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 major source of cellular energy; a six-carbon aldose sugar
	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 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	• A structural polysaccharide in 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 monomers • A major component of fungal cell walls and arthropod exoskeletons

2. Proteins

a. Amino acid

Amino acids are the monomers that make up proteins.
The central α-carbon is bonded to an amino group, a carboxyl group, a hydrogen, and a variable side chain (R group).
Each of the 20 common amino acids has a different R group.

b. Polypeptide

Amino acids are linked by peptide bonds.
Proteins function in catalysis, hormonal signaling, storage, regulation, defense, transport, structural support, and movement.
Heat or extreme pH can disrupt a protein’s secondary, tertiary, or quaternary structure and reduce or eliminate its function.

Structures	Features
Primary (1°) structure	• The unique linear sequence of amino acids in a polypeptide • Amino acids are connected by covalent peptide bonds
Secondary (2°) structure	• Local folding into α-helices and β-pleated sheets • Stabilized by hydrogen bonds between atoms of the polypeptide backbone
Tertiary (3°) structure	• The overall three-dimensional shape of a single polypeptide • Stabilized by interactions among R groups, including hydrogen bonds, ionic interactions, disulfide bonds, van der Waals forces, and hydrophobic interactions
Quaternary (4°) structure	• The association of two or more polypeptide subunits into one functional protein • The subunits may be identical or different • Examples: hemoglobin and collagen

3. Lipid

a. Fat

Cis double bonds in unsaturated fatty acids introduce pronounced kinks, reduce packing, and increase fluidity. Trans double bonds do not create the same kink and can pack more like saturated fatty acids.

– Examples: oils

Saturated fatty acids have no carbon–carbon double bonds, so their straight tails pack tightly and reduce fluidity.

– Example: butter

Fat provides ~9 kcal/g of nutritional energy.

Carbohydrate and protein provide ~4 kcal/g.

– Examples of lipid-related molecules: glycerol, fatty acids, and triacylglycerols

b. Phospholipid

A phospholipid is amphipathic, with a hydrophilic head and hydrophobic tails. Phospholipids form a bilayer in cell membranes.

c. Steroids

Four fused carbon rings.
Cholesterol helps regulate membrane fluidity and decreases permeability to many small water-soluble molecules.
Found in most animal cell membranes.
Examples: cholesterol

4. Nucleic acids

Molecules that store genetic information of organisms.
Composed of nucleotide (five carbon sugar, nitrogenous base, and phosphate group).
A phosphodiester linkage joins the 3′ oxygen of one sugar to the 5′ phosphate of the next nucleotide.
DNA is typically double-stranded, with complementary bases joined by hydrogen bonds.
DNA strands are antiparallel. RNA is typically single-stranded but can form base-paired regions.

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

	DNA	RNA
Sugar	Deoxyribose sugar	Ribose sugar
Bases	A, G, C, T	A, G, C, U
Shape	Usually double-stranded	Usually single-stranded
Bond	Hydrogen bonds (between strands) and phosphodiester bonds	RNA nucleotides are connected by phosphodiester bonds; RNA can also form hydrogen-bonded base-paired regions.

B. Shapes and functions of the cells

1. Cell theory

All living organisms are composed of one or more cells.
The cell is the basic unit of structure and function in living organisms.
All cells arise from preexisting cells.

2. The difference 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 (with a nuclear envelope) • Organelles with membrane

3. Structure of prokaryotic and eukaryotic cells

	Prokaryote	Eukaryote
	Prokaryote	Plant	Animal
Cell wall	Many bacteria: peptidoglycan walls. Archaea: no peptidoglycan. Some bacteria (e.g., Mycoplasma): no cell wall.	Present (cellulose)	None
Cytoplasm	Present	Present	Present
Ribosome	Present	Present	Present
Cytoskeleton	Present	Present	Present
Nucleoid	Present	None	None
Nucleus	None	Present	Present
Mitochondria	None	Present	Present
ER, Golgi	None	Present	Present
Chloroplast	None	Present	None
Vacuole	None	Present (major)	Present (minor)
Centriole	None	None	Present
Lysosome	None	None	Present

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. • Grow and divide from preexisting peroxisomes and may also arise 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 • Typical motile eukaryotic cilia and flagella: 9+2 axoneme. Primary/nonmotile cilia: commonly 9+0; exceptions exist. • 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 the most abundant structural protein in animals and forms a triple-helix structure.

e. Endomembrane system

Simplified pathway for DAT review. Some lipids may follow alternative intracellular transport pathways.

f. Growth of cell

If linear dimensions increase 10-fold:

Surface area increases 100-fold (10²).
Volume increases 1,000-fold (10³).

C. Cell communication

Cells communicate with one another to coordinate growth, development, and responses to environmental signals.

1. Signal

a. Direct cell-to-cell communication

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

– Signaling molecules diffuse through the extracellular fluid to nearby target cells.

– Local distance

– Examples: Growth factors, clotting factors, histamines, nitric oxide

Synaptic signal

– Release of neurotransmitters into the synaptic cleft.

c. Long distance signal

Endocrine signal

– Hormones are released into the bloodstream and travel to distant target cells.

– Long distance

– Examples: Estradiol, testosterone, adrenaline, insulin

2. Reception

a. Cell surface reception

Cell-surface receptors bind signaling molecules at the plasma membrane.

Ligand-gated ion channels

– Ligand-gated ion channels open or close in response to ligand binding, allowing specific ions to cross the membrane.

G-protein linked receptors

– Activate G proteins, which relay signals to intracellular effector proteins and enzymes.

Receptor Tyrosine kinases

– Ligand binding activates receptor tyrosine kinases, which use ATP to phosphorylate themselves and intracellular proteins.

b. Intracellular reception

Intracellular receptors bind hydrophobic signaling molecules, such as steroid hormones, inside the cell.

3. Transduction

a. Phosphorylation cascade

A series of enzyme activations in which one protein kinase activates the next by phosphorylation.

Phosphorylation

– Protein kinase: Enzyme that transfers phosphate groups from ATP to target proteins.

– Protein phosphatases: Enzymes that remove phosphate groups from proteins.

b. G-protein signaling pathway

First messenger (signal molecules): activates G-protein-linked receptor.
Adenylyl cyclase produces cAMP, which activates protein kinase A (PKA).

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 on the ER, causing Ca²⁺ to be released into the cytosol.

– Ca²⁺ activates calmodulin and many other intracellular proteins.

Phospholipase C (PLC) hydrolyzes PIP₂ into the second messengers IP₃ and DAG.
IP₃ releases Ca²⁺ from the endoplasmic reticulum, whereas DAG, together with Ca²⁺, activates protein kinase C (PKC).

4. Response

Results in changes in gene expression 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 – amphipathic molecules with hydrophilic heads and hydrophobic tails that form a membrane bilayer.
Proteins – integral proteins are embedded in the bilayer; peripheral proteins associate with membrane surfaces.
Glycolipids.

3. Passive transport

Passive transport moves substances down their concentration or electrochemical gradients without direct energy input.

Does not directly consume ATP.
Examples: diffusion, osmosis, and facilitated diffusion (including proton flow through mitochondrial ATP synthase).

a. Diffusion

Random movement of molecules from the area of higher concentration to the area of lower concentration.
Examples: movement of O₂ and CO₂ across the cell membrane and diffusion of solutes in a solution.

b. Osmosis

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

– hypotonic solution → animal cells swell and may lyse; plant cells become turgid

* Water enters cells by osmosis; the plant cell wall limits expansion.

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

– isotonic solution → animal cell: normal volume and shape; plant cell: flaccid

– hypertonic solution → animal cells shrink; plant cells undergo plasmolysis

* Water leaves cells by osmosis; in plant cells, the plasma membrane pulls away from the cell wall.

4. Active transport

Active transport moves substances against their concentration or electrochemical gradients using cellular energy, directly or indirectly.

Requires energy.
Examples: Sodium–potassium pumps in axonal membranes, electrogenic pump, cotransport (symport and antiport), proton pump.

5. Bulk transport

: movement of large molecules across the membrane.

Classification		Features
Endocytosis	Pinocytosis	Uptake of extracellular fluid by small membrane vesicles.
	Phagocytosis	Engulfment of large particles by the plasma membrane.
	Receptor-mediated endocytosis	Selective uptake of specific molecules through receptor proteins in the plasma membrane.
Exocytosis		Release of materials from vesicles by fusion with the plasma membrane.

E. Energy and life

1. Metabolism

Metabolism is the sum of chemical reactions that sustain life.

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.
Examples: Chemical energy converts into kinetic energy after eating food.

b. Second law of thermodynamics

Universal law of increasing entropy.
Examples: Organisms release heat as they perform work.

3. Homeostasis

Homeostasis is the maintenance of relatively stable internal conditions despite changes in the external environment.

Negative feedback.

– A response opposes a deviation in the regulated variable and tends to restore it toward a set point or range.

– Most homeostatic control mechanisms in animals use negative feedback.

Positive feedback – a response amplifies a deviation or change in the regulated variable until a terminating event.

F. Enzymes

An enzyme is a biological catalyst, usually a protein, that speeds up a chemical reaction by lowering its activation energy without being consumed.

Substrate binding can cause a conformational change in the enzyme (induced fit).
Enzymes speed both forward and reverse reactions without changing the equilibrium position or equilibrium concentrations, K_eq, ΔS, or ΔG.
Enzyme activity is influenced by temperature, pH, enzyme concentration, and substrate concentration.
Each enzyme has an optimal temperature and pH.
Enzymes can be reused after catalyzing a reaction.

1. Reaction

Exergonic reaction: release of free energy.
Endergonic reactions require a net input of free energy (ΔG > 0).

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 – binding an inhibitor at an allosteric site decreases enzyme activity.
Cooperativity.

– Binding at one site can change the affinity or activity of other sites.

– Cooperativity may be positive or negative.

b. Enzyme with inhibition

Allosteric inhibition

– Allosteric regulators bind outside the active site and alter enzyme conformation and activity. Allosteric inhibition can affect substrate affinity, catalytic activity, or both. Pure noncompetitive inhibition is one specific kinetic case, not a synonym for allosteric inhibition.

Competitive inhibition

– A competitive inhibitor competes with the substrate for the enzyme’s active site.

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

Oxidation is the loss of electrons.
In some reactions, oxidation involves loss of hydrogen or gain of oxygen; these are context-dependent descriptions.

b. Reduction

Reduction is the gain of electrons.
In some reactions, reduction involves gain of hydrogen or loss of oxygen; these are context-dependent descriptions.

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

2. Chloroplast

An organelle enclosed by two membranes that converts light energy into chemical energy.

a. Structure of chloroplast

b. Larger to smaller structure

c. Photosynthesis

Photosynthesis converts light energy into chemical energy, producing ATP and NADPH that are used to synthesize carbohydrates.

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

i. Light dependent (light reaction)

Takes place in the thylakoid membrane.
Photosynthetic pigments (light receptors).

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

– chlorophyll a: primary pigment that absorbs mainly violet-blue and red wavelengths and appears blue-green.

– chlorophyll b: accessory pigment with a different absorption spectrum that appears yellow-green.

– 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

Photosystem II (P680) oxidizes water and transfers electrons into the photosynthetic electron transport chain. Electron transport contributes to the proton gradient used by ATP synthase to make ATP. ATP is a product of the light reactions overall, not a direct product of PSII alone.
Final product of photosystem I (P700) is NADPH from electron transport system.
Electron transport through the cytochrome b₆f complex contributes to proton translocation into the thylakoid lumen, helping establish the proton gradient.
H⁺ moves down its electrochemical gradient through ATP synthase, driving ATP synthesis.

ii. Light-independent reactions (Calvin cycle)

Takes place in stroma.
The Calvin cycle uses ATP and NADPH generated by the light reactions to produce sugar. It is light-independent, not limited to darkness, and normally operates when these products are available.
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 a three-carbon sugar phosphate that can be used to synthesize glucose and other organic molecules. Fixing 3 CO₂ produces 1 net G3P.

d. Photosynthesis in C3, C4, CAM plants

C3 plants

– Examples: 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.

– Examples: 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.

– Examples: 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.

Glycolysis consumes 2 ATP and produces 4 ATP, yielding a net gain of 2 ATP per glucose molecule.
Harvesting 2NADH, 2H⁺, 2H₂O, 2Pyruvates.

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

2. Fermentation

: Fermentation regenerates NAD⁺ so glycolysis can continue; ATP comes from substrate-level phosphorylation in glycolysis. Fermentation differs from anaerobic respiration, which uses an electron transport chain with a terminal electron acceptor other than O₂.

Glycolysis supplies pyruvate for fermentation.
Lactic acid fermentation: pyruvate → lactate (e.g., in muscle cells).
Alcoholic fermentation: pyruvate → ethanol + CO₂ (e.g., in yeast cells).
In the Cori cycle, lactate from anaerobic glycolysis—especially in exercising muscle and continuously in RBCs—travels through blood to the liver. Gluconeogenesis converts lactate to glucose, which can return to peripheral tissues.
Regeneration of NAD⁺

3. Mitochondria

An organelle enclosed by two membranes where oxidative metabolism produces ATP.

Aerobic respiration

a. Structure of mitochondria

Double membrane
Cristae
Matrix

The Krebs (citric acid) cycle is a metabolic pathway that occurs primarily in the mitochondrial matrix in eukaryotic cells.

b. Acetyl CoA

Aerobic metabolism in mitochondria before moving into Krebs cycle
Per glucose molecule: 2 pyruvate → 2 acetyl-CoA + 2 CO₂ + 2 NADH (with 2 H⁺ released)

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

Aerobic metabolism in mitochondria
Acetyl CoA + oxaloacetate acid → citrate
Produces 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 (CoQ) is a lipid-soluble mobile electron carrier. Cytochrome c is a small water-soluble heme protein that transfers electrons on the outer surface of the inner mitochondrial membrane.
Electron transport chain pumps protons from matrix to intermembrane space to increase a proton gradient.
The created proton gradient synthesizes ATP.
Oxidative phosphorylation produces ~26–28 ATP per glucose, using approximate values of ~2.5 ATP per NADH and ~1.5 ATP per FADH₂. Exact yield varies with shuttle systems, membrane leak, and cellular conditions.
O₂ is the terminal electron acceptor in the electron transport chain and is reduced to H₂O.

4. Overall reaction between photosynthesis and cellular metabolism

a. Chloroplasts

PSII oxidizes water, releases O₂, and transfers electrons into the electron transport chain. Electron transport builds a proton gradient; ATP synthase produces ATP. Fixing 6 CO₂ in the Calvin cycle requires 18 ATP.
PSI and electron transport produce NADPH; fixing 6 CO₂ requires 12 NADPH.
Calvin cycle, for fixation of 6 CO₂: 12 G3P (PGAL) form during reduction; 10 regenerate RuBP, leaving 2 net G3P that can contribute to one glucose.

b. Mitochondria

Krebs cycle: 4 CO₂, 6 NADH, 2ATP, and 2 FADH₂/ per 2 pyruvates
Oxidative phosphorylation: ~26–28 ATP per glucose and H₂O; exact ATP yield varies with shuttle systems, membrane leak, and cellular conditions.

c. Typical total ATP production in eukaryotic cellular respiration: ~30–32 ATP per glucose

Glycolysis: 2 ATP
Krebs cycle: 2 ATP
Oxidative phosphorylation: ~26–28 ATP per glucose. Exact yield varies with shuttle systems, membrane leak, and cellular conditions.

d. Mitochondria and chloroplasts

Semiautonomous organelles containing their own DNA and ribosomes
Endosymbiosis