3.1

Review of Biomolecules and Macromolecular Structure

• Monomers of proteins are amino acids.

• There are $20$ distinct amino acids utilized in biological systems.

• The variable group ($R$ group) is the sole structural difference between the $20$ amino acids.

• Directionality of protein polypeptide chains proceeds from the $N$--terminus (amino terminus) to the $C$--terminus (carboxyl terminus).

• The $N$--terminus refers to the amine functional group ($NH_2$), which contains nitrogen.

• The $C$--terminus refers to the carboxyl/carboxy functional group (carboxylic acid).

• The term amino acid is derived directly from its functional chemical components: amino carboxylic acid.

• Monomers of nucleic acids are nucleotides.

• Nucleotide structure consists of a sugar-phosphate backbone attached to a nitrogenous base.

• Both $DNA$ and $RNA$ utilize $4$ distinct nitrogenous bases.

• Nitrogenous bases in $DNA$: Thymine ($T$), Cytosine ($C$), Guanine ($G$), and Adenine ($A$).

• Nitrogenous bases in $RNA$: Uracil ($U$), Cytosine ($C$), Guanine ($G$), and Adenine ($A$). Thymine is substituted by Uracil in $RNA$.

• Directionality of $DNA$ strands runs from the $3'$ end to the $5'$ end ($3' \rightarrow 5'$).

• Role of $DNA$: Genes located on $DNA$ code directly for proteins.

• Indirect role of $DNA$ in protein synthesis: $DNA$ is indirectly involved in synthesizing proteins because it stores and carries genetic instructions rather than executing translation directly.

• Secondary protein structure reinforcement: Hydrogen bonds stabilize the secondary folding structures of proteins.

• Tertiary protein structure reinforcement: Maintained by interactions between the variable $R$ groups of different amino acids, including disulfide bonds, ionic bonds, covalent bonds, hydrophobic interactions, and hydrophilic interactions.

• Denaturation: The process where a protein misfolds and deactivates when removed from its native environmental conditions.

• Causes of denaturation: Changes in environmental factors such as temperature, $pH$, salinity, and chemical concentrations.

• Egg white albumin denaturation example: Cooking egg whites applies thermal energy, causing the albumin protein to denature. The physical properties change from a transparent, clear fluid to an opaque, solid white structure.

• Sickle cell anemia pathophysiology: A genetic disorder caused by a mutation in the gene coding for hemoglobin.

• Tissue hypoxia mechanism: Abnormal hemoglobin causes red blood cells to sickle, blocking capillary beds and starving surrounding tissues of oxygen ($O_2$).

• Enzyme substrate specificity: Enzymes are specific to the substrate molecule upon which they act.

• Enzyme reusability: Enzymes are catalysts that are not consumed during a chemical reaction and do not become part of the final product.

• Adenosine Triphosphate ($ATP$): The primary nucleotide energy carrier in cells used to perform cellular work.

• Nitrogenous component of $ATP$: Adenine / Adenosine.

Fundamentals of Cellular Organization and Microscopy

• Examination timing: Scheduled for Monday, with an absolute completion deadline no later than Wednesday.

• Micrograph: A photograph captured through a microscope.

• Fluorescence staining analysis of a cell undergoing mitosis:

  • Red fluorescence stain: Identifies the plasma membrane (cell membrane).

  • Blue fluorescence stain: Identifies condensed chromosomes ($DNA$).

  • Green fluorescence stain: Identifies cytoskeletal elements, specifically the microtubules forming the mitotic spindle (originating from centriole pairs).

• Primary objective of cell staining: Provides visual contrast.

• Water content of cells: Cells are composed of $70\%$ to $90\%$ water, rendering them naturally transparent under direct light.

• Visual contrast analogy: Locating a clear glass tumbler thrown into a swimming pool vs. locating a bright red Solo cup. The glass tumbler requires specific light angles to generate minimal contrast, whereas the opaque red Solo cup is immediately visible due to distinct color contrast.

Cellular Pigmentation and Specialization Constraints

• Pigmentation in human body cells: Human cells generally lack inherent color. Only $2$ specific cell types possess natural pigmentation:

  • Red blood cells (erythrocytes): Contain hemoglobin bound to iron ($Fe$). Oxidation of iron imparts a red color. The red color itself serves zero physiological function.

  • Melanocytes: Produce melanin, which transfers into skin cells. Melanin pigment functions specifically to protect cellular $DNA$ against ultraviolet radiation.

• Visual appearance of desanguinated tissue: Without blood, dissected human body tissues appear exclusively white and gray. Blood provides red and pink coloration to internal organs.

• Commercial meat pigmentation dynamics: Fresh beef appears red due to oxygenated myoglobin (stored hemoglobin in skeletal muscle). When turned over or depleted of oxygen, beef turns gray or brown. Butcher display counters spray gases (such as ethylene gas) to react with myoglobin in muscle cells, artificially oxidizing it to maintain a bright red aesthetic.

• Definition of a Cell: The smallest unit of life that can exist independently or as part of a multicellular organism.

• Multicellular viability and loss of function: Cell specialization in multicellular organisms results in a loss of certain broad biological functions to optimize specific tasks.

• Red blood cell specialization constraints:

  • Lack of Nucleus: Maturing red blood cells eject their nucleus (the largest cellular organelle) to maximize physical space for hemoglobin and increase oxygen transport capacity. Consequently, red blood cells cannot undergo mitosis or cell division.

  • Lack of Mitochondria: Red blood cells lack mitochondria. Mitochondria generate $ATP$ via aerobic respiration, which consumes oxygen ($O_2$). Lacking mitochondria prevents red blood cells from consuming the oxygen they transport.

• Hematopoiesis: Red blood cells, white blood cells, and thrombocytes (platelets) cannot reproduce themselves; they are continuously generated by hematopoietic stem cells located in the red bone marrow.

Taxonomic Domains and Prokaryotic vs. Eukaryotic Cellular Architecture

• Eukaryotic Cells: "Eu" means true, and "karyon" means kernel/nucleus. Defined by the presence of membrane-bound organelles and a true nucleus separating genetic material ($DNA$) from the cytoplasm.

• Prokaryotic Cells: "Pro" means before, and "karyon" means kernel/nucleus. Defined by the absence of membrane-bound organelles and a true nucleus. Encompasses Domain Bacteria and Domain Archaea.

• Corn kernel structural metaphor: Eukaryotic cell structure resembles a corn kernel (niblet) containing an outer coating surrounding an inner seed/core. The outer hull is composed of cellulose (indigestible plant fiber), while the inner core consists of digestible starch.

• Taxonomic Domain System: Modern biological taxonomy utilizes a $3$--Domain system consisting of Domain Archaea, Domain Bacteria (prokaryotes), and Domain Eukarya (eukaryotes).

• Defined Eukaryotic Kingdoms: Domain Eukarya contains $3$ definitively categorized kingdoms: Kingdom Animalia, Kingdom Plantae, and Kingdom Fungi. The former Kingdom Protista lacks definitive single-group categorization.

• Outdated Five-Kingdom System: The traditional Five-Kingdom model is obsolete and does not accurately reflect modern phylogenetic taxonomy.

Structure and Properties of the Plasma Membrane

• Plasma Membrane: The outer limiting membrane separating intracellular contents from the extracellular environment.

• Organelles: Translated as "little organs"; membrane-bound sub-compartments within eukaryotic cells executing dedicated physiological functions.

• Phospholipids: Main structural component of all biological membranes.

• Chemical structure of phospholipids: $1$ glycerol molecule attached to $2$ fatty acid tails and $1$ phosphate head covalently bonded to the third carbon.

• Amphipathic nature: Phospholipids possess distinct polar and nonpolar regions within the same molecule.

  • Phosphate head: Polar / Hydrophilic (water-attracting).

  • Fatty acid tails: Nonpolar / Hydrophobic (water-repelling).

• Lipid Bilayer Formation: When placed in aqueous environments, phospholipids spontaneously self-assemble into a double-layer sheet (bilayer).

  • Outer layer heads face extracellular water.

  • Inner layer heads face intracellular cytosol water.

  • Hydrophobic tails orient inward toward each other, completely shielded from water.

• Structural distinction analogy: A lipid bilayer behaves like a hollow, air-filled basketball (or "balón" in Spanish) containing liquid both inside and outside, distinct from a solid triglyceride oil drop which resembles a solid baseball.

The Fluid Mosaic Model and Membrane Dynamics

• Fluid Mosaic Model: Describes the plasma membrane as a dynamic, non-static structure composed of a mosaic of phospholipids, proteins, and lipids.

• Mosaic Components:

  • Integral Membrane Proteins: Proteins embedded directly within the hydrophobic core of the lipid bilayer (e.g., channel proteins, active transport pumps).

  • Peripheral Membrane Proteins: Proteins attached to either the internal or external surface of the membrane.

  • Glycoproteins: Membrane proteins covalently bound to short carbohydrate chains. Act as cell-identity markers for cell-to-cell recognition and immune identification (e.g., antibody targeting).

  • Cholesterol: Steroid lipids embedded among phospholipid tails to stabilize membrane structural integrity and modulate fluidity.

• Fluidity Mechanisms:

  • Lateral Movement: Continuous, rapid side-to-side shifting of phospholipids and membrane proteins along the plane of the membrane layer.

  • Transverse Flipping ("flip-flop"): Extremely rare event where a phospholipid flips from one leaflet of the bilayer to the other. Flipping forces nonpolar tails through aqueous environments, creating a high energy barrier that prevents frequent spontaneous inversion.

• Experimental Demonstration of Membrane Fluidity:

  • Mouse-Human Hybrid Cell Experiment: Mouse membrane proteins were stained with green fluorescent dye, and human membrane proteins were stained with purple fluorescent dye.

  • Mouse and human cells were hybridized into a single combined cell.

  • At $t = 0$, green proteins remained localized strictly on one half of the cell and purple proteins on the other.

  • Following $1\,\text{hour}$ of incubation, green and purple proteins were completely homogenized across the entire surface membrane, proving lateral fluidity. (Note: Hybridized cells are non-viable long-term).

Principles of Selective Permeability and Transport Mechanisms

• Selective Permeability: Property of the plasma membrane allowing only specific substances to pass freely across the lipid bilayer.

  • Small, nonpolar molecules: Lipid-soluble molecules cross the membrane readily via simple diffusion.

  • Large, polar, or charged molecules: Cannot cross the membrane unassisted due to the hydrophobic core.

  • Polarity and Charge Restrictions: Starch cannot enter directly and must be hydrolyzed into individual glucose monomers. Glucose is polar and requires protein assistance. Ions ($Na^+$, $Ca^{2+}$, $K^+$) carry electric charges and are strictly blocked by hydrophobic fatty acid tails.

• Passive Transport:

  • Solute movement requiring zero cellular energy expenditure ($ATP$).

  • Simple Diffusion: Net movement of solute particles down their concentration gradient (from an area of higher concentration to an area of lower concentration).

  • Chemical Equilibrium: State reached when solute concentration is uniform, resulting in equal movement rates in both directions across the membrane.

  • Kayak Analogy: Moving downstream on a river requires no kinetic paddling energy because movement is driven passively along an elevation gradient; simple diffusion operates similarly along a concentration gradient.

• Independent Solute Diffusion:

  • Distinct solutes diffuse down their own individual concentration gradients independently of other dissolved substances.

• Osmolarity: Total overall concentration of all dissolved solutes within a given solution.

• Independent Gradient Example: In a system with Solution A (high total osmolarity, high concentration of solute $X$) and Solution B (lower total osmolarity, high concentration of solute $O$), solute $X$ diffuses from Solution A to Solution B, while solute $O$ diffuses from Solution B to Solution A until individual equilibria are reached.

• Facilitated Diffusion:

  • Passive movement of polar, charged, or large solutes across a membrane aided by specialized transport proteins.

  • Channel Proteins: Provide a continuous hydrophilic passageway through the hydrophobic membrane interior.

  • Carrier Proteins: Bind specific solutes and undergo conformational shape changes to move solutes across.

  • Amphipathic Structure of Transport Proteins: Channel proteins are amphipathic—the outer surface contacting lipid tails is nonpolar, while the inner channel lumen is polar.

Osmosis and Solvent Movement Mechanics

• Osmosis: The diffusion of solvent (water) molecules across a selectively permeable membrane.

• Mechanism of Osmosis: Occurs when solutes are physically prevented from crossing a semipermeable membrane. Water moves down its own concentration gradient—from a region of lower solute concentration (hypotonic / higher water concentration) to a region of higher solute concentration (hypertonic / lower water concentration).

• Osmotic Equilibrium: Chemical equilibrium is achieved via changes in solvent volume rather than solute movement across the membrane.

• Concentration Adjustment Principle: Solution concentration can be increased either by adding solute or by removing solvent (water). Osmosis alters concentration by shifting solvent volume.

Questions and Discussion

• Question: What are the monomers for proteins?

  • Answer: Amino acids ($20$ distinct types).

• Question: What is the only difference between the $20$ amino acids?

  • Answer: The variable group ($R$ group).

• Question: What are the monomers for nucleic acids?

  • Answer: Nucleotides, consisting of a sugar-phosphate backbone plus a nitrogenous base.

• Question: How many nitrogenous bases exist for nucleic acids, and which base is substituted in $RNA$?

  • Answer: There are $4$ nitrogenous bases for both $DNA$ and $RNA$. In $RNA$, Thymine is substituted by Uracil.

• Question: What are the four nitrogenous bases in $DNA$?

  • Answer: Thymine, Cytosine, Guanine, and Adenine.

• Question: What do genes on $DNA$ code for?

  • Answer: Proteins.

• Question: Is $DNA$ directly or indirectly involved in protein synthesis?

  • Answer: Indirectly involved, because it carries the genetic instructions.

• Question: What type of bonds reinforce the secondary structure of proteins?

  • Answer: Hydrogen bonds.

• Question: What reinforces the tertiary structure of proteins?

  • Answer: Interactions between variable $R$ groups (disulfide bonds, ionic bonds, covalent bonds, hydrophobic interactions, and hydrophilic interactions).

• Question: What is the term for when a protein misfolds and deactivates due to environmental changes?

  • Answer: Denaturation (caused by changes in temperature, $pH$, salinity, or chemical concentrations).

• Question: What is an example of denaturation in egg whites during cooking?

  • Answer: The albumin protein changes from a clear fluid to an opaque white solid, altering both color and texture.

• Question: What causes sickle cell anemia?

  • Answer: It is a genetic disorder affecting the gene that codes for hemoglobin.

• Question: Why do tissues become starved of oxygen in sickle cell anemia?

  • Answer: Sickled cells block capillary beds.

• Question: What is the target of an enzyme, and are enzymes consumed in chemical reactions?

  • Answer: The target is a substrate. Enzymes are not consumed in reactions and do not become part of the product (they are reusable).

• Question: What is the main energy carrier in a cell, and what is its nitrogenous base?

  • Answer: $ATP$ (Adenosine Triphosphate); Adenine / Adenosine.

• Question: What is the directionality of $DNA$ and protein synthesis?

  • Answer: $DNA$ directionality runs $3' \rightarrow 5'$; protein synthesis proceeds from the $N$--terminus (amine group, $NH_2$) to the $C$--terminus (carboxyl group).