STEM Readiness: Biology Readiness - Evolution/Ecology: Phylogenetics - Cladograms, Shared Derived Characters, Parsimony, Reading Trees

Must?Know

• Prokaryotic cells range from 0.1–5.0 ?m in diameter; eukaryotic cells range from 10–100 ?m.
• Prokaryotes lack a membrane-bound nucleus; DNA resides in the nucleoid region.
• Eukaryotes have a membrane-bound nucleus housing linear DNA complexed with histones.
• Prokaryotic ribosomes are 70S (50S + 30S subunits); eukaryotic cytoplasmic ribosomes are 80S (60S + 40S).
• Mitochondria and chloroplasts contain 70S ribosomes, supporting their origin via endosymbiosis.
• Bacterial cell walls contain peptidoglycan; archaea lack peptidoglycan but may have pseudopeptidoglycan.
• Plant cell walls are composed of cellulose; fungal cell walls contain chitin.
• Animal cells lack a cell wall; Mycoplasma (a bacterium) also lacks a cell wall.
• Both prokaryotes and eukaryotes have a phospholipid bilayer plasma membrane.
• Eukaryotes have extensive internal membranes forming organelles; prokaryotes generally do not.
• Endoplasmic reticulum (ER) is present only in eukaryotes; rough ER synthesizes proteins, smooth ER synthesizes lipids.
• Golgi apparatus modifies, sorts, and packages proteins for secretion or delivery; absent in prokaryotes.
• Mitochondria generate ATP via oxidative phosphorylation; have double membranes and their own DNA.
• Chloroplasts perform photosynthesis in plants and algae; contain chlorophyll and thylakoids.
• Lysosomes contain hydrolytic enzymes for degradation; found in animal cells, rare in plant cells.
• Vacuoles in plant cells are large and central, maintaining turgor pressure; smaller and transient in animal cells.
• Nuclear envelope is a double membrane with nuclear pores regulating transport; absent in prokaryotes.
• Nucleolus within the nucleus synthesizes ribosomal RNA and assembles ribosome subunits.
• Cytoskeleton (microtubules, actin filaments, intermediate filaments) is present in eukaryotes; prokaryotes have homologous proteins (e.g., FtsZ).
• Binary fission is the primary mode of reproduction in prokaryotes; eukaryotes divide by mitosis and cytokinesis.
• Archaea are prokaryotes in structure (no nucleus, 70S ribosomes) but share some molecular similarities with eukaryotes (e.g., RNA polymerase).
• Red blood cells in mammals lack a nucleus and mitochondria, maximizing hemoglobin capacity.
• Plasmids are small, circular DNA molecules found in prokaryotes and some eukaryotes (e.g., yeast).
• Endosymbiotic theory is supported by mitochondria and chloroplasts having circular DNA, 70S ribosomes, and double membranes.
• Gram-positive bacteria have thick peptidoglycan layers; Gram-negative have thin peptidoglycan and an outer membrane.

Difficulty Level

Intermediate – requires distinguishing structural and functional differences across domains and organelles, with attention to exceptions.

Common Traps

Trap: All cells with cell walls have peptidoglycan – Fact: Only bacteria have peptidoglycan; plants (cellulose), fungi (chitin), and archaea (no peptidoglycan) differ.
Trap: Ribosome size correlates with organism complexity – Fact: Mitochondria and chloroplasts have 70S ribosomes despite being in eukaryotic cells.
Trap: Prokaryotes have no internal structure – Fact: Prokaryotes have nucleoids, ribosomes, and some have protein-based cytoskeletal elements.
Trap: The nucleus is the only organelle with a double membrane – Fact: Mitochondria and chloroplasts also have double membranes.
Trap: All eukaryotic cells have a cell wall – Fact: Animal cells lack a cell wall; only plants, fungi, and some protists have one.

Practice MCQs

Question: Which of the following is a feature shared by both prokaryotic and eukaryotic cells?
A) Membrane-bound nucleus
B) 80S ribosomes
C) Phospholipid bilayer plasma membrane
D) Mitochondria
Answer: C
Explanation: Both cell types have a phospholipid bilayer as the plasma membrane.
Why the top distractor is wrong: D (mitochondria) are present only in eukaryotes.

Question: A cell is observed to contain 70S ribosomes, a nucleoid, and peptidoglycan in its cell wall. Which domain does it most likely belong to?
A) Eukarya
B) Archaea
C) Bacteria
D) Protista
Answer: C
Explanation: Peptidoglycan is unique to bacteria among prokaryotes.
Why the top distractor is wrong: B (Archaea) lack peptidoglycan despite having 70S ribosomes and a nucleoid.

Question: Which organelle is responsible for modifying and packaging proteins for secretion in eukaryotic cells?
A) Nucleolus
B) Smooth endoplasmic reticulum
C) Golgi apparatus
D) Lysosome
Answer: C
Explanation: The Golgi apparatus modifies, sorts, and packages proteins from the ER.
Why the top distractor is wrong: B (smooth ER) synthesizes lipids and detoxifies compounds but does not package proteins.

Question: Which of the following is an exception to the presence of a nucleus in eukaryotic cells?
A) Yeast cells
B) Neurons
C) Mature mammalian red blood cells
D) Plant root cells
Answer: C
Explanation: Mature mammalian red blood cells lack a nucleus to accommodate more hemoglobin.
Why the top distractor is wrong: A (yeast) are eukaryotes and have a nucleus.

Question: What is the primary evidence supporting the endosymbiotic theory for mitochondria?
A) They are surrounded by a single membrane
B) They contain 80S ribosomes
C) They have circular DNA and 70S ribosomes
D) They replicate by meiosis
Answer: C
Explanation: Mitochondria have circular DNA and 70S ribosomes, similar to bacteria.
Why the top distractor is wrong: A is incorrect because mitochondria have a double membrane, not single.

Question: Which of the following structures is found in plant cells but not in animal cells?
A) Lysosome
B) Centriole
C) Large central vacuole
D) Plasma membrane
Answer: C
Explanation: A large central vacuole is a defining feature of mature plant cells.
Why the top distractor is wrong: A (lysosomes) are common in animal cells and sometimes present in plant cells.

Question: What distinguishes the nucleoid from the nucleus?
A) The nucleoid contains RNA, while the nucleus contains DNA
B) The nucleoid is membrane-bound, while the nucleus is not
C) The nucleoid lacks a surrounding membrane, while the nucleus has a nuclear envelope
D) The nucleoid is found in eukaryotes, while the nucleus is found in prokaryotes
Answer: C
Explanation: The nucleoid is an unenclosed region in prokaryotes; the nucleus is enclosed by a double membrane.
Why the top distractor is wrong: D reverses the domains—nucleoids are in prokaryotes, nuclei in eukaryotes.

Last?Minute Revision

• Prokaryotic cell size: 0.1–5.0 ?m
• Eukaryotic cell size: 10–100 ?m
• Prokaryotic ribosome = 70S (50S + 30S)
• Eukaryotic cytoplasmic ribosome = 80S (60S + 40S)
• Mitochondria and chloroplasts have 70S ribosomes
• Mitochondria have circular DNA – evidence of endosymbiosis
• Bacterial cell walls contain peptidoglycan
• Plant cell walls = cellulose
• Fungal cell walls = chitin
• Animal cells = no cell wall
• Mycoplasma = bacterium without cell wall
• Nuclear envelope = double membrane with pores
• Nucleolus = site of rRNA synthesis and ribosome assembly
• Smooth ER = lipid synthesis, detoxification
• Rough ER = protein synthesis for secretion/membranes
• Golgi apparatus = modifies, sorts, packages proteins
• Lysosomes = contain hydrolytic enzymes, found in animal cells
• Mature mammalian red blood cells lack nucleus and mitochondria
• Archaea have 70S ribosomes but share transcription machinery with eukaryotes
• Endosymbiotic theory supported by: double membrane, 70S ribosomes, circular DNA, binary fission in mitochondria/chloroplasts
• Both prokaryotes and eukaryotes have phospholipid bilayer membranes
• Cytoskeleton components: microtubules, actin filaments, intermediate filaments – eukaryote-specific
• Gram-positive bacteria = thick peptidoglycan
• Gram-negative bacteria = thin peptidoglycan + outer membrane
• Plasmids = small circular DNA, common in bacteria, also in yeast
• Verify from standard textbook: exact protein composition of archaeal cell walls