Ultra cell structure - Vocabulary flashcards

Magnification and Resolution

• Magnification: the number of times an image is larger than its actual size.
  • Examples of units and conversions from the transcript:
  • 1 cm = 10 mm
  • 1 mm = 1000 μm
  • 1 μm = 1000 nm
  • 1 mm = 1,000,000 nm
• Resolution: the ability to distinguish between two points as separate; the shortest distance between two points that can be seen as different.
• How resolution is measured:
  • R = 1/2 × (shortest wavelength of the beam used)
  • For a light microscope (LM):
  • Uses light; shortest wavelength ≈ $ext{λ}_{min} = 400~ ext{nm}$
  • Resolution: $R = \frac{1}{2} \times 400~\text{nm} = 200~\text{nm}$
  • Magnification examples: up to around $M \approx 1500\times$
  • For an electron microscope (EM):
  • Uses electron beams (much shorter wavelength)
  • Resolution ≈ $0.5~\text{nm}$
  • Higher magnifications, up to ≈ $5\times 10^{5}\times$
• Relationship between resolution and magnification:
  • A lower resolution value means a higher ability to distinguish small details (higher resolution).

Light microscope vs Electron microscope

• Light microscope (LM)
  • Features:
  • Portable, relatively cheap, do not require extensive technical training
  • Can observe living cells
  • Real colour images (though colours can be added digitally for contrast)
  • Water drops can be added to observe movement of cells
  • Disadvantages:
  • Lower resolution and magnification compared with EM
  • Smaller organelles may be difficult or impossible to see
  • Artefacts can be introduced by staining/preserving samples; colours added digitally
• Electron microscope (EM)
  • Features:
  • Uses electron beams; very high resolution and magnification (up to 500,000×)
  • Higher detail allows observation of smaller organelles
  • Disadvantages:
  • Not portable; very expensive; requires technical training
  • Specimens are examined in vacuum; cannot observe living cells
  • Samples undergo treatments that can introduce artefacts
  • Images are black and white; colours are added digitally
• TEM (Transmission Electron Microscope) vs SEM (Scanning Electron Microscope)
  • TEM:
  • Produces 2D images of internal structures
  • Very high magnification and resolution
  • SEM:
  • Produces 3D-like images of surfaces
  • Also high magnification but generally provides surface detail rather than internal structure
• Notes on staining and contrast:
  • Stains/contrast agents are used to differentiate structures and enhance visibility in LM
  • In EM, electron-dense coatings or staining improve contrast; colours are added digitally after imaging

Parts of the light microscope

• Eyepiece (ocular)
• Eyepiece graticule (scale)
• Objective lens with different magnifications
• Stage with stage micrometer (calibrated scale)
• Coarse focus knob
• Fine focus knob
• Light source

Measuring specimens and calibration

• Stage micrometer provides a known scale; eyepiece graticule provides a relative scale.
• Example from transcript:
  • Stage micrometer: 0.1 mm corresponds to 100 μm
  • 1 eyepiece unit = 0.0025 mm = 2.5 μm
  • If a cell spans 20 units on the eyepiece graticule: cell length ≈ 20 × 2.5 μm = 50 μm
• Practical takeaway: calibration is necessary to translate graticule units to actual sizes.

Practical measurement: pollen growth rate (example from diagram)

• Setup: pollen grains grown in a sugar solution; observed with eyepiece graticule; diagram 1 (start) and diagram 2 (after 4 hours)
• Diagram data (as provided):
  • From diagram 1 to diagram 2, measurement differences observed correspond to a growth rate estimate.
  • Calculation example (interpreting the transcript):
  • Difference in unit measurement = 20 units over 4 hours
  • 1 unit ≈ 2 μm
  • Total growth = 20 × 2 μm = 40 μm in 4 h
  • Growth rate = 40 μm / 4 h = 10 μm h⁻¹
  • The transcript also shows a choice of possible rates; the derived rate from the given numbers is 10 μm h⁻¹ (aligns with option B in the slide).
• Note: The exact numerical values in the diagram are sketchy in the transcript, but the method is to measure the change in pollen grain/tube length by comparing diagram 1 and diagram 2 using the stage micrometer/eyepiece graticule calibration.
• Historical note: Epulopiscium fishelsoni (giant bacterium) was discovered in 1985.

Ultrastructure: membrane organization of organelles

• Classifications by membrane envelope:
  • Double membrane bound organelles:
  • Nucleus
  • Mitochondrion
  • Chloroplast
  • Amyloplast
  • (Some slides list endoplasmic reticulum as double-membrane, but the ER is typically a single membrane bound organelle; see notes below.)
  • Single membrane bound organelles:
  • Endoplasmic reticulum (RER and SER)
  • Golgi body
  • Vesicles
  • Lysosomes
  • Large vacuole
  • Non-membrane bound organelles:
  • Ribosomes
  • Nucleolus
  • Centrioles
• Important notes:
  • The rough endoplasmic reticulum (RER) has ribosomes on its surface and acisternal space; the ribosomes are sites of protein synthesis.
  • The smooth endoplasmic reticulum (SER) consists of tubules with no ribosomes and synthesizes lipids and steroid hormones.
  • The Golgi body consists of flattened sacs (cisternae) with vesicles at the ends; it receives proteins from the RER, modifies them (e.g., glycosylation), sorts/packages them into vesicles; it has a forming (cis) face and a maturing (trans) face.
  • Vesicles transport proteins between organelles and to the cell surface; secretory vesicles carry proteins to the plasma membrane for exocytosis; lysosomes contain hydrolytic enzymes.
  • The RER and Golgi operate together in the secretory pathway:
  • Ribosome -> RER (translation) -> cis face of Golgi (modification) -> trans face of Golgi -> secretory vesicle -> plasma membrane (exocytosis)

Protein trafficking: from ribosome to cell surface

• Step 1: Ribosomes on the RER translate mRNA into polypeptides.
• Step 2: Newly formed polypeptides enter the cisternal space of the RER for folding and initial modifications.
• Step 3: Transport vesicles bud off the RER carrying modified proteins toward the Golgi body (forming face / cis face).
• Step 4: In the Golgi, proteins undergo further modifications (e.g., glycosylation) and are packaged into Golgi vesicles.
• Step 5: Modified proteins are carried in secretory vesicles that bud from the maturing face (trans face) of the Golgi and move toward the cell surface.
• Step 6: Vesicles fuse with the plasma membrane and release their contents by exocytosis, using ATP.
• Note: Other vesicles may be directed to lysosomes for intracellular digestion.

Mitochondrion: structure and function

• Structure:
  • Double-membrane bound organelle
  • Outer membrane and inner membrane with folds called cristae to increase surface area
  • Intermembrane space between membranes; matrix inside inner membrane
  • Inner membrane contains ATP synthase; matrix contains loop of DNA and 70S ribosomes
  • Often rod-shaped
• Key features:
  • Cristae increase surface area for ATP synthase activities
  • Outer membrane is more permeable than inner membrane
  • Matrix contains genetic material (loop of DNA) and ribosomes
• Function:
  • Site of aerobic respiration and ATP production
  • Also contributes to lipid synthesis

Chloroplasts and amyloplasts

• Chloroplast:
  • Double membrane bound organelle
  • Site of photosynthesis
  • Internal structures:
  • Thylakoids arranged into stacks called granum (plural: grana)
  • Grana contain chlorophyll and are connected by stroma lamellae
  • Stroma is the fluid around thylakoids where the Calvin cycle occurs
  • Genetic features:
  • Loop of DNA
  • 70S ribosomes
  • Additional notes:
  • Both chloroplasts and mitochondria have their own DNA and ribosomes and a double membrane with an inner folded membrane (cristae in mitochondria; thylakoids in chloroplasts) to maximize surface area for metabolic reactions
• Amyloplast:
  • Double membrane bound organelle
  • Stores starch (amylose and amylopectin) as granules
  • Found in plant parts with large starch storage (e.g., tubers like potatoes)

Lysosomes

• Structure:
  • Dark spherical sacs
  • Single membrane bound
  • Contain hydrolytic enzymes for digestion
• Functions:
  • Digestion of worn-out organelles (autophagy) and foreign material via phagocytosis
  • Fusion with phagosomes to digest engulfed bacteria
  • Role in apoptosis (programmed cell death)
  • Some lysosome-like processes contribute to exocytosis in specialized cells (e.g., acrosome content release in sperm)
• Note: Lysosomes are an important digestive compartment for intracellular turnover and defense

Centrioles and nucleus

• Centrioles:
  • Non-membrane bound organelle found in animal cells only
  • Usually two centrioles at right angles to one another in the centrosome
  • Structure: each centriole composed of nine triplets of microtubules
  • Function: act as microtubule organizing centers (MTOC); organize spindle fibers during cell division to separate chromosomes
• Nucleus:
  • Double membrane bound organelle; nuclear envelope with nuclear pores
  • Outer membrane continuous with rough endoplasmic reticulum
  • Contains chromatin (DNA with histone proteins) in a loosely coiled form when not dividing
  • Contains nucleolus (site of rRNA synthesis) and ribosomal subunit assembly
  • Nuclear pores regulate transport between nucleus and cytoplasm

Nucleus, ribosomes, and chromatin

• Chromatin/Chromosome:
  • DNA wound around histone proteins
  • Before mitosis: chromatin is loosely packed; genes are active and transcription occurs; mRNA formed in the nucleus
  • During mitosis: chromatin condenses into visible chromosomes
• Nucleolus:
  • Region within nucleus where ribosomal RNA (rRNA) synthesis occurs and ribosomal subunits begin to assemble with proteins
• Nuclear envelope:
  • Double membrane that protects DNA from cytoplasmic enzymes; pore complexes regulate exchange with cytoplasm
• Ribosomes:
  • Non-membrane bound
  • Two subtypes:
  • 80S ribosomes in eukaryotes (e.g., cytoplasm and rough ER); size ≈ 25 nm
  • 70S ribosomes in mitochondria and chloroplasts (and in prokaryotes); smaller (~18 nm)
  • Sites of translation and protein synthesis

Prokaryotes vs Eukaryotes

• Prokaryotes:
  • No membrane-bound organelles
  • Circular DNA (naked, not enclosed by a nucleus) in a nucleoid region
  • 70S ribosomes
  • Cell wall made of peptidoglycan (murein)
  • Additional structures: flagellum, pili, capsule, plasmids, mesosomes (historical term)
• Eukaryotes:
  • Membrane-bound organelles present (nucleus, mitochondria, chloroplasts, etc.)
  • Linear DNA associated with histone proteins, enclosed in a nucleus
  • 80S ribosomes (cytoplasm and RER); 70S ribosomes in mitochondria/chloroplasts
  • Plant and fungal cell walls differ (cellulose in plants, chitin in fungi)
• Shared features:
  • Cytoplasm, cell membrane, ribosomes present in both
• Other notes from the transcript:
  • Prokaryotes may have plasmids carrying antibiotic resistance genes
  • Some historical terms like mesosomes are less emphasized in modern textbooks

Plant cell ultrastructure vs animal cell features

• Plant cell features in the transcript include:
  • Large central vacuole with tonoplast (vacuolar membrane)
  • Chloroplasts with thylakoids, grana, stroma, and chlorophyll
  • Amyloplasts for starch storage
  • Plasmodesmata (cytoplasmic channels) between plant cells
  • Middle lamella (cell-cell adhesion layer between cell walls)
  • Cell wall made of cellulose
• Animal cell features (where applicable):
  • Typically lack chloroplasts and large central vacuoles
  • Lysosomes and centrioles are common
• Shared features:
  • Nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, ribosomes, cytoskeleton, plasma membrane

Large-scale organization: tissue and organ definitions

• Level of organization:
  • Cell: smallest unit of life
  • Tissue: group of similar cells performing a specific function
  • Organ: group of different tissues working together to perform a function
• Types of tissues mentioned in the transcript:
  • Muscle
  • Nervous
  • Connective tissue (with extracellular matrix such as bone, cartilage, and blood)
  • Epithelium (epithelial cells) – a layer lining surfaces
• Epithelium types mentioned:
  • Squamous epithelium: flat cells lining ducts and vessels (e.g., alveoli, blood vessels)
  • Columnar epithelium: tall, rectangular cells (e.g., trachea, oviduct)
  • Endothelium: one layer of squamous cells lining inner surfaces of organs

Summary from the plant and animal cell ultrastructure comparison

• Size order (from largest to smallest, as given):
  • Nucleus > Chloroplast > Mitochondrion > Nucleolus > Lysosomes > Centrioles > Ribosomes
• LM vs EM visibility:
  • LM can show nucleus, chloroplast, mitochondrion, nucleolus, cell membrane, cell wall, vacuole
  • EM reveals more organelles: lysosomes, centrioles, ribosomes, ER, Golgi, grana of chloroplasts, vesicles

Tracing the secreted protein: radioactive amino acid pathway

• Pathway: Ribosomes -> RER -> Golgi body (cis face) -> Golgi vesicles -> secretory vesicles -> cell surface membrane
• Steps:
  1. Ribosomes synthesize proteins on the RER (translation occurs here).
  2. Proteins enter the cisternal space of the RER for folding and initial modifications.
  3. Transport vesicles bud off the RER and migrate to the Golgi (forming face / cis face).
  4. Proteins are further modified (e.g., glycosylation) in the Golgi and packed into Golgi vesicles.
  5. Modified proteins are packed into secretory vesicles and bud off from the trans face of the Golgi.
  6. Vesicles move to the plasma membrane and fuse with it via exocytosis, releasing contents outside the cell; ATP is used in the process.
• Additional destination: some vesicles fuse with lysosomes for intracellular use

Plant cell-specific ultrastructure details (from the plant cell diagram and text)

• Chloroplast:
  • Double membrane bound; stroma contains enzymes of the Calvin cycle; thylakoids contain chlorophyll; granum/grana are stacks of thylakoids
  • Contains loop of DNA and 70S ribosomes
• Large vacuole and tonoplast:
  • Single membrane bound; stores sap (water, salts, sugars)
  • Functions: turgidity, lowering water potential to enable water influx by osmosis, storage of sugars and salts
• Amyloplast:
  • Stores starch; double membrane bound; abundant in plant storage tissues (e.g., potatoes)
• Middle lamella and plasmodesmata:
  • Middle lamella between adjacent plant cell walls; plasmodesmata allow transport and communication between plant cells

Trace: key numerical references and units relevant to microscopy

• Resolution values:
  • LM resolution ≈ $200~\text{nm}$
  • EM resolution ≈ $0.5~\text{nm}$
• Wavelengths (example):
  • Light: $\lambda_{ ext{min}} \approx 400~\text{nm}$
• Magnifications mentioned:
  • LM up to about $1500\times$
  • EM up to about $5 \times 10^{5}\times$
• Measurement calibrations:
  • 0.1 mm stage micrometer corresponds to 100 μm (relationship example)
  • 1 eyepiece unit ≈ 0.0025 mm ≈ 2.5 μm
  • If a cell spans 20 units on the eyepiece, cell length ≈ 20 × 2.5 μm = 50 μm

Check list (study aids)

• Magnification definition
• Resolution definition
• Units: mm, μm, nm
• LM vs EM: advantages and disadvantages
• Why stain cells in LM
• TEM (2D) vs SEM (3D) characteristics
• Stage micrometer calibration for eyepiece graticule
• Labels of common animal cell organelles
• Double membrane vs single membrane vs non-membrane bound organelles
• RER and SER: structure and function
• Golgi apparatus: cis and trans faces; protein processing and trafficking
• How proteins reach the cell membrane (secretory pathway)
• Mitochondrion: structure and function
• Chloroplasts and amyloplasts: structure and function
• Lysosomes: structure and functions (including autophagy and apoptosis)
• Centrioles and centrosomes: role in mitosis
• Nucleus: structure (nuclear envelope, pores, chromatin, nucleolus)
• Ribosomes: 80S vs 70S and their locations
• Prokaryotes vs Eukaryotes: key differences
• Plant cells: vacuole, chloroplasts, amyloplasts, plasmodesmata
• Level of organization: cell, tissue, organ; tissue types

Note on expressions and symbols

• All formulas and numerical relations are presented with LaTeX formatting in this note. For example:
  • Resolution: $R = \frac{1}{2} \lambda_{\min}$
  • Light microscope resolution with a 400 nm wavelength: $R = \frac{1}{2} \times 400~\text{nm} = 200~\text{nm}$
  • Example of growth rate calculation: if a length increases by 20 μm over 4 h, growth rate = $\frac{20~\mu\text{m}}{4~\text{h}} = 5~\mu\text{m}\,\text{h}^{-1}$

End of notes