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	Existence (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	Existence	None
Vacuole	None	Existence (major)	Existence (minor)
Centriole	None	None	Existence
Lysosome	None	None	Existence

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 • The axoneme of cilia and flagella has a 9+2 microtubule 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: glycoprotein of triple helix structure in animal cells.

e. Endomembrane system

f. Growth of cell

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 blood cells.

– long distance

– eg/ Estradiol, testosterone, adrenaline, insulin

2. Reception

a. Cell surface reception

: receptor that binds signal on plasma membrane.

Ion channel linked receptors

– acting as gate controlling synaptic signaling by. neurotransmitter.

G-protein linked receptors

– helping G protein to act as an inactive enzyme.

Receptor Tyrosine kinases

– activated tyrosine kinases by ATP molecules helps to activate an inactive enzyme.

b. Intracellular reception

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

3. Transduction

a. Phosphorylation cascade

: sequence of enzyme activities, in which activated enzyme by protein kinase reads an inactivated enzyme.

Phosphorylation

– protein kinase: Activated enzyme by accepting phosphate groups from ATP.

– protein phosphatases: Inactivated enzyme by losing phosphate groups.

b. G-protein signaling pathway

First messenger (signal molecules): activates G-protein-linked receptor.
Second messenger (c AMP): activates protein kinase A from adenylyl cyclase.

c. Calcium and IP₃ in signaling pathway

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

– IP₃activates IP₃– gated calcium channel to flow out Ca²⁺ from ER to cytosol.

– Ca²⁺ activates various proteins.

4. Response

: leading transcription or cytoplasmic activities

D. Membrane

1. Function

Separation between inside and outside of cell.
Selective transporting of molecules (lipids and small hydrophobic molecules) into and out of cell.
Growth and movement.
Communication with other cells.

2. Components of structure

Phospholipids – bilayer with amphipathic (hydrophilic and hydrophobic molecules).
Proteins – integral proteins (hydrophobic) and peripheral proteins (hydrophilic).
Cholesterols – embedded in cell membranes and function in keeping membrane fluidity to environment condition.
Glycolipids.

3. Passive transport

: diffusing down any substance of concentration gradient.

Does not require energy.
Eg/ Diffusion, osmosis, facilitated diffusion (chemiosmosis in the mitochondria).

a. Diffusion

Random movement of molecules from the area of higher concentration to the area of 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 → Lysed, 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 → Flattened, flaccid

– hypertonic solution → Shrunken, plasmolyzed

* Because of losing water, the cell size shrinks.

4. Active transport

: movement of substances from an area of low concentration to an area of high concentration by using chemical energy.

Requires energy.
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

: energy property from the chemical reaction to maintain living organisms

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.

– reversal change of internal condition against outside environmental changes.

– most homeostatic animal cells operate on negative feedback.

Positive feedback – same directional change of internal condition with outside environmental change.

F. Enzymes

: a biological catalyst (mainly protein) increasing the chemical reaction by lowering the activation energy without being used up.

Enzymatic conformational change by binding substrate.
No changing concentration of product, K_eq, ΔS, or ΔG by enzyme.
Influenced enzyme by temperature, pH level, concentration of enzyme, and concentration of substrate.
Each enzyme having certain optimum temperature and pH.
Reusable enzyme after finishing catalytic activity.

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 – products are produced by binding of activator at allosteric site.
Inhibition – products are not produced by binding of inhibitor at allosteric site.
Cooperativity.

– binding one substrate to active site causes the rest of the subunits to be stimulated and become active.

– amplify the activity of enzyme.

b. Enzyme with inhibition

Non-competitive inhibition

– binding inhibitor to the allosteric site causes the enzyme to be inactive.

Competitive inhibition

– binding inhibitor to the active site hinders the binding activator to active site and becomes inactive.

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 with reflection of blue-green light.

– chlorophyll b: accessory pigment with reflection green-yellow light.

– carotenoid: accessory pigment with reflection of yellow-red light and photoprotection (protection of chlorophyll by dissipating excessive light energy).

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

H₂O (split into) → e^–, H⁺, O₂

Final product of photosystem II (P680) is ATP from electron transport system.
Final product of photosystem I (P700) is NADPH from electron transport system.
The movement of H⁺ across a membrane through cytochrome complex is active transport.
The movement of H⁺ across a membrane through ATP synthase is facilitated diffusion.

ii. Light independent (dark reaction)

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 (PGAL): immediate food nutrient, glucose formation, and end product of Calvin cycle

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

Glycolysis, fermentation, mitochondria (TCA cycle, electron transport chain)

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

: ATP production in anaerobic respiration.

Glucose → pyruvate → lactate (lactic acid), ethanol.
Lactate reaction in muscle cell.
Ethanol reaction in yeast cell.
Lactic acid goes the cori cycle in the liver to regenerate glucose again.
Regeneration of 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. Acetyl CoA

Aerobic metabolism in mitochondria before moving into Krebs cycle
Production of 2CO₂, 2NADH, and 2H⁺

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

Aerobic metabolism in mitochondria
Acetyl CoA + oxaloacetate acid → citrate
Producing 6 NADH, 2 FADH₂, 2 ATP (2 GTP), and 4 CO₂ per 2 pyruvates (1 glucose molecule = 2 pyruvates)

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 and cytochrome c are mobile lipid-soluble carriers of electron.
Electron transport chain pumps protons from matrix to intermembrane space to increase a proton gradient.
The created proton gradient synthesizes ATP.
Production 32 or 34 ATP (1NADH=3ATP, 1FADH₂=2ATP).
O₂ is final source for acceptance of electron from NADH and FADH₂ to become H₂O.

4. Overall reaction between photosynthesis and cellular metabolism

a. Chloroplasts

PS II and electron transport: O₂and 18 ATP/6 turns (1 glucose = 6 turns)
PS I and electron transport: 12NADPH/6 turns
Calvin cycle: 12 PGAL/ 6 turns, glucose

b. Mitochondria

Krebs cycle: 4 CO₂, 6 NADH, 2ATP, and 2 FADH₂/ per 2 pyruvates
Electron transport chain: 32 – 34 ATP, H₂O

c. ATP producing in cellular respiration per 1mole glucose: 36 – 38 ATP

Glycolysis: 2 ATP
Krebs cycle: 2 ATP
Electron transport chain: 32~34 ATP

d. Mitochondria and chloroplasts

Semiautonomous containing DNA and ribosome
Endosymbiosis