Biology Foundations: Atoms, Bonds, Water, Vitamins/Minerals, Macromolecules, Lipids, Proteins, and Nucleic Acids

A set of question-and-answer flashcards covering atoms, bonds, water properties, minerals/vitamins, macromolecules, lipids, proteins, and nucleic acids, based on the lecture notes.

What are the smallest building blocks of matter that biology focuses on?

Atoms and the biomolecules they form through chemical bonds.

What subatomic particles make up an atom?

Neutrons, protons, and electrons.

What determines the type of bond formed between two atoms?

The difference in electronegativity between the atoms.

What is electronegativity?

The ability of an atom to attract electrons, leading to partial charges between atoms.

What is a hydrogen bond?

A weak bond between a hydrogen covalently bonded to a highly electronegative atom and another electronegative atom.

Which two conditions must be met for hydrogen bonding to occur?

A hydrogen bonded to F, O, or N in one molecule, and the hydrogen attracted to a second electronegative atom (F, O, or N) in another location.

How do covalent bonds within a molecule differ from hydrogen bonds?

Covalent bonds are strong bonds within a molecule; hydrogen bonds are weaker and can be between molecules (intermolecular) or within a molecule (intramolecular).

Are van der Waals interactions true chemical bonds?

No. They are weak attractions due to transient charge distributions between close-lying atoms or molecules.

What real-world example illustrates van der Waals interactions?

Gecko foot hairs interacting with a wall to enable climbing.

Why are water’s properties important in biology?

Water is essential as a solvent, has high heat capacity, a unique density behavior, and participates in cohesion and adhesion that support processes like capillary action.

Why is water an excellent solvent in cells?

Water is highly polar and surrounds charged ions and polar substances, helping them dissolve.

What causes water to have a high heat capacity?

Strong hydrogen bonding and molecular interactions require substantial energy to change temperature.

Why is ice less dense than liquid water?

Hydrogen bonds form a crystal lattice in ice that keeps molecules farther apart than in liquid water.

What is the significance of water’s phase diagram slope for solid vs liquid phases?

Water’s solid-liquid line has a negative slope, meaning solid water (ice) is less dense than liquid water.

What is cohesion in water?

Attraction between like water molecules, contributing to surface tension.

What is adhesion in water?

Attraction between water molecules and other materials or surfaces.

What is capillary action and what drives it?

Water rising in narrow tubes due to cohesion and adhesion.

What plant process illustrates capillary action and water movement?

Transpiration—water moves from roots to leaves and evaporates from stomata.

What are minerals and how do they function in the body?

Inorganic ions required for bone health, electrochemical gradients, and as components of biomolecules like hemoglobin and chlorophyll.

What are vitamins and how are they categorized?

Organic molecules required in small amounts; categorized as water-soluble or fat-soluble.

How do fat-soluble vitamins differ from water-soluble vitamins in terms of storage and excretion?

Fat-soluble vitamins are stored in tissues and can accumulate; water-soluble vitamins are not stored and are excreted in urine.

Which vitamins are water-soluble and what are some key examples and roles?

B vitamins (coenzymes and precursors in metabolism) and vitamin C (synthesis of collagen).

Which vitamins are fat-soluble and what are their main roles?

Vitamins A (vision), D (calcium absorption), E (antioxidant), K (blood clotting).

What are macromolecules and what are the four major biological macromolecules?

Macromolecules are large polymers; the four major ones are carbohydrates, lipids, proteins, and nucleic acids.

What are the monomers for carbohydrates, proteins, nucleic acids, and lipids?

Carbohydrates: monosaccharides; Proteins: amino acids; Nucleic acids: nucleotides; Lipids: not a true polymer with a single monomer (examples include glycerol + fatty acids in triglycerides, glycerol + phosphate head in phospholipids, cholesterol as a steroid).

What are the polymer forms for carbohydrates, proteins, and nucleic acids?

Carbohydrates form polysaccharides; Proteins form polypeptides; Nucleic acids form DNA and RNA; Lipids are not formed by repeating monomer units in the same way.

What is dehydration synthesis and why is it important for macromolecules?

A reaction where two monomers join to form a polymer with the release of water; hydrolysis reverses this by adding water.

What is the common byproduct of forming macromolecules via dehydration synthesis?

Water (H2O) is produced.

What are glycosidic bonds and how are they formed or broken in carbohydrates?

Glycosidic bonds link monosaccharides in polysaccharides; formed by dehydration synthesis and broken by hydrolysis.

How are monosaccharides classified and what are examples?

Monosaccharides are simple sugars like glucose, fructose, and galactose; they can be classified as aldoses or ketoses and by stereochemistry (alpha or beta forms).

What is the difference between alpha and beta glycosidic bonds?

Alpha glycosidic bonds form between alpha glucose units (both OH groups point down); beta glycosidic bonds form between beta glucose units (one OH points up, the other down).

Which polysaccharides are formed by alpha glucose and are branched, and which are beta glucose and linear?

Starch and glycogen (alpha) are branched; cellulose and chitin (beta) are linear.

Why can humans digest starch and glycogen but not cellulose?

Humans have enzymes to break alpha glycosidic linkages (starch/glycogen) but not beta linkages found in cellulose; some animals rely on gut microbes to digest cellulose.

What are the major lipid types you should know for the exam?

Triglycerides, phospholipids, steroids, and porphyrins.

What makes a phospholipid amphipathic?

It has a polar (hydrophilic) head (phosphate group) and nonpolar (hydrophobic) tails (fatty acids).

What is membrane fluidity and how is it regulated?

The viscosity of the cell membrane; regulated by lipid composition and cholesterol; unsaturated fatty acids increase fluidity, saturated fatty acids decrease it, with cholesterol modulating both.

What is the structure and function of triglycerides?

Glycerol backbone with three fatty acid tails; primarily energy storage and insulation; fatty acids can be saturated or unsaturated.

What are phospholipids and why are they critical for cell membranes?

Glycerol backbone with two fatty acids and a phosphate head; amphipathic and form the bilayer of cell membranes.

What are steroids and porphyrins in the lipid category?

Steroids are four fused rings (e.g., cholesterol, hormones, vitamin D); porphyrins are four fused rings with a central metal (e.g., heme with iron, chlorophyll with magnesium).

What are the monomer units of proteins and the bonds that link them?

Amino acids are the monomers; peptide bonds link them.

What are the four levels of protein structure?

Primary (linear sequence), secondary (alpha helix and beta sheet), tertiary (3D folding), and quaternary (multi-subunit assemblies).

What stabilizes alpha helices in proteins?

Hydrogen bonds between the amino and carboxyl groups of nearby amino acids.

What is disulfide bonding and in which macromolecule is it most characteristic?

Covalent bonds between cysteine sulfur atoms; characteristic of proteins.

What is protein denaturation and can it be reversible?

Loss of secondary, tertiary, and quaternary structure with retention of primary; reversibility depends on the cause and extent of denaturation.

What are nucleic acids and what are their monomers?

DNA and RNA are nucleic acids; monomers are nucleotides.

What bonds hold nucleotides together within a strand and between strands in DNA?

Phosphodiester bonds link nucleotides within a strand; hydrogen bonds between bases (A-T with 2 bonds, G-C with 3 bonds) hold opposing strands together.

What makes DNA antiparallel and complementary?

Two strands run in opposite directions (5' to 3' and 3' to 5'); bases pair specifically (A with T, G with C) forming a complementary double helix.

What is Chargaff’s rule?

In double-stranded DNA, the amount of A equals T and the amount of G equals C; purine and pyrimidine counts are balanced.

If a DNA sample has 15% adenine, what percent cytosine does it have?

35% cytosine (and 35% guanine); A and T each 15% (A=T; G=C).

What is the difference between a nucleotide and a nucleoside?

A nucleotide has a phosphate group; a nucleoside lacks the phosphate group.

What distinguishes ribonucleosides from deoxyribonucleosides?

Ribonucleosides have ribose with an extra OH group; deoxyribonucleosides have deoxyribose lacking the 2' OH.

What is ATP and why is it important?

Adenosine triphosphate; a ribonucleoside with three phosphate groups that stores and provides energy for cellular processes.

What is the backbone of DNA and how is it formed?

Phosphodiester bonds between the phosphate of one nucleotide and the sugar of the next; forms the sugar-phosphate backbone.

What is the difference in nitrogenous bases between DNA and RNA?

DNA uses A, T, G, C with thymine; RNA uses A, U, G, C with uracil replacing thymine.

Beyond subatomic particles, what fundamental chemical entities are considered the basic building blocks in biological systems, and how do they form complex structures?

Atoms, which subsequently form biomolecules through various types of chemical bonds (e.g., covalent, ionic, hydrogen bonds) to enable cellular functions.

Compare and contrast the key properties (charge, location, relative mass, and primary role in chemical interactions) of the three principal subatomic particles found in an atom.

Protons (+1 charge, in nucleus, relative mass of 1 amu, determines atomic number/element identity); Neutrons (0 charge, in nucleus, relative mass of 1 amu, contributes to mass number/isotope); Electrons (-1 charge, in electron cloud, negligible mass, determines chemical reactivity and bonding).

Explain how the difference in electronegativity between two atoms dictates the nature of the chemical bond formed, specifically differentiating between nonpolar covalent, polar covalent, and ionic bonds.

The difference in electronegativity:1. Nonpolar Covalent: Small/negligible difference (e.g., < 0.5), electrons shared equally.2. Polar Covalent: Moderate difference (e.g., 0.5 - 1.7), unequal sharing, resulting in partial charges ($\delta+$ and $\delta-$).3. Ionic: Large difference (e.g., > 1.7), complete transfer of electrons, forming full ions and electrostatic attraction.

Define electronegativity and describe its general trend across a period and down a group in the periodic table, providing examples of highly electronegative elements relevant in biology.

Electronegativity is an atom's intrinsic ability to attract shared electrons in a chemical bond. It generally increases across a period (due to increasing nuclear charge) and decreases down a group (due to increased shielding and atomic radius). Highly electronegative elements in biology include Fluorine (F), Oxygen (O), and Nitrogen (N).

Describe the nature of a hydrogen bond, distinguishing it from a covalent bond, and explain its typical strength relative to other intermolecular forces.

A hydrogen bond is a relatively weak, electrostatic attraction (not a true covalent bond) that forms between a partially positively charged hydrogen atom (covalently bonded to a highly electronegative atom like F, O, or N) and another nearby highly electronegative atom with a lone pair of electrons. It is stronger than van der Waals forces but significantly weaker than covalent or ionic bonds.

Identify the two essential structural prerequisites for the formation of a hydrogen bond and provide a biological example where these conditions are met.

1. A hydrogen atom must be covalently bonded to a highly electronegative atom (Fluorine (F), Oxygen (O), or Nitrogen (N)) – this creates the partial positive charge on hydrogen. 2. A second highly electronegative atom (F, O, or N) with an available lone pair of electrons must be in close proximity to the partially positive hydrogen. Example: Water molecules forming hydrogen bonds with each other, or base pairing in DNA (G-C, A-T).

Elaborate on the fundamental differences between covalent bonds and hydrogen bonds, considering their nature, relative strengths, and typical biological roles (e.g., structural integrity vs. dynamic interactions).

• Covalent Bonds: Formed by the sharing of electron pairs between atoms, typically strong (bond energy ~50-110 kcal/mol), primarily responsible for intramolecular stability and the permanent structure of molecules.- Hydrogen Bonds: Electrostatic attractions, not true sharing of electrons, much weaker (~2-10 kcal/mol), crucial for dynamic interactions within and between molecules (e.g., protein folding, DNA base pairing, water's properties). Covalent bonds involve a single molecule or macromolecule, hydrogen bonds typically involve multiple molecules.

Describe van der Waals interactions, outlining the three distinct types and their mechanisms of attraction, and explain why they are not considered true chemical bonds.

No, they are not true chemical bonds but rather weak, transient attractive forces between electrically neutral atoms or molecules due to temporary, fluctuating dipoles. The three types are:1. Dipole-dipole interactions: Between two permanent dipoles.2. Dipole-induced dipole interactions: Between a permanent dipole and a nonpolar molecule (inducing a temporary dipole).3. London Dispersion Forces (Induced dipole-induced dipole): Between two nonpolar molecules due to instantaneous, temporary dipoles arising from electron movement. They are very weak and short-range but collectively significant.

Explain how the specialized structure of gecko foot hairs effectively utilizes van der Waals interactions to enable their climbing ability on various surfaces.

Gecko foot hairs (setae) branch into millions of tiny spatulae, which come into extremely close contact with a surface. This close proximity allows the cumulative effect of numerous weak van der Waals forces between the spatulae and the surface to generate enough adhesive force to support the gecko's weight, facilitating climbing.

Identify and briefly explain at least four unique physicochemical properties of water that are crucial for sustaining life, providing a concise biological implication for each.

1. Excellent Solvent: Its polarity allows it to dissolve many ionic and polar substances, facilitating transport of nutrients and waste.2. High Heat Capacity: Resists temperature changes, helping to stabilize cellular and environmental temperatures.3. Unique Density Behavior: Ice is less dense than liquid water, allowing aquatic life to survive under frozen surfaces.4. Cohesion and Adhesion: Enable capillary action (e.g., water transport in plants), and contribute to surface tension and transport processes.5. High Heat of Vaporization: Effective cooling mechanism through evaporation.

Elaborate on the molecular basis for water’s exceptional solvent properties, specifically explaining how it interacts with both ionic compounds and polar non-ionic substances to facilitate their dissolution, using the concept of hydration shells.

Water's high polarity, due to its bent shape and the electronegativity difference between oxygen and hydrogen, allows it to form hydration shells.- Ionic Compounds: The partially negative oxygen atoms surround positive ions (cations), and partially positive hydrogen atoms surround negative ions (anions), effectively separating and dissolving them.- Polar Non-ionic Substances: Water forms hydrogen bonds with polar groups (e.g., -OH or -NH_2) on the solute molecules, disrupting solute-solute interactions and allowing the substance to dissolve.

Explain the molecular mechanism behind water's remarkably high heat capacity, specifically attributing it to the extensive network of hydrogen bonds.

Water's high heat capacity stems from the extensive network of strong hydrogen bonds that exist between its molecules. A significant amount of thermal energy (heat) must first be absorbed to break these hydrogen bonds before the kinetic energy of the water molecules can increase, thus raising the temperature. Conversely, a large amount of energy must be released to form these bonds when water cools, slowing down temperature decreases.

Describe the structural transformation that water undergoes upon freezing, explaining how the arrangement of hydrogen bonds in ice results in a lower density compared to liquid water.

When water freezes, each water molecule forms stable hydrogen bonds with four other water molecules, creating a crystalline, open hexagonal lattice structure. This specific arrangement holds the molecules at a greater average distance from each other than in the more transiently bonded, densely packed liquid state. The increased volume for the same mass results in ice being less dense than liquid water.

In the phase diagram for water, the solid-liquid equilibrium line exhibits a negative slope. What is the fundamental physical implication of this unique characteristic, and how does it relate to the behavior of ice in aquatic environments?

The negative slope of water's solid-liquid line signifies that solid water (ice) is less dense than liquid water. This means that as pressure increases, the melting point decreases (or freezing point decreases). Consequently, ice floats on liquid water. Biologically, this is crucial for aquatic life, as ice forms on the surface of bodies of water, insulating the liquid water below and preventing complete freezing, allowing organisms to survive.

Define cohesion in the context of water and explain the molecular forces responsible for this property, including its contribution to biological phenomena like surface tension.

Cohesion is the strong intermolecular attraction between water molecules themselves, primarily due to the extensive network of hydrogen bonds. This force contributes significantly to water's high surface tension (allowing small insects to walk on water) and plays a key role in supporting the column of water during capillary action within plant vascular tissues.

Define adhesion with respect to water and differentiate it from cohesion by explaining the molecular basis of each interaction with respect to different types of surfaces.

Adhesion is the attraction between water molecules and other polar or charged surfaces/molecules (dissimilar substances). This attraction occurs because water can form hydrogen bonds or electrostatic interactions with polar groups on other materials (e.g., glass, plant cell walls). While cohesion is water-water attraction, adhesion is water-other substance attraction, and both are critical for phenomena like capillary action.

Explain how the interplay of cohesion and adhesion drives the phenomenon of capillary action, particularly in narrow tubes, and why this is biologically significant.

Capillary action is the upward movement of water in narrow tubes or spaces against the force of gravity. It is driven by:- Adhesion: Water molecules are attracted to the polar surfaces of the tube (e.g., xylem walls), causing them to 'climb' the walls.- Cohesion: As water molecules adhere to the walls and move up, they pull other water molecules with them due to the strong hydrogen bonds between them. This combined force allows water to move to significant heights in plants.

Describe the complete 'transpiration-cohesion-tension' mechanism that accounts for water transport in plants, detailing the roles of cohesion, adhesion, and evaporation.

Transpiration, combined with the cohesion-tension theory, explains water movement in plants. Water evaporates from stomata in leaves, creating a negative pressure (tension) that pulls a continuous column of water upwards through the xylem. This column is maintained by:- Cohesion: Strong hydrogen bonds between water molecules.- Adhesion: Water molecules adhering to the hydrophilic xylem walls. These forces collectively overcome gravity, allowing water to be drawn from roots to leaves.

Define minerals in a biological context and elaborate on their diverse roles in the body, providing specific examples for structural support, electrochemical gradients, and as cofactors or components of biomolecules.

Minerals are inorganic elements or ions typically obtained through diet, essential for various bodily functions.- Structural Support: Calcium (Ca^{2+}) and Phosphate (PO_4^{3-}) in bones and teeth.- Electrochemical Gradients & Nerve Impulses: Sodium (Na^+), Potassium (K^+), Chloride (Cl^-).- Components of Biomolecules: Iron (Fe^{2+}) in hemoglobin (oxygen transport), Magnesium (Mg^{2+}) in chlorophyll (photosynthesis) and as an enzyme cofactor, Iodine (I^-) in thyroid hormones (metabolism).

What are vitamins and how are they categorized?

Organic molecules required in small amounts; categorized as water-soluble or fat-soluble.

Compare and contrast fat-soluble and water-soluble vitamins with respect to their absorption, storage, excretion, and potential for toxicity.

• Fat-soluble Vitamins (A, D, E, K): Absorbed with dietary fats, stored in adipose tissue and the liver, not readily excreted, higher risk of toxicity with excessive intake because of accumulation.- Water-soluble Vitamins (B-complex, C): Absorbed directly into the bloodstream, generally not stored (except B12), readily excreted in urine when consumed in excess, lower risk of toxicity.

Enumerate the major water-soluble vitamins and detail at least two specific examples of their coenzyme forms or crucial metabolic roles.

Water-soluble vitamins include the B vitamins (Thiamine (B1), Riboflavin (B2), Niacin (B3), Pantothenic Acid (B5), Pyridoxine (B6), Biotin (B7), Folate (B9), Cobalamin (B12)) and Vitamin C.- B Vitamins: Function as coenzymes or precursors to coenzymes (e.g., B1 as TPP in carbohydrate metabolism, B2 as FAD in redox reactions, B3 as NAD^+ in electron transport, B5 as CoA in fatty acid synthesis). They are critical for various metabolic pathways.- Vitamin C (Ascorbic Acid): Essential for collagen synthesis, acts as an antioxidant, and aids in iron absorption.

List the fat-soluble vitamins and provide a more detailed explanation of their primary physiological functions beyond a simple association.

• Vitamin A (Retinol, Retinal, Retinoic Acid): Crucial for vision (as retinal in rhodopsin), cell growth and differentiation, immune function, and epithelial tissue maintenance.- Vitamin D (Calciferol): Functions as a hormone to regulate calcium and phosphate homeostasis, promoting their absorption in the gut and reabsorption in the kidneys, essential for bone health.- Vitamin E (Tocopherols): A powerful antioxidant that protects cell membranes from oxidative damage by scavenging free radicals.- Vitamin K (Phylloquinone, Menaquinone): Essential coenzyme for gamma-carboxylation of specific proteins involved in blood coagulation (e.g., prothrombin) and bone metabolism.

Define biological macromolecules and list the four primary classes, briefly noting which are true polymers and which are not, and why.

Macromolecules are large, complex organic molecules essential for life processes. The four major biological macromolecules are:1. Carbohydrates (Polysaccharides): True polymers of monosaccharides.2. Proteins (Polypeptides): True polymers of amino acids.3. Nucleic Acids (DNA, RNA): True polymers of nucleotides.4. Lipids: Generally not considered true polymers (with repeating monomeric units) but are large biological molecules with diverse structures (e.g., triglycerides, phospholipids, steroids).

What are the monomers for carbohydrates, proteins, nucleic acids, and lipids?

Carbohydrates: monosaccharides; Proteins: amino acids; Nucleic acids: nucleotides; Lipids: not a true polymer with a single monomer (examples include glycerol + fatty acids in triglycerides, glycerol + phosphate head in phospholipids, cholesterol as a steroid).

What are the polymer forms for carbohydrates, proteins, and nucleic acids?

Carbohydrates form polysaccharides; Proteins form polypeptides; Nucleic acids form DNA and RNA; Lipids are not formed by repeating monomer units in the same way.

Describe the process of dehydration synthesis (or condensation reaction) and its significance in macromolecule formation, contrasting it with the hydrolysis reaction and outlining the energetic requirements for each process.

Dehydration synthesis (or condensation reaction) is a metabolic process where two smaller molecules (monomers) are covalently linked to form a larger molecule (polymer) with the concomitant removal of a water molecule (H_2O). This is an anabolic, energy-requiring process. Its importance lies in building virtually all biological macromolecules from their respective monomeric units. Hydrolysis is the reverse catabolic process, breaking polymers into monomers by adding a water molecule, typically releasing energy.

What is the common byproduct of forming macromolecules via dehydration synthesis?

Water (H_2O) is produced.

Define a glycosidic bond, explain which specific carbon atom of a monosaccharide is typically involved in its formation, and describe the process of its synthesis and cleavage.

A glycosidic bond is a covalent bond that links a carbohydrate (sugar) molecule to another group, which can be another carbohydrate or a non-carbohydrate group. Specifically, it involves the anomeric carbon (the carbonyl carbon, C1 for aldoses or C2 for ketoses) of one monosaccharide reacting with a hydroxyl group of another monosaccharide. It is formed by a dehydration synthesis reaction and broken by a hydrolysis reaction, often catalyzed by specific glycosidases.

Beyond general examples, delineate the primary classification criteria for monosaccharides, including their carbonyl group type and carbon chain length, in addition to relevant stereochemical forms.

Monosaccharides are classified by:1. Type of Carbonyl Group:- Aldoses: Contain an aldehyde group (e.g., glucose, galactose).- Ketoses: Contain a ketone group (e.g., fructose).2. Number of Carbon Atoms: Trioses (C3), Pentoses (C5 such as ribose, deoxyribose), Hexoses (C_6 such as glucose, fructose, galactose).3. Stereochemistry: Cyclized monosaccharides can exist in alpha or beta anomeric forms, depending on the orientation of the anomeric hydroxyl group relative to the O-bridge.

Precisely distinguish between alpha and beta glycosidic bonds in terms of the stereochemical orientation of the hydroxyl group involved in bonding at the anomeric carbon, and their implications for polysaccharide structure.

The distinction lies in the orientation of the anomeric hydroxyl group of the first monosaccharide relative to the CH2OH group (C6) on the same ring in the cyclic form:- Alpha (\alpha) Glycosidic Bond: The anomeric hydroxyl group is below the plane of the ring (or trans to the CH2OH group) when linearizing to form the bond.- Beta (\beta) Glycosidic Bond: The anomeric hydroxyl group is above the plane of the ring (or cis to the CH_2OH group) when linearizing to form the bond.These orientations critically influence the 3D structure and digestibility of polysaccharides.

Categorize the major storage and structural polysaccharides based on their constituent monosaccharides, the type of glycosidic linkages (alpha or beta), and their macroscopic structural characteristics (linear vs. branched).

• Alpha Glucose Polysaccharides (Energy Storage):- Starch: Amylose (unbranched, \alpha-1,4 linkages) and Amylopectin (branched, \alpha-1,4 and \alpha-1,6 linkages).- Glycogen: Highly branched, \alpha-1,4 and \alpha-1,6 linkages (more branched than amylopectin).- Beta Glucose Polysaccharides (Structural):- Cellulose: Linear, unbranched, \beta-1,4 linkages.- Chitin: Linear, unbranched, \beta-1,4 linkages, derived from N-acetylglucosamine.

Why can humans digest starch and glycogen but not cellulose?

Humans possess enzymes such as amylase (in saliva and pancreas) and disaccharidases that are specific for hydrolyzing the \alpha-1,4 and \alpha-1,6 glycosidic linkages found in starch and glycogen. In contrast, cellulose consists of \beta-1,4 glycosidic linkages. Humans lack the enzyme (beta-glucosidase or cellulase) required to break these beta linkages. Therefore, cellulose passes through the human digestive tract as indigestible fiber.

What are the major lipid types you should know for the exam?

Triglycerides, phospholipids, steroids, and porphyrins.

Explicate the molecular structure of a phospholipid that confers its amphipathic character, detailing the specific components of both the hydrophilic and hydrophobic regions.

A phospholipid is amphipathic because it possesses both hydrophilic (water-loving) and hydrophobic (water-fearing) regions:- Hydrophilic Head: Composed of a phosphate group (which is negatively charged) and typically a small, polar organic molecule (e.g., choline, ethanolamine) attached to the phosphate. This region readily interacts with water.- Hydrophobic Tails: Consist of two long hydrocarbon chains (fatty acids), which are nonpolar and repel water. This dual nature is crucial for forming biological membranes.

Define membrane fluidity and explain, at a molecular level, precisely how the composition of fatty acid tails (saturation level) and the presence of cholesterol regulate this essential property of biological membranes across varying temperatures.

Membrane fluidity refers to the viscosity of the lipid bilayer, which allows embedded components to move laterally. It is regulated by:- Fatty Acid Saturation:- Unsaturated fatty acids: Have one or more double bonds, creating "kinks" in the hydrocarbon tails. These kinks prevent tight packing, increasing membrane fluidity.- Saturated fatty acids: Have no double bonds, allowing for tight, regular packing of tails. This increases van der Waals interactions between tails, decreasing fluidity and making the membrane more rigid.- Cholesterol: Acts as a fluidity buffer. At warm temperatures, it restricts phospholipid movement, decreasing fluidity. At cold temperatures, it prevents phospholipids from packing too closely, thereby increasing fluidity and preventing solidification.

Describe the complete chemical structure of a triglyceride, including the specific type of bond that links its components, and elaborate on its primary biological functions, distinguishing between saturated and unsaturated forms.

A triglyceride consists of a glycerol molecule (a three-carbon alcohol) covalently bonded to three fatty acid tails via ester linkages.- Function: Primarily serves as a highly efficient form of long-term energy storage, insulation against cold, and protection for organs.- Saturation: Fatty acids can be saturated (no double bonds, solid at room temp, e.g., animal fats) or unsaturated (one or more double bonds, liquid at room temp, e.g., plant oils).

Beyond their amphipathic nature, explain how phospholipids spontaneously assemble into a bilayer structure in aqueous environments and why this specific arrangement is absolutely critical for the cell membrane's function.

Phospholipids are lipids composed of a glycerol backbone, two fatty acid tails, and a phosphate group (often with an additional polar head group). They are critical for cell membranes because their amphipathic nature (hydrophilic head, hydrophobic tails) causes them to spontaneously arrange into a lipid bilayer in an aqueous environment. The hydrophobic tails face inwards, shielded from water, while the hydrophilic heads face outwards, interacting with the aqueous intracellular and extracellular fluids. This bilayer forms a selectively permeable barrier, regulating passage of substances, providing cell compartmentalization, and maintaining cellular integrity.

Describe the defining structural features of steroids and porphyrins, and provide key biological examples for each, explaining their broad functional categories within biological systems.

• Steroids: Characterized by a distinctive four-fused-ring carbon skeleton. Examples include cholesterol (a precursor for other steroids and a membrane fluidity modulator), sex hormones (e.g., estrogen, testosterone), and Vitamin D (hormone for calcium regulation). Their functions are diverse, ranging from membrane structure to signaling.- Porphyrins: While not lipids in the classical sense, they are often grouped due to their hydrophobic properties or association with lipid-like structures. Structurally, they consist of four modified pyrrole rings joined in a cyclic fashion, often chelating a central metal ion. Examples include heme (with central iron, found in hemoglobin for oxygen transport) and chlorophyll (with central magnesium, for photosynthesis). They primarily function in oxygen binding, electron transport, and light absorption.

Identify the monomeric units of proteins and precisely describe the chemical bond that links these monomers, detailing the atoms involved and the type of reaction that forms it.

The monomeric units of proteins are amino acids. They are linked by peptide bonds, which are covalent bonds formed between the carboxyl group of one amino acid and the amino group of an adjacent amino acid, with the release of a water molecule (dehydration synthesis). This bond forms the polypeptide backbone.

Enumerate the four hierarchical levels of protein structure, and for each level, briefly describe its defining characteristics and the primary types of molecular interactions or bonds responsible for its stability.

1. Primary Structure: The unique, linear sequence of amino acids in a polypeptide chain. Stabilized by covalent peptide bonds.2. Secondary Structure: Local folding patterns of the polypeptide backbone, primarily \alpha-helices and \beta-sheets. Stabilized by hydrogen bonds between the carbonyl oxygen and amide hydrogen atoms within the backbone.3. Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between amino acid side chains (R-groups). Stabilized by various interactions: hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions, and van der Waals forces.4. Quaternary Structure: The arrangement of multiple polypeptide subunits (if present) into a functional protein complex. Stabilized by the same non-covalent interactions as tertiary structure, and sometimes disulfide bonds.

Detail the specific molecular interactions responsible for stabilizing the alpha-helical secondary structure in proteins, indicating which parts of the amino acid residues participate in these bonds.

Alpha helices are stabilized by regularly spaced hydrogen bonds formed between the carbonyl oxygen of one amino acid residue and the amide hydrogen of an amino acid residue located four positions along the polypeptide backbone (i to i+4). These hydrogen bonds are entirely within the polypeptide backbone, not involving the R-groups, and run parallel to the helix axis, giving the structure its stability.

Describe the formation of a disulfide bond, including the specific amino acid involved and the type of chemical reaction required, and explain its significance in stabilizing protein structure.

A disulfide bond (-S-S-) is a strong covalent bond formed between the sulfur atoms of two cysteine residues. This bond is formed through an oxidation reaction (removal of two hydrogen atoms). It is highly characteristic of proteins, especially extracellular or secreted proteins, and plays a crucial role in stabilizing tertiary and sometimes quaternary protein structures, contributing significantly to their overall stability and rigidity.

Define protein denaturation, specifying which levels of protein structure are affected while identifying common denaturing agents. Discuss the conditions under which denaturation might be reversible (renaturation).

Protein denaturation is the process by which a protein loses its specific three-dimensional (secondary, tertiary, and sometimes quaternary) structure, leading to a loss of its biological function, while its primary amino acid sequence remains intact.- Common Denaturing Agents: Extreme heat, drastic changes in pH, high concentrations of salts (heavy metals), strong reducing agents (for disulfide bonds), organic solvents, and detergents.- Reversibility: Denaturation can sometimes be reversible (renaturation) if the primary structure is undamaged, and the denaturing conditions are mild enough to allow the protein to refold into its native conformation, often aided by chaperones. However, severe or prolonged denaturation usually leads to irreversible loss of function.

What are nucleic acids and what are their monomers?

DNA and RNA are nucleic acids; monomers are nucleotides.

Identify the type of covalent bond that forms the backbone of a single nucleic acid strand, detailing which specific components of the nucleotides are involved. Additionally, specify the non-covalent bonds responsible for holding two complementary DNA strands together, noting the quantitative difference between specific base pairs.

• Within a strand: Phosphodiester bonds link nucleotides. These are covalent bonds formed between the phosphate group attached to the 5' carbon of one nucleotide's sugar and the hydroxyl group on the 3' carbon of the next nucleotide's sugar, creating the sugar-phosphate backbone.- Between strands (in DNA): Hydrogen bonds between complementary nitrogenous bases: Adenine (A) forms two hydrogen bonds with Thymine (T), and Guanine (G) forms three hydrogen bonds with Cytosine (C).