BIO45 ‑ Exam 3 Comprehensive Study Notes

PROTEIN & AMINO ACIDS

  • Definition & Basic Chemistry

    • Protein = large, nitrogen-containing macromolecule composed of chains of amino acids (AAs).
    • Amino acid (AA) = carbon skeleton with:
    • Central (α) carbon (Cα)
    • Amine group ((-NH_2))
    • Carboxylic acid group ((-COOH))
    • Hydrogen (H)
    • Side chain ((R) group) → unique feature of each AA.
    • All AAs share the first four components; the R-group dictates polarity, charge, hydrophobicity & hence 3-D folding of proteins.
    • Peptide bond = covalent bond formed between (-COOH) of one AA and (-NH_2) of the next; formed via dehydration synthesis.

  • Essential vs. Non-essential AAs

    • Essential (indispensable) = cannot be synthesized (or not rapidly enough) by humans → must be supplied by food.
    • Non-essential (dispensable) = can be synthesized from other carbon skeletons & N.

  • Transamination & Deamination

    • Transamination: transfer of an amino group from an AA to a keto-acid → produces a new AA + new keto-acid. Requires vitamin B6B_6 as coenzyme (pyridoxal phosphate).
    • Deamination: removal of (-NH2) → yields keto-acid + ammonia (NH3). Ammonia is converted to urea in liver and excreted by kidneys.

  • Denaturation of Protein

    • Disruption of secondary/tertiary/quaternary structure (not primary).
    • Causes: heat (cooking, fever), acid (stomach HCl, lemon juice), alkali, alcohol, heavy metals (Hg, Pb).
    • Foods: cooked egg whites, yogurt, cheese, grilled meat.
    • Biological consequence: loss of biological activity but ↑ digestibility.

  • Levels of Structure & Role of Side Chains

    • Primary (sequence) → Secondary (α-helix, β-sheet) → Tertiary (folded) → Quaternary (multi-subunit).
    • Interactions among R-groups (H-bond, ionic, hydrophobic, disulfide bridge) determine folding → folding determines function (e.g., enzyme active site, antibody specificity). Mis-folding can produce disease (e.g., sickle-cell).

  • Major Functions in the Body (BIO45 focus)

    • Enzymes, transporters (hemoglobin, albumin), structural (collagen, keratin), hormones (insulin), antibodies, fluid balance (oncotic pressure), acid-base buffering, energy (4 kcal g⁻¹), gluconeogenesis substrate.

  • Protein Synthesis (overview)

    • Occurs on ribosomes.
    • DNA (nucleus) → transcription → mRNA → cytosol → ribosome.
    • mRNA codons read; tRNA delivers specific AAs; peptide bond formed; requires energy (ATP → GTP) & magnesium, adequate AA pool.

  • Protein Turnover & AA Pool

    • Constant breakdown/resynthesis (≈ 250–300 g250–300\,g protein/d).
    • AA pool = free AAs available in cells & blood (~ 100 g100\,g); sources: dietary intake + recycled from catabolism.
    • Significance: explains why daily dietary need is much smaller than body protein mass; enables adaptation to short fasting.

  • Fate of Cellular AAs (4 destinations)

    1. Protein synthesis (major, growth/repair)
    2. Synthesis of non-protein N-compounds (neurotransmitters, creatine, niacin, purines)
    3. Energy production (deamination → TCA)
    4. Conversion to fat or glucose (when energy/protein intake > need)

  • Handling of Removed Amino Group

    • NH₃ → urea cycle (liver) → urea transported in blood → kidney → urine. Urea formula: (NH<em>2)</em>2CO(NH<em>2)</em>2CO.

  • Dietary Requirements & Assessment

    • RDA: 0.8 g⋅kg−1 (healthy BW)0.8\,\text{g·kg}^{-1}\,(\text{healthy BW}) day⁻¹.
    • Calculation: 70 kg person → 0.8×70=56 g0.8 \times 70 = 56\,g protein.
    • Use healthy weight for obese individuals to avoid overestimation (lean tissue correlates with need).
    • AMDR: 10%–35%10\%–35\% of total kcal; too wide for evaluating adequacy (g depends on kcal, not lean mass).

  • Excess Dietary Protein

    • Surplus AAs deaminated → carbon skeletons → acetyl-CoA or pyruvate → stored as fat; NH₃ → urea.
    • Risks: kidney stress (urea load), potential Ca²⁺ loss, displacing fruits/veg/fiber, may raise CVD risk when animal-protein rich, environmental cost.

  • Protein Quality Concepts

    • Complete protein: supplies all essential AAs in adequate amounts (animal foods, soy, quinoa).
    • Incomplete: missing/low in ≥1 essential AA (most plants).
    • Limiting AA: the essential AA in shortest supply relative to need (e.g., lysine in grains, methionine in legumes).
    • Complementary proteins: combine two incomplete proteins whose limiting AAs differ so meal provides full profile (rice + beans, hummus + pita, peanut butter + whole-wheat bread). Need not be same bite; same day suffices.

  • Protein-Energy Malnutrition (PEM)

    • Marasmus: chronic deficiency of kcal & protein → severe wasting, stunted growth.
    • Kwashiorkor: adequate kcal, insufficient protein → edema, fatty liver, impaired immunity; often after weaning to starchy gruel.

  • Digestion & Absorption

    • Begins in stomach: HCl (pH ≈ 2) denatures proteins & activates pepsin (endopeptidase).
    • Small intestine: pancreatic proteases (trypsin, chymotrypsin, carboxypeptidase) + brush-border peptidases → dipeptides, tripeptides, free AAs.
    • End products absorbed via Na⁺-dependent carriers into enterocytes → portal vein → liver.
    • Proteins must be hydrolyzed to peptides/AAs; intact absorption only in early infancy (IgA).

  • Protein Supplements / Fortified Foods

    • Only required for: critical illness, severe malabsorption, very high-volume training athletes, some elderly with low intake.
    • Downsides: expense, heavy metal contamination, excess kcal/protein load, displacing whole foods.
    • Most people easily meet needs from mixed diet; protein-fortified snacks unnecessary.

  • Vegetarian Patterns

    • Vegetarian: excludes meat/fish; variants:
    • Lacto-ovo: includes dairy & eggs.
    • Vegan: excludes all animal products.

  • Nutrients of Concern for Vegetarians

    • Vitamin B12B_{12}, Vitamin D, Calcium, Iron, Zinc, Iodine, long-chain ω!–3\omega!–3 (EPA/DHA), sometimes protein (vegan children).

  • Potential Benefits

    • Lower LDL-C & blood pressure, lower BMI, reduced T2 diabetes, lower CVD & certain cancer risk, higher fiber/phytochemical intake, environmental sustainability.

  • Why Often Healthier

    • ↑ whole grains, legumes, fruits, veg → fiber & antioxidants; ↓ saturated fat; overall lower energy density.

  • Possible Pitfalls

    • Over-reliance on refined carbs, inadequate protein variety, deficiencies listed above, high sodium (meat analogs), caloric inadequacy in children.

ENERGY METABOLISM

  • Definitions

    • Metabolism: all chemical reactions in cells sustaining life.
    • Energy metabolism: reactions involved in acquiring & using energy from nutrients.
    • Anabolic = build (require ATP). Catabolic = break down (release ATP).
    • Coupled reactions: energy from catabolism drives anabolism (ATP is the link).
    • Energy in food exists as chemical potential energy in covalent bonds.

  • ATP (Adenosine Triphosphate)

    • Universal energy currency.
    • Hydrolysis: ATP→ADP+Pi+7.3 kcal (30.5 kJ)ATP \rightarrow ADP + P_i + 7.3\,kcal\,(30.5\,kJ).
    • Regenerated via substrate-level phosphorylation & oxidative phosphorylation in mitochondria.

  • Key Coenzymes in Energy Metabolism

    1. NAD⁺ / NADH – contains vitamin B3B_3 (niacin).
    2. FAD / FADH₂ – contains B2B_2 (riboflavin).
    3. CoA (Coenzyme A) – contains B5B_5 (pantothenic acid).

  • Four Parts of Glucose Catabolism (BIO45)

    1. Glycolysis (cytosol): glucose (6C) → 2 pyruvate (3C) + net 2 ATP + 2 NADH.
    2. Pyruvate → Acetyl-CoA (mitochondrial matrix): produces 1 NADH / pyruvate, releases CO₂; irreversible.
    3. Citric Acid Cycle (TCA/Krebs): Acetyl-CoA + oxaloacetate → citrate … → regenerates oxaloacetate. Yields per acetyl-CoA: 3 NADH, 1 FADH₂, 1 GTP (≈ATP), 2 CO₂.
    4. Electron Transport Chain (ETC) & Oxidative Phosphorylation: NADH/FADH₂ donate electrons → O₂ final acceptor → H₂O; proton gradient powers ATP synthase; ~ 28–32 ATP28–32\,ATP/glucose.
    • Complete oxidation of glucose: C<em>6H</em>12O<em>6+6O</em>2→6CO<em>2+6H</em>2O+≈30–34 ATPC<em>6H</em>{12}O<em>6 + 6O</em>2 \rightarrow 6CO<em>2 + 6H</em>2O + \approx 30–34\,ATP.

  • Lactic Acid System

    • Under anaerobic/high-intensity, pyruvate + NADH → lactate (cytosol) regenerating NAD⁺ for glycolysis.
    • Produced in muscle, RBCs; transported to liver → Cori cycle (lactate → glucose) using ATP.
    • Excess lactate ↓ pH → fatigue/burning sensation; cleared within ~1 h.

  • Significance of the Irreversibility of Pyruvate → Acetyl-CoA

    • Once past this step, carbons cannot form glucose → explains need for glucose-forming pathways (gluconeogenesis) from other substrates.

  • Oxaloacetate (OAA)

    • 4-carbon TCA intermediate.
    • Roles:
    1. Condenses with acetyl-CoA to start TCA (must be available; produced from pyruvate, some AAs).
    2. Precursor for gluconeogenesis → maintains blood glucose.

  • Entry of Fats & Protein into Pathways

    • Fat: Triglyceride → glycerol (→ glycolysis) + fatty acids.
    • Fatty acids enter mitochondria via carnitine shuttle, undergo β-oxidation → multiple acetyl-CoA + NADH + FADH₂.
    • Protein: AAs deaminated: glucogenic AAs → pyruvate/OAA; ketogenic AAs → acetyl-CoA or acetoacetate.
    • Significance: FA & ketogenic AAs entering at acetyl-CoA cannot yield glucose; glucogenic AAs & glycerol can.

  • Carnitine

    • Quaternary amine synthesised in liver/kidney (from lysine & methionine).
    • Transfers long-chain fatty acyl-CoA into mitochondria.
    • Supplements do NOT increase fat oxidation unless person is carnitine-deficient (rare).

  • Terminology

    • Lipolysis: hydrolysis of TG → glycerol + 3 FA.
    • β-oxidation / FA oxidation: sequential removal of 2-C units as acetyl-CoA; each cycle yields 1 NADH + 1 FADH₂.
    • Example: 16-C palmitate → 8 acetyl-CoA, 7 NADH, 7 FADH₂; total ATP ≈ 106106.

  • Metabolic States

    • Feasting (Excess intake)
    • ↑ insulin → glycogen synthesis (liver/muscle) till stores full, then de novo lipogenesis, FA re-esterified → adipose TG.
    • Excess protein deaminated → fat.
    • Short-term fasting (3–24 h)
    • Glycogenolysis maintains blood glucose (~12–18 h supply).
    • ↑ lipolysis → FA oxidation; glycerol + AA begin gluconeogenesis.
    • Long-term fasting (>24 h)
    • Liver gluconeogenesis from AAs, lactate, glycerol; ketosis begins (brain adapts to ketones, ↓AA catabolism).

  • Gluconeogenesis (GNG)

    • Formation of glucose from non-CHO precursors (lactate, glycerol, glucogenic AAs).
    • Starts in mitochondria (pyruvate → OAA) or cytosol; requires ATP + biotin ((B_7)).

  • Protein-Sparing Action of Carbohydrate

    • Adequate CHO intake prevents excess AA catabolism for glucose, preserving lean tissue.

  • Ketone Production & Ketosis

    • When acetyl-CoA accumulation > OAA (low CHO), liver converts excess acetyl-CoA → ketone bodies (acetoacetate, β-hydroxybutyrate, acetone).
    • Occurs during prolonged fasting, very-low-CHO diet, uncontrolled T1 diabetes.
    • Ketones exported; used by brain, muscle → spare glucose & protein.
    • Ketosis suppresses appetite (possible mechanism in ketogenic diets).

  • Ketoacidosis

    • Pathologic accumulation of ketones → blood pH < 7.357.35; seen in diabetic ketoacidosis, starvation with impaired renal excretion.
    • Risks: dehydration, electrolyte imbalance, coma, death without treatment.

  • Therapeutic Use of Ketones

    • Epilepsy (refractory pediatric cases) – ketogenic diet reduces seizure frequency.