Microscope, Cell Structure, and Cell Cycle Notes

Microscope Safety, Setup, and Basics

• Attendance and access policy: password stays the same to prevent home logins from earning credit; attendance in lecture and lab tied to completing attendance questions during lab after the password change.

• Lab safety and practices: ensure Laboratory Safety Agreement is completed; a new handout on abdominal quadrant/regions and organs will be posted under Lab 1 Study Materials > Tables and Figures; look for additional chapter-related tables/figures.

• General logistics: instructor plans to post materials and continue to update study aids; questions from last week were answered; today’s focus is microscopy and foundational cell biology.

Microscope Safety and Handling

• Carrying the microscope: use two hands; one around the arm (the back portion) and the other at the base.

• The stage and cord: wrap the cord around, lower the stage fully before carrying; power should be off when storing.

• Storage orientation: the ocular lens should face the wall when stored; improper storage will incur a penalty per incident per instructor’s joke about lunch.

• Cleaning and lens care: wipe lenses with lens paper (special paper in the drawer); do not use regular paper towels.

• Optional maintenance: a white booklet in the common drawer contains tissue paper for lens cleaning; optional but recommended use after and before viewing.

Parts of the Microscope and Basic Terminology

• Base: bottom of the microscope; power button may be at the back or front.

• Illuminator: light source located under the stage; a light bulb may burn out and require replacement.

• Rheostat: side-control knob (or dial) to adjust brightness of the light.

• Coarse focus knob (big knob): moves the stage up and down; provides major focus adjustments.

• Fine focus knob: small inner knob; moves the stage in tiny increments for precise focusing.

• Stage: the black square where the slide sits; the stage has a hole in the center for light to pass through.

• Diaphragm (aperture): lower assembly consisting of a disc under the stage that regulates light amount.

• Condenser: another disc under the stage that focuses light onto the specimen.

• Clips/slide holder: two small clips (described visually as Reese’s Mini cups) hold the slide in place; clips resemble an L-shaped silver piece and a claw-like mechanism.

• Stage movement knobs: two knobs on the side (often described as small Reese’s cups) control left-right and forward-back movement of the stage.

• Ocular lens (eyepiece): binoculars or single lens at the top; magnification typically 10× and adjustable by eyepiece.

• Objective lenses (turret): rotating nosepiece containing multiple lenses of different magnifications (commonly 4×, 10×, 40×, and sometimes 100× for oil immersion).

• Arm and body tube: the curved back (arm) for carrying; the body tube houses prisms to direct light to the oculars.

• Objective magnifications and color codes: 4×, 10×, 40×, (and sometimes 100× for oil immersion) with color ribbons sometimes used to indicate magnification level.

• Oculars/eyepieces: typically 2 if the microscope is binocular; total magnification depends on both ocular and objective.

• Lens terminology: ocular lens (eye piece) vs. lens; make sure spelling is correct (ocular vs. eye piece).

• Common storage note: the stage should be lowered for safe storage; ensure stage is down and light is off.

Magnification, Resolution, and Light Path

• Total magnification formula: the final image magnification equals the objective magnification multiplied by the ocular magnification.

  • M = m{ ext{objective}} imes m{ ext{ocular}}

• Examples:

  • 4× objective with 10× ocular yields M = 4 imes 10 = 40.

  • 10× objective with 10× ocular yields M = 10 imes 10 = 100.

  • 40× objective with 10× ocular yields M = 40 imes 10 = 400.

• Light path through the microscope: illuminator → condenser → specimen → objective lens → body tube → prism → ocular lens (eye piece).

• Resolution (clarity) and resolving power: the ability to distinguish two close objects as separate.

• Typical resolving power mentioned: 0.4 nanometers (the lab context uses this value for discussion of limits of resolution).

• Refractive index concept: light bends (refracts) when passing between media; the refractive index depends on the medium.

• Immersion oil and high magnification: for 100× objective, an immersion oil is often used between the slide and the objective to match refractive indices and increase resolution; in this lab, immersion oil is not commonly used unless directed.

• A practical note: 99% of the lab sessions do not use immersion oil unless specifically required for a slide.

Anatomy of the Light Path and Why Refractive Index Matters

• Glass slide → cover slip → specimen → objective lens → oculars: light travels through glass, specimen, and air; air has a different refractive index than glass/oil, affecting resolution.

• Oil immersion uses a drop of oil between the slide and 100× objective to improve refractive index matching, enhancing resolution.

• When not using oil, air in the gap reduces imaging quality at high magnifications.

The Living Cell: Basic Structure and Organization

• Cells are the fundamental units of life; there are about 250 distinct cell types in the human body; many variations in size, shape, and function.

• Cell boundary and contents: plasma membrane encloses cytoplasm and organelles; nucleus contains genetic material.

• Key organelles mentioned for context (not all are visible with basic microscopy): mitochondria, Golgi apparatus, etc.

• Nucleus and genetic information: nucleus contains genetic material (DNA) enclosed by a nuclear envelope.

• Chromatin: DNA packaged with histone proteins forming chromatin (DNA + histones).

• Diploid genome: humans have 2 sets of chromosomes; somatic (non-gamete) cells have 46 chromosomes (2n = 46).

  • 2n = 46

• Haploid genome: gametes (egg and sperm) have 23 chromosomes (n = 23) after meiotic reduction.

  • n = 23

• Chromosome structure during cell division: chromosomes become visible as condensed chromatin during mitosis; sister chromatids held together at the centromere.

• Chromosome: two sister chromatids (each a duplicate of a single chromosome) held together by a centromere.

• Nuclear envelope: in different phases, the nuclear envelope dissolves (prophase) and re-forms (telophase).

• The nucleus contains DNA; not all organelles are visible at light microscopy; nucleus often visible, other organelles require higher resolution.

The Cell Cycle: Phases and Checkpoints

• Two major cell-cycle phases:

  • Interphase: growth, metabolism, and DNA replication in preparation for division.

  • M phase (Mitosis or Meiosis): cell division and formation of daughter cells.

• Interphase subdivisions:

  • G1 (Gap 1): cell growth and normal metabolism; major checkpoint occurs here.

  • S (Synthesis): DNA replication occurs; chromosomes are duplicated.

  • G2 (Gap 2): final preparation for division; organelles duplicated; checkpoint prior to M phase.

• G0: some cells may exit the cell cycle into a non-dividing state (G0); cells may re-enter the cycle later.

• Checkpoints and cancer: checkpoints regulate whether the cell proceeds to the next phase; cancer can arise when a cell overrides checkpoints and divides inappropriately.

• M phase overview: mitosis or meiosis; in this course, emphasis is on mitosis (the reproductive division in somatic cells) for the context of the lesson.

• DNA replication in S phase ensures each daughter cell will receive a full set of genetic information.

• After mitosis, cytokinesis completes cell division by physically separating the cytoplasm into two daughter cells.

Mitosis: Stages and Key Events (PMAT + Cytokinesis)

• Prophase

  • Nuclear envelope dissolves.

  • Chromatin condenses into visible chromosomes (shortens and thickens).

  • Centrosomes move to opposite poles and organize spindle fibers.

• Metaphase

  • Chromosomes align single file along the metaphase plate (the cell’s equatorial plane).

  • Spindle fibers attach to centromeres of chromosomes.

• Anaphase

  • Centromeres split and sister chromatids are pulled toward opposite poles by shortening of spindle fibers.

• Telophase

  • Nuclear envelopes re-form around two clusters of chromosomes, creating two nuclei.

  • Chromosomes begin to de-condense.

• Cytokinesis

  • Cytoplasm divides; the cell membrane pinches inward at the cleavage furrow to form two separate cells.

  • Incomplete or faulty cytokinesis can lead to conditions like conjoined twins when cells remain connected.

• Visualization cues: in lab slides (fish embryo examples), look for mitotic stages; early metaphase shows chromosomes aligned; anaphase shows separation; cytokinesis shows cleavage.

Key Structural Details for Mitosis

• Chromosome structure during S phase: chromosomes replicate to form sister chromatids; chromatids are held together at the centromere.

• Centrosomes/centrioles: organize spindle apparatus; microtubules emanate to separate chromatids.

• Centromere: constricted region where sister chromatids are held together; attachment point for spindle fibers via kinetochores.

• Sister chromatids: identical copies of a chromosome held together at the centromere until separation in anaphase.

• Metaphase plate: the imaginary plane in the center of the cell where chromosomes line up during metaphase.

The DNA Packaging and Gene Content in the Nucleus

• DNA packaging: DNA is wrapped around histone proteins to form chromatin; chromatin condenses into visible chromosomes during mitosis.

• Chromatin vs. chromosomes: chromatin is the relaxed form; chromosomes are condensed for segregation during mitosis.

• Cells contain many chromosomes; in humans, 46 in somatic cells after packaging; 23 pairs (diploid).

• During mitosis, the chromosome number remains the same (no change in chromosome number): the purpose of mitosis is growth and replacement, not changing the chromosome count.

Life Cycle and Cellular Growth: Analogies and Examples

• Human life cycle stages (for context): egg fertilizes sperm → zygote → embryo → baby → newborn → toddler → adolescent → adult → middle age → elderly → death.

• Cell life cycle analogy: interphase = cell’s “working life” (growth, metabolism, function); M phase = cell division to produce new cells.

• Relevance of checkpoint controls: checkpoints ensure cells only proceed when conditions are right; failures can lead to uncontrolled division (cancer).

Practical Lab Notes and Visuals

• Slide handling practice: red-dot slides (2740) and blue-dot slides (2840) indicate different sample sets; look for red or blue dot cues.

• Stage and slide orientation: the stage clip secures the slide; the letter e slide is used to demonstrate inverted/left-right reversal due to light path, so sketch observed orientation on scratch paper.

• Observation strategy: for tissue samples, examine under 4×, 10×, and 40× objectives when possible; anticipate being asked to identify tissue type or organ in practical exams.

• Light and image orientation: the image seen through the eyepiece is inverted and flipped due to light path; this is normal and should be noted when sketching observed cells.

• Fish embryo slides: examples of cells in different mitotic stages can appear in lab imagery; look for single stripes (metaphase) and multiple chromosomes aligned in the center or pulled apart in anaphase.

Quick Reference: Common Terms and Definitions

• Plasma membrane: boundary of the cell; separates internal environment from external.

• Cytoplasm: fluid inside the cell that contains organelles and cytosol.

• Nucleus: contains DNA; enclosed by nuclear envelope.

• Nuclear envelope: membrane surrounding the nucleus; dissolves during prophase and re-forms during telophase.

• Chromatin: DNA + histone proteins; condenses to form chromosomes during mitosis.

• Chromosome: condensed chromatin; comprises two sister chromatids joined at the centromere.

• Centromere: region where sister chromatids are held together; focal point for spindle attachment.

• Sister chromatids: identical copies of a chromosome after S phase; separated during anaphase.

• Kinetochore: protein structure at the centromere that attaches spindle fibers.

• Centrosome/Centrioles: organizing centers for spindle apparatus; move chromosomes to opposite poles.

• Metaphase plate: imaginary plane where chromosomes align during metaphase.

• Spindle fibers: microtubules that separate chromatids during mitosis.

• Ocular lens (eyepiece): usually 10× magnification; combined with objective magnification to yield total magnification.

• Objective lenses: 4×, 10×, 40×, (and sometimes 100× oil immersion).

• Immersion oil: used with 100× objective to improve resolution by refractive-index matching.

• Numerical concepts: diploid vs. haploid, 2n = 46, n = 23.

• Resolution: ability to distinguish two close objects as separate; typical reference value discussed was 0.4 nm resolving power.

• Refractive index: measure of how much light bends when crossing media; oil immersion changes the refractive path to increase resolution.

• PMAT: the sequence of mitotic stages: Prophase, Metaphase, Anaphase, Telophase; Cytokinesis follows.

• G0, G1, S, G2: phases of interphase; checkpoints control progression and can contribute to cancer if overridden.

• Cancer concept: bypassing checkpoints leads to uncontrolled cell division.

• Practical tips: practice looking at samples under multiple objectives; always be mindful of orientation and measurement when identifying tissues.

Summary of Core Takeaways

• Microscopes require careful handling, labeling, and maintenance; safety and proper storage are essential.

• Understanding magnification and resolution is foundational to interpreting microscopic images; total magnification is the product of objective and ocular magnifications.

• Light path, refractive index, and the use of immersion oil affect image clarity; know when oil is appropriate.

• Cells are organized into a nucleus containing DNA packaged as chromatin; during mitosis, chromatin condenses into chromosomes with sister chromatids held at centromeres.

• The cell cycle includes interphase (G1, S, G2) and M phase (mitosis and cytokinesis); checkpoints help ensure fidelity, and bypassing them can lead to cancer.

• Mitosis consists of prophase, metaphase, anaphase, and telophase, followed by cytokinesis, producing two genetically identical diploid daughter cells.

• Practical lab observations reinforce the importance of examining samples under multiple magnifications and recognizing orientation changes due to optical paths.