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📘 Biochemistry & Metabolism – Protein Metabolism (AV-7)

Seminar prep guide based on your lecture slides

Slide 1–3 | Introduction: Amino Acids & Peptide Bonds

The presentation covers protein metabolism — how the body handles dietary proteins from ingestion to final nitrogen disposal. It opens with the structural basics: amino acids are the building blocks of proteins, linked together by peptide bonds (the covalent bond between the carboxyl group of one amino acid and the amino group of the next).

Slide 4 | Nitrogen Balance

This is a key concept — it measures the body's protein status by comparing nitrogen intake vs. output (since ~16% of protein mass is nitrogen):

State	Condition	Who
Nitrogen balance (Vin = Vout)	Synthesis = breakdown	Healthy adults
Positive balance (Vin > Vout)	Synthesis > breakdown	Growing children, pregnant women, athletes recovering, patients healing
Negative balance (Vin < Vout)	Breakdown > synthesis	Starving individuals, critically ill patients

Slide 5–6 | What Makes a "Complete Protein"?

A complete (full-value) protein must satisfy four criteria:

Quantity: 100–120 g/day for adults; 2–3 g/kg for infants; ~1.5–2 g/kg for older children
Essential amino acid ratio: at least 32% essential amino acids
Amino acid profile similarity to average human body protein
Digestibility in the GI tract

Chicken egg protein is the gold standard — closest to ideal human protein composition.

Limiting amino acid: The amino acid present in the smallest amount relative to need. Its absence blocks utilization of ALL other amino acids, even if those are abundant. The relative requirements (ratio):

Tryptophan – 1
Threonine – 2
Lysine, Valine, Isoleucine – 3
Phenylalanine, Leucine, Methionine – 4.5

Slides 7–14 | Protein Digestion in the Stomach

HCl Production (Slide 8)

Parietal cells secrete hydrochloric acid via the H⁺/K⁺-ATPase proton pump.

Functions of HCl (Slide 9) — expect questions on this:

Antibacterial — kills ingested pathogens
Protein denaturation — unfolds proteins, exposing peptide bonds to enzymes
Releases iron from protein complexes (critical for Fe²⁺ absorption)
Releases vitamins bound to proteins (B1/TPP, FAD, FMN, B6/PLP, B12, biotin)
Activates pepsinogen → pepsin (partial proteolysis)
Sets pH 1.5–2.5 — optimal for pepsin activity
Stimulates duodenal hormones (secretin, CCK) → triggers pancreatic juice and bile release

Proteolytic Enzymes (Slides 10–13)

Enzymes are secreted as inactive zymogens (inactive precursors) and activated by partial proteolysis (cleavage of an inhibitory peptide fragment):

Zymogen	Activator	Active Enzyme	Site
Pepsinogen	HCl, pepsin (autocatalytic)	Pepsin (pH 1.5–2)	Stomach
—	—	Gastrixin (pH 3.2–3.5)	Stomach (milk/plants)
Trypsinogen	Enterokinase/enteropeptidase	Trypsin	Duodenum
Chymotrypsinogen	Trypsin	Chymotrypsin	Duodenum
Procarboxypeptidase	Trypsin	Carboxypeptidase	Duodenum

Endopeptidases cleave internal peptide bonds; exopeptidases cleave terminal amino acids.

Stomach Cell Types (Slide 14):

Mucous cells → mucus (protects gastric lining)
Chief cells → pepsinogen
Parietal cells → HCl + Intrinsic factor (required for vitamin B12 absorption)

Slides 15–16 | Protein Digestion in the Small Intestine

Pancreatic juice is alkaline (rich in HCO₃⁻), neutralizing acid chyme:

HCl + HCO₃⁻ → Cl⁻ + H₂CO₃ → H₂O + CO₂↑

This raises pH to 7.0–8.0, the optimal range for pancreatic proteases (trypsin, chymotrypsin, carboxypeptidase, elastase). Trypsin is the master activator — once enterokinase generates a small amount of trypsin, it auto-activates more trypsinogen and activates all other zymogens.

Slide 17 | Absorption of Amino Acids & Oligopeptides

Transport mechanisms across the intestinal epithelium:

Secondary active transport with Na⁺ cotransporters (5 distinct systems for different amino acid groups)
Glutathione transport system — carries amino acids intracellularly
Pept1 transporter — carries di- and tripeptides intact into enterocytes

Slides 18–20 | Metabolic Fates of Amino Acids

Once absorbed, amino acids can be:

Used for protein synthesis
Deaminated — the amino group (-NH₂) is removed, leaving a carbon skeleton for energy or gluconeogenesis

Types of deamination:

Type	Product
Intramolecular	Unsaturated fatty acid
Reductive	Saturated fatty acid
Hydrolytic	Hydroxy carboxylic acid
Oxidative (main in humans)	α-Keto acid + NH₄⁺

The released NH₄⁺ (ammonium) is toxic — it must be eliminated.

Slides 21–26 | Ammonia Disposal: The Urea Cycle

Different species excrete nitrogen differently:

Ammoniotelic (fish, aquatic): excrete NH₄⁺ directly
Uricotelic (birds, reptiles): excrete uric acid
Ureotelic (mammals, including humans): excrete urea — less toxic, water-soluble

The Ornithine Cycle (Krebs-Henseleit Cycle) — Slides 23–25

This cycle occurs in liver hepatocytes (partly in mitochondria, partly in cytoplasm):

NH₃ + CO₂ → Carbamoyl phosphate (mitochondria; enzyme: CPS-I)
Carbamoyl phosphate + Ornithine → Citrulline
Citrulline + Aspartate → Argininosuccinate
Argininosuccinate → Arginine + Fumarate
Arginine → Ornithine + Urea (arginine regenerated, cycle continues)

Net: 2 NH₃ + CO₂ → Urea

Regulation (Slide 26):

Long-term: Gene-level regulation of enzyme biosynthesis; regulated by blood ammonia levels
Short-term: Allosteric activation of carbamoyl phosphate synthetase I (CPS-I) by N-acetylglutamate (the obligatory positive modulator)

Slides 27–30 | Bioactive Amines from Amino Acids (α-Decarboxylation)

Amino acids undergo α-decarboxylation (removal of -COOH) to form biologically active amines:

Histamine (from Histidine) — Slide 27

Stimulates gastric acid secretion
Modulates sleep (histaminergic neurons)
Involved in allergic reactions and immune disorders
Anticonvulsant/protective neurological roles

GABA (from Glutamate) — Slide 28

Inhibitory neurotransmitter — suppresses synaptic transmission
Clinical use: basis of antiepileptic drugs

Serotonin (from Tryptophan) — Slide 29

Neurotransmitter controlling: appetite, sleep, memory, learning, mood, temperature, behavior, cardiovascular function, muscle contraction, endocrine regulation
Potent vasoconstrictor

Catecholamines (from Tyrosine) — Slide 30

Dopamine → Norepinephrine → Epinephrine (synthesis pathway)

Correlated with blood pressure regulation
Dopamine deficiency → Parkinson's disease

Key Concepts to Know Cold for the Seminar

Topic	Key Point
Limiting amino acid	Blocks utilization of all others if absent
HCl functions	7 functions — especially pepsinogen activation & B12 release
Zymogen activation	Enterokinase activates trypsinogen → trypsin activates everything else
Parietal cells	Make HCl and Intrinsic factor (B12 absorption)
Urea cycle	Liver; N-acetylglutamate activates CPS-I
Nitrogen balance	Positive = anabolic state; Negative = catabolic/starvation
Bioactive amines	Histamine (His), GABA (Glu), Serotonin (Trp), Catecholamines (Tyr)

Good luck with your seminar tomorrow!

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