B1.1-B4.2 Notes

Molecules

B1.1 Carbohydrates and Lipids

1. Bonding of Carbon Atoms

• Carbon atoms have 6 electrons, with 4 in the outer shell, enabling them to form 4 covalent bonds.
• Carbon can bond with other carbon atoms or different types of atoms (hydrogen, oxygen, nitrogen, phosphorus).
• Methane (CH₄) has single covalent bonds between carbon and hydrogen.
• Carbon dioxide (CO₂) features a carbon atom with two double covalent bonds with oxygen atoms.
• Carbon's ability to form links with four other atoms is critical for forming complex molecular structures (rings or chains).
• Rings can be single or multiple. Chains can be branched or unbranched and extend to any number of atoms.

2. Condensation Reactions

• Living organisms produce macromolecules from subunits (monomers) linked by covalent bonds to form polymers.
• Examples: Polypeptides (amino acid monomers), nucleic acids (nucleotide monomers), polysaccharides (monosaccharide monomers).
• Condensation reactions join two molecules to form a larger molecule, releasing a molecule of water.
• Water is formed by removing a hydroxyl group (-OH) from one molecule and a hydrogen from the other.
• Diagram example: Two glucose molecules forming maltose (a disaccharide) via condensation. Polysaccharides form as more glucose molecules are linked via condensation.
• This process leads to a diverse range of carbon compounds crucial for life in all organisms.

3. Hydrolysis Reactions

• Hydrolysis is the reverse of condensation: a large molecule is broken down into smaller molecules using water.
• Water is split into -H and -OH groups (hydro = water, lysis = splitting).
• These -H and -OH groups are needed to form new bonds after the large molecule has been broken.
• Hydrolysis is crucial for digesting food.
• Examples:
  • Polypeptide + water → amino acids
  • Polysaccharide + water → monosaccharides
  • Glyceride + water → fatty acids + glycerol
• Diagram: A bond linking two nucleotides broken by hydrolysis; -OH from water bonds to C, and H from water bonds to O.

4. Recognizing Monosaccharides

• Monosaccharides are simple sugars that cannot be further broken down and are monomers.
• They typically contain three, five, or six carbon atoms (trioses, pentoses, and hexoses).
• Composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio; pentoses have the formula $C<em>5H</em>{10}O<em>5$, hexoses have the formula $C</em>6H<em>{12}O</em>6$.
• One oxygen atom in monosaccharides is bonded only to carbon, either by a double bond or two single bonds.
• The other oxygen atoms are part of -OH groups.
• Pentoses and hexoses usually exist in ring form, characterized by:
  • One or two side chains with -OH and two H groups bonded to a carbon atom.
  • A ring of atoms, all of which are carbon, apart from one oxygen.
  • A single H group on the carbon atom of the side chain.
  • H and OH groups attached to carbon atoms in the ring (except those with a $CH_2OH$ side chain).
• Example: D-ribose; the 'D' indicates the right-handed form. Living organisms do not use left-handed forms of ribose and glucose.
• D-glucose exists in alpha and beta forms, differing in the orientation of the -OH groups on C₁ and C₄.

5. Polysaccharides

• Plants store energy as starch, while mammals and some fungi/bacteria use glycogen.
• Both starch and glycogen are composed of alpha glucose monomers linked by glycosidic bonds, formed by condensation reactions.
  $C<em>1$ can link to $C</em>4$, and hydrogen is removed from the OH group on $C_1$ of one glucose. H from glucose and OH from the polysaccharide combine to produce water. Also, an OH is removed from a carbon atom on a glucose that is already part of the polysaccharide.
• $C<em>1$ can also link to $C</em>6$, creating 1-6 glycosidic bonds that result in a branched structure.
• Approximately 25% of starch is unbranched (amylose), with only 1-4 bonds. About 75% is branched (amylopectin), containing some 1-6 bonds.
• Glycogen is similar to amylopectin but has twice as much branching.
• Starch and glycogen are effective energy stores due to:
  • Their compact, coiled, and branched structure.
  • Relative insolubility, preventing excessive water intake by osmosis.
  • Easy addition or removal of glucose units, which is more rapid in branched chains.

6. Structure of Cellulose

• Cellulose consists of beta glucose molecules linked by 1-4 glycosidic bonds.
• Glucose molecules alternate in orientation (up-down-up-down) due to the arrangement of OH groups on C₁ and C₄ of beta-glucose.
• This results in straight chains, unlike the helical structure of amylose (alpha-glucose).
• Cellulose molecules pack together in parallel, forming hydrogen bond cross-links and creating cellulose microfibrils.
• Cellulose microfibrils possess high tensile strength and are the main component of plant cell walls.

7. Cell-Cell Recognition

• Glycoproteins and glycolipids are plasma membrane components with short sugar chains (oligosaccharides) projecting outwards.
• Carbohydrates are attached to proteins (glycoproteins) or lipids (glycolipids).
• Interactions between oligosaccharides and carbohydrate-binding proteins allow cell-cell recognition.
• Oligosaccharides link cells together into tissues.
• Cells recognize foreign or infected cells via the oligosaccharides of glycoproteins and glycolipids.
• ABO blood groups in humans are determined by a glycoprotein and glycolipid in red blood cells.
  • Individuals with only H antigens have type O blood.
  • Those with an A allele have an enzyme that adds an extra sugar to some glycoprotein and glycolipid.
  • Those with a B allele have an enzyme that adds a different sugar to some glycoprotein and glycolipid.

8. Lipids are Hydrophobic

• Lipids are defined by their solubility in non-polar solvents (e.g., toluene) and insolubility in water.


• Lipid molecules have few charged groups and form few hydrogen bonds.


• Lipids are chemically diverse, including fats, oils, waxes, and steroids.


• Have higher C:O and H:O ratios than carbohydrates.


• The table shows the CHO composition of four lipids and glucose for comparison:
  

• Triglycerides (fats and oils) are formed by combining fatty acids with glycerol.
• Fatty acids have a carboxyl group (-COOH), which is acidic, and an unbranched hydrocarbon chain.
• Glycerol is an alcohol with three hydroxyl (-OH) groups.
• A fatty acid is linked to glycerol via a condensation reaction, forming a monoglyceride.
• Two more fatty acids can link to the monoglyceride, forming a triglyceride via ester bonds.
• Phospholipids are made by combining two fatty acids and one phosphate group with glycerol.
• Condensation reactions create ester bonds and release water.
• Phosphate groups are hydrophilic, while hydrocarbon chains of fatty acids are hydrophobic, placing them on opposite sides of the molecule.

10. Differences Between Fatty Acids

• Fatty acids vary in the number of carbon atoms in the hydrocarbon chain and the type of bonding between these atoms.
• Saturated fatty acids have all carbon atoms connected by single covalent bonds.
• Monounsaturated fatty acids possess one double bond between two carbon atoms.
• Polyunsaturated fatty acids have two or more double bonds.
• The position of the double bond nearest to the $CH_3$ terminal is significant in omega-3 and omega-6 fatty acids.
• Double bonds create kinks in the hydrocarbon chain.
• Unsaturated fatty acids do not pack together as neatly as saturated fatty acids, leading to lower melting points.

*Triglycerides with mostly unsaturated fatty acids are liquid at room temperature (oils), while those with saturated fatty acids are solid at 20°C and liquid at 37°C (fats).
*Stores of triglyceride must remain liquid, so birds and mammals with constant high body temperatures can store fats. Plants and other organisms must use oils instead as their tissues are sometimes below the melting point of fats.

11. Triglycerides in Adipose Tissues

• Adipose cells accumulate large amounts of triglyceride.
• Fats and oils are inert and coalesce into compact droplets, which do not cause osmosis.
• They are efficient energy stores, releasing twice as much energy per gram as carbohydrates during cell respiration.
• Adipose tissue is often located next to the skin for thermal insulation.

12. Formation of Phospholipid Bilayers

• Phospholipids are the basic component of all biological membranes.
• Phospholipid molecules are amphipathic (part hydrophilic, part hydrophobic).
• The phosphate head is hydrophilic, and the fatty acid tails are hydrophobic.
• In water, phospholipids arrange into bilayers with hydrophilic heads facing outwards and hydrophobic tails facing inwards.
• This structure is stable because hydrophobic tails are more attracted to each other than to water, while hydrophilic heads are more attracted to water.

13. Steroids

*Steroids are a group of lipids with molecules similar to that of sterol.
*They have four fused rings of carbon atoms, three with six and one with five carbon atoms.
*There are hundreds of different steroids, which differ in the position of C=C double bonds and the functional groups such as -OH that are attached to the four-ring structure.
*Steroids are mostly hydrocarbon and therefore hydrophobic.
*This allows them to pass through phospholipid bilayers and therefore enter or leave cells.

B1.2 Proteins

1. Amino Acid Structure

• Amino acids have a central carbon atom linked to four different groups:
  • Hydrogen atom (H)
  • Amine group (-NH₂)
  • Carboxyl group (-COOH)
  • R-group (R)
• Each of the 20 amino acids used has a unique R-group.

2. Formation of Dipeptides

• Amino acids link together via condensation reactions to form a peptide bond.
  $H_2O$ is lost during the condesation reaction between the amine group of one amino acid and the carboxyl group of the next
• A molecule with two amino acids is a dipeptide. Many amino acids linked together form polypeptides.

3. Essential Amino Acids

• Plants produce all 20 amino acids via photosynthesis. Animals obtain these amino acids from their food.
• Animals can convert some amino acids into others (non-essential amino acids).
• Essential amino acids cannot be synthesized in sufficient quantities by an animal and must be obtained from the diet.
• Nine of the 20 amino acids are essential in humans.
• Animal foods supply amino acids in the proportions needed in the human diet, but plant-based foods may lack certain amino acids.
• Vegans must ensure they consume enough of each essential amino acid.

4. Variety of Peptide Chains

• A peptide is an unbranched chain of amino acids.
  • Oligopeptides contain 2-10 amino acids.
  • Polypeptides contain more than 20 amino acids, potentially over 10,000 (typically 50-2,000).

• The genetic code specifies twenty amino acids; the first amino acid in a peptide chain (and every subsequent amino acid) can be any of these 20.
• There are effectively infinite numbers of possible peptide chains.
• The amino acid sequence of a polypeptide is coded by a gene; the DNA sequence determines the amino acid sequence.
• Over two million polypeptides have been identified in living organisms.

5. Denaturing Proteins

• Denaturation occurs when a protein's three-dimensional shape is damaged by changes to chemical or physical conditions.
  • Heat causes vibrations that break intramolecular bonds, changing the conformation irreversibly.
  • Changes in pH disrupt intramolecular bonds, denaturing the protein if the pH deviates too far from the optimum.

6. R-Groups of Amino Acids

• The R-groups of amino acids largely determine protein properties.
• Half of the R-groups are hydrophobic.
• About a third of the hydrophilic R-groups are polar but do not ionize, and can form hydrogen bonds.
• Another third of the hydrophilic R-groups are basic and can accept a proton, becoming positively charged.
• Another third of the hydrophilic R-groups are acidic and can donate a proton, becoming negatively charged and forming ionic bonds.
• One R-group is mildly hydrophilic and contains an -SH group, which can form a covalent S-S bond called a disulfide bridge.
• R-groups vary in size and shape, from simple to rings.

7. Conformations of Proteins

• Conformation is the arrangement of atoms in space.
• Cells construct proteins with each amino acid in a precise position to ensure a predictable conformation.
• Software like AlphaFold has been developed to predict conformations, but predictions can still be false.
• As a polypeptide is synthesized, it gradually develops its conformation, guided by chemical properties.
• The primary structure (amino acid sequence) determines the distinctive conformation.

8. Secondary Structure of Proteins

• When amino acids are linked by peptide bonds, a repeating sequence (N-C-C-N-C-C) forms the polypeptide backbone.
• Hydrogen bonds can form between N-H and C=O groups in the polypeptide.
• If polypeptide sections run parallel, they form a beta-pleated sheet.
• If the polypeptide is wound into a right-handed helix, hydrogen bonds form between adjacent turns, creating an alpha helix.
• Alpha helices and beta-pleated sheets stabilized by hydrogen bonds are the secondary structure of a polypeptide.

9. Tertiary Structure of Proteins

• Tertiary structure is the three-dimensional conformation of a polypeptide.
• It is formed when a polypeptide folds up after translation, stabilized by intramolecular bonds and interactions between amino acid R-groups.
• Four main types of interaction:
  • Hydrogen bonds between polar R-groups
  • Ionic bonds between $NH_3^+$ and $COO^−$ groups
  • Disulfide bonds (S-S covalent bonds) between cysteines
  • Hydrophobic interactions between non-polar R-groups

10. Effects of Amino Acid Polarity

• Proteins with hydrophilic amino acids on their outer surface dissolve in water and often have hydrophobic amino acids in their core.
• Proteins with hydrophobic amino acids on their outer surface are attracted to the non-polar core of membranes and become integral membrane proteins.
• The distribution of polar and non-polar amino acids determines tertiary structure and location within cells.

11. Quaternary Structure of Proteins

• Some proteins contain a non-polypeptide structure called a prosthetic group (conjugated proteins), e.g., hemoglobin with haem groups.
• Quaternary structure is the linking of two or more polypeptides to form a single protein.
• The same types of intramolecular bonding are used as in tertiary structure.

12. Globular and Fibrous Proteins

• Form and function are closely related in proteins.
• Fibrous proteins have unfolded polypeptides and structural roles.
• Globular proteins have folded polypeptides and varied roles.
• Collagen is a fibrous protein with three polypeptides wound into a triple helix; it can withstand pulling forces.
• Insulin is a globular protein (hormone) with a hydrophilic surface that is soluble in blood plasma and binds to specific receptor proteins.

B2 . 1 Cells: Membranes and Membrane Transport

1. Cell Membranes are Made from Lipid Bilayers

• Phospholipids naturally form continuous sheet-like bilayers in water.
• Other amphipathic lipids like cholesterol join phospholipids to form the bilayers of cell membranes.
• This applies to both the plasma membrane (outer boundary) and organelle membranes in eukaryotes.

2. Membranes Form Barriers

• Large molecules and hydrophilic particles cannot easily pass through the hydrophobic core of a membrane.
• This gives membranes low permeability to these substances, making them effective barriers between aqueous solutions.
• Membranes maintain concentration gradients.
• The plasma membrane is essential for keeping useful substances inside the cell and preventing entry of harmful substances.
  • Examples of low permeability: large molecules like proteins and starch; polar molecules like glucose and amino acids; and ions like chloride and sodium.

3. Simple Diffusion Across Cell Membranes

• Diffusion is the net movement of particles from a region of higher concentration to lower concentration.
• It is a passive process due to the random motion of particles in liquids or gases, not solids.
• Small non-polar molecules can diffuse across membranes by passing between phospholipid molecules.
• The rate depends on the concentration gradient.
• If the concentration is the same on both sides, there is no net movement.
• If there is a concentration gradient, more molecules move from the higher to the lower concentration.
• Oxygen and carbon dioxide enter or leave cells by simple diffusion.
• Oxygen is non-polar due to equal sharing of electrons. Carbon dioxide is non-polar because the polarity of the carbon-oxygen bonds cancels out.

4. Diversity of Membrane Proteins

• Cell membranes contain proteins in addition to the phospholipid bilayer.
• Proteins are mostly globular, with diverse structures, functions, and positions.
• Integral proteins are embedded in the phospholipid bilayer and have a hydrophobic surface.
• Peripheral proteins are attached to the membrane surface on one side or the other.
• Transmembrane proteins stretch across the entire membrane.

5. Osmosis

• Water is the solvent in cytoplasm and extracellular fluids.
• Particles dissolve in water by forming hydrogen bonds.
• Water and solutes are in constant random motion.
• Membranes are highly permeable to water but less so to solutes.
• Water moves across membranes readily due to its attraction to solutes, resulting in net movement from lower to higher solute concentration.
• Osmosis is the passive movement of water molecules from a region of lower solute concentration to higher solute concentration across a partially permeable membrane.
• The overall concentration of solutes governs water movement, not individual substances.
• Plasma membrane permeability can be increased by aquaporins, transmembrane proteins with pores for water molecules.
  *Aquaporins do not use energy to make water move. Water movement across membranes is always passive-water molecules are never pumped.

6. Facilitated Diffusion

• Ions (e.g., chloride, sodium) and polar molecules (e.g., glucose) pass slowly between phospholipids.
• Channel proteins are needed to facilitate diffusion at biologically relevant rates.
• A pore allows particles to pass across the membrane in either direction.
• The pore's diameter and charges on amino acids lining the pore make channel proteins specific.
• Potassium channels only allow potassium ions (K+) through.
• Facilitated diffusion is passive movement of particles from higher to lower concentration via channel proteins.
• Some channel proteins can open and close their pores.
  *No energy from ATP is used.

7. Active Transport

• Active transport is the movement of substances across membranes using energy from ATP.
• It moves substances against the concentration gradient (from lower to higher concentration).
• Protein pumps in the membrane carry out active transport, working in a specific direction.
• The pump alternates between two conformations.
• ATP causes a change from more stable to less stable conformation.
• The reverse change happens without input of energy.

8. Membranes are Selectively Permeable

• Membranes are semi-permeable or partially permeable.
• Simple diffusion allows small, non-polar particles to pass through down the concentration gradient.
• Facilitated diffusion and active transport allow more control over membrane permeability.
• Channel proteins are specific to one type of particle; cells can select which particles enter or exit.
• Pump proteins move particles in one direction and can generate concentration gradients.
• Thus, membranes are selectively permeable, controlling which substances can move through them.

9. Glycoproteins and Glycolipids

• Glycoproteins are polypeptides with attached carbohydrates.
• Glycolipids are lipids with attached carbohydrates.
• The protein or lipid is embedded in the membrane, and the carbohydrate part projects outwards.
• They have two main roles:
  • Cell adhesion: they form a carbohydrate-rich layer (glycocalyx) that binds cells into tissues.
  • Cell recognition: differences in glycoproteins and glycolipids allow cells to recognize other cells, aiding tissue development and enabling the immune system to distinguish self from non-self cells.

10. Fluid Mosaic Model

• The fluid mosaic model describes membrane structure as proteins floating in a lipid bilayer.
• Hydrophobic protein parts are embedded in the core, while hydrophilic parts are on the surface.
• Lipids and proteins can rotate or move laterally.
• Differences between the two sides of the membrane persist.

11. Fluidity of Lipid Bilayers

• Saturated fatty acids have straight chains, allowing tight packing and reducing fluidity.
• Unsaturated fatty acids have kinks, making membranes more fluid and flexible.
• The relative amounts of saturated and unsaturated fatty acids are regulated to maintain required membrane properties.
• The ideal ratio depends on temperature; e.g., fish from Antarctic waters have more unsaturated fatty acids.

12. Cholesterol and Membrane Fluidity

• Cholesterol makes up 20-40% of lipids in eukaryotic plasma membranes.
• Membranes are in a liquid-ordered phase, with densely packed lipids that can still move laterally.
• Cholesterol maintains phospholipid arrangement at high temperatures and prevents solidification at low temperatures.

13. Endocytosis and Exocytosis

• A vesicle is a small spherical sac of membrane with fluid inside.
• Vesicles move materials around inside cells via formation, movement, and fusion.
• Examples of intracellular vesicle movement:
  • Proteins synthesized by ribosomes on the rough ER are carried to the Golgi apparatus.
  • Proteins processed by the Golgi apparatus are carried to the plasma membrane.
  • Phospholipids and cholesterol synthesized by the smooth ER are carried to the plasma membrane.
• Endocytosis is the formation of vesicles in the cytoplasm by pinching off a piece of plasma membrane. *Vesicles made by endocytosis contain water and solutes from outside the cell. They may contain larger molecules needed by the cell that cannot pass through the plasma membrane
  • Example: WBC absorbing pathogens
• Exocytosis is fusion of a vesicle with the plasma membrane, expelling the contents of the vesicle from a cell.
• Example: gland cells secreting proteins

14. Ion Channels in Neurons

• Gated ion channels open briefly to allow a pulse of ions to diffuse through, used in nerve impulses and synaptic transmission.
• Voltage-gated sodium and potassium channels change conformation in response to changes in voltage.
• If the voltage is below -50 mV, $Na^+$ and $K^+$ channels remain closed. If it rises above -50 mV, $Na^+$ channels open
• When it reaches +40 mV, $K^+$ channels open, allowing potassium ions to diffuse out, returning the voltage to its original level of -70 mV.
• Nicotinic acetylcholine receptors at synapses have proteins in the postsynaptic membrane that are both receptors and channels.
• Binding of acetylcholine is reversible.

15. Sodium-Potassium Pumps

• Exchange transporters move different substances in opposite directions.
• Sodium-potassium pumps transport three sodium ions out and two potassium ions in with each cycle.
• Energy from ATP is needed to pump against the concentration gradients.
• The sodium-potassium pump generates concentration gradients of both Na+ and K+ across the membrane.

16. Indirect Active Transport

• Sodium-glucose cotransporters move $Na^+$ and glucose together into a cell.
• The concentration gradient of $Na^+$ drives glucose movement against its concentration gradient.
• Movement of glucose is indirect active transport, depending on ATP use to pump $Na^+$ out of the cell.
• Examples: kidney and small intestine

17. Adhesion of Cells to Form Tissues

• Cell-cell adhesion molecules (CAMs) link adjacent animal cells.
• CAMs are integral membrane proteins that protrude into the extracellular environment.
• A cell-cell junction is formed by the extracellular parts of CAMs.
• Cells of the same type have the same CAMs, while different cell types have different CAMs.

B2.2 Organelles and Compartmentalization

1. Organelles

• Eukaryote cells contain a variety of organelles, each adapted to perform specific functions.
• The plasma membrane, nucleus, vesicles, and ribosomes are all organelles.
• Structures that are not organelles:
  *cell wall-outside the plasma membrane so outside the boundary of the cell (extracellular)
  *cytoplasm?has diverse rather than specific functions
  *cytoskeleton-very extensive structure that extends through the cytoplasm and is not discrete.

2. Separation of the Nucleus and Cytoplasm

• Eukaryotes modify mRNA inside the nucleus before translation in the cytoplasm.
• The nuclear membrane ensures post-transcriptional modification before mRNA meets ribosomes.
• Prokaryotes lack a nuclear membrane, so ribosomes can translate mRNA as soon as it is produced, and post-transcriptional modification is not possible.

3. Advantages of Compartmentalization

• Organelles like lysosomes enclose contents and create a compartment separate from the cytoplasm.
• Advantages include:
  • Concentrating enzymes and substrates to speed up activity.
  • Maintaining ideal pH levels.
  • Separating incompatible biochemical processes.
    *Lysosomes contain many hydrolytic enzymes that digest proteins and other macromolecules. If not confined within a membrane, they would digest much of the cell.

4. Adaptations of the Mitochondrion

• Structure and function are closely related in mitochondria.
• Outer mitochondrial membrane separates contents from the rest of the cell.
• Inner mitochondrial membrane contains electron transport chains and ATP synthase for ATP production.
• Cristae increase surface area for ATP production.
  *Naked loop of DNA and 70S ribosomes allow the mitochondrion to synthesize some of its own proteins
  *Matrix contains enzymes and substrates for the Krebs cycle and link reaction
  *Intermembrane space has a very small volume and quickly develops a high proton concentration

5. Adaptations of the Chloroplast

*Thylakoid membranes contain photosystems, electron carriers and ATP synthase
Portions of the the chloroplast include:
*Grana-give a large total surface area of membrane for the light-dependent reactions
*Thylakoid spaces-with a very small volume, so a high proton concentration builds up
*Naked loop of DNA and 70S ribosomes allow the chloroplast to synthesize some its own proteins
*Stroma contains enzymes and substrates for the light-independent reactions
*Chloroplast envelope creates a compartment with optimal conditions for photosynthesis

6. Advantages of the Double Nuclear Membrane

• A double nuclear membrane has these advantages:
  • Pores can be formed by joining the outer membrane to the inner membrane for ribosome and mRNA movement.
  • The nuclear membrane can easily break up during mitosis and meiosis, releasing the chromosomes to move within the cell.

7. Free Ribosomes and the Rough ER

• Free ribosomes synthesize proteins released into the cytoplasm.
• Ribosomes bound to the rough ER make proteins for transport to other organelles.
• Proteins enter the lumen of the rough ER and are transported in vesicles.
• Many proteins pass to the Golgi apparatus and then the plasma membrane for secretion.

8. The Golgi Apparatus

• The Golgi apparatus modifies polypeptides as they move from the cis to the trans side.
• Enzymes modify polypeptides by adding non-amino acid structures or cutting and crosslinking.
• Vesicles bud off to carry mature proteins to the plasma membrane or other organelles.

9. Clathrin-Coated Vesicles

• Clathrin is a protein that forms a spherical cage to pull a membrane inwards and form a vesicle.
• Vesicles remain coated in clathrin molecules.

B2.3 Cell Specialization

1. Differentiation in Early Embryo

• Fertilization produces a zygote that divides repeatedly to form an embryo.
• Embryo cells have all the genes in the genome but become specialized for specific functions through differentiation.
• Morphogens are signalling chemicals that determine cell position in the embryo and the pathway of differentiation it should follow.
  Morphogens are regulators of gene expression-they determine which genes are transcribed to produce mRNA and therefore which proteins are made in each cell.

2. Stem Cells

• Stem cells have two key properties:
  • Self-replicating: they can divide to produce more stem cells.
  • Undifferentiated: they can differentiate along different pathways.

3. Stem Cell Niches

• Most cells produced by division of stem cells become differentiated.
• Stem cell niches are the precise locations of stem cells within a tissue that must provide conditions for stem cells to remain inactive or proliferate and differentiate.

4. Types of Stem Cells

• Stem cells can be totipotent, pluripotent, or multipotent.
  • Totipotent stem cells can differentiate into any cell type.
  • Pluripotent stem cells can differentiate into many, but not all, cell types.
  • Multipotent stem cells can differentiate into several cell types.

5. Specialization - Cell Size

• Each cell type has an ideal size for efficient function.
• Examples in humans:
  • Male gametes
  • 3 um wide which makes it easier for a sperm to swim to the egg
  • Red blood cells
  • 7 um in diameter and 1-2 um thick, allowing passage through narrow capillaries and giving a large surface area-to-volume ratio so entry and exit of oxygen is rapid
  • White blood cells
  • 10-12 um in diameter when inactive, and 30 um when plasma cells. This allows antibodies to be produced in bulk.
    female gametes
  • 110 um in diameter, with a very large volume of cytoplasm that contains enough food to sustain the embryo during the early stages of development
    neurons
  • Motor neurons have a diameter of 20 um, allowing signals to be carried this far
    Striated muscle fibres
  • very large cells with large and powerful muscle contractions.

6. Limits to Cell Size

• As size increases, the surface area-to-volume ratio decreases, meaning a cell might not be able to take in essential materials or excrete waste substances quickly enough.

7. Increasing the SA/V Ratio

• A sphere has the smallest surface area-to-volume ratio; any change in shape increases the ratio.
• Cells specialized for exchange increase plasma membrane area through:
• Flattening (e.g., red blood cells)
• Microvilli (e.g., kidney tubule cells)
• Invaginations (e.g., kidney tubule cells)

8. Type I and Type II Pneumocytes

• Alveoli in the lungs are lined by an epithelium with two cell types:
  Type I pneumocytes:
  *make up 95% but adapted to carry out gas exchange
  Type II pneumocytes:
  *5% of the area of alveolus wall but are more numerous, and reduces surface tension, so preventing the sides of the alveoli from sticking together.

9. Adaptations of Muscles

• Muscle tissue exerts pulling forces as it contracts.
• Cardiac muscle helps pump blood.
• Striated muscle exerts force on a bone for posture, locomotion, or ventilation.
• Both have contractile myofibrils and mitochondria to supply ATP.

10. Egg cells and sperm adaptions

*Male gametes travel to female gametes
*Male gametes are motile they can swim and produce ATP to swim
*Faster they swim, the more chance of reaching the egg first and fertilizing it, so small size and an efficient propulsion system are needed.
*Female gametes have a mechanism for allowing one sperm to penetrate but not more.
Contains several features:

• Acrosome has enzymes
• Haploid nucleas.
• Mid-piece with many mitochondria that prouduce atp
• Microtubles in tail to swim
• Protien fibres for strenght

B3. 1 all organisms must absorb one gas from the environment and release another one

1. Gas Exchange

• Gas exchange involves absorbing one gas from the environment and releasing another.
  Redwood trees absorb carbon dioxide for use in photosynthesis and release oxygen produced in the process. Humans absorb oxygen for cell respiration and release the carbon dioxide produced
• The relationship between surface area and volume has consequences for gas exchange:
• * Unicellular organisms have a large surface area-to-volume ratio and use their outer surface for gas exchange.
• In larger organisms, the surface area-to-volume ratio is smaller, so the outer surface of the organism cannot carry out gas exchange rapidly enough. A specialized gas exchange surface is required that is much larger than the outer surface, for example alveoli in lungs or the spongy mesophyll in a leaf

2. Features