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Cell Biology & Metabolism: Descriptive Questions (1-32)

Fundamental Knowledge: Cell Biology & Metabolism

Part 1: Cell Structure & Function

Eukaryotes vs. Prokaryotes vs. Viruses

FEATUREEUKARYOTESPROKARYOTESVIRUSES
Nucleus 🧠Present, membrane-boundAbsent, has nucleoid regionAbsent, is acellular
Organelles 🏭Present, membrane-boundAbsentAbsent, not a cell
Ribosomes ⚫80S (60S + 40S)70S (50S + 30S)Uses host's ribosomes
Genetic Material 🧬Linear DNA with histonesCircular DNA, no histonesDNA or RNA
Cell Wall 🧱Plants (cellulose), Fungi (chitin)PeptidoglycanProtein capsid instead
Size 📏10–100 µm0.1–5.0 µm20–300 nm
Reproduction 🔄Mitosis, MeiosisBinary FissionHijacks host cell machinery
Prokaryotic vs Eukaryotic Cells

Prokaryotic vs. Eukaryotic Cells

Virus Structure

Basic Structure of a Virus

🔬 Relative Biological Sizes

ObjectApproximate Size
Amino Acid~1 nm
Antibody (Protein)~10 nm
Virus~100 nm
Mitochondrion~2 µm
Bacterium (E. coli)~3 µm
Red Blood Cell~7 µm
Animal Cell (generic)~10-30 µm
Plant Cell~10-100 µm

💧 Osmosis in Animal & Plant Cells

SolutionAnimal Cell 🦓Plant Cell 🌳
Hypotonic SolutionLysed (bursts)Turgid (normal)
Isotonic SolutionNormalFlaccid
Hypertonic SolutionShriveledPlasmolyzed
Osmosis in Red Blood Cells

Osmosis in Animal Cells

Osmosis in Plant Cells

Osmosis in Plant Cells

Key Cellular Organelles and Structures 🏭

OrganelleKey Function(s)
NucleusContains DNA, controls cell activities
RibosomeSynthesizes proteins
Rough ERProtein synthesis/modification for secreted/membrane proteins
Smooth ERLipid synthesis, detoxification, calcium storage
Golgi ApparatusModifies, sorts, and packages proteins and lipids
LysosomeDigestion of macromolecules, recycling cellular components
PeroxisomeMetabolizes fatty acids; neutralizes toxic compounds (H₂O₂)
MitochondrionCellular respiration, ATP production
ChloroplastPhotosynthesis (in plants and algae)
VacuoleStorage (water, nutrients, waste), turgor pressure (plants)
CentrosomeMicrotubule organizing center, forms spindle fibers in mitosis (animal cells)
Animal Cell

Diagram of an Animal Cell

Plant Cell

Diagram of a Plant Cell

Nucleus and ER

Nucleus & Endoplasmic Reticulum

Ribosome

Structure of a Ribosome

Golgi Apparatus

Golgi Apparatus & Endomembrane System

Peroxisome

Structure of a Peroxisome

Hierarchical Structure of Proteins 💪

LevelDescriptionStabilizing Bonds
1° PrimaryLinear sequence of amino acidsPeptide bonds
2° Secondaryα-helices and β-sheetsHydrogen bonds (backbone)
3° TertiaryOverall 3D shape of one polypeptideR-group interactions (hydrophobic, ionic, disulfide)
4° QuaternaryAssembly of multiple polypeptidesSame as tertiary

Cytoskeleton 🏗️

ComponentFunctions
Microfilaments (Actin)Cell shape/motility, muscle contraction, cytokinesis
Intermediate FilamentsMechanical strength, nuclear lamina, anchoring
Microtubules (Tubulin)Intracellular transport (rails), cilia/flagella, mitotic spindle
Cytoskeleton Components

Microfilaments, Intermediate Filaments, Microtubules

Major Motor Proteins 🚚

ProteinTrack & Role
KinesinMicrotubules (Moves toward (+) end (cell periphery))
DyneinMicrotubules (Moves toward (-) end (cell center), cilia/flagella motion)
MyosinActin filaments (Muscle contraction, cytokinesis)
Motor Proteins

Kinesin and Dynein on Microtubule

Substance Transport Across the Membrane 🚪

Transport TypeEnergy? ⚡Examples
Simple DiffusionNoO₂, CO₂, lipids
Facilitated DiffusionNoGlucose, ions (via channels)
OsmosisNoMovement of water across a semipermeable membrane
Active TransportYes (ATP)Na⁺/K⁺ pump
Bulk TransportYes (ATP)Endocytosis, Exocytosis
Fluid Mosaic Model

Fluid Mosaic Model

Sodium Potassium Pump

Sodium-Potassium Pump

Bulk Transport

Endocytosis and Exocytosis

Cell Adhesion & Junctions 🤝

Junction TypeFunctionKey Proteins
Tight JunctionsSeals cells, prevents leakageOccludins, Claudins
Adherens JunctionsConnects actin filamentsCadherins
DesmosomesAnchors cells (mechanical strength)Cadherins
HemidesmosomesAnchors cells to basement membraneIntegrins
Gap JunctionsAllows communicationConnexins
Cell Junctions

Tight Junction, Desmosome, Gap Junction

Part 2: Metabolism & Enzymes

Cellular Respiration & Fermentation ⚡

ProcessLocationKey Outputs
GlycolysisCytoplasm2 Pyruvate, 2 ATP (net), 2 NADH
Pyruvate OxidationMitochondrial Matrix2 Acetyl-CoA, 2 CO₂, 2 NADH
Citric Acid CycleMitochondrial Matrix4 CO₂, 2 ATP, 6 NADH, 2 FADH₂
Oxidative PhosphorylationInner Mitochondrial Membrane~28 ATP, H₂O
FermentationCytoplasmLactate or Ethanol, NAD⁺
Mitochondria

Structure of a Mitochondrion

Photosynthesis ☀️🌿

ProcessLocationKey I/O
Light-Dependent ReactionsThylakoid MembraneIN: Light, H₂O → OUT: O₂, ATP, NADPH
Calvin CycleStromaIN: CO₂, ATP, NADPH → OUT: G3P (sugar)
Chloroplast

Structure of a Chloroplast

Part 3: Genetics & Molecular Biology

Core Genetic Processes (Central Dogma) 📜

ProcessTemplate → ProductKey Enzyme/Machinery
ReplicationDNADNADNA Polymerase
TranscriptionDNARNARNA Polymerase
TranslationmRNAProteinRibosome

Mitosis vs. Meiosis

FeatureMitosis (👯‍♀️ Identical)Meiosis (🎲 Diverse)
PurposeGrowth, repairGamete production
Daughter Cells2, diploid (2n), identical4, haploid (n), diverse
Key EventSeparation of sister chromatidsCrossing over & separation of homologs

Gene Regulation 🧬 On/Off

FeatureProkaryotes (🦠 Simple)Eukaryotes (🦓 Complex)
Primary ControlTranscription (Operons)Multiple levels (Chromatin, Transcription, Post-transcriptional)
RNA ProcessingMinimalExtensive (splicing, 5' cap, poly-A tail)

PCR Steps 🧪

StepProcess
1. Denaturation (~95°C)Separate DNA strands
2. Annealing (~55°C)Primers bind to template
3. Extension (~72°C)Taq polymerase synthesizes new DNA

Recombinant DNA Tools 🛠️

ToolFunction
Restriction EnzymesCut DNA at specific sequences
DNA LigaseJoin DNA fragments
PlasmidsVectors to carry foreign DNA into cells

🎲 Patterns of Inheritance

PatternDescription
Monohybrid CrossTracks one trait (e.g., Rr x Rr → 3:1 phenotype).
Dihybrid CrossTracks two traits (e.g., RrYy x RrYy → 9:3:3:1 phenotype).
Incomplete DominanceHeterozygote has an intermediate phenotype (e.g., red + white = pink).
CodominanceBoth alleles are fully expressed in the heterozygote (e.g., AB blood type).
Sex-Linked InheritanceInheritance of a trait on a sex chromosome (X or Y).
Lethal AlleleAn allele that causes death when homozygous.
Genetic LinkageGenes on the same chromosome tend to be inherited together.
Test CrossCrossing an unknown dominant with a homozygous recessive to find its genotype.

💥 Types of Mutations

CategoryTypeDescription
Gene MutationsPoint Mutation
Changes a single base. Can be silent, missense, or nonsense.
Gene MutationsFrameshift
Insertion or deletion of bases not in a multiple of three. Highly disruptive.
Chromosomal MutationsStructural
Deletion, duplication, inversion, translocation.
Chromosomal MutationsNumerical
Abnormal number of chromosomes (e.g., Trisomy).

Part 4: Advanced Topics

The Cell Cycle: Phases & Checkpoints

PhaseKey Events
G1 PhaseCell growth, protein synthesis, organelle duplication. Ends at G1 checkpoint.
S PhaseDNA replication (synthesis) occurs. Chromosomes are duplicated.
G2 PhaseFurther growth and preparation for mitosis. Ends at G2 checkpoint.
M PhaseMitosis (nuclear division) and Cytokinesis (cytoplasmic division).
CheckpointChecks ForKey Proteins
G1 CheckpointCell size, nutrients, DNA damagep53, Rb
G2 CheckpointDNA replication complete, DNA damageMPF (Cdk1/Cyclin B)
M (Spindle) CheckpointChromosome attachment to spindleAPC/C

💀 Cell Death: Apoptosis vs. Necrosis

FeatureApoptosisNecrosis
ApoptosisCell shrinks, forms apoptotic bodiesNo inflammation, clean removal
NecrosisCell swells and bursts (lysis)Causes inflammation

📡 Signal Transduction Pathways

PathwayBasic Steps
GPCR PathwayLigand → GPCR → G-protein → Enzyme → 2nd Messenger (cAMP)
RTK PathwayLigand → RTK dimerization → Autophosphorylation → Relay proteins activated

🌱 Stem Cells

TypePotencySource
Embryonic (ES) CellsPluripotentInner cell mass of blastocyst
Adult Stem CellsMultipotentVarious tissues (e.g., bone marrow)
iPS CellsPluripotentReprogrammed adult cells

Theme 1: Eukaryotic and Prokaryotic Cells

#1

Describe the most important differences between eukaryotic and prokaryotic cells from the three perspectives of the nucleus, organelles, and ribosomes.

Theme 2: Structure of the Cell Membrane

#2

Describe the 'fluid mosaic model,' which is the basic structure of the cell membrane, including its components and characteristics.

Theme 3: Protein Structure

#3

Protein structure has a hierarchy from primary to quaternary structure. Explain what determines each of these structural levels.

Theme 4: Active and Passive Transport

#4

Explain the difference between active and passive transport from the perspectives of the concentration gradient and the requirement for energy (ATP).

Theme 5: Enzyme Reaction Rate and Temperature

#5

Explain how the rate of an enzyme reaction changes at low, optimal, and high temperatures, including the reasons for these changes.

Theme 6: Enzyme Reaction Rate and Substrate Concentration

#6

When the amount of enzyme is constant, how does the reaction rate change as the substrate concentration is increased from low to high? Explain the reason using the term 'active site.'

Theme 7: Competitive Inhibition

#7

What is 'competitive inhibition' in an enzyme reaction? Explain by focusing on the structure of the inhibitor and where it binds.

Theme 8: Electron Transport Chain

#8

Regarding the role of the electron transport chain in cellular respiration, explain three points: where it takes place, the final electron acceptor, and the mechanism by which ATP is generated.

Theme 9: Calvin-Benson Cycle

#9

Describe the three main stages of the Calvin-Benson cycle, and state what is consumed and what is produced in the cycle as a whole.

Theme 10: C₄ Plants

#10

Explain why the C₄ pathway is advantageous compared to the C₃ pathway, especially in hot, dry environments, mentioning the initial CO₂-fixing enzyme and photorespiration.

Theme 11: CAM Plants

#11

Describe the mechanism of photosynthesis in CAM plants, focusing on how they conserve water. Also, state the difference in their activities between day and night.

Theme 12: Differences in Photosynthetic Mechanisms

#12

Compare C₃, C₄, and CAM plants on two points: (1) the initial CO₂-fixing enzyme, and (2) the environmental conditions under which each is most advantageous.

Theme 13: The Cell Cycle

#13

The eukaryotic cell cycle is broadly divided into M phase and interphase. State that interphase is further divided into three phases, and describe the main events that occur in each. Also, name the two main groups of proteins that regulate the progression of the cell cycle.

Theme 14: Apoptosis

#14

Explain the differences between apoptosis and necrosis from the perspectives of the morphological changes that occur in the cell and the effects on the living organism.

Theme 15: DNA Replication

#15

Explain why DNA replication is called 'semiconservative replication.' Also, describe the difference in the synthesis patterns of the leading and lagging strands in relation to the function of DNA polymerase.

Theme 16: Transcription and Translation

#16

Describe the processes of 'transcription' and 'translation' in the central dogma, from the perspectives of where they occur, the template molecule, the molecule synthesized, and the main machinery or enzymes involved.

Theme 17: Regulation of Gene Expression

#17

Regarding the lactose operon (lac operon), a representative example of gene expression regulation in prokaryotes, explain how gene expression is regulated in the absence and presence of lactose.

Theme 18: The Cytoskeleton

#18

Name the three main types of fibers that make up the cytoskeleton, and for each, describe its main protein component and two of its main functions within the cell.

Theme 19: Signal Transduction

#19

Describe the general process of information transmission, from the binding of an extracellular signal molecule (ligand) to a receptor to the final response within the cell, by dividing it into the three stages of 'reception,' 'transduction,' and 'response.' Also, state the role of a 'second messenger' with a specific example.

Theme 20: Cancer

#20

List three characteristics of cancer cells that are different from normal cells. Also, explain how 'oncogenes' and 'tumor suppressor genes' are involved in carcinogenesis from the perspective of the effects of their mutations.

Theme 21: Protein Sorting and Vesicular Transport

#21

Describe the pathway (secretory pathway) by which a protein synthesized in the endoplasmic reticulum is transported through the Golgi apparatus and secreted outside the cell. Mention how the protein is transported by vesicles in this process.

Theme 22: Cell Adhesion and the Extracellular Matrix

#22

Name the three main types of cell-cell adhesion junctions in animal tissues and describe the structure and main function of each.

Theme 23: Meiosis and Genetic Diversity

#23

Explain the differences that meiosis brings about in the chromosome number and genetic composition of daughter cells compared to mitosis. Also, name the two main mechanisms by which genetic diversity is generated during meiosis.

Theme 24: Cellular Respiration: Glycolysis and Citric Acid Cycle

#24

Regarding the initial stages of aerobic respiration, glycolysis and the citric acid cycle, state where in the cell each takes place, what the main starting material and final products are. Also, explain the main purpose of these processes.

Theme 25: Stem Cells and Cell Differentiation

#25

Define the two fundamental abilities of stem cells. Also, explain the mechanism by which 'cell differentiation' occurs, from the perspective of gene expression.

Theme 26: DNA and RNA Structure

#26

After describing the structure of a nucleotide, the basic unit of DNA and RNA, explain the structural differences between DNA and RNA from the two perspectives of 'sugar' and 'base.'

Theme 27: Properties of the Genetic Code

#27

Among the characteristics of the genetic code (codons), explain what the properties of 'universality' and 'degeneracy (redundancy)' are.

Theme 28: Mendel's Laws: The Law of Segregation

#28

What is Mendel's 'Law of Segregation'? Explain using the terms allele, gamete, and genotype.

Theme 29: Mendel's Laws: The Law of Independent Assortment

#29

What is Mendel's 'Law of Independent Assortment'? Explain using an example of two pairs of alleles located on different homologous chromosomes.

Theme 30: Gene Mutation Types and Effects

#30

Regarding mutations that occur in the base sequence of a gene, describe what 'point mutations' and 'frameshift mutations' are, and state the difference in their effects on protein function.

Theme 31: Chromosomal Abnormalities

#31

Broadly classify chromosomal abnormalities into 'structural abnormalities' and 'numerical abnormalities,' and explain what each type of abnormality is. Also, state which chromosome is affected and what kind of abnormality occurs to cause Down syndrome.

Theme 32: Epigenetics

#32

Explain what 'epigenetics' is. Also, describe how its representative molecular mechanisms, 'DNA methylation' and 'histone modification,' regulate gene expression.