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Chapter 4 Notes — Proteins

Protein Chapter 4 – Comprehensive Exam Notes

Key idea: protein shape determines function

  • Protein function is driven by structure: primary, secondary, tertiary, and quaternary structures.

  • Primary structure: sequence of amino acids (the order of amino acids). Visual: beads on a string; the order matters.

  • Secondary structure: folding patterns caused by hydrogen bonds between amino acids; common forms are:

    • alpha helix (coil)

    • beta pleated sheet (zigzag)

  • Tertiary structure: 3D folding of the chain (kinks and folds) creating a unique shape; like a necklace twisted into a ball/ blob.

  • Quaternary structure: multiple folded chains coming together to form a larger functional complex; when several proteins stick together, they form a larger blob that defines the protein’s overall shape and function.

  • Implication: protein shape determines function in digestion (enzymes), drug interactions, and enzyme–substrate compatibility.

Amino acids and their basic building blocks

  • All amino acids share a common carbon core with four bonding sites:

    • hydrogen (H)

    • amino group (–NH₂)

    • carboxyl group (–COOH)

    • side chain (R group) that differs among amino acids

  • The identity of each amino acid is determined primarily by its R group.

  • The sequence of amino acids (primary structure) determines all higher structural levels and hence function.

Protein functions (Box 4.2 overview)

  • Structural roles: components of skeletal muscles and other tissues.

  • Enzymes: catalyze virtually all body chemical reactions (e.g., pepsin).

  • Secretions: many body secretions are protein-based (e.g., antibodies).

  • Fluid balance: proteins influence osmotic pressure and water distribution; albumin is a key protein for maintaining fluid balance.

    • Low albumin can lead to edema due to fluid leakage/retention.

  • Acid–base balance: amino acids have acidic and basic properties; proteins help buffer pH (hemoglobin acts as an effective buffer).

  • Transport proteins: lipoproteins transport fats in blood; other proteins transport various molecules.

  • Clotting and hormones: thrombin and hormone-related proteins (e.g., tyrosine-related hormones).

  • General statement: proteins are involved in nearly every cell function and process in the body.

Essential vs nonessential vs conditional amino acids

  • Total amino acids: 20 standard amino acids.

  • Essential amino acids (9): cannot be synthesized by the body; must be supplied in the diet. ext{essential}
    ightarrow ext{must be supplied in the diet}

  • Nonessential amino acids (11): can be synthesized by the body if other essential amino acids are available.

  • Conditionally essential amino acids (6): usually nonessential, but under high demand or certain conditions (growth, illness, trauma) they may need to be supplied in the diet.

  • In short:

    • Essential: must come from diet.

    • Nonessential: body can synthesize.

    • Conditionally essential: may require dietary provision under stress or growth.

Complete vs incomplete proteins

  • Complete proteins: contain all 9 essential amino acids in sufficient amounts for protein synthesis.

    • Best sources: animal proteins (meat, poultry, fish, dairy, eggs).

    • Exceptions: gelatin (animal-derived) is not a complete protein.

    • Some plant sources are complete: soy and quinoa.

  • Incomplete proteins: lack one or more essential amino acids in sufficient amounts (common in most plant proteins: beans, rice, nuts, grains).

  • Complementary proteins: combining incomplete proteins to make a complete amino acid profile over the course of a day.

    • Example pairs: rice + beans; peanut butter + bread.

    • Important point: they do not need to be eaten at the same meal; variety throughout the day can yield a complete amino acid profile.

    • Box 4.4 reviews various complementary protein combinations.

  • Practical note: complementary protein concepts matter more when protein needs are high (growth, pregnancy, recovery, training) or in limited-diet situations (vegetarian/vegan, very low calories).

Digestibility and absorption

  • Animal proteins are typically digested more efficiently than plant proteins: ext{animal protein digestibility}
    ightarrow 90 ext{–}99\%

  • Plant proteins can be digested as low as 70 ext{–}90\%, affecting how many amino acids are available for use.

  • Plant-based protein shakes may have lower absorption depending on their amino acid profile.

Protein digestion and metabolism (concepts you should know now)

  • Synthesis vs metabolism:

    • Synthesis: building amino acids into proteins.

    • Metabolism: breaking down proteins and protein turnover (normal process of turnover to maintain function).

  • Protein turnover examples:

    • Hemoglobin turnover is about ext{90 days} (continuous breakdown and rebuilding in cells).

  • Metabolic pool: free amino acids circulating in blood; available for building/repair as needed.

  • Dietary carbohydrates and fats spare protein use for energy and allow more protein for growth/repair.

Nitrogen balance (concept and clinical use)

  • Nitrogen balance assessment (24-hour urine urea nitrogen) helps estimate protein status, especially in clinical settings (burns, ICU).

  • Balance definition:

    • Positive nitrogen balance: intake > losses → protein growth/recovery (e.g., pregnancy, muscle growth).

    • Negative nitrogen balance: intake < losses → increased protein breakdown; may require more protein.

  • Measurements compare dietary protein intake with urinary/other nitrogen losses (sweat, feces).

  • Not routinely tested for exams; Box 4.3 covers calculation details if needed.

Protein and genetics

  • Proteins are central to genetic expression; DNA encodes proteins, and proteins themselves influence cellular function and phenotype.

  • This topic is acknowledged but not a primary exam focus in this course.

Protein requirements and dietary ranges

  • AMDR (macronutrient distribution range) for protein: ext{protein calories}
    ightarrow 10 ext{–}35\% \, ext{of total calories}

  • RDA for protein: 0.8\ ext{g/kg body weight/day} for age 19+.

  • Needs vary by life stage and health status:

    • Growth (children/pregnancy) and healing increase needs.

    • Certain diseases (kidney disease, liver disease) may alter needs.

    • Burns, injuries, inflammation, infection also raise requirements.

    • PEM (protein-energy malnutrition) category: two main forms:

    • Kwashiorkor (protein deficiency with edema and fatty liver)

    • Marasmus (calorie and protein deficiency with wasting)

  • Special note on assessment in clinical practice: nitrogen balance may be used to gauge protein status in some patients, but not always practical outside ICU settings.

PEM: Protein-Energy Malnutrition

  • Kwashiorkor (protein deficiency):

    • Edema (fluid retention) and fatty liver common.

    • Appetite often reduced; abdominal distention can be prominent.

    • Common in contexts with limited protein intake despite adequate calories in some diets.

  • Marasmus (calorie and protein deficiency):

    • Severe wasting without edema; very frail appearance; alertness may be reduced.

  • Management emphasis:

    • Refeeding carefully to avoid refeeding syndrome (see below).

    • Severe cases require cautious rehabilitation with careful monitoring of fluids, electrolytes, and minerals.

  • Refeeding syndrome (major clinical risk when introducing nutrition in severely malnourished patients):

    • Fatal shifts in fluids and electrolytes when nutrition is reintroduced too quickly.

    • Hallmarks: hypophosphatemia, dysregulated sodium/water balance, changes in glucose, protein and fat metabolism, rapid thiamine (vitamin B1) deficiency leading to neurologic problems, hypokalemia, hypomagnesemia.

    • Prevention/management: very slow, cautious refeeding; monitor labs closely; use vitamin supplementation (including a multivitamin) and align calories/protein with recovery needs.

Protein sources and dietary quality

  • Animal proteins (complete): high absorption but can come with saturated fats and cholesterol depending on cut and preparation; lean options and seafood are preferable where possible.

  • Dairy and eggs (complete) often come with fat and/or carbohydrate depending on product; choose low-fat options when appropriate.

  • Plant proteins (incomplete): beans, rice, nuts, seeds, grains; generally healthier fats and more fiber, but may require careful pairing to meet essential amino acid needs.

  • Dietary considerations for proteins:

    • Balance energy intake with protein to support tissue repair and metabolic needs.

    • Choose nutrient-dense protein sources; be mindful of fat content in animal products.

    • For vegetarians/vegans or very-low-calorie diets, use complementary proteins and consider fortified foods or supplements as needed.

  • Caloric equivalence: proteins provide 4\ ext{calories per gram}.

    • Example: one cup of milk (~8 g protein) contains 8 \times 4 = 32\text{ calories from protein}; total calories vary with carbohydrate/fat content of the milk.

Dietary guidelines and seafood recommendations

  • US dietary patterns show suboptimal seafood intake: about 8 ext{–}12\ ext{ounces per week} recommended; plant-based protein intake often underutilized (4–6 oz/week) and meats/eggs/poultry at 23 ext{–}33\ ext{ounces per week}.

  • Methylmercury considerations:

    • High-mercury fish to limit: king mackerel, marlin, orange roughy, sharks, swordfish, tilefish, big-eye tuna.

    • Safer options: salmon, light canned tuna, trout, tilapia, cod, catfish, etc.

    • Pregnant women and young children should limit methylmercury exposure; adults can vary but should choose fish with lower mercury when possible.

  • Vegetarian diets: one of the identified healthy eating patterns; can be healthy if well-planned.

    • Benefits: lower saturated fat, lower cholesterol, higher fiber, vitamins/minerals/antioxidants; potential benefits for obesity, cardiovascular risk, diabetes, and some cancers.

    • Risks: poorly planned vegetarian diets can lack essential nutrients or adequate protein.

    • Practical tips for vegetarians: eat a variety of protein sources; include vitamin C with meals to enhance mineral absorption; use iodized salt or sea vegetables for iodine; limit high-fat cheese; supplement when necessary but not routinely.

Vegetarian diets and athletic performance

  • Protein alone does not build muscle; resistance training and adequate total calories are essential.

  • Protein intake guideline for athletes: 1.2\ ext{to } 2.0\ \mathrm{g/kg/day}; do not exceed ~2.0\ \mathrm{g/kg/day} as excess protein will be stored as fat if not used for energy or tissue repair.

  • Emphasis on whole foods over supplements when possible; plant-based proteins may require more careful planning to ensure complete amino acid profiles.

  • Timing matters: anabolic window – the timing of protein intake relative to workouts improves recovery, but total daily intake and distribution across meals is also important.

    • Suggested per-meal protein target: 20 ext{–}40\ \mathrm{g} of protein per meal or snack, spread throughout the day.

    • Post-workout strategy: combine protein with carbohydrate within approximately 1\ \text{hour} after exercise; examples include a glass of low-fat chocolate milk or a turkey-on-whole-grain wrap with veggies.

Practical notes and takeaways for exams

  • Remember the four levels of protein structure and the visual analogies used (beads on a string; alpha helix vs beta sheet; necklace folding into a blob; multiple chains forming a larger complex).

  • Know the definitions and implications of:

    • Essential vs nonessential vs conditional amino acids

    • Complete vs incomplete proteins

    • Complementary proteins and their day-long vs meal-long timing

    • Protein digestibility differences between animal and plant proteins

  • Be comfortable with the major numeric values:

    • Essential amino acids: 9\

    • Total amino acids: 20\

    • RDA for protein: 0.8\ \mathrm{g/kg/day}

    • AMDR for protein: 10\%\text{–}35\% of calories

    • Protein calories: 4\ \mathrm{cal/g}

    • Fish intake: 8 ext{–}12\ \mathrm{oz/week}; plant proteins: 4 ext{–}6\ \mathrm{oz/week}; meats/poultry/eggs: 23 ext{–}33\ \mathrm{oz/week}

    • Athlete guideline: 1.2\–2.0\ \mathrm{g/kg/day}

    • Per-meal target: 20\–\40\ \mathrm{g}

    • Anabolic window: within approximately 1\ \text{hour} post-workout

    • Digestibility ranges: ext{animal } 90\%\text{–}99\%, ext{plant } 70\%\text{–}90\%

    • Hemoglobin turnover: approximately 90\text{ days}

  • Clinical concepts to know (brief): nitrogen balance, PEM (Kwashiorkor vs Marasmus), refeeding syndrome, and the general approach to dietary planning in special populations (pregnant, elderly, kidney/liver disease, burns/injury).

  • Real-world relevance: dietary patterns influence chronic disease risk; vegetarian diets require planning to ensure complete amino acid profiles and adequate micronutrients; seafood choices affect mercury exposure and heart health; protein timing supports athletic recovery and performance.