Premed · Premed · Anatomy Physiology 1
Lecture 2: Chemical and Cellular Basis of Life (Review)
Anatomy and Physiology I
Learning Objectives
By the end of this lecture, students will be able to:
- Distinguish between atoms, elements, molecules, and compounds
- Describe the three types of chemical bonds relevant to biology
- Differentiate between the four major classes of biological macromolecules
- Identify the major organelles of a human cell and describe their functions
- Describe the structure of the plasma membrane and the fluid mosaic model
- Explain the key mechanisms of membrane transport (passive and active)
- Outline the basic stages of the cell cycle including mitosis
Lecture Content
I. Basic Chemistry Review
Atoms and Elements
An atom is the smallest unit of matter that retains the properties of an element. Each atom is composed of three types of subatomic particles: protons, which carry a positive charge, neutrons, which are electrically neutral, and electrons, which carry a negative charge. Protons and neutrons reside in the dense central nucleus, while electrons orbit around it in energy levels known as shells. The atomic number of an element equals its number of protons, while the mass number is the sum of protons and neutrons.
An element is a substance that cannot be broken down into simpler substances by ordinary chemical means. Twenty-six elements are found in the human body. The four major elements by mass are oxygen (65%), carbon (18.5%), hydrogen (9.5%), and nitrogen (3.2%). Lesser elements include calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium, while trace elements such as iron, iodine, and zinc are required in tiny amounts.
Isotopes are atoms of the same element that differ in their number of neutrons. Radioactive isotopes, or radioisotopes, are unstable and emit radiation as they decay, a property exploited in medical imaging and cancer treatment.
Chemical Bonds
Ionic bonds form when one atom transfers electrons to another, creating ions: a cation (positive, having lost an electron) and an anion (negative, having gained one). Ionic compounds dissociate in water to form electrolytes, as when sodium chloride separates into sodium and chloride ions.
Covalent bonds involve the sharing of electron pairs between atoms. When electrons are shared equally, the bond is nonpolar covalent, as seen in molecular oxygen and carbon-hydrogen bonds. When one atom is more electronegative and attracts the shared electrons more strongly, the bond is polar covalent, as in the oxygen-hydrogen bonds of water. Atoms can form single, double, or triple covalent bonds depending on how many electron pairs they share.
Hydrogen bonds are weak attractions between a slightly positive hydrogen atom, bonded to an oxygen or nitrogen, and a slightly negative oxygen or nitrogen atom on another molecule. Individually these bonds are weak, but collectively they are powerful. Hydrogen bonds are responsible for many of the remarkable properties of water and help stabilize the structures of proteins and DNA.
Water and Its Properties
Water makes up 60 to 80 percent of body mass and possesses several properties critical to life. Its high heat capacity means it resists temperature changes, helping to stabilize body temperature. Its high heat of vaporization makes sweating an effective cooling mechanism. As a polar solvent, water dissolves ionic compounds and other polar molecules, which are termed hydrophilic. Water participates directly in chemical reactions such as hydrolysis and dehydration synthesis. It also provides cushioning that protects organs, as in the case of cerebrospinal fluid surrounding the brain.
Acids, Bases, and pH
An acid is a proton donor that increases the hydrogen ion concentration in solution, while a base is a proton acceptor that decreases it. The pH scale measures hydrogen ion concentration on a scale from 0 (most acidic) to 14 (most basic), with 7 being neutral. Blood pH is tightly regulated between 7.35 and 7.45, a slightly alkaline range. Buffers resist changes in pH by accepting or releasing hydrogen ions as needed; the bicarbonate buffer system is especially critical for maintaining blood pH.
II. Biological Macromolecules
Carbohydrates
Carbohydrates are composed of carbon, hydrogen, and oxygen in a general ratio approximated by the formula CH2O. Monosaccharides such as glucose, fructose, and galactose are simple sugars. Disaccharides form when two monosaccharides are joined by dehydration synthesis, producing familiar molecules like sucrose, lactose, and maltose. Polysaccharides are long chains of monosaccharides; glycogen is the animal storage form of glucose, held in the liver and skeletal muscle, while starch serves the same purpose in plants. The primary functions of carbohydrates are to supply energy, particularly through glucose metabolism, and to play structural roles.
Lipids
Lipids are composed primarily of carbon and hydrogen with relatively little oxygen, making them hydrophobic. Triglycerides, the most common dietary fats, consist of a glycerol backbone linked to three fatty acid chains. Saturated fatty acids contain no double bonds between carbons and tend to be solid at room temperature, while unsaturated fatty acids have one or more double bonds and are typically liquid (oils). Triglycerides serve as concentrated energy stores, provide insulation, and cushion organs.
Phospholipids replace one fatty acid with a phosphate group, creating an amphipathic molecule with a hydrophilic head and two hydrophobic tails. This property enables phospholipids to form the lipid bilayer that is the structural basis of cell membranes. Steroids are built on a framework of four interlocking hydrocarbon rings; cholesterol, the most familiar steroid, stabilizes cell membranes and is the precursor for steroid hormones and bile salts. Eicosanoids, including prostaglandins and leukotrienes, are lipid-based local signaling molecules involved in inflammation.
Proteins
Proteins are composed of carbon, hydrogen, oxygen, and nitrogen, sometimes with sulfur. Their building blocks are amino acids, of which there are 20 types, each distinguished by its unique R group, or side chain. Amino acids are linked by peptide bonds through dehydration synthesis reactions to form polypeptide chains. Protein structure is described at four levels: primary structure is the amino acid sequence; secondary structure consists of local folding patterns such as alpha helices and beta pleated sheets, stabilized by hydrogen bonds between backbone atoms; tertiary structure is the overall three-dimensional shape of a single polypeptide, determined by interactions among R groups; and quaternary structure describes the arrangement of multiple polypeptide subunits.
Proteins perform a vast array of functions: enzymes catalyze biochemical reactions, structural proteins like collagen and keratin provide mechanical support, hemoglobin transports gases, antibodies defend against pathogens, hormones like insulin regulate physiology, and contractile proteins such as actin and myosin drive movement. Denaturation, the loss of a protein's three-dimensional shape due to heat, pH changes, or chemical exposure, destroys its ability to function.
Nucleic Acids
DNA (deoxyribonucleic acid) is a double-helical molecule that stores the cell's genetic information using four nitrogenous bases: adenine, thymine, guanine, and cytosine. RNA (ribonucleic acid) is typically single-stranded and participates in protein synthesis, using uracil in place of thymine. Both are polymers of nucleotide monomers, each consisting of a phosphate group, a pentose sugar, and a nitrogenous base. ATP (adenosine triphosphate) is the universal energy currency of the cell, storing readily accessible energy in its high-energy phosphate bonds.
<image>A summary panel of the four classes of biological macromolecules. Panel A: Carbohydrates — a glucose ring structure and a short glycogen chain. Panel B: Lipids — a triglyceride molecule showing glycerol backbone with three fatty acid tails, and a phospholipid with its hydrophilic head and hydrophobic tails. Panel C: Proteins — a polypeptide chain illustrating primary through quaternary structure with labels. Panel D: Nucleic Acids — a short segment of DNA double helix showing base pairing (A-T, G-C), sugar-phosphate backbone, and a single nucleotide enlarged to show its three components.</image>
III. Cell Structure and Function
The Plasma Membrane
The structure of the plasma membrane is described by the fluid mosaic model: it is a dynamic structure composed of a phospholipid bilayer in which a variety of proteins are embedded or associated. The phospholipid bilayer consists of two layers of phospholipids arranged so that their hydrophilic heads face outward toward the aqueous environments on either side and their hydrophobic tails face inward, shielded from water.
Membrane proteins fall into two categories. Integral, or transmembrane, proteins span the entire bilayer and serve as channels, carriers, and receptors. Peripheral proteins are loosely attached to the inner or outer surface of the membrane and function as enzymes or structural anchors. Cholesterol molecules are interspersed among the phospholipid tails and help stabilize membrane fluidity across a range of temperatures. The glycocalyx, a sugar-rich coat formed by glycoproteins and glycolipids on the extracellular surface, plays roles in cell-cell recognition, immune identification, and protection.
<image>A detailed cross-section of the plasma membrane illustrating the fluid mosaic model. The phospholipid bilayer is shown with hydrophilic heads (circles) facing the extracellular fluid and cytoplasm, and hydrophobic tails pointing inward. Integral proteins span the bilayer, including a channel protein with a central pore and a carrier protein. Peripheral proteins sit on the cytoplasmic surface. Cholesterol molecules are wedged between phospholipid tails. Glycoproteins and glycolipids extend from the extracellular surface forming the glycocalyx. All components are clearly labeled.</image>
Cytoplasm and Organelles
The cytoplasm encompasses all cellular contents between the plasma membrane and the nucleus, including the gel-like cytosol, the organelles, and temporary stores called inclusions such as glycogen granules, lipid droplets, and pigments.
The nucleus is the control center of the cell, enclosed by a double-membrane nuclear envelope studded with nuclear pores. Inside, chromatin, a complex of DNA and histone proteins, disperses throughout the nucleoplasm and condenses into visible chromosomes during cell division. The nucleolus within the nucleus is the site of ribosomal RNA synthesis and ribosome subunit assembly. The nucleus houses the genome and directs protein synthesis.
Ribosomes are the sites where proteins are assembled. Free ribosomes floating in the cytosol produce proteins used within the cell, while bound ribosomes attached to the rough endoplasmic reticulum manufacture proteins destined for secretion or incorporation into membranes.
The endoplasmic reticulum comes in two forms. The rough ER is studded with ribosomes and specializes in synthesizing and modifying proteins, packaging them into transport vesicles for shipment. The smooth ER lacks ribosomes and is involved in lipid synthesis, detoxification, and calcium storage.
The Golgi apparatus consists of stacks of flattened membrane sacs called cisternae. It receives proteins and lipids from the ER at its cis (receiving) face, modifies, sorts, and packages them, and dispatches them from its trans (shipping) face as lysosomes or secretory vesicles.
Lysosomes are membrane-bound sacs filled with digestive (hydrolytic) enzymes that break down ingested bacteria, worn-out organelles, and cellular debris. They function at an acidic pH of about 5. If lysosomes rupture, the released enzymes can digest the cell itself, a process called autolysis.
Mitochondria, often called the powerhouses of the cell, possess a double membrane: a smooth outer membrane and a folded inner membrane whose infoldings are called cristae. The matrix, the inner compartment, contains the enzymes of the Krebs cycle. Mitochondria are the primary site of aerobic cellular respiration and generate most of the cell's ATP. Notably, they carry their own DNA, which is inherited exclusively from the mother.
Peroxisomes are membrane-bound compartments containing oxidase enzymes that detoxify harmful substances such as alcohol and formaldehyde, break down fatty acids, and neutralize free radicals. They convert the toxic byproduct hydrogen peroxide to water using the enzyme catalase.
The cytoskeleton is an internal framework of protein filaments that gives the cell its shape and enables internal movement. Microfilaments made of actin support cell shape, drive muscle contraction, and facilitate cell motility. Intermediate filaments provide mechanical strength and resist tension. Microtubules, composed of tubulin, maintain cell shape, guide organelle movement, and form structures such as centrioles, cilia, and flagella.
Centrioles are paired cylindrical structures near the nucleus that organize the mitotic spindle during cell division. Cilia and flagella are motile extensions of the cell surface built from microtubules in a characteristic 9+2 arrangement. Cilia are short and numerous, moving substances over cell surfaces as in the respiratory tract, while a flagellum is a long, single appendage that propels the cell, as exemplified by the sperm tail.
<image>A large, labeled cross-sectional diagram of a generalized human cell. The cell is cut away to reveal internal structures. Labeled organelles include: nucleus with nuclear envelope, nuclear pores, chromatin, and nucleolus; rough ER with attached ribosomes; smooth ER; Golgi apparatus showing cis and trans faces with vesicles; free ribosomes; mitochondrion cut open to show cristae and matrix; lysosomes; peroxisomes; centrioles; cytoskeleton elements (microfilaments, intermediate filaments, microtubules); plasma membrane; and cilia projecting from the surface. The cytosol fills the space between organelles.</image>
IV. Membrane Transport
Passive Transport (no ATP required; substances move down their concentration gradient)
Simple diffusion allows nonpolar, lipid-soluble molecules to pass directly through the lipid bilayer without assistance. Oxygen, carbon dioxide, and fat-soluble vitamins cross the membrane in this way. Osmosis is a special case of diffusion in which water moves through a selectively permeable membrane from a region of higher water concentration to one of lower water concentration. The concept of tonicity describes the effect of a solution on cell volume: an isotonic solution produces no net water movement, a hypotonic solution causes water to enter the cell so that it swells, and a hypertonic solution draws water out so that the cell shrinks or crenates. Facilitated diffusion enables polar or large molecules to cross the membrane through protein channels or carriers, still moving down their concentration gradient. Ion channels allow specific ions such as sodium, potassium, and calcium to pass, while carrier proteins such as the GLUT transporters ferry glucose.
Active Transport (requires ATP; substances move against their concentration gradient)
Primary active transport uses ATP directly to power a pump. The most important example is the Na+/K+ ATPase, or sodium-potassium pump, which exports three sodium ions and imports two potassium ions per ATP molecule hydrolyzed, maintaining the electrochemical gradient essential for nerve and muscle function. Secondary active transport, also called cotransport, harnesses the energy stored in an ion gradient that was created by primary active transport. In symport, two substances travel in the same direction, as when the sodium-glucose symporter carries glucose into intestinal cells. In antiport, the substances move in opposite directions, as with the sodium-hydrogen exchanger.
Vesicular Transport
Endocytosis brings material into the cell within membrane-enclosed vesicles. Phagocytosis, or "cell eating," engulfs large particles such as bacteria, as when macrophages ingest pathogens. Pinocytosis, or "cell drinking," takes up small droplets of extracellular fluid along with dissolved solutes. Receptor-mediated endocytosis is more selective: specific molecules bind to surface receptors, triggering vesicle formation, as when cells take up cholesterol via LDL receptors. Exocytosis is the reverse process, in which intracellular vesicles fuse with the plasma membrane and release their contents outside the cell, as occurs during neurotransmitter release and hormone secretion.
V. The Cell Cycle
The cell cycle consists of two major periods: interphase, during which the cell grows and prepares for division, and the mitotic (M) phase, during which division actually occurs. Interphase accounts for roughly 90 percent of the cycle and is subdivided into G1 phase, when the cell grows and duplicates its organelles; S phase, when DNA is replicated so that each chromosome consists of two sister chromatids joined at the centromere; and G2 phase, when final preparations for division are completed, including replication of the centrioles.
The mitotic phase begins with mitosis, the division of the nucleus into two genetically identical daughter nuclei. During prophase, chromatin condenses into visible chromosomes, the mitotic spindle forms, the nucleolus disappears, and the nuclear envelope begins to break down. In metaphase, the chromosomes align at the metaphase plate, the equator of the cell. During anaphase, the centromeres split and the sister chromatids, now individual chromosomes, are pulled to opposite poles. In telophase, the nuclear envelope re-forms around each set of chromosomes, the chromatin decondenses, and nucleoli reappear. Cytokinesis follows, dividing the cytoplasm as a cleavage furrow pinches the cell in two, yielding two identical daughter cells.
The cell cycle is tightly regulated by checkpoints at the G1, G2, and M phases that verify DNA integrity and proper division. Growth factors stimulate division, and contact inhibition causes cells to stop dividing when they come into contact with neighboring cells. Cancer arises when these checkpoints fail and cell division becomes uncontrolled.
<image>A circular diagram of the cell cycle. The outer ring is divided into the major phases: G1 (large section), S phase, G2, and M phase (mitosis + cytokinesis). Inside the ring, the stages of mitosis are shown sequentially in small panels: Prophase (condensing chromosomes, forming spindle), Metaphase (chromosomes at the equator), Anaphase (chromatids moving to poles), Telophase (nuclear envelopes reforming), and Cytokinesis (cleavage furrow dividing the cell). Checkpoints are marked at G1/S boundary, G2/M boundary, and mid-M phase with small stop-sign icons.</image>
