CHAPTER 2

The Structure and Function of Animal Cells

CELLS: THE COMMON UNIT OF ALL LIFE

Properties and Varieties of Cells
 All living organisms share common cellular features, indicating a shared
evolutionary origin.
 Cells have a fundamentally similar organization and perform many common
functions.
 Most cells are very small, reflecting their efficiency in carrying out life processes.
 Despite 3.9 billion years of evolution, cellular diversity remains relatively limited.
Common Organization
 Plasma Membrane: Acts as the outer boundary, separating internal processes
from the environment.
 DNA (Deoxyribonucleic Acid): Serves as the genetic material, either enclosed
in a membrane system or loosely distributed in the cell.
 Cytoplasm: Found between the plasma membrane and DNA region, consisting
of:
o Cytosol: A semifluid substance.

o Organelles: Small structures with specific functions.

 Ribosomes: The only organelle shared by all cells, essential for protein
synthesis.
Limits on Size
 Most Cells Are Microscopic: Exceptions include vertebrate eggs (e.g., reptiles
and birds) and some long nerve cells.
 Reason for Small Size:
o Cells need to exchange nutrients, wastes, and chemicals efficiently.

o As cell size increases, volume grows faster than surface area, limiting
exchange capacity.
 Surface-to-Volume Ratio:
o Cells maximize exchange efficiency by increasing surface area.

o Adaptations include flattened shapes, concave surfaces, membrane

protrusions, and complex folds.
 Internal Cellular Membranes:
o Help compartmentalize materials and provide surfaces for reactions.
  Cellular Transport Mechanisms:
o Aid in the movement of reactants and products across the plasma
membrane.
Three Types of Cells
 Common Origin of Cells
o All cells share a common origin from 3.9 billion years ago.

o Evidence: Universal genetic molecules (DNA, RNA) and ATP (energy-

carrying molecule).
o Evolution has led to three major cell types, dividing life into three
domains: Bacteria, Archaea, and Eukarya.
 Prokaryotic Cells (Bacteria and Archaea)
o Lack membrane-bound nuclei and organelles.

o Bacteria: Common organisms, e.g., Escherichia coli.

o Archaea: Found in extreme environments, e.g., hot springs

(Crenarchaeota) and animal intestines (Methanobrevibacter).
o Similar in size (0.5–5 μm) and division but molecularly different.

 Eukaryotic Cells (Eukarya: Animals, Plants, Fungi, Protists)

o Larger (10–30 μm) and more complex than prokaryotes.

o Distinctive features:

 Membrane-bound nucleus.
 Organelles: Mitochondria, chloroplasts (in plants/protists), and
others.
 DNA complexed with proteins.
 Unique cell division and metabolism.
CELLULAR MEMBRANES AND MEMBRANE TRANSPORT
 Membrane Systems in Animal Cells
o Compartmentalization: Membranes enclose organelles to carry out
specific functions.
o Mitochondria: Use an extensive membrane system for energy
processing.
o Endomembrane System: Includes the endoplasmic reticulum and
Golgi apparatus, which work together to package and transport
proteins.
o Nuclear Envelope: Defines eukaryotic cells and shares properties with
other cellular membranes.
o Plasma Membrane: Separates the cell from its surroundings,
distinguishing life from nonlife.
The Plasma Membrane
 Structure:
o The plasma membrane is a phospholipid bilayer with proteins and
other macromolecules.
o Each phospholipid molecule has:

 Two hydrophobic tails (water-fearing).

 One hydrophilic head (water-loving).
o The bilayer forms spontaneously in a watery medium and remains fluid,
essential for its function.
 Cholesterol in Membranes:
o Modulates membrane fluidity:

 Prevents excessive fluidity at high temperatures.

 Prevents excessive rigidity at low temperatures.
o Reduces permeability to small ions and molecules.

 Membrane Proteins:
o Monolayer-associated proteins: Attach to the inner and outer surfaces.

o Transmembrane proteins: Embedded in the membrane.

o Functions include:

 Transporting ions and molecules.

  Attachment points for cellular structures.
 Forming junctions between cells.
 Acting as hormone receptors and enzymes.

 Carbohydrate Layer (Glycocalyx):

o Found on the outer surface of eukaryotic cell membranes.

o Carbohydrate chains attach to:

 Proteins (forming glycoproteins).

 Lipids (forming glycolipids).
o Functions:

 Protection from mechanical and chemical damage.

 Cell-to-cell recognition and adhesion (e.g., egg cell recognition
by sperm).
Membrane Transport
 More Than Just Barriers:
o Cellular membranes are not merely barriers; they regulate precise
balances of materials inside and outside the cell.
o The lipid bilayer is the primary barrier to movement.

 What Can and Cannot Pass Through the Lipid Bilayer:

o Cannot Permeate: Hydrophilic molecules.

o Can Pass Easily:

 Small nonpolar molecules (e.g., O₂, CO₂).

 Lipid-soluble hormones (hydrophobic molecules).
 Membrane Channels and Protein Transporters:
o Some substances require channels or transporters to move across the
membrane.
o Example: Nerve cells

 Sodium (Na⁺): 10–30 times more concentrated outside the cell.

 Potassium (K⁺): 28 times more concentrated inside the cell.

 Negatively charged proteins remain inside, maintaining a charge
difference.
 Nerve impulses occur when ion channels open and close, allowing
Na⁺ and K⁺ to move.
  Protein transporters use energy to restore ion balance after an
impulse.
 Selective Permeability:
o Some substances can move across the membrane, while others are
blocked.
o This property is essential for maintaining cellular function.

Summary of Plasma Membrane Structure

Phospholipid Bilayer:
o Acts as a fluid, two-dimensional structure where phospholipids can
move within the membrane.
 Components Embedded in the Bilayer:
o Cholesterol molecules:
 Regulate membrane fluidity.
 Charged end associates with the hydrophilic head of
phospholipids.
 The rest of the cholesterol molecule associates with the
hydrophobic tail.
o Transmembrane proteins:
 Span the membrane, assisting in transport and signaling.
o Monolayer-associated proteins:
 Attach to inner and outer surfaces of the membrane.
 Glycocalyx:
o A carbohydrate coat on the outer surface.
o Functions in protection, cell-to-cell recognition, and adhesion.

Non-Transporter Gradient Exchanges

1. Diffusion
 Molecules move randomly due to heat energy.
 Movement occurs down a concentration gradient (from high to low
concentration).
 Simple diffusion: Small molecules (e.g., O₂, CO₂) move directly through the
lipid bilayer.
 Facilitated diffusion: Larger or charged molecules (e.g., ions) diffuse through
membrane channels.
2. Osmosis (Water Diffusion)
 Water moves down its concentration gradient across a selectively permeable
membrane.
 Water passes easily through membranes using aquaporins (water channels).
3. Tonicity (Effect of Solute Concentration on Water Movement)
  Isotonic Solution:
o Solute concentration is equal inside and outside the cell.

o No net water movement → cell maintains its shape.

 Hypertonic Solution:
o Higher solute concentration outside the cell.

o Water moves out, causing the cell to shrink (crenation).

 Hypotonic Solution:
o Lower solute concentration outside the cell.

o Water moves in, causing the cell to swell and possibly burst (lysis).

4. Filtration: A process that forces small molecules and ions across a selectively
permeable membrane using hydrostatic pressure (e.g., blood pressure).
 Example in Capillaries: Blood pressure pushes water and dissolved
molecules through the permeable walls of capillaries, but large molecules
(proteins) cannot pass through.
 Example in Kidneys: Blood pressure filters water, wastes, and other
molecules into kidney tubules, helping in urine formation.

Key Points on Diffusion Through Membrane Channels

 Diffusion: Movement of molecules from high to low concentration (down a
concentration gradient).
 Membrane Channels:
o Small polar molecules (e.g., water, ions) use protein channels to
cross the membrane.
o Nonpolar molecules (e.g., steroid hormones) can directly diffuse
through the phospholipid bilayer without channels.
 Selective Permeability: The membrane regulates what enters and exits
the cell to maintain balance.

Key Points on Osmosis

 Osmosis: The diffusion of water across a selectively permeable
membrane from higher to lower water concentration.
 Selective Permeability: The membrane allows water to pass but not large
solutes (e.g., sugar molecules).
 Process:
o Initially: Water moves from compartment 2 to compartment 1
because compartment 1 has dissolved sugar (lower water
concentration).
o Over Time: Water movement slows as osmotic pressure increases in
compartment 1.
o Osmotic Equilibrium: Water movement stops when osmotic
pressure counteracts further diffusion.
Key Points on Tonicity
 Tonicity: Describes the relative solute concentration inside and outside a
cell.
 Red Blood Cell (RBC) Response to Different Solutions:
1. Isotonic Solution:
 Equal solute concentration inside and outside the RBC.
 Water moves in and out at the same rate.
 Cell maintains normal shape (no volume change).
2. Hypertonic Solution:
 Higher solute concentration outside the RBC.
 Water moves out, causing the cell to shrink (crenation).
3. Hypotonic Solution:
 Lower solute concentration outside the RBC.
 Water moves in, causing the cell to swell and potentially
burst (lysis).

Key Points on Filtration

 Filtration: A process where hydrostatic pressure forces water, ions, and
small molecules through a selectively permeable membrane.
 Example: Capillary Filtration
o Blood pressure pushes small molecules (e.g., water, ions, nutrients)
out of the capillaries.
o Large molecules (e.g., proteins, blood cells) cannot pass through
and remain inside the capillary.
o This process is important in kidney function, where blood pressure
aids in filtering waste from the blood.

Carrier-Mediated Transport
Facilitated Diffusion
 Used for large or polar molecules that cannot diffuse through the lipid bilayer.
 Requires transport proteins to help molecules move across the membrane.
 Moves along a concentration gradient (high → low concentration).
 Does not require ATP (energy comes from the concentration gradient).
 Example: Glucose absorption from the digestive tract into the bloodstream.
Active Transport
 Moves molecules against their concentration gradient (low → high
concentration).
 Requires ATP for energy.
 Uses specific carrier proteins:
o Uniporters: Transport one type of molecule.

o Symporters: Transport two molecules in the same direction.

 o Antiporters: Transport two molecules in opposite directions.

 Examples:
o Sodium-Potassium Pump: Maintains nerve cell function.

o Calcium Pump: Regulates muscle contraction by keeping calcium levels

low in the cytosol.

Facilitated Diffusion (Figure 2.7) Summary

 Type of Transport: Passive (no ATP required).
 Movement: From high to low concentration (down the concentration
gradient).
 Molecule Type: Large or polar molecules (e.g., glucose).
 Transport Protein Role:
o Binds to the molecule.
o Changes shape (conformational change).
o Releases the molecule on the other side of the membrane.
 Energy Source: The concentration gradient itself provides energy.
 Example: Glucose uptake from the digestive tract into the blood.

ENERGY, ENZYMES, AND REACTIONS

Energy in Animals
 Energy is essential for survival, movement, and response to the environment.
 Animals are heterotrophs (consume other organisms for energy).
 Metabolism: The sum of all cellular energy-requiring reactions.
ATP: The Energy Currency
 ATP (Adenosine Triphosphate) stores and provides energy for cellular
processes.
 The high-energy bond between the second and third phosphate is broken to
release energy.
 ATP Cycle: ATP is continuously broken down and regenerated.
Role of Enzymes in Metabolism
 Enzymes are proteins that speed up biochemical reactions by lowering
activation energy.
 They bind to substrates, stress their bonds, and facilitate reactions.
 Enzymes enable reactions to occur at body temperature, preventing heat
damage.
Metabolic Pathways
 Multistep reactions allow controlled energy release and multiple regulation
points.
 These pathways ensure energy is released in small, safe steps for cellular use.
 They also provide branch points for alternative reactions.
Active Transport Summary (Figure 2.8)
 Definition: Active transport moves molecules against their concentration
gradient (low → high concentration).
 Energy Requirement: Requires ATP (cellular energy).
 Transport Proteins:
o Bind to molecules on one side of the membrane.
o Change shape using ATP.
o Release the molecule on the other side, where it accumulates.
 Examples:
o Sodium-Potassium Pump: Maintains ion balance in nerve cells.
o Calcium Pump: Essential for muscle contraction.
This process ensures cells get necessary nutrients and maintain proper function
even when natural diffusion isn't enough!

ATP and the ATP Cycle (Figure 2.9)

(a) ATP Structure:
 ATP (Adenosine Triphosphate) = Adenosine (Adenine + Ribose) + Three
Phosphate Groups.
 Functions as the energy carrier in cells.
(b) The ATP Cycle:
1. ATP Breakdown (Energy Release)
o The third phosphate is removed → ATP becomes ADP (Adenosine
Diphosphate) + Pi (Inorganic Phosphate).
o This releases energy for cellular work (e.g., making DNA/proteins,
muscle contraction).
2. ATP Formation (Energy Storage)
o Energy from food is used to re-attach the phosphate to ADP,
regenerating ATP.
o This cycle repeats constantly to keep cells functioning.

CELLULAR RESPIRATION
Aerobic Cellular Respiration: How Animals Use Oxygen for Energy
With few exceptions, animals need oxygen to survive because it is essential for
aerobic cellular respiration, the process of breaking down glucose (C₆H₁₂O₆) with
oxygen (O₂) to form ATP (energy).
Overall Reaction:
C6H12O6+6O2→6CO2+6H2O+energy (ATP)C_6H_{12}O_6 + 6O_2 → 6CO_2 + 6H_2O
+ \text{energy (ATP)}C6H12O6+6O2→6CO2+6H2O+energy (ATP)
 Glucose + Oxygen → Carbon Dioxide + Water + Energy
 This is a catabolic pathway because a large molecule (glucose) is broken down
into smaller molecules, releasing energy.
 The released energy is then used for anabolic pathways (building proteins,
DNA, etc.).
Three Major Phases of Aerobic Cellular Respiration:
1. Glycolysis (Occurs in the cytoplasm)
 o Glucose is split into two smaller molecules (pyruvate).

o Produces a small amount of ATP.

o Can occur with or without oxygen (aerobically or anaerobically).

2. Citric Acid Cycle (Krebs Cycle) (Occurs in the mitochondria)

o Requires oxygen.

o Produces molecules that carry electrons to the next step.

3. Electron Transport Chain (ETC) (Occurs in the mitochondria)

o Requires oxygen.

o Produces most of the ATP used by animal cells.

Glycolysis
Carbohydrates and Glycolysis: The First Step in Energy Production
Carbohydrates are essential in animal diets because they are broken down into
glucose, which fuels cellular respiration.
Glycolysis: The First Stage of Cellular Respiration
 Where? Cytosol (the fluid part of the cell)
 What happens?
1. A molecule of glucose (6-carbon sugar) is split into two 3-carbon
molecules.
2. Two ATP are used to start the process.
3. The three-carbon molecules are modified into pyruvate, which is
crucial for the next phase (Citric Acid Cycle).
4. Four ATP are produced, giving a net gain of two ATP.

5. NAD⁺ molecules pick up electrons, forming NADH, which carries high-

energy electrons to the Electron Transport Chain.
This ATP production is called substrate-level phosphorylation, where a
phosphate group is directly transferred to ADP, forming ATP.
Glycolysis is the starting point for energy production, setting the stage for the
Citric Acid Cycle and Electron Transport Chain to maximize ATP production.

Figure 2.10: Glycolysis and Its Pathways

Glycolysis takes place in the cytoplasm and is the first step in breaking down
glucose for energy.
Pathways After Glycolysis:
1. Aerobic Pathway (Oxygen Present) → Citric Acid Cycle & Electron
Transport Chain
o Pyruvate enters the mitochondrion, where it is further broken down
to produce more ATP.
o This is the most efficient way to generate energy.
2. Anaerobic Pathway (Oxygen Lacking) → Lactate Fermentation
 o During intense exertion, muscles may not receive enough oxygen
from the blood.
o Instead of entering the mitochondria, pyruvate is converted into
lactate.
o This process produces small amounts of ATP to temporarily support
muscle activity.

Transition Events
Mitochondria: The Powerhouse of the Cell
The remaining steps of aerobic respiration happen inside the mitochondria,
where energy is extracted from pyruvate to generate ATP efficiently.
Structure of Mitochondria
 Double membrane: Outer membrane + inner membrane.
 Cristae: Folds of the inner membrane that increase surface area for energy
production.
 Matrix: The fluid-filled space inside the inner membrane, containing enzymes for
further reactions.
Transition Step: Prepping Pyruvate for the Citric Acid Cycle
 Pyruvate enters the mitochondrial matrix.
 It undergoes oxidation, losing one CO₂ molecule.

 NAD⁺ is reduced to form NADH, a high-energy electron carrier.

 The remaining two-carbon fragment attaches to Coenzyme A (CoA) to form
Acetyl-CoA.
Why Is This Important?
 Acetyl-CoA fuels the Citric Acid Cycle, a crucial step in ATP production.
 CO₂ is a waste product and must be eliminated, or it will interfere with
metabolic processes.

Mitochondria: The Powerhouse of the Cell

The mitochondrion is the center of ATP production in the cell, where pyruvate
from glycolysis is further broken down for energy.
Key Structures & Functions
 Matrix : Inner space where the Citric Acid Cycle occurs.
 Cristae : Folded inner membrane where the Electron Transport Chain (ETC)
takes place.
 Intermembrane Space : The area between the inner and outer membranes,
crucial for proton gradient formation in ATP production.
 Mitochondrial DNA & Ribosomes: Allow the mitochondrion to self-
replicate and produce essential proteins.
Energy Production Breakdown
1. Pyruvate enters the matrix → Begins Citric Acid Cycle (Krebs Cycle).
 2. Electron Transport Chain (ETC) & Chemiosmosis occur in the cristae,
leading to massive ATP production.
3. Oxygen is required to accept electrons at the end of the ETC, forming water
(H₂O) as a byproduct.

Citric Acid Cycle (Krebs Cycle)

The Citric Acid Cycle is a crucial step in aerobic cellular respiration, occurring in
the mitochondrial matrix.
Step-by-Step Breakdown
1. Acetyl-CoA (C₂) joins oxaloacetate (C₄) → Forms citrate (C₆)
2. Citrate undergoes a series of reactions → Converts into 8 intermediate
molecules
3. Key Outputs per Cycle:
o 2 CO₂ (waste product)

o 1 ATP (substrate-level phosphorylation)

o 3 NADH & 1 FADH₂(electron carriers for the Electron Transport Chain)

4. Two cycles occur for every glucose molecule (since glycolysis produces 2
pyruvates).
Total Yield for 2 Cycles (1 Glucose)
✅4CO₂
✅2ATP
✅6NADH
✅2FADH₂
The NADH & FADH₂ carry high-energy electrons to the Electron Transport Chain
(ETC) in the cristae, where massive ATP production occurs!

1️⃣ Transition Events (Prepping for the Citric Acid Cycle)

✔ Pyruvate (C₃) is oxidized:
 1 carbon is removed as CO₂.
 NAD⁺ is reduced to NADH.
 The remaining 2-carbon molecule (acetyl group) binds to Coenzyme A
(CoA) → Acetyl-CoA (C₂-CoA).
✔ Each glucose produces 2 pyruvate, so this happens twice!

2️⃣ The Citric Acid Cycle (Krebs Cycle)

 Acetyl-CoA (C₂) enters the cycle, combining with oxaloacetate (C₄) to
form citrate (C₆).
 The cycle breaks citrate down step by step, releasing energy & high-
energy electron carriers:
🔹2CO₂ molecules released (waste product ).
🔹1ATP (via substrate-level phosphorylation).
🔹3NADH & 1FADH₂ produced (electron carriers ).
🔹 Oxaloacetate is regenerated to continue the cycle.
✔ Each glucose fuels TWO turns of the cycle (since 2 pyruvates enter).
 3️⃣ ATP & Electron Carrier Summary from the Citric Acid Cycle
For each glucose molecule (2 turns of the cycle):
✅4CO₂released(waste).
✅2ATPproduced.
✅ 6 NADH & 2 FADH₂ generated (carry electrons to the ETC).
These NADH & FADH₂ molecules then move to the Electron Transport Chain
(ETC) to fuel massive ATP production!

Electron Transport Chain

The Electron Transport Chain (ETC) is the final and most ATP-producing phase of
aerobic cellular respiration, taking place in the inner mitochondrial membrane
(cristae).
Key Processes in ETC
1. Electron Donation & Proton Pumping
o NADH & FADH₂ donate high-energy electrons to the ETC.

o These electrons move through protein complexes (proton pumps)

embedded in the inner mitochondrial membrane.

o Protons (H⁺) are pumped into the intermembrane space, creating a

proton gradient (potential energy).
2. Oxygen as the Final Electron Acceptor
o The last protein complex donates electrons to oxygen (O₂).

o Oxygen binds with H⁺ to form H₂O .

o This is why oxygen is essential for aerobic respiration!

3. ATP Production via Chemiosmosis

o The accumulated protons (H⁺) rush back into the matrix through ATP
synthase (a protein channel).
o This movement releases energy, allowing ATP synthase to
phosphorylate ADP into ATP.
ATP Yield from ETC
✅3ATPperNADH
✅2ATPperFADH₂
✅ Total ATP from ETC: ~30-34 ATP
Total Theoretical ATP from Cellular Respiration
🔹Glycolysis:2ATP
🔹CitricAcidCycle:2ATP
🔹ElectronTransportChain:~30-34ATP
🔹 Total Yield: 36-38 ATP per glucose molecule
Efficiency: Cellular respiration is 52-55% efficient, much higher than most
machines!
Electron Transport System & Chemiosmosis: The Powerhouse of ATP
Production
The Electron Transport System (ETS) and Chemiosmosis occur in the inner
mitochondrial membrane and are responsible for generating most of the ATP in
aerobic respiration.

1️⃣ Electron Transport System (ETS)

✔ NADH & FADH₂ donate high-energy electrons to the electron transport chain
(ETC), a series of proteins embedded in the inner mitochondrial membrane.
✔ Electrons are passed along protein complexes, releasing energy with each
transfer.
✔ This energy powers proton pumps, which actively transport H⁺ ions (protons)
into the intermembrane space, creating a proton gradient (potential energy
buildup).
✔ Final electron acceptor = Oxygen (O₂), which combines with H⁺ to form
water (H₂O).

📌 Key takeaway: The ETS transfers electrons and pumps protons, setting up
conditions for ATP production.

2️⃣ Chemiosmosis (ATP Production)

✔ The proton gradient created by the ETS results in high H⁺ concentration in the
intermembrane space and low H⁺ concentration in the matrix.
✔ H⁺ ions flow back into the matrix through a special enzyme called ATP
Synthase—this process is called chemiosmosis.
✔ As H⁺ flows through ATP Synthase, it spins like a turbine, using the released
energy to phosphorylate ADP into ATP.
✔ Each NADH → Produces 3 ATP
✔ Each FADH₂ → Produces 2 ATP
📌 Key takeaway: Chemiosmosis harnesses stored energy in the proton
gradient to produce ATP, like a dam generating electricity from flowing water!

3️⃣ ATP Yield from Cellular Respiration

Step ATP Produced
2 ATP (substrate-level
Glycolysis
phosphorylation)
2 ATP (substrate-level
Citric Acid Cycle
phosphorylation)
Electron Transport &
~26-34 ATP
Chemiosmosis
Total ATP Yield ~30-38 ATP per glucose
📌 Key takeaway: ETS & Chemiosmosis are responsible for most of the ATP
production!

Final Thoughts
✔ The electron transport chain extracts energy from NADH and FADH₂.
✔ Protons are pumped across the membrane to create a gradient.
✔ ATP Synthase converts proton flow into ATP, the cell’s energy currency.
✔ Oxygen is crucial—without it, the whole process stops, leading to anaerobic
respiration instead.
ETS & Chemiosmosis = The Grand Finale of Cellular Respiration!
Alternative Pathways
Anaerobic Respiration & Alternative Metabolic Pathways
Even though aerobic respiration is the most efficient way to generate ATP, animals
can survive without oxygen for short periods using anaerobic respiration or by
metabolizing non-glucose molecules when needed.
1️⃣ Anaerobic Respiration (Lactate Fermentation)
✔ Used during intense activity when oxygen is scarce (e.g., escaping predators or
deep diving).
✔ Only produces 2 ATP per glucose (vs. 30-38 ATP in aerobic respiration).
✔ Pyruvate is converted into lactate (lactic acid) instead of entering the
mitochondria.
✔ Lactic acid buildup causes muscle fatigue, so it must be transported to the
liver, where it is converted back to pyruvate when oxygen is available again.
📌 Key takeaway: Anaerobic respiration is fast but inefficient, used for short bursts of
energy.
2️⃣ Alternative Energy Sources When Glucose is Scarce
Animals don’t always rely on carbohydrates! When glucose is unavailable, the body can
metabolize fats and proteins instead.
🔹 Fat Metabolism (Lipolysis)
✔ Fat is energy-dense and provides more ATP per molecule than glucose.
✔ Glycerol (from fats) → Converted to pyruvate → Feeds into glycolysis.
✔ Fatty acids → Broken down into acetyl-CoA → Enter the Citric Acid Cycle.
✔ Excess calories are stored as fat for future energy needs.
📌 Key takeaway: Fats provide long-term energy storage but breaking them down takes
longer than using glucose.

🔹 Protein Metabolism (Amino Acid Catabolism)

✔ When carbs and fats are unavailable, the body breaks down proteins for energy.
✔ Amino acids lose their amino group (NH₂) → Carbon skeleton enters
glycolysis or the Citric Acid Cycle.
✔ The removed NH₂ forms ammonia (NH₃), which is toxic and must be quickly
converted into urea or uric acid and excreted.
📌 Key takeaway: Proteins are a last-resort energy source since they are needed for
muscle and enzyme function.
3️⃣ Storing & Releasing Energy
✔ Glycogen (stored glucose) can be quickly broken down into glucose when needed.
✔ The liver can synthesize glucose from pyruvate & lactic acid via
gluconeogenesis (reverse glycolysis).
✔ Excess nutrients → Stored as fat for long-term energy.
Final Thoughts
📌 Cellular respiration is flexible!
 If oxygen is available → aerobic respiration (efficient ATP production).
 If oxygen is limited → anaerobic respiration (quick but inefficient ATP).
 If glucose is unavailable → fats & proteins can be used for energy.

THE NUCLEUS, RIBOSOMES, AND VAULTS

The Protein Production Team: Nucleus, Ribosomes, and Vaults
Three key cellular structures work together to code for and produce proteins:
1️⃣ The Nucleus: The Command Center
✔ Stores genetic information (DNA), which contains instructions for making
proteins.
✔ Transcribes DNA into RNA—specifically, messenger RNA (mRNA), which carries the
genetic instructions.
✔ Surrounded by the nuclear envelope, a membrane with nuclear pores that
control what enters and leaves the nucleus.
📌 Key takeaway: The nucleus is where DNA → RNA transcription happens.
2️⃣ Ribosomes: The Protein Factories
✔ Translate mRNA into proteins (site of protein synthesis).
✔ Made of ribosomal RNA (rRNA) and proteins.
✔ Found in two locations:
 Attached to the rough endoplasmic reticulum (RER) → Proteins made here
are often exported or used in membranes.
 Free-floating in the cytoplasm → Proteins made here stay inside the cell.
✔ Ribosomes can form polyribosomes (polysomes)—multiple ribosomes
translating the same mRNA simultaneously.
📌 Key takeaway: Ribosomes translate RNA into protein—the final product of
genetic instructions!
3️⃣ Vaults: The Transport Units
✔ Shaped like octagonal barrels and found in large numbers in the cytoplasm.
✔ Assist in transporting RNA and other materials between the nucleus and
cytoplasm.
✔ Complexed with nuclear pores, helping regulate cellular activity (cell signaling).
📌 Key takeaway: Vaults help shuttle RNA out of the nucleus so protein synthesis
can occur.
Protein Production Process (Summary)
1. DNA in the nucleus is transcribed into RNA.
2. RNA exits through nuclear pores (assisted by vaults).
 3. Ribosomes translate RNA into proteins (either in the cytoplasm or on the
rough ER).
4. Proteins are used for cellular functions or exported out of the cell.
💡FinalThought:
The nucleus, ribosomes, and vaults form a highly efficient protein production
system, ensuring the cell can grow, function, and respond to its environment!

THE ENDOMEMBRANE SYSTEM

The endomembrane system is an interconnected network of membranes that
manages material flow within the cell. It includes:
1️⃣ Endoplasmic Reticulum (ER): The Factory 🏭
✔ Rough ER (RER) → Covered in ribosomes, makes proteins for export or membranes.
✔ Smooth ER (SER) → No ribosomes, makes lipids, detoxifies substances, stores
calcium.
📌 Key Role: Synthesizes proteins and lipids, sends them to the Golgi for
processing.
2️⃣ Golgi Apparatus: The Packaging & Shipping Center 📦📮
✔ Receives proteins & lipids from the ER.
✔ Modifies, sorts, and packages them into vesicles.
✔ Ships vesicles to their final destinations (inside or outside the cell).
📌 Key Role: Final processing & distribution of cell products.
3️⃣ Vesicles: The Delivery Trucks 🚚
✔ Small membrane-bound sacs that transport proteins, lipids, and waste.
✔ Types of vesicles:
 Transport vesicles → Move materials between ER and Golgi.
 Secretory vesicles → Release substances outside the cell.
 Lysosomes → Contain digestive enzymes to break down waste.
📌 Key Role: Transport materials between organelles.
4️⃣ Nuclear Envelope: The Headquarters Wall 🏢🚪
✔ Surrounds the nucleus and controls material exchange.
✔ Connected to the ER, allowing RNA and proteins to move freely between them.
📌 Key Role: Regulates traffic in and out of the nucleus.
🔄 How It Works (Step-by-Step) 🔄
1. ER synthesizes proteins & lipids.
2. Vesicles transport them to the Golgi.
3. Golgi modifies & packages them.
 4. Vesicles ship the final products inside or outside the cell.
💡FinalThought:
The endomembrane system is like a highly organized supply chain, ensuring
proteins, lipids, and other materials reach the right place at the right time! 🚀

The Endoplasmic Reticulum and the Golgi Apparatus

Summary: Endoplasmic Reticulum and Golgi Apparatus
 Endoplasmic Reticulum (ER)
o A membrane-bound network of flattened sheets, sacs, and tubules
spreading throughout the cytoplasm.
o Continuous from the nuclear envelope to the plasma membrane.

o Functions as a channel for material transport and storage for

enzymes and proteins.
o Two types:

 Rough ER – has attached ribosomes, synthesizes proteins.

 Smooth ER – lacks ribosomes, involved in lipid production,
detoxification of organic molecules, and calcium storage
(e.g., in muscle cells).
o Most cells contain both types, but the proportion varies.

 Golgi Apparatus
o Named after Camillo Golgi, who discovered it in 1898.

o Physically and functionally connected to the ER.

o Made of flattened stacks of membrane-bound cisternae (fluid

reservoirs).
o Functions:

 Sorts, packages, and secretes proteins and lipids.

 Receives proteins from ribosomes via the ER in transfer
vesicles.
 Chemically modifies proteins to mark and sort them for different
destinations.
 Packages proteins into membrane-enclosed vesicles for
transport.
o Abundant in cells that secrete substances, such as:

 Pancreatic cells (secreting digestive enzymes).

 Nerve cells (secreting neurotransmitters).
  Hormone-producing cells and tissues.

Vesicles and Cellular Transport

 Cellular Transport
o Materials diffuse through the cytosol or move between organelles.

o Proteins move from ribosomes into the ER during production.

o Vaults may aid material transport from the nucleus to the cytoplasm.

o Vesicles, part of the endomembrane system, form from or receive

materials from the ER or Golgi apparatus.
 Types of Vesicles
o Transfer vesicles – Carry proteins from the ER to the Golgi apparatus.

o Secretory vesicles – Move materials to the plasma membrane for

release.
o Vacuoles – Used for temporary storage and transport.

 Contractile vacuoles in freshwater sponges remove excess

water for homeostasis.
 Food vacuoles store ingested food for intracellular digestion.
o Endosomes – Formed when the plasma membrane engulfs materials
from outside the cell.
 Lysosomes
o Membrane-bound organelles containing acid hydrolase enzymes
(40+ types).
o Break down extracellular material, intracellular waste, and worn-out
organelles.
o Formation process:

1. Enzymes synthesized by ribosomes.

2. Transported in vesicles from the ER to the Golgi apparatus.

3. Processed and secreted by the Golgi into vesicles that become

or fuse with lysosomes.
o Function:

 Digest food, waste, and cellular debris.

 Recycle breakdown products for energy or anabolic functions.
 Regulate metabolism, cell longevity, and influence
neurodegenerative diseases.
Endocytosis and Exocytosis
 Vesicles transport materials by endocytosis and exocytosis.
 Endocytosis (Gr. endon, within + cyto, cell) moves large particles and
molecules into the cell by enveloping them with the plasma membrane.
o Three forms of endocytosis:

 Pinocytosis (Gr. pinein, to drink) – Nonspecific uptake of small

extracellular fluid droplets.
 Phagocytosis (Gr. phagein, to eat) – The cell engulfs solid
material rather than liquid.
 Receptor-mediated endocytosis – A specific receptor protein
on the plasma membrane binds to extracellular molecules,
forming a vesicle.
 Exocytosis (Gr. exo, outside) – A secretory vesicle fuses with the plasma
membrane and releases its contents outside the cell.
o This process replaces plasma membrane material lost during
endocytosis.

Summary: Endocytosis and Exocytosis

 Endocytosis and exocytosis facilitate the transport of large molecules
into and out of cells.
 These processes are essential for protein packaging by the ER and Golgi
apparatus.
 Endocytosis – The plasma membrane engulfs materials, forming vesicles
that transport substances into the cell.
Exocytosis – Vesicles fuse with the plasma membrane, releasing their contents
outside the cell.

PEROXISOMES
 Peroxisomes are vesicle-like structures that may originate from the division
of preexisting peroxisomes, though evidence is contradictory, so they are
not classified as part of the endomembrane system.
 They contain enzymes that remove electrons and hydrogen atoms from
acids (amino acids and fatty acids).
 Functions:
o Detoxify alcohol

o Break down hydrogen peroxide into water and oxygen to prevent

DNA damage and cell death
 Hydrogen peroxide is produced in the mitochondria during the electron
transport chain, and its breakdown is crucial in inflammation, aging, and
cancer metabolism.
THE CYTOSKELETON AND CELLULAR MOVEMENT
Cytosol and Cytoskeleton
 The cytosol is not just a fluid interior with floating organelles; it is highly
structured and dynamic.
 It contains a complex network of filaments and tubules called the
cytoskeleton, which:
o Connects structures, giving the cell shape and texture.

o Projects from the cell, aiding in locomotion (e.g., sperm cell

movement) or moving materials across outer surfaces (e.g., egg
transport through the oviducts in female mammals).

Microtubules, Intermediate Filaments, and Microfilaments

 The cytoskeleton is composed of microtubules, intermediate

filaments, and microfilaments.

Microtubules
 Hollow, slender, cylindrical structures made of paired tubulin
subunits.
 Functions:
o Assist in the movement of organelles (e.g., secretory
vesicles).
o Play a role in chromosome movement during cell division.
o Serve as a transport system (e.g., transporting materials in
nerve cells).
o Contribute to cell shape changes during specialization.
 Assembled at the Microtubule-Organizing Center (MTOC),
which:
o Contains centrioles surrounded by pericentriolar material.
o Helps form structures like cilia, flagella, basal bodies, and
the mitotic apparatus.
o Replicates during cell division, forming centrosomes at
opposite poles of the cell.

Intermediate Filaments
 Heterogeneous group of protein fibers, varying by cell type.
 Functions:
o Maintain cell shape and organize organelles.
o Support mechanical activities within the cytoplasm.

Microfilaments (Actin Filaments)

 Solid protein filaments composed of actin.
 Functions:
 o Present in muscle cells as myofibrils, aiding in contraction.
o Provide mechanical support and help maintain cell shape
in nonmuscle cells.
Summary: Cytoskeletal Protein Fibers
 The cytoskeleton consists of three classes of protein fibers
(figure 2.19):
(a) Microtubules
 Composed of paired globular proteins called tubulin subunits,
arranged in parallel rows.
(b) Intermediate Filaments
 Chemically heterogeneous; their protein subunits vary among
different cell types.
(c) Microfilaments
 Actin is the primary subunit.
 Supports mechanical functions and helps maintain cell shape.

Cilia and Flagella

 Cilia (L. cilium, eyelash) and flagella (L. flagrum, whip) are
elongated appendages that aid in cell movement and material
transport.
 Unicellular organisms (e.g., Giardia) use flagella for propulsion.
 Stationary cells use cilia to move materials over their surfaces.
 Primary cilium functions as a cell-signaling antenna, regulating
cell division, differentiation, and cilia motility.
Differences Between Cilia and Flagella
Feature Cilia Flagella
Length Shorter Longer
Few (1-3 per
Number Numerous
cell)
Moveme Coordinated Planar wave
nt waves motion
Structural Composition
 Both cilia and flagella follow a 9 + 2 microtubule
arrangement, called the axoneme, surrounded by the plasma
membrane.
 Dynein arms enable bending through ATP-powered
conformational changes.
Basal Body & Microtubule Organization
 Basal body anchors cilia and flagella within the cytoplasm.
 Features a 9 + 0 microtubule triplet arrangement, similar to
centrioles.

LEVELS OF ORGANIZATION IN AN ANIMAL

Multicellularity & Levels of Organization
Animals are multicellular and exhibit different levels of cellular
organization:
1. Tissue Level – Groups of similar cells with a common function.
2. Organ Level – Structures composed of multiple tissue types
working together.
3. Organ-System Level – Organs grouped to perform broader
functions (e.g., digestive system).

Tissue Types in Animals (Histology: Gr. histos, tissue + logos,

discourse)
1. Epithelial Tissue
o Function: Covers or lines surfaces (e.g., epidermis of the skin,
digestive tract lining).
o Structure: Rests on a basement membrane containing
collagen proteins.
o Examples:
 Small intestine: Secretes enzymes & absorbs nutrients.
 Epidermis: Protects against external harm.
2. Connective Tissue
o Function: Provides support and binding.
o Structure: Consists of fibers embedded in a ground
substance (fluid to solid).
o Examples:
 Blood (fluid matrix)
 Cartilage & bone (solid matrix)
3. Nervous Tissue
o Function: Communication & coordination within the body.
o Structure: Contains:
 Neurons – Conduct impulses.
 Neuroglia – Support & nourish neurons.
o Examples: Nerves, ganglia, brain.
4. Muscle Tissue
o Function: Enables movement.
o Examples:
 Skeletal muscle – Moves body parts.
 Smooth muscle – Moves food through the digestive
tract.
 Cardiac muscle – Pumps blood.
Higher Levels of Organization
 Organs: Structures composed of multiple tissues (e.g., heart,
stomach).
 Organ Systems: Groups of organs working together (e.g.,
digestive, circulatory, respiratory systems).
Animal complexity increases from simple tissues to integrated organ
systems, allowing diverse functions across species.