading to neurodevelopmental impairments.

Endogenous proteins

Proteins made within the body

Importance of dietary protein

Needed to synthesize some endogenous proteins

Body cannot synthesize certain amino acids called essential amino acids

Essential amino acids

Valine

tryptopan

threorine

leucine

lysine

Histadine

isoleucine

methione

phenylalanine

protein turn over

The balance between protein synthesis and degradation by the continual renewal or replacement of proteins.

Importance of protein turnover

To maintain optimal functioning of proteins

Factors influencing protein turn- over

Type of tissue

relative contribution of varying tissues

age

adaptation of various levels of protein in take

Steady state protein turn over

Protein synthesis and degradation rates are balanced

Constant protein levels within cells

Transcriptome and metablome are not affected

Transcriptome

Total amount of mRNA molecules expressed from a gene of an organism.

Metablome

Total number of metabolites within a system

Amino acid pool expansion

1. Increased synthesis of proteome, unchanged degradation of proteome to amino acid→ transcriptome regulated

2. Unchanged synthesis of proteome, decreased degradation of proteome to amino acid→ metablome regulated

Amino acid pool contraction

1. Unchanged synthesis + decreased degradation of proteome→ Metablome regulation

2. Decreased synthesis + unchanged degradation → Transcriptome regulation

Protein degradation pathways

Ubiquitin- proteasome system

Macro autophagy/ Mitophagy

Chaperone mediated autophagy

Ubiquitin- proteasome system (UPS)- second definition

A major selective pathway for the degradation of misfolded, damaged or unneeded proteins to maintain homeostasis within eukaryotic cells

Step 1 of Ubiquitin - proteasome system

E1- Ubiquiting activating enzyme activate Ubiquiting in an ATP dependent manner.

Proteostasis network

The collective processes that maintain the stability and functionality of the proteome, ensuring that proteins are correctly folded, assembled, and degraded as necessary.

Step 1 of proteostasis network: Protein Synthesis

Proteins are synthesized from amino acids based on the instructions coded in the DNA.

Step 2 of proteostasis network: Protein Folding

Newly synthesized proteins must fold into their specific three-dimensional structures, facilitated by molecular chaperones.

Step 3 of proteostasis network: Quality Control

Misfolded or unfolded proteins are identified and either refolded or targeted for degradation.

Step 4 of proteostasis network: Protein Assembly

Proteins may need to assemble into larger complexes, requiring precise interactions with other proteins.

Step 5 of proteostasis network: Protein Turnover

Proteins have a lifespan and are continuously degraded and replaced; this balance is crucial for cellular health.

Step 6 of proteostasis network: Response to Stress

Cells activate protective mechanisms in response to stress conditions to maintain proteostasis.

Step 2 of Ubiquitin - proteasome system

E2- Ubiquiting conjugating enzyme transfers activated Ubiquiting with the help of E3

Step 3 of Ubiquitin - proteasome system

E3 facilitates the transfer of Ubiquitin from E2 to the lysine residue on the target cell

Step 4 of Ubiquitin - proteasome system

The first Ubiquitin attaches to the amino acid of the side chain of a lysine residue on the isopeptide bond

Step 5 of Ubiquitin - proteasome system

Additional ubiquitins are added to form a multi-ubiquitin chain which acts as a marker for proteasome to recognize.

Steps 6 of Ubiquitin - proteasome system

Proteosome recognized marker, targets protein, degrades it into peptides and also degrades the ubiquitins to be reused