I. Cell

Key focus of this chapter: biological macromolecules

This chapter focuses on biological macromolecules and gives concise summaries of the important things about cell membrane and cellular respiration in more detail.

A. Biological Macromolecules

Most biological molecules are composed primarily of carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), and sulfur (S), collectively known as CHNOPS.

• Nucleic acids: C, H, O, N, and P

• Proteins: primarily C, H, O, and N; some proteins also contain S

1. Carbohydrates (Sugars)

Composed primarily of carbon, hydrogen, and oxygen, often in an approximate 1:2:1 ratio
Functions: energy source, energy storage, structural support, and cell recognition

Carbohydrates (sugar)	Classification	Description
Monosaccharide	Glucose	• A six-carbon aldose sugar; the primary energy source for most cells
	Ribose	• A five-carbon sugar found in RNA
	Deoxyribose	• A five-carbon sugar found in DNA
	Galactose	• A component of lactose
	Fructose	• A six-carbon ketose sugar found in many fruits; a component of sucrose
Disaccharide	Sucrose	• Glucose + fructose • α(1→2)β glycosidic linkage
	Maltose	• Glucose + glucose • α(1→4) glycosidic linkage
	Lactose	• Glucose + galactose • β(1→4) glycosidic linkage
Polysaccharide	Starch	• A glucose-storage polysaccharide in plants • Composed of amylose and amylopectin • Contains α(1→4) linkages and α(1→6) branch points
	Glycogen	• A highly branched glucose-storage polysaccharide in animals and fungi • Contains α(1→4) linkages and α(1→6) branch points • More highly branched than starch
	Cellulose	• The primary structural polysaccharide of plant cell walls • Composed of β-glucose monomers joined by β(1→4) glycosidic linkages • Parallel cellulose chains are linked by hydrogen bonds to form microfibrils
	Chitin	• A structural polysaccharide composed of N-acetylglucosamine (NAG) monomers • A major component of fungal cell walls and arthropod exoskeletons

2. Proteins

a. Amino acids

Amino acids are the monomers of proteins.
Each amino acid contains a central α-carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).
The 20 common amino acids differ in the chemical properties of their R groups.

b. Polypeptides

Amino acids are joined by peptide bonds through dehydration (condensation) reactions to form polypeptide chains.
Peptide bonds are formed by dehydration synthesis and broken by hydrolysis.
Functions of proteins include enzymatic catalysis, signaling, regulation, transport, storage, defense, structural support, and movement.
High temperatures, extreme pH conditions, or certain chemicals can denature proteins by disrupting their secondary, tertiary, or quaternary structure, often causing loss of biological function.
Denaturation usually does not break the peptide bonds of the primary structure.

Structures	Features
Primary (1º) structure	• Unique linear amino acid sequence; peptide bonds.
Secondary (2º) structure	• α-helices and β-pleated sheets; stabilized by hydrogen bonds between backbone atoms.
Tertiary (3º) structure	• Overall 3D shape of a single polypeptide; stabilized by hydrogen bonds, ionic interactions, disulfide bonds, van der Waals forces, and hydrophobic interactions among R groups.
Quaternary (4º) structure	• Association of two or more polypeptide subunits into one functional protein; Example: hemoglobin.

3. Lipids

a. Fats

Unsaturated fatty acids contain one or more carbon–carbon double bonds.
Cis double bonds create kinks in hydrocarbon tails, preventing tight packing and increasing membrane fluidity.
Unsaturated fats are commonly liquid at room temperature (e.g., many plant oils).
Saturated fatty acids contain no carbon–carbon double bonds.
Their straight hydrocarbon tails pack tightly together, decreasing membrane fluidity.
Saturated fats are commonly solid at room temperature (e.g., butter).
Fats are more energy-dense than carbohydrates and proteins.
A triacylglycerol (triglyceride) consists of one glycerol molecule joined to three fatty acids by ester linkages.

b. Phospholipids

Phospholipids are amphipathic molecules with hydrophilic heads and hydrophobic fatty-acid tails.
They spontaneously form a phospholipid bilayer, the basic structure of cell membranes.

c. Steroids

Steroids are lipids characterized by four fused carbon rings.
Examples include cholesterol, testosterone, estradiol, cortisol, and vitamin D.
Cholesterol is an essential component of animal cell membranes and helps regulate membrane fluidity and permeability.
Cholesterol is also a precursor of steroid hormones, bile acids, and vitamin D.
Waxes are hydrophobic lipids that provide protective, water-resistant coatings.

4. Nucleic acids

Nucleic acids are biological macromolecules that store and transmit genetic information.
Each nucleotide consists of a five-carbon sugar, a nitrogenous base, and a phosphate group.
Adjacent nucleotides are linked by phosphodiester bonds to form a sugar-phosphate backbone.
In DNA, two antiparallel strands are held together by hydrogen bonds between complementary bases.

Classification	Description
Nucleoside	Five-carbon sugar + nitrogenous base
Nucleotide	Five-carbon sugar + nitrogenous base + phosphate group
Nucleic acids	Polymer of nucleotides linked by phosphodiester bonds

	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, G, C, T	A, G, C, U
Structure	Usually double-stranded	Usually single-stranded
Bonds	Hydrogen bonds (between strands) and phosphodiester bonds	Phosphodiester bonds

B. Shapes and functions of the cells

1. Cell theory

The cell is the smallest unit of life.
Cells are the basic structural and functional units of all living organisms.
All cells arise from preexisting cells.

2. The differences between prokaryotic and eukaryotic Cells

Prokaryotic cell	Eukaryotic cell
• Cell division by binary fission • Can exchange genetic material by conjugation • Nucleoid (lacks a nuclear envelope)	• Mitotic and meiotic division • Generally larger than prokaryotic cells • Nucleus (w/ nuclear envelope) • Organelles with membrane

3. Structure of prokaryotic and eukaryotic cells

Structures	Prokaryote	Eukaryote
Structures	Prokaryote	Plant	Animal
Cell wall	Many bacteria have peptidoglycan cell walls; archaeal cell walls lack peptidoglycan.	Existence (cellulose)	None
Cytoplasm	Existence	Existence	Existence
Ribosome	Existence	Existence	Existence
Cytoskeleton	Existence	Existence	Existence
Nucleoid	Existence	None	None
Nucleus	None	Existence	Existence
Mitochondria	None	Existence	Existence
ER, Golgi	None	Existence	Existence
Chloroplast	None	Present in photosynthetic plant cells	None
Vacuole	None	Existence (major)	Existence (minor)
Centriole	None	Usually absent in typical flowering-plant somatic cells	Usually present in typical animal cells
Lysosome	None	Lytic vacuoles perform comparable digestive functions	Typically present in animal cells

a. The functions of organelles

Organelles	Functions and features
Flagella	• Cell locomotion
Nucleus	• DNA replication and transcription • Stores genetic information
Ribosomes	• Site of protein synthesis. • Ribosomal subunits are assembled in the nucleolus. • Functional ribosomes are found in the cytoplasm, mitochondria, and chloroplasts. • Free in the cytoplasm or bound to the rough endoplasmic reticulum (ER). • Composed of rRNA and proteins.
Rough ER	• Studded with ribosomes. • Synthesizes secretory proteins, membrane proteins, and membrane components.
Smooth ER	• Lacks ribosomes • Lipid synthesis (including steroid hormones) • Calcium storage • Carbohydrate metabolism • Detoxification
Golgi Apparatus	• Receives proteins and lipids from the ER. • Modifies, sorts, and packages proteins and lipids. • Ships vesicles from the trans face to the plasma membrane or other destinations.
Lysosomes	• Membrane-bound organelles containing hydrolytic enzymes. • Formed through the Golgi apparatus. • Primarily found in animal cells.
Peroxisomes	• Contains oxidative enzymes that produce and break down H₂O₂. • Oxidizes fatty acids and detoxifies harmful compounds. • Formed from the ER.
Vacuole	• Stores nutrients and waste products. • Isolates harmful substances. • Maintains internal pH and turgor pressure. • Surrounded by the tonoplast membrane.
Mitochondria	• Site of aerobic cellular respiration and ATP production. • Contains its own ribosomes and DNA. • Double membrane, cristae, and matrix. • Originated through endosymbiosis.
Chloroplasts	• Site of photosynthesis. • Contains its own ribosomes and DNA. • Double membrane, stroma, thylakoids, and chlorophyll. • Originated through endosymbiosis.
Cytosol	• Main site of many metabolic reactions, including glycolysis.
Centriole	• Organizes microtubules • Helps form the mitotic spindle during cell division • Found primarily in animal cells

b. Cytoskeletons

Cytoskeletons	Functions and features
Microtubules	• Hollow tubes composed of tubulin • Form the mitotic spindle during cell division • Most motile eukaryotic cilia and flagella have a 9+2 microtubule arrangement; primary cilia usually have a 9+0 arrangement • Major component of centrosomes and centrioles • Form cilia and flagella (with dynein for movement) • Serve as tracks for intracellular transport by kinesin and dynein
Microfilaments (Actin filament)	• Cleavage furrow in cytokinesis • Cell crawling (amoeboid movement) • Support the cell cortex and microvilli • Interact with myosin during muscle contraction
Intermediate filaments	• Tensile strength • Nuclear lamina • Keratin provides mechanical strength to epithelial cells.

c. Different layers of membranes

Membranes	Organelles
No membrane	Centriole, Ribosome
Single membrane	Peroxisome, Lysosome, ER, Golgi apparatus, Vacuole
Double membrane	Chloroplast, Mitochondria, Nucleus

d. Extracellular matrix

• Collagen is a major fibrous structural protein of the animal extracellular matrix. Its molecules form a triple helix.

e. Endomembrane system

f. Growth of cell

If a cell’s linear dimensions increase tenfold:

Area: 10² increase
Volume: 10³ increase

C. Cell communication

: cells need to communicate with each other to defend against pathogens and exterior environment and to grow and develop.

1. Signal

a. Direct signal and connection

Cell types	Classification	Features
Animal cell	Tight junction	Tightly associated membranes between two cells
	Gap junction	Channels that directly connect the cytoplasm of adjacent cells
	Desmosomes	Anchoring junctions held together by adhesion proteins
Plant cell	Plasmodesmata	Perforated channels in plant cell wall

b. Local signal

Paracrine signal

– diffusing signal through extracellular matrix to near target cells.

– local distance

– eg/ Growth factors, clotting factors, histamines, nitric oxide

Synaptic signal

– releasing neurotransmitter into synapse

c. Long distance signal

Endocrine signal

– releasing of extracellular signal known as hormones into the bloodstream.

– long distance

– eg/ Estradiol, testosterone, adrenaline, insulin

2. Reception

a. Cell surface reception

: receptor that binds signal on plasma membrane.

Ion channel linked receptors

– Ligand binding opens or closes an ion channel, changing ion flow across the membrane.

G-protein linked receptors

– A ligand-bound GPCR activates a heterotrimeric G protein by promoting GDP–GTP exchange on its α subunit.

Receptor Tyrosine kinases

– Ligand binding activates receptor tyrosine kinases, which use ATP to phosphorylate tyrosine residues and initiate downstream signaling.

b. Intracellular reception

: receptor that binds hydrophobic hormones (steroid hormones) on the inside of a cell.

3. Transduction

a. Phosphorylation cascade

: a sequence of protein phosphorylation events that relays a signal.

Phosphorylation

– Protein kinases transfer phosphate groups, usually from ATP, to target proteins.

– Protein phosphatases remove phosphate groups from target proteins.

Phosphorylation can activate or inhibit a protein, depending on the target and site. The figure below illustrates an example in which phosphorylation activates the protein.

b. G-protein signaling pathway

First messenger (signal molecules): activates G-protein-linked receptor.
Activated G protein → adenylyl cyclase → cAMP production → protein kinase A activation.
Adenylyl cyclase converts ATP to cAMP, the second messenger.

c. Calcium and IP₃ in signaling pathway

First messenger (signal molecules): activates G-protein-linked receptor.
Second messenger (IP₃ and Ca²⁺).

– IP₃ binds to IP₃-gated calcium channels in the ER membrane, releasing Ca²⁺ into the cytosol.

– Ca²⁺ activates various proteins.

4. Response

: leading transcription or cytoplasmic activities

D. Membrane

1. Function

Separation between inside and outside of cell.
Selectively regulates transport into and out of the cell. Small hydrophobic molecules can diffuse through the lipid bilayer; ions and many polar solutes require transport proteins.
Growth and movement.
Communication with other cells.

2. Components of structure

Phospholipids – amphipathic molecules with hydrophilic heads and hydrophobic tails, arranged in a bilayer.
Proteins – integral proteins have membrane-embedded hydrophobic regions; peripheral proteins associate with membrane surfaces.
Cholesterol – embedded in animal cell membranes and helps regulate membrane fluidity.
Glycolipids.

3. Passive transport

: net movement of substances down their concentration or electrochemical gradients.

Does not require direct cellular energy input.
Examples: simple diffusion, osmosis, and facilitated diffusion through ion channels or carrier proteins.
Chemiosmosis couples proton movement down an electrochemical gradient through ATP synthase to ATP production.

a. Diffusion

Random molecular motion produces net diffusion from higher to lower concentration.
Eg/ Movement of O₂ and CO₂ through cell membrane and movement of solutes substances dissolved in a solution.

b. Osmosis

Diffusion of water from high water potential area to low water potential area across a semi-permeable membrane.
Eg/ Water movement through aquaporins of vacuoles.
If cell is placed in

– hypotonic solution → Animal cell: swelling or lysis; plant cell: turgid

* Because of absorption of water, the cell size becomes bigger.

* Eg/ A red blood cell swells up and bursts when it is placed in distilled water.

– isotonic solution → Animal cell: normal; plant cell: flaccid

– hypertonic solution → Animal cell: shriveled; plant cell: plasmolyzed

* Because of losing water, the cell size shrinks.

4. Active transport

: Active transport moves substances against their concentration or electrochemical gradients using energy, either directly from ATP or indirectly from an ion gradient.

Primary active transport uses energy directly; secondary active transport uses energy stored in an ion gradient.
Eg/ Sodium-potassium pump of axon, electrogenic pump, cotransport (symport and antiport), proton pump.

5. Bulk transport

: movement of large molecules across the membrane.

Classification		Features
Endocytosis	Pinocytosis	Engulfing liquid by using vesicle of membrane
	Phagocytosis	Engulfing particles by using of membrane
	Receptor-mediated endocytosis	Engulfing molecules by specific receptor of vesicle membrane
Exocytosis		Ejection of stuff in vesicle by plasma membrane

E. Energy and life

1. Metabolism

: Metabolism is the sum of all chemical reactions in a living organism, including catabolic and anabolic pathways.

Catabolic pathways – breakdown pathway or digestive process.
Anabolic pathways – the process of building complicated molecules from smaller units by using energy.

2. Laws of energy

a. First law of thermodynamics

Principle of conservation of energy – energy can be transferred and transformed, but not created or destroyed.
Eg/Chemical energy converts into kinetic energy after eating food.

b. Second law of thermodynamics

Universal law of increasing entropy.
Eg/ Heat energy emit when organisms work.

3. Homeostasis

: control system to maintain the stable internal condition from outside environmental changes.

Negative feedback.

– responses oppose deviations from a set point.

– most homeostatic control systems use negative feedback.

Positive feedback – responses amplify the initial change.

F. Enzymes

: biological catalysts (mostly proteins) that speed chemical reactions by lowering activation energy without being consumed.

Substrate binding can induce a conformational change in the enzyme.
Enzymes speed the approach to equilibrium without changing K_eq or the reaction’s ΔG.
Enzyme activity depends on temperature, pH, and enzyme and substrate concentrations.
Each enzyme has an optimum temperature and pH.
Enzymes can be reused after catalysis.

1. Reaction

Exergonic reaction: release of free energy.
Endergonic reaction: obtaining free energy.

2. Structure of enzyme

Allosteric site

– meaning different site.

– regulatory molecules (activator, inhibitor) binding site.

Active site – substrate binding site

3. Regulation of enzyme

a. Allosteric Enzyme

: enzyme can be active or inactive by the binding of regulatory molecule to allosteric site.

Activation – binding of an activator at an allosteric site increases enzyme activity.
Inhibition – binding of an inhibitor at an allosteric site reduces enzyme activity.

Positive cooperativity.

– binding of substrate to one subunit increases substrate affinity at other subunits.

– amplify the activity of enzyme.

b. Enzyme with inhibition

Non-competitive inhibition

– A noncompetitive inhibitor reduces enzyme activity by binding at a site distinct from the active site; it does not necessarily prevent substrate binding.

Competitive inhibition

– A competitive inhibitor binds to the active site and competes with the substrate.

Allosteric regulation includes activation or inhibition at regulatory sites; it is not identical to noncompetitive inhibition.
Feedback inhibition

– the end product of a long series of enzymatic reaction inhibits the beginning reaction of the series.

G. Photosynthesis

1. Redox reaction

a. Oxidation

Losing electron and hydrogen.
Gaining oxygen.

b. Reduction

Gaining electron and hydrogen.
Losing oxygen.

** OILRIG – Oxidation Is Losing electron and Reduction Is Gaining electron.

2. Chloroplast

: double membraned organelle of cell, which is to convert light energy to chemical energy.

a. Structure of chloroplast

b. Larger to smaller structure

c. Photosynthesis

: converting light energy to ATP free energy and reducing NADP to NADPH to make sugar as a final product.

Light + 6H₂O + 6CO₂ → C₆H₁₂O₆ + 6O₂
Occurring in some bacteria, algae, and plants.

i. Light dependent (light reaction)

Taking place at thylakoid membrane.
Photosynthetic pigments (light receptors).

: magnesium-containing porphyrin ring and hydrocarbon tail in Chlorophyll.

– chlorophyll a: primary pigment that absorbs primarily blue-violet and red light and reflects relatively more green light.

– chlorophyll b: accessory pigment that broadens the range of light absorbed for photosynthesis.

– carotenoid: accessory pigment that absorbs mainly blue-green wavelengths and contributes to photoprotection (protection of chlorophyll by dissipating excessive light energy).

H₂O is source of electron, hydrogen, and oxygen at photosystem II.

2H₂O → O₂ + 4H⁺ + 4e⁻

PSII oxidizes water and supplies electrons to the photosynthetic electron transport chain, contributing to proton-gradient formation.
PSI transfers excited electrons to ferredoxin, enabling NADP⁺ reduction to NADPH.
Electron transport through the cytochrome complex drives proton movement from the stroma into the thylakoid lumen.
ATP synthase uses the proton gradient across the thylakoid membrane to synthesize ATP as H⁺ flows into the stroma.

ii. Calvin cycle (light-independent reactions)

Takes place in stroma.
Uses ATP and NADPH to produce sugar in Calvin cycle.
Calvin cycle

RuBP (Ribulose bisphosphate) + CO₂ (by Rubisco enzyme)

→ Two 3-phosphoglycerate (PGA) per turn of Calvin cycle

Glyceraldehyde 3-phosphate (G3P, also called PGAL) is the net carbohydrate product. Three CO₂ fixed yield one net G3P; six yield two net G3P for carbohydrate synthesis. Light-independent does not mean that these reactions occur only in darkness.

d. Photosynthesis in C3, C4, CAM plants

C3 plants

– Eg/ Most crops (rice, wheat, soybeans).

C4 plants

– adaptation in hot and dry conditions.

– spatial separation: CO₂fixation in mesophyll cell and then working of Calvin cycle in bundle sheath cell.

– eg/ sugarcane, corn.

CAM plants

– adaptation in arid conditions.

– temporal separation (night, day) – CO₂enter into stomata during night and then working of Calvin cycle during day.

– open stomata during the night and close stomata during the day.

– eg/ Cacti, pineapples.

H. Cellular respiration

: metabolic reaction, which is to convert nutrients into energy in organism cells

Aerobic respiration: glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation. Fermentation provides an alternative means of regenerating NAD⁺ for glycolysis.

C₆H₁₂O₆ + 6O₂→ 6H₂O + 6CO₂+ Energy (ATP)

1. Glycolysis

: metabolic pathway, which is to convert one glucose into two pyruvates in cytosol.

Investing 2ATP and harvesting 4ATP, therefore harvesting net 2ATP.
Harvesting 2NADH, 2H⁺, 2H₂O, 2Pyruvates.

Glucose + 2NAD⁺ + 2Pi + 2ADP → 2Pyruvates + 2NADH + 2ATP(NET) + 2H⁺ + 2H₂O

2. Fermentation

: Fermentation regenerates NAD⁺ from NADH, allowing glycolysis to continue without an electron transport chain.

ATP is produced by substrate-level phosphorylation in glycolysis, not by the fermentation reactions themselves. Fermentation differs from anaerobic respiration, which uses an electron transport chain.

Lactic acid fermentation converts pyruvate to lactate; alcoholic fermentation produces ethanol and CO₂.
Lactate fermentation occurs in muscle cells; alcoholic fermentation occurs in yeast.
In the Cori cycle, lactate travels to the liver and is used to regenerate glucose.
Both fermentation pathways regenerate NAD⁺.

3. Mitochondria

: double membraned organelle of cell, which is place for oxidative metabolism to make ATP.

Aerobic respiration

a. Structure of mitochondria

Double membrane
Cristae
Matrix
Krebs cycle

b. Pyruvate oxidation (acetyl-CoA formation)

A separate step before the Krebs cycle, occurring in the mitochondrial matrix in eukaryotic cells.
Per glucose: 2 pyruvate → 2 acetyl-CoA + 2 CO₂ + 2 NADH.

c. Krebs cycle (Citric acid cycle, TCA cycle)

Aerobic metabolism in mitochondria
Acetyl CoA + oxaloacetate → citrate
Producing 6 NADH, 2 FADH₂, 2 ATP (2 GTP), and 4 CO₂ per 2 acetyl-CoA (derived from one glucose); pyruvate oxidation separately produces 2 NADH and 2 CO₂

d. Catabolism of various macromolecules

Gluconeogenesis – glucose generation of metabolic pathway from amino acid, glycerol, and lactate.

e. Electron transport

Electron transport chain and chemiosmosis at inner mitochondrial membrane are called oxidative phosphorylation.
Ubiquinone (coenzyme Q) is a lipid-soluble mobile electron carrier within the inner mitochondrial membrane.
Cytochrome c is a small, water-soluble peripheral protein that transfers electrons between complexes III and IV.
Electron transport chain pumps protons from matrix to intermembrane space to increase a proton gradient.
ATP synthase uses the proton motive force to synthesize ATP.
Oxidative phosphorylation typically produces approximately 26–28 ATP per glucose in eukaryotic cells.
Typical P/O ratios: NADH ≈ 2.5 ATP; FADH₂ ≈ 1.5 ATP.
O₂ is the final electron acceptor and is reduced to H₂O.

4. Overall reaction between photosynthesis and cellular metabolism

a. Chloroplasts

Light reactions: PSII releases O₂; electron transport and ATP synthase generate ATP, while PSI supports NADPH production.
For 6 CO₂ fixed, the Calvin cycle consumes 18 ATP and 12 NADPH.
The cycle forms 12 G3P (PGAL); 10 regenerate RuBP and 2 are net products available for carbohydrate synthesis.

b. Mitochondria

Krebs cycle: 4 CO₂, 6 NADH, 2 ATP (or GTP), and 2 FADH₂ per 2 acetyl-CoA (one glucose)
Oxidative phosphorylation: approximately 26–28 ATP per glucose; O₂ is reduced to H₂O

c. ATP yield from aerobic respiration

Glycolysis: 2 ATP
Krebs cycle: 2 ATP
Oxidative phosphorylation: approximately 26–28 ATP

Total ATP yield from aerobic respiration is approximately 30–32 ATP per glucose, depending on the shuttle system and cellular conditions.

d. Mitochondria and chloroplasts

Semiautonomous containing DNA and ribosome
Endosymbiosis