Course Book for General Biology I under Biochemistry
General Biology I: Cell Biology & Genetics
Biology, the study of life, is a vast and intricate field that seeks to understand the mechanisms, processes, and diversity of living organisms. General Biology I, often focusing on Cell Biology and Genetics, serves as a foundational course, delving into the fundamental units of life – cells – and the principles governing heredity. This exploration unveils the remarkable complexity underlying even the simplest forms of life and provides the essential vocabulary and concepts for further biological study.
Part 1: The Cell – The Fundamental Unit of Life
The concept of the cell as the basic unit of life is one of the most profound discoveries in biology. Robert Hooke first observed "cells" in cork in 1665, but it was the work of Matthias Schleiden and Theodor Schwann in the 19th century that established the unifying cell theory. This theory, in its modern form, postulates three key principles:
All living organisms are composed of one or more cells.
The cell is the basic unit of structure and organization in organisms.
All cells arise from pre-existing cells.
Understanding the cell involves dissecting its various components and appreciating how they work in concert to sustain life.
1.1. Prokaryotic vs. Eukaryotic Cells
The biological world is broadly divided into two major cell types: prokaryotic and eukaryotic. This distinction is based primarily on the presence or absence of a membrane-bound nucleus and other organelles.
Prokaryotic Cells: These are the simpler and generally smaller cell types, characteristic of bacteria and archaea. Key features include:
No true nucleus: Genetic material (a single circular chromosome) is located in a region called the nucleoid.
No membrane-bound organelles: Ribosomes are present for protein synthesis, but there are no mitochondria, endoplasmic reticulum, Golgi apparatus, etc.
Cell wall: Typically present, providing structural support and protection.
Capsule: An outer protective layer found in some bacteria.
Pili/Fimbriae: Hair-like appendages for attachment.
Flagella: For locomotion.
Reproduction: Primarily by binary fission.
Eukaryotic Cells: These are larger, more complex cells found in protists, fungi, plants, and animals. Their defining characteristics include:
True nucleus: Contains the cell's genetic material (linear chromosomes) enclosed within a double membrane.
Membrane-bound organelles: A diverse array of specialized compartments, each performing specific functions.
Larger size: Generally significantly larger than prokaryotic cells.
More complex organization: Allows for specialization and the formation of multicellular organisms.
Reproduction: Involves mitosis and meiosis.
The evolution of eukaryotic cells from prokaryotic ancestors is a cornerstone of evolutionary biology, with the endosymbiotic theory proposing that mitochondria and chloroplasts originated from free-living prokaryotes engulfed by ancestral eukaryotic cells.
1.2. Eukaryotic Cell Organelles and Their Functions
The intricate division of labor within a eukaryotic cell is facilitated by its various organelles.
Nucleus: The control center of the cell.
Nuclear Envelope: A double membrane perforated by nuclear pores, regulating transport between the nucleus and cytoplasm.
Nucleoplasm: The fluid inside the nucleus.
Chromatin: A complex of DNA and proteins (histones) that condenses into chromosomes during cell division.
Nucleolus: A dense region involved in ribosomal RNA (rRNA) synthesis and ribosome assembly.
Ribosomes: Sites of protein synthesis (translation). They can be free in the cytoplasm or attached to the endoplasmic reticulum.
Endoplasmic Reticulum (ER): A network of interconnected membranes involved in synthesis and transport.
Rough ER (RER): Studded with ribosomes, involved in the synthesis and folding of proteins destined for secretion, insertion into membranes, or delivery to other organelles.
Smooth ER (SER): Lacks ribosomes, involved in lipid synthesis, detoxification of drugs and poisons, and storage of calcium ions.
Golgi Apparatus (Golgi Complex): A stack of flattened membrane-bound sacs (cisternae) involved in modifying, sorting, and packaging proteins and lipids synthesized in the ER. It acts as the cell's "post office."
Lysosomes: Membrane-bound sacs containing hydrolytic enzymes, responsible for breaking down waste materials, cellular debris, and foreign invaders (e.g., bacteria). They are the cell's "recycling centers."
Vacuoles: Large membrane-bound sacs with diverse functions.
Central Vacuole (plants): Stores water, nutrients, pigments, and waste products; maintains turgor pressure.
Contractile Vacuole (protists): Pumps excess water out of the cell.
Food Vacuoles (animals/protists): Formed by phagocytosis, containing ingested food particles.
Mitochondria: The "powerhouses" of the cell, responsible for cellular respiration, generating ATP (adenosine triphosphate) – the cell's primary energy currency. They have their own circular DNA and ribosomes, supporting the endosymbiotic theory.
Chloroplasts (plants and algae): Sites of photosynthesis, converting light energy into chemical energy (sugars). Like mitochondria, they have their own DNA and ribosomes and are key players in the endosymbiotic theory.
Peroxisomes: Small, membrane-bound organelles containing enzymes that produce and break down hydrogen peroxide, involved in various metabolic processes.
Cytoskeleton: A network of protein filaments extending throughout the cytoplasm, providing structural support, facilitating cell movement, and guiding organelle transport.
Microtubules: Hollow tubes involved in maintaining cell shape, organelle movement, and chromosome separation during cell division (form spindle fibers).
Microfilaments (Actin Filaments): Solid rods involved in muscle contraction, cell division (cytokinesis), and maintenance of cell shape.
Intermediate Filaments: Provide tensile strength and help anchor organelles.
Cell Wall (plants, fungi, bacteria): A rigid outer layer that provides structural support, protection, and prevents excessive water uptake. Composed mainly of cellulose in plants.
Extracellular Matrix (ECM) (animal cells): A complex network of glycoproteins and proteoglycans secreted by cells, providing structural support, cell adhesion, and communication.
1.3. Cell Membrane: Structure and Function
The cell membrane, or plasma membrane, is a crucial boundary that separates the internal environment of the cell from its external surroundings. It is a selectively permeable barrier, regulating the passage of substances into and out of the cell.
Fluid Mosaic Model: This widely accepted model describes the cell membrane as a fluid structure with a "mosaic" of various proteins embedded in or associated with a phospholipid bilayer.
Phospholipid Bilayer: The fundamental structure, composed of phospholipids with hydrophilic (water-loving) heads facing outwards and hydrophobic (water-fearing) tails facing inwards, forming a barrier to water-soluble molecules.
Membrane Proteins: Diverse proteins with various functions:
Integral Proteins: Span the entire lipid bilayer (transmembrane proteins) or are embedded within it.
Peripheral Proteins: Loosely associated with the surface of the membrane.
Functions: Transport (channels, carriers), enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, attachment to the cytoskeleton and ECM.
Cholesterol (animal cells): A steroid embedded in the bilayer, regulating membrane fluidity across a range of temperatures.
Glycocalyx (carbohydrates): Short chains of sugars attached to lipids (glycolipids) or proteins (glycoproteins) on the outer surface, involved in cell-cell recognition and adhesion.
1.4. Membrane Transport
The cell membrane's selective permeability is vital for maintaining cellular homeostasis. Transport across the membrane can be categorized as passive or active.
Passive Transport: Does not require cellular energy (ATP). Substances move down their concentration gradient (from high to low concentration).
Diffusion: Movement of molecules from an area of higher concentration to an area of lower concentration until equilibrium is reached.
Osmosis: The diffusion of water across a selectively permeable membrane from an area of higher water concentration (lower solute concentration) to an area of lower water concentration (higher solute concentration).
Isotonic solution: Solute concentration is the same inside and outside the cell; no net water movement.
Hypotonic solution: Solute concentration is lower outside the cell; water moves into the cell, potentially causing lysis (bursting).
Hypertonic solution: Solute concentration is higher outside the cell; water moves out of the cell, causing crenation (shriveling) in animal cells or plasmolysis in plant cells.
Facilitated Diffusion: Movement of molecules across the membrane with the help of transport proteins (channel proteins or carrier proteins), still down their concentration gradient. Examples include glucose transport.
Active Transport: Requires cellular energy (ATP) to move substances against their concentration gradient (from low to high concentration).
Primary Active Transport: Uses ATP directly to power a pump (e.g., sodium-potassium pump).
Secondary Active Transport (Cotransport): Uses the energy stored in an ion gradient (established by primary active transport) to move another substance against its gradient (e.g., SGLT transporters for glucose).
Bulk Transport: For larger molecules or particles.
Endocytosis: Cell takes in substances by forming vesicles.
Phagocytosis: "Cellular eating"; engulfment of large particles or whole cells.
Pinocytosis: "Cellular drinking"; engulfment of extracellular fluid and dissolved solutes.
Receptor-Mediated Endocytosis: Specific uptake of molecules bound to receptors on the cell surface.
Exocytosis: Cell releases substances by fusing vesicles with the plasma membrane.
1.5. Cell Signaling and Communication
Cells constantly communicate with each other and their environment through complex signaling pathways, essential for coordination, development, and response to stimuli.
Signal Transduction Pathway: A series of steps by which a signal from outside the cell is converted into a cellular response.
Reception: A signaling molecule (ligand) binds to a specific receptor protein on the cell surface or inside the cell.
G-Protein Coupled Receptors (GPCRs): Common type, involving a G protein and often leading to the production of second messengers.
Receptor Tyrosine Kinases (RTKs): Receptors that, when activated, phosphorylate tyrosine residues on other proteins, initiating a cascade of events.
Ligand-Gated Ion Channels: Open or close in response to ligand binding, allowing specific ions to pass through.
Transduction: The binding of the ligand triggers a change in the receptor, initiating a cascade of intracellular events, often involving protein phosphorylation and second messengers (e.g., cAMP, Ca2+).
Response: The final cellular activity, such as gene expression, enzyme activation, or changes in cell shape/movement.
1.6. Cell Cycle and Cell Division
The cell cycle is the series of events that take place in a cell leading to its division and duplication. It consists of interphase (growth and DNA replication) and the M phase (mitosis or meiosis and cytokinesis).
Interphase: The longest phase, where the cell grows and prepares for division.
G1 Phase (First Gap): Cell grows and carries out normal metabolic functions.
S Phase (Synthesis): DNA replication occurs, resulting in two identical sister chromatids for each chromosome.
G2 Phase (Second Gap): Cell continues to grow and synthesizes proteins necessary for mitosis.
M Phase (Mitotic Phase): The actual division of the cell.
Mitosis (Nuclear Division): Division of the nucleus, resulting in two genetically identical daughter nuclei. Occurs in somatic cells for growth, repair, and asexual reproduction.
Prophase: Chromosomes condense, mitotic spindle begins to form.
Prometaphase: Nuclear envelope breaks down, kinetochore microtubules attach to centromeres.
Metaphase: Chromosomes align at the metaphase plate.
Anaphase: Sister chromatids separate and move to opposite poles.
Telophase: Chromosomes decondense, nuclear envelopes reform, mitotic spindle disappears.
Cytokinesis (Cytoplasmic Division): Division of the cytoplasm, typically overlapping with telophase.
Animal cells: Formation of a cleavage furrow.
Plant cells: Formation of a cell plate.
Meiosis (Reductional Division): A specialized type of cell division that produces four haploid (n) daughter cells (gametes) from a single diploid (2n) parent cell. Essential for sexual reproduction.
Meiosis I (Reductional Division): Homologous chromosomes separate.
Prophase I: Chromosomes condense, homologous chromosomes pair up (synapsis) to form tetrads, crossing over occurs (exchange of genetic material).
Metaphase I: Homologous pairs align at the metaphase plate.
Anaphase I: Homologous chromosomes separate and move to opposite poles.
Telophase I & Cytokinesis: Two haploid cells are formed, each with duplicated chromosomes.
Meiosis II (Equational Division): Sister chromatids separate, similar to mitosis.
Prophase II: Chromosomes condense.
Metaphase II: Chromosomes align at the metaphase plate.
Anaphase II: Sister chromatids separate.
Telophase II & Cytokinesis: Four haploid daughter cells are formed, each with unduplicated chromosomes.
Part 2: Genetics – The Science of Heredity
Genetics is the branch of biology concerned with the study of heredity and variation in living organisms. It explores how traits are passed from parents to offspring and the molecular mechanisms underlying this inheritance.
2.1. Mendelian Genetics
Gregor Mendel, an Austrian monk, is considered the "father of modern genetics" for his pioneering work with pea plants in the mid-19th century. His experiments revealed the fundamental principles of heredity.
Key Concepts:
Genes: Discrete units of heredity, segments of DNA that code for specific traits.
Alleles: Alternative forms of a gene (e.g., tall vs. dwarf pea plants).
Locus: The specific location of a gene on a chromosome.
Genotype: The genetic makeup of an individual (e.g., TT, Tt, tt).
Phenotype: The observable physical or biochemical characteristics of an individual (e.g., tall, dwarf).
Dominant allele: An allele that expresses its phenotype even when paired with a recessive allele.
Recessive allele: An allele whose phenotype is only expressed when two copies are present.
Homozygous: Having two identical alleles for a particular gene (e.g., TT, tt).
Heterozygous: Having two different alleles for a particular gene (e.g., Tt).
P generation: Parental generation.
F1 generation: First filial generation (offspring of P generation).
F2 generation: Second filial generation (offspring of F1 generation).
Mendel's Laws:
Law of Segregation: During gamete formation, the two alleles for a heritable character separate (segregate) from each other so that each gamete carries only one allele for each character. This is demonstrated by monohybrid crosses (involving one trait).
Law of Independent Assortment: When considering two or more genes, each pair of alleles segregates independently of any other pair of alleles during gamete formation. This applies to genes located on different chromosomes or far apart on the same chromosome and is demonstrated by dihybrid crosses.
Punnett Squares: A graphical tool used to predict the genotypes and phenotypes of offspring from a genetic cross.
2.2. Extensions of Mendelian Genetics
While Mendel's laws provide a strong foundation, many inheritance patterns are more complex.
Incomplete Dominance: The heterozygous phenotype is intermediate between the two homozygous phenotypes (e.g., red + white = pink flowers).
Codominance: Both alleles are expressed equally and distinctly in the heterozygote (e.g., ABO blood groups, where A and B alleles are codominant).
Multiple Alleles: More than two alleles exist for a single gene in the population (e.g., ABO blood groups have three alleles: IA, IB, i).
Epistasis: The expression of one gene modifies or masks the expression of another gene at a different locus (e.g., coat color in Labrador retrievers).
Polygenic Inheritance: Multiple genes contribute to a single phenotypic trait, often resulting in continuous variation (e.g., human height, skin color).
Pleiotropy: A single gene affects multiple phenotypic traits (e.g., sickle cell anemia affects multiple systems).
Environmental Influence: The environment can also influence the expression of genes (e.g., nutrition affecting height, temperature affecting fur color in some animals).
2.3. Chromosomal Basis of Inheritance
The work of Sutton and Boveri in the early 20th century linked Mendel's abstract "factors" to physical chromosomes, forming the chromosomal theory of inheritance.
Chromosomes: Structures made of DNA and proteins that carry genetic information.
Autosomes: Non-sex chromosomes.
Sex Chromosomes: Determine an individual's sex (e.g., X and Y in humans).
Sex-Linked Genes: Genes located on the sex chromosomes. In humans, X-linked genes are particularly important, as males (XY) only have one X chromosome, making them more susceptible to X-linked recessive disorders (e.g., color blindness, hemophilia).
Linkage and Crossing Over:
Linked Genes: Genes located on the same chromosome tend to be inherited together more often than not.
Recombination: The process of forming new combinations of alleles during meiosis, primarily through crossing over between homologous chromosomes.
Genetic Maps: Created by measuring recombination frequencies between linked genes; closer genes have lower recombination frequencies.
Chromosomal Abnormalities:
Nondisjunction: The failure of homologous chromosomes or sister chromatids to separate properly during meiosis, leading to an abnormal number of chromosomes in gametes (aneuploidy).
Monosomy: Missing one chromosome (2n-1).
Trisomy: Having an extra chromosome (2n+1), e.g., Trisomy 21 (Down syndrome).
Structural Aberrations: Deletions, duplications, inversions, and translocations of chromosomal segments.
2.4. Molecular Genetics
The discovery of the structure of DNA by Watson and Crick in 1953, building on the work of Rosalind Franklin and Maurice Wilkins, ushered in the era of molecular genetics, explaining heredity at the molecular level.
DNA (Deoxyribonucleic Acid): The genetic material.
Structure: A double helix composed of two polynucleotide strands.
Nucleotides: Building blocks of DNA, each consisting of a deoxyribose sugar, a phosphate group, and a nitrogenous base (Adenine A, Guanine G, Cytosine C, Thymine T).
Base Pairing: A always pairs with T (two hydrogen bonds); G always pairs with C (three hydrogen bonds) – Chargaff's rules.
Antiparallel Strands: The two strands run in opposite 5' to 3' directions.
DNA Replication: The process of making an identical copy of a DNA molecule.
Semiconservative Replication: Each new DNA molecule consists of one original (parental) strand and one newly synthesized strand.
Key Enzymes:
Helicase: Unwinds the DNA double helix.
DNA Polymerase: Synthesizes new DNA strands by adding nucleotides, also has proofreading activity.
Primase: Synthesizes RNA primers to initiate DNA synthesis.
Ligase: Joins DNA fragments (Okazaki fragments on the lagging strand).
Topoisomerase: Relieves supercoiling ahead of the replication fork.
Leading Strand: Synthesized continuously in the 5' to 3' direction.
Lagging Strand: Synthesized discontinuously in short segments (Okazaki fragments) in the 5' to 3' direction, which are later joined.
RNA (Ribonucleic Acid): Involved in gene expression.
Structure: Single-stranded, contains ribose sugar instead of deoxyribose, and Uracil (U) instead of Thymine (T).
Types:
mRNA (messenger RNA): Carries genetic information from DNA to ribosomes.
tRNA (transfer RNA): Carries specific amino acids to ribosomes during protein synthesis.
rRNA (ribosomal RNA): A structural and catalytic component of ribosomes.
Gene Expression: From Gene to Protein (The Central Dogma)
Transcription: The synthesis of RNA from a DNA template.
RNA Polymerase: Enzyme that synthesizes RNA.
Promoter: DNA sequence where RNA polymerase binds.
Terminator: DNA sequence signaling the end of transcription.
mRNA Processing (Eukaryotes):
5' cap: Added to the 5' end.
Poly-A tail: Added to the 3' end.
Splicing: Removal of non-coding introns and joining of coding exons.
Translation: The synthesis of a polypeptide (protein) from an mRNA template.
Genetic Code: A set of rules by which information encoded in genetic material is translated into proteins.
Codon: A three-nucleotide sequence on mRNA that specifies a particular amino acid.
Start Codon (AUG): Specifies methionine and signals the beginning of translation.
Stop Codons (UAA, UAG, UGA): Signal the termination of translation.
Degeneracy: Most amino acids are specified by more than one codon.
Universality: The genetic code is nearly universal across all life forms.
Ribosomes: Sites of translation, composed of rRNA and proteins.
tRNA: Molecules with an anticodon (complementary to mRNA codon) and an attached amino acid.
Steps:
Initiation: mRNA, tRNA with methionine, and ribosomal subunits assemble.
Elongation: Amino acids are added one by one to the growing polypeptide chain.
Termination: A stop codon is reached, and the polypeptide is released.
Mutations: Changes in the DNA sequence.
Point Mutations: Changes in a single nucleotide pair.
Silent Mutation: No change in amino acid due to degeneracy of the genetic code.
Missense Mutation: Changes one amino acid to another.
Nonsense Mutation: Changes an amino acid codon to a stop codon, leading to a truncated protein.
Frameshift Mutations: Insertions or deletions of nucleotides that are not multiples of three, leading to a shift in the reading frame and often a nonfunctional protein.
Causes: Spontaneous errors during DNA replication or recombination, or exposure to mutagens (chemicals, radiation).
Significance: Source of genetic variation, which is the raw material for evolution; can also cause genetic diseases.
2.5. Regulation of Gene Expression
Not all genes are expressed at all times or in all cells. Gene regulation is crucial for cell differentiation, development, and adaptation to the environment.
Prokaryotic Gene Regulation (Operons):
Operon: A functional unit of DNA containing a cluster of genes under the control of a single promoter.
Operator: A DNA segment within the promoter where a repressor protein can bind, blocking RNA polymerase.
Repressor: A protein that binds to the operator, inhibiting transcription.
Inducible Operons (e.g., lac operon): Usually off, but can be turned on by an inducer molecule (e.g., lactose) that inactivates the repressor.
Repressible Operons (e.g., trp operon): Usually on, but can be turned off by a corepressor molecule (e.g., tryptophan) that activates the repressor.
Eukaryotic Gene Regulation: More complex and occurs at multiple levels.
Chromatin Remodeling: Altering the structure of chromatin to make genes more or less accessible for transcription.
Histone Acetylation: Loosens chromatin, promoting transcription.
DNA Methylation: Tightly compacts chromatin, inhibiting transcription.
Transcriptional Control:
Transcription Factors: Proteins that bind to DNA regulatory sequences (enhancers, silencers) to activate or repress transcription.
Mediator Complex: Helps regulate RNA polymerase activity.
Post-Transcriptional Control:
Alternative Splicing: Different combinations of exons can be joined to produce different mRNA molecules from the same gene.
mRNA Degradation: The lifespan of mRNA molecules can be regulated.
Translational Control:
Initiation Factors: Proteins that regulate the rate of translation initiation.
Post-Translational Control:
Protein Modification: Chemical modifications (e.g., phosphorylation, glycosylation) can activate or inactivate proteins.
Protein Degradation: Regulated breakdown of proteins (e.g., via ubiquitin-proteasome system).
Conclusion
General Biology I, with its focus on Cell Biology and Genetics, provides a comprehensive overview of the fundamental building blocks and hereditary principles that govern all life. From the intricate machinery within a single cell to the elegant mechanisms of genetic inheritance and expression, these topics lay the groundwork for understanding the complexity and diversity of biological systems. This foundational knowledge is indispensable for students pursuing further studies in biology, medicine, biotechnology, and related scientific disciplines, illuminating the wonders of the living world at its most fundamental levels.
