DC

Chapter 2 Chemistry of life pt 1

Water, electrolytes, and pH basics

  • Water in the body is a central medium; we can’t “control” its intrinsic properties, so we work with them rather than against them.

  • Everyday analogy: spilled water soaks into a towel due to water’s properties (polarity, electron arrangement) that enable it to be absorbed and to spread.

  • Electrolyte balance is key to controlling water movement in the body.

  • Thirst and fluids: after a salty meal, you drink because water follows sodium (electrolyte balance drives water distribution).

  • pH scale basics (acid–base):

    • Acid: pH 0–7

    • Neutral: pH 7

    • Base: pH 7–14

  • You don’t need to memorize covalent vs. ionic details for this course; focus on core ideas and how pH/electrolytes affect body chemistry.

  • Textbook as a reference: chapter 2 can be used for quick review if memory is fuzzy.

Major, trace, and mineral elements

  • Four major elements make up about 96% of body mass:

    • Oxygen (O)

    • Carbon (C)

    • Hydrogen (H)

    • Nitrogen (N)

  • Among these, Oxygen is the most abundant; Carbon accounts for about 18% of body mass in organic molecules.

  • Mineral elements (seven essential minerals) comprise <4% of body mass:

    • Sodium (Na)

    • Potassium (K)

    • Calcium (Ca)

    • Chlorine (Cl)

    • Magnesium (Mg)

    • Phosphorus (P)

    • Sulfur (S)

  • Major/mineral distinction helps with electrolyte balance and body chemistry, but you should know the list of seven minerals.

  • Trace elements (less abundant but essential): Zinc, Iodine, Copper, Iron, etc. (others exist; not all are listed in this transcript).

  • Why this matters: these elements form electrolytes and are essential in diet (e.g., iron in hemoglobin).

  • Note on memorization: the color-coding in the visuals is for location reference only; don’t memorize the periodic table layout from these slides.

  • Test prep tip: be able to identify which substances are mineral elements in a given list (e.g., sodium, potassium, phosphorus, iodine, nitrate, sulfur) and pick not-a-mineral from choices.

Metabolism: types of chemical reactions and enzyme roles

  • Metabolism refers to all chemical reactions in the body that process chemicals to sustain life.

  • Three main types of reactions:

    • Catabolic reactions: large molecules are broken down into smaller ones (e.g., digestion of food into amino acids).

    • Anabolic reactions: smaller molecules are built into larger ones (e.g., synthesis of muscle tissue from amino acids).

    • Exchange reactions: parts of molecules are rearranged (e.g., swapping ions like sodium and chloride or shuffling amino acids).

  • Energy transformation: reactions convert chemical energy into a usable form (e.g., ATP).

  • A mnemonic to remember the two building directions: “anabolic” means building up; “catabolic” means breaking down.

  • Enzymes are catalysts that speed up reactions; in biology they are highly specific and are essential for life (e.g., lactase breaks down lactose).

  • Temperature and enzyme activity: extremely high temperatures denature enzymes; very low temperatures slow them down.

  • Enzyme concepts:

    • Lock-and-key model: substrates fit into an enzyme’s active site like a key fits a lock.

    • Active site: the region of the enzyme where the substrate binds.

    • Enzymes are not permanently altered by the reaction; they catalyze and reset.

  • Real-world enzyme examples and disorders:

    • Lactase deficiency leads to lactose intolerance; lactose remains undigested in the gut.

    • Enzyme deficiencies can have severe consequences (see disease examples below).

  • Major disease examples tied to enzymes (brief):

    • Tay-Sachs disease: deficiency of hexosaminidase A; GM2 ganglioside accumulates in neurons; fatal in early childhood.

    • Severe Combined Immunodeficiency (SCID): deficiency of adenosine deaminase; near absence of immune function; example referenced as “boy in the bubble.”

    • Phenylketonuria (PKU): deficiency of phenylalanine hydroxylase; phenylalanine builds up and must be avoided in diet; testing at birth detects PKU; diet restrictions help manage/seize symptoms.

  • Practical point: enzyme-related conditions illustrate why metabolism is tightly regulated and why diet and genetics can have profound consequences.

  • Exercise and heat question (discussion prompt): Why do you feel hot during and after exercise?

    • Exercise raises metabolic rate; cells require more fuel, increasing metabolism and enzyme activity, generating heat; cooling takes time due to sustained metabolic rate, blood flow, and heat production from ongoing metabolic processes.

  • An emphasis on the real-world relevance of metabolism: nutrition, disease, and physical performance all hinge on metabolic rates and enzyme function.

Organic compounds and hydrocarbon basics

  • We are organic, carbon-based organisms; hydrocarbons are carbon–hydrogen compounds and the backbone of most organic molecules.

  • Carbon’s tetravalence: each carbon forms four covalent bonds, either to hydrogens or to other carbons; this enables chain and ring structures.

  • Metabolism and energy release: breaking covalent bonds releases energy, which can be captured in ATP; energy release is central to nutrient processing.

  • Carbons can form chains and rings; carbohydrates, lipids, and proteins all incorporate hydrocarbon frameworks.

  • Note on visuals: you don’t need to memorize specific hydrocarbon structures for tests, but you should understand the concept of bonds and energy release when bonds break.

Carbohydrates: structure, function, and metabolism

  • Carbohydrates are made of carbon, hydrogen, and oxygen (C, H, O).

  • Primary functions: energy fuel; some structural roles on cell surfaces (markers) via glycoproteins and glycolipids; also important in cell recognition and communication.

  • Monomer, dimer, and polymer terminology:

    • Monosaccharide: single sugar unit (monomer).

    • Disaccharide: two monosaccharides linked together; typically used for transport (e.g., sucrose, lactose).

    • Polysaccharide: many monosaccharides linked; for storage or structure (e.g., starch in plants, glycogen in animals).

  • Common monosaccharides (3–7 carbon atoms): glucose, fructose, galactose; also ribose and deoxyribose (essential for DNA/RNA).

  • Glyco-prefix means sugar (e.g., glycoprotein = sugar attached to a protein; glycolipid = sugar attached to a lipid).

  • Glucose chemistry: empirical formula for glucose is ext{C}6 ext{H}{12} ext{O}_6; breaking it releases energy used to form ATP.

  • Disaccharides: formed by dehydration synthesis; example: sucrose (table sugar) and lactose (milk sugar).

    • Dehydration synthesis example: when glucose and fructose join, a water molecule is removed: ext{Glucose} + ext{Fructose}
      ightarrow ext{Sucrose} + ext{H}_2 ext{O}

    • Hydrolysis: reverse reaction; add water to split disaccharides back into monosaccharides.

  • Polysaccharides: storage forms of glucose

    • Plants store as starch.

    • Animals store as glycogen, primarily in the liver and muscles.

    • Carb loading (pre-competition): build up glycogen stores for quick energy during activity.

  • Carbohydrates and health:

    • Brain and neural tissue require glucose; cells strategically convert dietary sugar to glucose as needed.

    • Diabetes concerns arise from dysregulated glucose handling; ketosis can occur with fat/protein metabolism in the absence of sufficient glucose.

  • Important caveats from the lecture:

    • Carbs are not “evil”; the body relies on glucose for brain function and energy.

    • Sugars differ in properties and effects; monosaccharides vs disaccharides vs polysaccharides have different roles.

  • Glycogen storage sites and energy strategy:

    • Glycogen stored in liver and muscles; a larger glycogen reserve supports rapid energy during activity.

Lipids: structure, function, and diversity

  • Lipids are primarily composed of carbon and hydrogen with relatively less oxygen; common role is energy storage, but they also form cell membranes and steroid hormones.

  • Major lipid categories and components:

    • Fatty acids: hydrocarbon chains with a carboxyl group (COOH) at one end; chain length varies; may have zero, one, or multiple double bonds.

    • Triglycerides (neutral fats): glycerol backbone with three fatty acids; a primary energy storage form; formed via dehydration synthesis and broken via hydrolysis.

    • Phospholipids: glycerol backbone, two fatty acids, and a phosphate group; amphipathic (polar head, nonpolar tails) which enables bilayer membranes (cell membranes).

    • Steroids: four-ring hydrocarbon nucleus; cholesterol is a key steroid with roles in membranes and as a precursor to other steroids (bile acids, estrogen, testosterone); cholesterol is essential but dysregulated levels can contribute to health issues (hypercholesterolemia).

  • Fatty acid saturation and health implications:

    • Saturated fats: no double bonds; typically solid at room temperature (e.g., animal fats like bacon grease, coconut oil).

    • Monounsaturated fats: one double bond; usually liquid at room temperature (plant oils).

    • Polyunsaturated fats: two or more double bonds; also liquid at room temperature (plant and fish oils); include omega-3s; location of double bonds matters for metabolic effects.

    • Trans fats: produced by hydrogenating unsaturated fats; associated with higher cardiovascular risk when consumed in excess.

  • Phospholipids and membranes:

    • Phospholipid bilayer forms the fundamental structure of cell membranes; phosphate head is hydrophilic (water-loving) and faces the aqueous environment, while fatty acid tails are hydrophobic (water-hating) and form the interior barrier.

  • Energy and storage considerations:

    • Fat stores a lot of energy per gram because many carbon–carbon bonds can be broken to release energy.

    • Triglycerides are stored rather than floating freely in the bloodstream; storage in liver or adipose tissue is metabolically favorable compared to circulating lipids.

  • Diet considerations mentioned in the lecture:

    • Omega-3 fats are highlighted as beneficial; essential fatty acids cannot be synthesized by the body and must be consumed.

    • Saturated fats are generally less favorable for cardiovascular health, though not all are equally problematic; trans fats are particularly problematic.

  • Summary note on cholesterol: essential for membranes and steroid hormones, but overproduction or misplacement can cause health problems; hypercholesterolemia has genetic components.

Nucleic acids (brief mention in the transcript)

  • Nucleic acids involve sugars such as ribose (RNA) and deoxyribose (DNA).

  • They are essential for genetic information storage and transfer; the transcript emphasizes ribose (RNA) and deoxyribose (DNA) in the context of carbohydrates and nucleic acids.

Proteins: structure, synthesis, and functions

  • Core elements: carbon, hydrogen, oxygen, nitrogen (N is essential because amino groups contain nitrogen).

  • Protein mass and diversity:

    • Proteins make up a large portion of body mass (roughly 20%); humans possess a vast diversity of proteins (tens of thousands, with estimates ranging from 50,000 to 100,000 different types).

    • Protein synthesis is encoded by DNA; proteins sculpt the body’s structure and function.

  • Protein functions:

    • Structural roles (e.g., connective tissue, muscle components).

    • Enzymatic roles (catalyzing biochemical reactions).

    • Immune defense (antibodies and immune signaling).

    • Cellular communication and signaling.

    • Muscle contraction and movement.

    • Can be used as an energy source if needed when carbohydrates/fats are insufficient.

  • Amino acids: the monomer units of proteins

    • About 21 amino acids are discussed; typically, humans use 20 standard amino acids to form proteins, with additional variants like selenocysteine sometimes recognized in special cases.

    • Structure of an amino acid (common representation):

    • Central carbon (C)

    • Amino group (–NH₂)

    • Carboxyl group (–COOH)

    • Hydrogen (–H)

    • R group (side chain) that makes each amino acid unique

    • Represented as: ext{NH}_2- ext{CH}( ext{R})- ext{COOH}

  • Protein monomers and polymers:

    • Dipeptides: two amino acids linked together.

    • Tripeptides: three amino acids linked together.

    • Polypeptides: sequences of many amino acids (10+).

  • Peptide bonds: the bonds formed between amino acids during dehydration synthesis; also the bond that links amino acids in proteins.

  • Protein structure and folding:

    • Primary structure: the linear amino acid sequence.

    • Secondary structure: localized folding patterns (alpha helices and beta sheets) due to hydrogen bonding.

    • Tertiary structure: the overall three-dimensional shape of a single polypeptide.

    • Quaternary structure: assembly of multiple polypeptide chains into a functional protein.

    • Globular proteins: generally spherical and functional (e.g., enzymes, hormones, cell signaling molecules).

    • Fibrous proteins: long, thread-like, often structural (e.g., hair, nails, tendons, bones).

  • Protein misfolding and disease (examples discussed):

    • Cystic fibrosis: wrong amino acid in a protein causes misfolding and altered receptor function, affecting mucus regulation and other cellular processes.

  • Enzymes (protein catalysts):

    • Enzymes are highly specific; each enzyme works best with a particular substrate (lock-and-key concept).

    • Example: Lactase enzyme acts on lactose; lactose intolerance occurs when lactase is deficient.

    • Temperature sensitivity: enzymes can be denatured by heat or slowed by cold; loss of activity has broad physiological consequences.

  • The role of enzymes in disease and health contexts:

    • Enzyme deficiencies can be fatal if essential reactions do not proceed (e.g., Tay-Sachs, SCID, PKU as described in slides).

  • Practical takeaways for study:

    • You don’t need to memorize every amino acid name for exams in this course, but you should understand how amino acids compose proteins and how the enzyme system and genetic encoding influence protein structure and function.

Real-world applications and implications

  • Exercise physiology and metabolism:

    • Exercise increases cellular fuel demands; metabolism speeds up; enzyme activity increases; body temperature rises; cooling takes time due to sustained metabolic activity.

  • Diet and health considerations:

    • Carbohydrates are essential for brain function and energy; the body can convert ingested nutrients to glucose as needed.

    • The brain’s glucose demand influences how dietary sugar is processed and allocated to other tissues.

    • Diet composition and fat types influence cardiovascular health; saturated fats and trans fats have different health implications; omega-3 fats are highlighted as beneficial.

    • Cholesterol is essential in membranes and steroid hormone synthesis, but overproduction or misplacement can contribute to disease risk (hypercholesterolemia).

  • Carbohydrate handling and glycogen storage:

    • Liver and muscle glycogen stores provide rapid energy during activity; training can increase glycogen storage capacity.

  • Enzyme-based disorders and newborn screening:

    • PKU screening at birth allows dietary management to prevent severe symptoms.

    • Other enzyme-related diseases (e.g., Tay-Sachs, SCID) illustrate the deep connections between genetics, metabolism, and health.

  • Doping and ethics:

    • Anabolic remarks and steroids were used as a mnemonic to differentiate anabolic vs. catabolic processes, but the teacher cautioned against using anabolic steroids in practice.

Quick study prompts and test-style ideas

  • Explain how water’s properties influence tissue hydration and fluid balance.

  • List the four major elements and the seven mineral elements; give examples of where they appear in biology and why they matter for electrolytes.

  • Define catabolic, anabolic, and exchange reactions with a simple example for each (e.g., digestion, muscle synthesis, rearranging ions).

  • Describe how enzymes work using lactase and lactose as an example; discuss how temperature and pH affect enzyme activity.

  • Compare saturated vs unsaturated fats; explain how trans fats are formed and why they are harmful.

  • Explain the structure and function of phospholipids in cell membranes; why membranes are amphipathic.

  • Outline the four levels of protein structure and give a disease example caused by misfolding.

  • Summarize the PKU disorder and why newborn screening matters; discuss dietary management implications.

  • Describe glucose as a key energy source with its chemical formula; explain how dehydration synthesis and hydrolysis apply to disaccharides using sucrose and lactose as examples.

  • Explain glycogen storage in liver and muscle and why carb loading can improve athletic performance.

  • Discuss the role of cholesterol in membranes and steroid hormones, and explain the concept of hypercholesterolemia in broad terms.

ext{Glucose (monosaccharide): } ext{C}6 ext{H}{12} ext{O}6 ext{Disaccharide formation (dehydration synthesis): } ext{Glucose} + ext{Fructose} ightarrow ext{Sucrose} + ext{H}2 ext{O}
ext{Hydrolysis (disaccharide breakdown): } ext{Sucrose} + ext{H}2 ext{O} ightarrow ext{Glucose} + ext{Fructose} ext{Triglyceride formation (neutral fat): glycerol} + 3 ext{ fatty acids} ightarrow ext{Triglyceride} + 3 ext{H}2 ext{O}
ext{Phospholipid bilayer: hydrophilic phosphate heads (polar) on the outside; hydrophobic tails inside}
ext{Amino acid general structure: } ext{NH}2- ext{CH}( ext{R})- ext{COOH} ext{Peptide bond formation (dehydration synthesis): } ext{Amino Acid}1- ext{Amino Acid}2 ightarrow ext{Dipeptide} + ext{H}2 ext{O}
ext{Protein energy concept (general): } ig( ext{Energy of bonds broken}ig) - ig( ext{Energy of bonds formed}ig) = ext{Net } riangle E