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

: almost all living cells are composed of carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphate (P), and sulfur (S).

Nucleotide: C, H, O, N, P
Protein: C, H, O, N, S

1. Carbohydrates (sugar)

1:2:1 of C:H:O ratio
Function as building materials and energy storage.

Carbohydrates (sugar)	Classification	Description
Monosaccharide	Glucose	• Chief source of energy in living organisms
	Ribose	• 5 carbon sugar in RNA
	Galactose
	Fructose
Disaccharide	Sucrose	• Glucose + Fructose • 1,2 glycosidic linkage
	Maltose	• Glucose + Glucose • 1, 4 glycosidic linkage
	Lactose	• Polymerized glucose in plants • a glucose monomers with 1, 4 linkage
Polysaccharide	Starch	• Polymerized glucose in plants • α glucose monomers with 1, 4 linkage
	Glycogen	• Polymerized glucose in animals
	Cellulose	• Cell wall of plant • Connected and joined by microfibrils • β glucose monomers with 1, 4 linkage
	Chitin	• Composed of nitrogenous group and sugar base • Cell wall component of fungi • Main elements in exoskeletons of arthropods

2. Proteins

a. Amino acid

Subunit of proteins as a monomer.
Consisting of amino group, carboxyl group, a carbon, functional group, and hydrogen.
Each of 20 common amino acids has different functional group.

b. Polypeptide

Amino acids are linked by peptide bonds.
Multiple functions such as enzyme catalysis, hormone, storage, regulation, defense, transport, support, and motion.
Heating or changing condition of pH causes protein to lose its secondary, tertiary, or quaternary structure and becomes inactive.

Structures	Features
Primary (1º) structure	• Structure of linear amino acids sequence • Only peptide bond
Secondary (2º) structure	• α helix and β pleated sheet by hydrogen bond
Tertiary (3º) structure	• Hydrogen bond, disulfide bond, ionic bond, and hydrophobic interaction • Interaction between the R side chains
Quaternary (4º) structure	• Functional macromolecule • Interaction between two or more different proteins

3. Lipid

a. Fat

Unsaturated fat presences of double bond, which causes kink in fatty acid tail, increases fluidity.

– eg/oil

Saturated fat presences of no double bond, which causes no kink, decreases fluidity.

– eg/butter

Greatest source of energy producing 9 calories/gram.

** Carbohydrate and protein produce 4 calories/gram.

– eg/ glycerol, fatty acid, triacylglycerol

b. Phospholipid

Forming amphipathic (hydrophilic and hydrophobic) bilayers of cell membrane.

c. Steroids

Four fused carbon rings.
Keep fluids inside the membrane.
Found in most animal cell membranes.
eg/cholesterol

4. Nucleic acids

Molecules that store genetic information of organisms.
Composed of nucleotide (five carbon sugar, nitrogenous base, and phosphate group).
Phosphate groups connected by phosphodiester bonds.
Two nucleic acids connected by hydrogen bonds.
Anti-paralleled strands.

Classification	Description
Nucleoside	Five carbon sugar + nitrogenous base
Nucleotide (basic unit)	Five carbon sugar + nitrogenous base + phosphate group
Nucleic acids	Nucleotide + more nucleotides

	DNA	RNA
Sugar	Deoxyribose sugar	Ribose sugar
Bases	Adenine(A) Guanine(G) Cytosine(C) Thymine (T)	Adenine(A) Guanine(G) Cytosine(C) Uracil(U)
Shape	Double stranded	Single stranded
Bond	Hydrogen bond, phosphodiester bond	Phosphodiester bond

B. Shapes and functions of the cells

1. Cell theory

The smallest unit of life functions
Basic units of all living organisms
All cells coming from other cells

2. The difference between prokaryotic and eukaryotic cells

Prokaryotic cell	Eukaryotic cell
• Cell division by binary fission • Share genetic information by conjugation • Nucleoid (no nuclear envelope)	• Mitotic and meiotic division • 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 and RNA synthesis • Storage place of genetic information
Ribosomes	• Site of protein synthesis from the genetic code of nucleic acids • Found in nucleus, chloroplast, mitochondria, and cytoplasm • Bound to rough endoplasmic reticulum (ER) and free ribosomes in cytoplasm • Composed of rRNA and protein
Rough ER	• Carries ribosome on its membrane • Glycoproteins (secretory proteins) and membranes synthesis
Smooth ER	• No ribosome • Lipid synthesis (production of hormones) • Calcium storage • Carbohydrate metabolism • Detoxification
Golgi Apparatus	• Made from ER • Receiving (cis) & modifying proteins with polysaccharide and lipid • Storing & shipping (trans) the protein vesicles to cell membrane or other destinations
Lysosomes	• Digestive vesicle containing hydrolytic enzyme • Produced by rough ER • Found in animal cells
Peroxisomes	• Vesicle containing H2O2 to break down fatty acid • Oxidize toxin • Produced by ER
Vacuole	• Isolating harmful material and containing waste molecules • Storing nutrients • Maintaining internal pH and hydrostatic pressure • Tonoplast membrane
Mitochondria	• Site of aerobic cellular respiration to make ATP • Containing Ribosome and DNA • Double membrane, cristae, matrix • Evolution from bacterial symbiosis
Chloroplasts	• Site of photosynthesis • Containing Ribosome and DNA • Double membrane, stroma, Thylakoid disk, chlorophyll • Evolution from bacterial symbiosis
Cytosol	• Main site of chemical reaction in cell

b. Cytoskeletons

Cytoskeletons	Functions and features
Microtubules	• Hollow rods of tubulin, 9+2 arrangement • Centrosomes and centrioles • Intracellular transport by cilia and flagella (combine with dynein)
Microfilaments (Actin filament)	• Cleavage furrow in cytokinesis • Cell surface, crawling of amoeboid movement • Cell cortex, microvilli as a serving anchor of intermediate filaments • Myosin and actin filament in muscle cell
Intermediate filaments	• Tensile strength • Nuclear lamina • Keratin filament

c. Different layers of membranes

Membranes	Organelles
No membrane	Centriole, Ribosome
Single membrane	Peroxisome, Lysosome, ER, Golgi Complex, 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	Communication junction, which is direct connection of cytoplasm between two 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