intro micro
Exam context and scoring overview
About five questions out of a larger set; this specific question is described as the hardest one for the class. The surrounding questions typically yield ~78% class performance, but this one drops lower.
Instructor encourages reviewing wrong answers by scheduling an appointment or visiting office hours to go over questions from the quiz/exam.
Classroom score and thresholds
You should see a current classroom score in your credit book.
There is a 50% threshold for the classroom score; most students are at or above 50%, but some are not. If you don’t hit the threshold, you won’t receive today’s points until you meet the threshold.
Normal class questions will be administered today, contributing to the overall score.
Reading questions and exam boosting
Reading questions provide a boost that is half participation points and half correctness.
If you answer all reading questions incorrectly but still complete them, you would get a 2.5% boost on the exam.
If you answer all reading questions correctly, you get a 5% boost on the exam (two chances to achieve this 5% boost).
The message is to do the homework/questions to maximize this boost in future assessments.
Exam normalization (scaling) policy
Each exam is scaled so that the highest score becomes 100.
If the top score is 90 or higher, scores are scaled proportionally so that the top score maps to 100.
In this particular exam iteration, the class reported unusually high extra credit, with estimated top scores around 105% (i.e., some students exceeded 100% due to extra credit).
The resulting average (including extra credit) tends to be around 80% for the class.
What to expect in future assessments
The instructor notes that the course will continue to alternate focus: bacteria, then viruses, then eukaryotes.
There will be chemistry-based questions for biochemistry students; other students may find them challenging.
There will be genetics-based questions on a subsequent exam.
Some material may touch on eukaryotic pathogens, helminths, fungi, and other microbiology topics; there will be a mix of microbe types covered.
Endosymbiotic theory and the origin of organelles
Core idea
Organelles such as mitochondria and chloroplasts originated from free-living bacteria that were assimilated by an ancestral archaean/early eukaryotic cell (endosymbiotic theory).
The long-term result is the presence of 70S ribosomes in these organelles, which are prokaryote-like, versus the 80S ribosomes in the cytoplasm of eukaryotic cells.
Ribosome sizes and implications
Prokaryotic ribosomes: 70S
Eukaryotic cytoplasmic ribosomes: 80S
The growth of both these ribosome types is discussed in the context of their respective cellular domains.
Taxonomic framework referenced
The Woese-style, ribosomal RNA–based classification places all cellular life into three domains: ext{Domains} = \{ ext{Bacteria}, ext{Archaea}, ext{Eukarya} \}
Viruses are not included in this scheme because they do not contain ribosomes.
Practical takeaway
This framing helps explain why some organelles resemble bacteria and why ribosomal characteristics are used for classification.
Bacterial cell walls, the glycocalyx, and related components
Cell wall types discussed
Gram-positive and Gram-negative cell walls were introduced when thinking about which components are present in the cell wall and which are not.
The glycocalyx was described as an anti-coagulant “of the cell wall,” though in standard biology the glycocalyx is a layer of polysaccharides that aids in protection and adhesion; it is not primarily an anticoagulant.
Components embedded in peptidoglycan layer
Some molecules are embedded in the peptidoglycan layer; these contribute to the overall structure and properties of Gram-positive cell walls.
A common example (alluded to in class) is teichoic acids, which are embedded in the Gram-positive cell wall.
Fungal cell walls
Fungal cell walls were noted as not covered in the current line of discussion, so questions about fungal cell wall components were expected to be avoided for this particular item.
Takeaway about Gram-positive vs Gram-negative
The thickness of the peptidoglycan layer and the presence/absence of an outer membrane differentiate Gram-positive from Gram-negative bacteria, and these differences influence which molecules are embedded and how the wall interacts with dyes and antibiotics.
Bacterial flagella: structure and components
Base unit and assembly of the flagellum
The base is connected to a basal body and a sheath; embedded within the sheath is the flagellar filament.
A common misperception corrected here: bacterial flagella do not contain tubulin.
Key structural components
Filament: made of flagellin; extends outward from the basal body.
Basal body: anchors flagellum to the cell envelope and acts as the motor
Hook: connects the basal body to the filament (implied by the description of the sheath/basal body arrangement).
Important distinction emphasized
Bacterial flagella operate via a reversible or rotational mechanism that is more like a tail beating than a simple spin; the motion is generated by a motor in the basal body powered by proton or sodium ion gradients.
Common misconceptions addressed
The presence of microtubules (tubulin) is characteristic of eukaryotic flagella/cilia, not bacterial flagella.
Eukaryotic flagella and cilia: structure, size, and motion
Size and scale contrasts
Prokaryotic organisms (bacteria) typically have very small cells (roughly 1–2 μm in length; some measurements mention ~0.2 μm thickness for the flagellum).
Eukaryotic cells and their flagella/cilia are generally larger (e.g., visible on electron micrographs at tens of micrometers in a cell and longer flagella/cilia depending on the organism).
Structural core: microtubules
The core filament in eukaryotic flagella and cilia is made of microtubules arranged in a characteristic 9+2 pattern: nine outer doublets and two central singlets.
In the basal body, the arrangement is 9 triplets with no central pair (9+0).
Major structural difference from bacteria
Eukaryotic flagella/cilia are built from microtubules and rely on dynein-driven bending motions, not a simple rotary motor like bacterial flagella.
The majority of the flagellum’s structure is extracellular relative to the cytoplasmic membrane, unlike many bacterial components.
Function and movement
Eukaryotic flagella/cilia move by a bending or whipping motion generated by dynein arms on the microtubules, producing coordinated waves or strokes rather than simple rotation.
Notable differences in morphology and mechanism
Bacteria: basal body, hook, and filament; propulsion through rotation.
Eukaryotes: core axoneme with nine doublets plus two central microtubules; dynein motors drive bending; movement is more like a wave than a spin.
Additional notes on motility structures
Cilia and flagella in eukaryotes are structurally the same kind of organelle (axoneme) but differ in length, number, and motion patterns; cilia are typically shorter and more numerous, often used for moving fluid rather than locomotion.
Nucleus, chromatin, and nuclear architecture
Chromatin states
Euchromatin: lighter-staining regions; less condensed; actively transcribed and being used to make RNA.
Heterochromatin: darker-staining regions; more condensed; less transcriptionally active.
Nuclear organization and the lamina
The nucleus is supported/stabilized in the cell by the nuclear lamina, a network of intermediate filaments.
The lamina helps maintain nuclear shape and provides structural support.
Role of intermediate filaments
Intermediate filaments contribute to the nuclear lamina and overall nuclear positioning within the cell.
Nucleolus and ribosome assembly context
The discussion touches on how chromatin states relate to ribosome production/assembly and rough endoplasmic reticulum activities, as these relate to protein synthesis and ribosome biology.
Rough endoplasmic reticulum (RER) and Golgi apparatus: protein synthesis and trafficking
Rough ER: site of protein synthesis for secreted and membrane-associated proteins
Ribosomes on the rough ER synthesize proteins that will be secreted or presented on the cell surface.
Proteins destined for the cytoplasm are typically synthesized by free ribosomes in the cytosol.
Pathway from RER to Golgi
Nascent proteins enter the rough ER lumen where initial folding and possible co-translational modifications occur.
Proteins are packaged into vesicles that bud off the ER and move toward the Golgi apparatus.
The Golgi modifies, sorts, and further packages proteins for their final destinations.
Vesicle trafficking and sorting
Proteins that stay in the cytoplasm are usually retained by ribosomes free in the cytosol.
Proteins destined for the outside of the cell or for the cell membrane pass through the rough ER and Golgi on vesicles to reach their final destinations.
Some proteins require specific localization signals (tags) to direct them to the nucleus, mitochondria, lysosomes, or other compartments.
Functional implications of sorting
The sorting process ensures proteins reach the correct cellular location, enabling proper function and regulation.
Smooth ER and other organelles (briefly mentioned)
Smooth ER was noted as a counterpart to the rough ER, with distinct roles (e.g., lipid synthesis, detoxification) though not elaborated in depth in this segment.
Putting it together: organelles, trafficking, and cellular organization
The course emphasizes a progression from bacterial to viral to eukaryotic life, with emphasis on how organelles evolved and how their components differ across domains.
The lecture integrates structural biology with functional pathways:
Endosymbiotic theory explains mitochondria/chloroplasts as former bacteria.
Ribosome composition (70S vs 80S) reflects prokaryotic vs eukaryotic origin.
Eukaryotic cytoskeleton (microtubules) underpins spindle dynamics during cell division and motility via flagella/cilia.
Nuclear architecture (chromatin state and lamina) governs gene expression and genome stability.
Protein trafficking pathways (RER → Golgi → vesicles) ensure proper protein localization and function.
Biological scale, imaging, and real-world relevance
Size scales mentioned
Bacterial cells: typically 1–2 μm in length; flagella are thin and often not visible under standard light microscopy without special staining.
Eukaryotic cells: overall sizes range larger; visible differences in organelle size and flagellar length between prokaryotes and eukaryotes.
Imaging contrasts used as teaching tools
Electron micrographs illustrate the large scale differences between prokaryotic and eukaryotic cells and their appendages (e.g., flagella/cilia).
Practical significance
Understanding these differences informs how we study pathogens, how drugs target bacterial components, and why certain cellular processes differ across domains.
Study strategy and takeaways for exam preparation
Focus on key contrasts and relationships
70S vs 80S ribosomes and their evolutionary implications.
Endosymbiotic theory as a framework for organelle origins.
Differences in bacterial cell wall components that distinguish Gram-positive vs Gram-negative bacteria.
Structural differences between bacterial flagella and eukaryotic flagella/cilia, including microtubule-based architecture (9+2 vs 9+0) and motion.
Nuclear organization: euchromatin vs heterochromatin and the role of the nuclear lamina.
Protein trafficking pathway: rough ER → Golgi → vesicles and final destinations; role of signal sequences and localization tags.
Reminder on practical assessment details
Use office hours to review incorrect items.
Complete reading questions to maximize the potential exam boost.
Be mindful of the normalization policy and how scores are scaled.
Real-world relevance and cross-topic connections
The material bridges foundational cell biology with microbiology, highlighting how structural differences underlie function and disease processes across bacteria, viruses, and eukaryotes.
Key formulas and technical terms (LaTeX)
Ribosome sizes: 70S ext{ (prokaryotic)} \ 80S ext{ (eukaryotic)}
Domain-based taxonomy reference: ext{Domains} = \{ ext{Bacteria}, ext{Archaea}, ext{Eukarya} \}
Normalization/scaling of exam scores: S{ ext{norm}} = rac{S}{S{ ext{max}}} imes 100
Nuclear structure terminology:
Euchromatin (less condensed, transcriptionally active)
Heterochromatin (more condensed, transcriptionally inactive)
Flagellar architecture (eukaryotic): ext{axoneme} = 9 ext{ outer doublets} + 2 ext{ central microtubules (9+2)}
Basal body architecture (eukaryotic analogy): 9 ext{ triplets (9+0)}
General trafficking pathway (protein sorting): rough ER → Golgi → vesicles → final destination