foundations of biology

Introduction to Cell Biology

  • A human body consists of trillions of cells organized to maintain distinct internal compartments.

    • These compartments keep body cells separated from external environmental threats.

    • They also separate internal body fluids from microorganisms on body surfaces (e.g., intestinal tract has more bacterial cells than human cells).

  • Skin acts as a physical barrier with tightly packed epidermal cells preventing harmful microorganisms from entering.

  • Respiratory tract lined with specialized cells that trap and expel pathogens while enabling gas exchange (oxygen and carbon dioxide).

  • These examples highlight cellular organization's role in maintaining internal stability and defending against external threats.

The Basic Unit of Life

  • All living organisms exhibit key characteristics that distinguish them from non-living matter:

    • Cellular organization

    • Metabolism (energy transformation)

    • Growth and development

    • Reproduction

    • Response to stimuli

    • Homeostasis

    • Adaptation

    • Heredity through genetic material

  • Cells are the basic unit of life because:

    • They are the smallest structures capable of performing all life processes independently.

    • They contain DNA that directs activities, maintain internal stability, and generate new cells.

    • Cells provide structural and functional foundation for life, enabling survival, reproduction, and evolution.

General Cell Structure: Plasma Membrane, Cytoplasm, and Nucleus

  • Cell membrane (plasma membrane) separates internal cell contents from the external environment.

    • Provides a protective barrier and regulates material passage in and out of the cell.

    • Composed primarily of phospholipids arranged in two layers, containing cholesterol and proteins.

  • Cytoplasm: Internal compartment of a living cell, made of cytosol and organelles.

    • Cytosol: Jelly-like substance providing the fluid medium for biochemical reactions; primarily consists of water.

  • Organelles: Membrane-enclosed bodies within the cell, each performing unique functions alongside each other for cellular health.

  • The nucleus: Central organelle containing the cell's DNA.

Endoplasmic Reticulum (ER)

  • Endoplasmic reticulum (ER) is a system of channels continuous with the nuclear membrane, composed of lipid bilayer material.

  • Functions:

    • Rough ER (RER): Dotted with ribosomes; involved in protein synthesis and modification.

    • Ribosome: Organelle serving as the protein synthesis site; ribosomes can be bound (to ER) or free (in cytosol).

    • Smooth ER (SER): Lacks ribosomes, synthesizes phospholipids and steroid hormones, sequesters and regulates cellular calcium ions (Ca2+).

    • Rough ER synthesizes proteins destined for cell membranes or export, often undergoing glycosylation before vesicle transport to the Golgi apparatus.

Golgi Apparatus

  • The Golgi apparatus consists of stacked, flattened discs resembling pancakes, membranous.

  • Roles:

    • Modified proteins and lipids (via glycosylation, phosphorylation, sulfation, proteolytic cleavage).

    • Sorts and packages products for their destinations.

    • Two sides:

    • Cis face: Receives vesicles with products.

    • Trans face: Releases newly packaged vesicles containing processed products, e.g., for cell export.

Lysosomes

  • Lysosomes are organelles containing enzymes to break down and digest unnecessary cellular components.

  • Enzymes are packaged in transport vesicles (lysosomes) from the Golgi apparatus.

    • Autophagy: Process where a cell digests its own damaged organelles/proteins.

    • Purposes include promoting cell survival under stress, recycling nutrients, and removing damaged components.

    • Lysosomal membranes include proteins such as proton pumps, transporters, and protective glycoproteins.

Mitochondria

  • Mitochondria (plural of mitochondrion): Membranous, bean-shaped organelles functioning as "energy transformers".

    • Structure: Outer and inner lipid bilayer membranes; inner membrane formed into cristae for increased surface area.

    • Biochemical reactions of cellular respiration occur along the inner membrane to convert stored energy in nutrients (e.g., glucose) into ATP.

    • ATP is the usable energy for cells that require it constantly (notably in high ATP cells like muscle and nerve cells).

Cell Nucleus

  • The nucleus is the largest organelle often considered the cell's control center.

    • It stores genetic instructions for protein synthesis.

    • Some cells (e.g., muscle cells) are multinucleated, while mammalian red blood cells lack nuclei altogether.

    • Contains DNA, the blueprint for cellular function and product synthesis.

    • Nuclear envelope: Surrounds the nucleus, consisting of two lipid bilayers with nuclear pores for protein, RNA, and solute transport between cytoplasm and nucleus.

    • Nucleolus: Dark-staining mass within the nucleus responsible for synthesizing rRNAs to construct ribosome subunits, exported to the cytoplasm for protein synthesis (ribosome biogenesis).

The Flow of Information in the Cell

  • Genetic instructions are arranged in ordered strands of DNA, which wrap around histone proteins forming nucleosomes (basic unit of chromatin).

    • Each nucleosome consists of ~147 base pairs of DNA wrapped around an octamer of histones (H2A, H2B, H3, H4).

    • Histone H1 links nucleosomes together.

    • Nucleosomes coil and fold into chromatin fibers that compact DNA further into chromosomes during cell division.

  • Humans have approximately 22,000 genes on 46 chromosomes.

  • The central dogma of molecular biology states that information flow is as follows:

    • DNA is transcribed into mRNA in the nucleus.

    • mRNA travels to ribosomes (in cytoplasm) to be translated into proteins.

  • Proteins have varied functions within the cell, maintenance, growth, and response to environmental changes.

Structures and Functions of DNA, RNA, and Proteins

  • DNA: Double-stranded molecule made up of nucleotides containing deoxyribose sugar, a phosphate group, and nitrogenous bases (adenine, thymine, cytosine, guanine).

    • Function: Acts as the genetic blueprint for growth, development, and reproduction; sequences encode protein-building instructions.

  • RNA: Single-stranded molecule similar to DNA, containing ribose sugar and uracil instead of thymine.

    • Types of RNA:

    • mRNA: Messenger RNA, carries genetic code from DNA to ribosomes.

    • tRNA: Transfer RNA, brings amino acids to the ribosomes for protein synthesis.

    • rRNA: Ribosomal RNA, forms part of ribosome structure.

  • Proteins: Large molecules composed of amino acids linked by peptide bonds, executing majority cellular functions.

    • Functions range from catalyzing reactions (enzymes) to providing structural support and regulating processes (hormones).

Transcription Regulatory Elements

  • A gene includes a promoter upstream of the transcription start site, with a 5′ untranslated region (5′ UTR) followed by coding exons interrupted by introns spliced out of mRNA.

  • Transcription factors: Proteins that bind specific DNA sequences controlling gene expression via promoters, enhancers, and silencers.

    • Promoters are position-specific and located upstream; enhancers and silencers may be located almost anywhere in relation to a gene.

Alternative Splicing

  • Alternative splicing allows for one gene to code for multiple proteins by varying the exon composition of the messenger RNA.

  • During RNA splicing, exons of pre-messenger RNA are reconnected in different arrangements, leading to various mature mRNAs and proteins.

Cell Cycle

  • Cell cycle: Ordered sequence of events for cell growth, DNA replication, and division into two daughter cells.

    • Consists of interphase (G1, S, G2) followed by M phase (mitosis and cytokinesis).

    • G0: Resting state where cells may stop dividing temporarily or permanently.

  • Phases:

    • G1: Cell growth, organelle synthesis in preparation for DNA replication.

    • S: DNA replication occurs, duplicating genetic material.

    • G2: Additional growth, protein synthesis, DNA repair in preparation for mitosis.

    • M: Chromosome segregation and division producing two daughter cells.

  • Checkpoints at G1/S, G2/M, and metaphase ensure DNA is undamaged and chromosomes are properly aligned.

  • M phase subphases:

    • Prophase: Chromosomes condense, mitotic spindle begins to form.

    • Prometaphase: Nuclear envelope breaks down, spindle microtubules attach to chromosomes.

    • Metaphase: Chromosomes align at the cell's center.

    • Anaphase: Sister chromatids are pulled apart to opposite poles.

    • Telophase: Chromosomes reach poles, nuclear membranes reform, spindle disassembles.

  • Actin and microtubules are cytoskeletal systems crucial for cell division.

Somatic Cells

  • Somatic cells: All body’s cells excluding germ cells (sperm and egg).

    • Typically diploid, containing two sets of chromosomes.

Examples of Somatic Cells

  • Endothelial Cells: Form the endothelium lining blood vessels, regulate blood flow, act as selective filters for gas and immune cell passage.

    • Human endothelial cells can be isolated for studying angiogenesis, cancer therapy, and wound healing.

  • Cardiomyocytes: Specialized muscle cells controlling heart contractions; elongated and branched for interconnection.

  • Keratinocytes, fibroblasts, melanocytes: Forms of somatic cells in skin, contributing to structure and pigmentation.

  • Erythrocytes: Red blood cells carrying hemoglobin for oxygen transport.

Neurons and Their Characteristics

  • Neurons: Major signaling units in the central nervous system, dynamically polarized with distinct structural functionality.

    • Polarity refers to asymmetrical organization necessary for directional processes; different parts perform specialized tasks.

  • Neuronal morphology in 2D culture:

    • Dendrites: Short, branching extensions for signal reception.

    • Axon: Long extension sending signals.

    • Soma: Round cell body containing nucleus.

    • Synapses: Areas where signals are transmitted between axons and dendrites.

Hepatocytes and Epithelial Cells

  • Human Hepatocytes: Liver cells responsible for metabolism, detoxification, bile production, nutrient storage, and contributing to immunity.

    • Generally polygonal when cultured, distinct from their cuboidal organization in liver tissue.

  • Bronchial Epithelial Cells: Main cells lining bronchi, crucial for respiratory health and homeostasis; maintain tight junctions and structural integrity.

2D vs. 3D Culture Techniques

  • 2D Culture: Cells grown in a flat monolayer on a solid surface such as a petri dish or plastic flask; this setup lacks the height dimension, leading to superficial interactions.

    • Advantages:

      • Easy setup: Requires minimal equipment and can be conducted in standard laboratory conditions.

      • Lower costs: Materials and consumables are cheaper compared to 3D cultures.

      • Efficient screening: High throughput screening compatibility allows for rapid analysis of compound effects on cell behavior.

      • Reproducibility: Consistent results due to uniformity in cell exposure to experimental conditions.

    • Disadvantages:

      • Lack of physiological relevance: Cells do not behave the same way as they would in vivo due to the absence of the natural three-dimensional extracellular matrix (ECM) and cell-cell interactions.

      • Limited signaling: Cells may not respond accurately to growth factors and signaling molecules.

      • Altered gene expression: Differences in gene expression profiles compared to cells in their natural environment.

  • 3D Culture: Cells grown in a matrix or scaffold that allows for a more realistic environment, mimicking in vivo cellular interactions and spatial arrangements.

    • Advantages:

      • Enhanced cell-cell interactions: Cells can interact in multiple dimensions, leading to more complex communications and functional behaviors as seen in tissues.

      • Improved cell-matrix interactions: Customized extracellular matrices can be used to replicate tissue-specific conditions, enhancing nutrient and oxygen gradients.

      • Realistic proliferation and differentiation: Cells demonstrate more appropriate growth patterns and specialized functions, leading to a more genuine representation of tissue behavior.

      • Better responses to drug therapies: 3D cultures allow researchers to observe how cells respond to drugs, predicting in vivo outcomes more effectively.

    • Disadvantages:

      • More complex setup: Requires specialized materials and techniques for cell culture which may involve increased cost and time.

      • Difficulty in analysis: Characterizing the cells within a 3D matrix can be more challenging compared to analyzing flat monolayers.

      • Variability: The complexity of 3D structures can lead to batch-to-batch variations affecting reproducibility in experiments.

    • 3D cultures may simulate specific tissue environments and support cell differentiation and maturity, enabling research on tissue regeneration, drug testing, and disease modeling. Overall, the choice between 2D and 3D culture techniques ultimately depends on the research question, desired outcomes, and available resources.

Advantages of 3D Mammalian Cell Culture

  • 3D cultures more accurately replicate in vivo cell behaviors through:

    • Enhanced cell-cell interactions

    • e.g., gap junctions, tight junctions, and adherens junctions for communication and structural integrity.

    • More complex cell-matrix interactions with tailored ECMs enabling physiological conditions.

    • Gradients for oxygen, nutrients, and metabolites mimicking tissue environments.

    • More realistic proliferation and differentiation behaviors and better responses to drug therapies.

2D Mammalian Cell Culture

  • Remains the gold standard in many research areas for its:

    • Cost-effectiveness and simplicity.

    • High throughput screening compatibility and reproducibility.

    • Easy analysis and monitoring of cell behavior.

  • Findings facilitate initial screening in drug development due to controlled conditions.