Unit 2 SBI4U

Matter

Anything that has mass and takes up space; made up of atoms.

Atoms

Basic unit of matter; made of protons, neutrons, and electrons.

Neutrons

Neutral subatomic particles found in the nucleus.

Protons

Positively charged subatomic particles found in the nucleus.

Electrons

Negatively charged subatomic particles that orbit the nucleus.

Bohr-Rutherferford Diagram

A model that depicts the arrangement of protons, neutrons, and electrons in an atom, showing electron orbits around the nucleus.

Electron behavior

• Cannot exist between orbits; move up or down in energy levels.

• More stable at lower energy levels (closer to nucleus).

• Always occupy the lowest available orbit first.

Shell capacity

• 1st shell: maximum 2 electrons.

• All other shells: maximum 8 electrons.

Valence electrons

• Valence electrons: Electrons in the outermost shell.

• Determine how an element reacts and bonds with other atoms.

• Maximum valence electrons:

  • 1st shell: 2 electrons.

  • Other shells: 8 electrons.

Atom is chemically inert

Stable and 8 valence electrons

Noble Gases

• Group VIII (far right column of periodic table).

• Most stable; full outer shell of electrons.

• Exception: Helium has only 2 total electrons.

• Very non-reactive.

Octet rule

Atoms gain/lose electrons to achieve a full outer shell like noble gases.

Ions

charged atoms (electrons ≠ protons).

Anion

Atom gains electrons → negative charge.

Cation

Atom loses electrons → positive charge.

Macromolecules

• Large, carbon-based molecules found in living organisms.

• Includes

  • Carbohydrates

  • Proteins

  • Lipids

  • Nucleic acids

Monomers

The smaller building blocks of macromolecules (like beads in a necklace).

Polymers

Chains of monomers linked together

Functional groups

Specific groupings of atoms that give macromolecules their function (e.g., carboxyl, amino, hydroxyl, phosphate)

Building macromolecules

• Building (anabolic)

• Dehydration Synthesis (Condensation Reaction):

  • Joins monomers to form polymers.

  • Water is removed.

  • Requires enzymes to catalyze the reaction.

Breaking down macromolecules

• Breaking Down (Catabolic)

• Hydrolysis Reaction:

  • Breaks polymers into monomers.
    Water is added.

  • Also enzyme-catalyzed.

Carbohydrates function

• Energy source

• Cell structure (plants)

• Cell recognition and communication

Carbohydrates composition

Carbon, Hydrogen, Oxygen (1:2:1 ratio)

Kinds of carbohydrates

• simple carbohydrates

• Complex carbohydrates

Monosaccharides

• Simple carbohydrates

• One sugar: glucose, galactose, fructose

  • Aldoses: Glucose, Galactose, Ribose
    Ketoses: Fructose, Ribulose
    Can exist as ring structures in water

  • Are isomers: same formula, different structures

Disaccharides

• Simple carbohydrates

• Two sugars

• Glucose + Glucose → Maltose + H₂O
  Glucose + Galactose → Lactose + H₂O

• Glucose + Fructose → Sucrose + H₂O

• Formed via glycosidic linkages (covalent bonds)

Oligosaccharides

• Simple carbohydrate

• 3–10 sugar units, also use glycosidic linkages

Alpha (fancy a) 1-4 glycosdic bonds

• carbon-1 on the first carbohydrate and the carbon-4 on the other carbohydrate are covalently bonded and the –OH group on the Carbon-1 below the glucose ring

• 

Beta (fancy b) 104 glycosidic bonds

means that the carbon-1 on the first carbohydrate and the carbon-4 on the other carbohydrate are covalently bonded and the –OH group on the Carbon-1 is above the glucose ring

Polysaccharides

• Hundreds to thousands of sugar units

• Starch: Plant storage (α1-4 and α1-6 bonds)

• Glycogen: Animal storage, highly branched (α1-4 and α1-6 bonds)

• Cellulose: Structural in plants (β1-4 bonds, not digestible by humans)

• Chitin: Exoskeletons, fungal walls (glucose with nitrogen group)

Protein function

Enzymes, structural support, immune response, transport, etc.

Protein composition

• Monomers: Amino acids (20 types)

  • Components: Amino group (NH₂), Carboxyl group (COOH), R-group (side chain)

  • R-group determines properties (polar, non-polar, charged)

  • 9 essential amino acids (from diet), 11 non-essential

Protein formation

Linked via peptide bonds through dehydration synthesis

Peptide bond: Between COOH of one amino acid and NH₂ of another

Protein structure

1. Primary: Sequence of amino acids

2. Secondary:

   • α-Helix (coiled)

   • β-Pleated sheet (folded)

3. Tertiary: Further folding due to R-group interactions

4. Quaternary: Multiple polypeptides combine to form a functional protein

Lipid function

Energy storage, insulation, cell membranes, hormone production

Lipid characteristics

• Non-polar (hydrophobic)

• More energy-dense than carbohydrates

Types of Lipids

• Fats (triglycerides)

• Phospholipids

• Steroids ( Sterols)

• Waxes

Fats (triglycerides)

• Made of 1 glycerol + up to 3 fatty acid chains

• Linked via ester bonds

• Formed by esterification (dehydration synthesis)
  Saturated: No double bonds (solid)
  Unsaturated: One or more double bonds (liquid)

• 

Phospholipids

• Found in cell membranes

• 1 glycerol + 2 fatty acids + phosphate group

• Hydrophilic head, hydrophobic tails

Steroids (Sterols)

• Four fused carbon rings

• E.g., cholesterol, hormones

Waxes

• Long-chain fatty acids + alcohol or carbon ring

• Waterproof (e.g., plant cuticles, beeswax)

Nucleic acids Function

Store and transmit genetic information

Nucleic acid types

• DNA

• RNA
  ATP (energy molecule)

• Nucleotide coenzymes (NAD⁺, FAD, NADP⁺)d

Nucleic structure

• Monomers: Nucleotides

  • Components: Nitrogenous base + 5-carbon sugar + phosphate group

  • Linked by phosphodiester bonds

Nitrogenous Bases

• Purines (double-ring): Adenine, Guanine

• Pyrimidines (single-ring): Cytosine, Thymine (DNA), Uracil (RNA)

Enzyme

• Enzymes are protein catalysts that speed up chemical reactions without being consumed.

• Made of amino acids folded into complex tertiary or quaternary structures.

• Enzyme names typically end in “-ase” (e.g., amylase, sucrase).

Enzyme function

• Enzymes either break down or join molecules.

• Activation Energy (Ea): The energy needed to start a reaction. Enzymes lower Ea by positioning reactants in an optimal way.

• Active Site: Specific region on enzyme where substrate binds.

• Substrate: Reactant molecule that fits into the active site.

• Induced Fit: Active site molds around the substrate for a tight fit.

• Enzyme-Substrate Complex forms during the reaction.

• After reaction, enzyme is released unchanged and can be reused.

• 

Enzyme-Catalyzed reactions

• Catabolic Reaction: Breaks a molecule into parts. Enzyme stretches/bends bonds to help them break.

•  Anabolic Reaction: Joins two molecules. Enzyme orients substrates to encourage bond formation.

• Example: Sucrase catalyzes breakdown of sucrose into glucose + fructose

Enzyme helpers

• Some enzymes need cofactors (inorganic) or coenzymes (organic, from vitamins).

• Coenzymes shuttle molecules between enzymes.

Pepsine

Breaks proteins into peptides in the stomach. Low or missing levels → incomplete digestion.

Cytochrome c oxidase

: Essential in respiration; inhibited by carbon monoxide.

 Acetylcholinesterase

Breaks down neurotransmitter acetylcholine. Inhibited → nerve signals stop → muscle paralysis.

Enzymes in industry

Used in food industries: baking, juice processing, cheese-making.

Improve texture, flavor, and nutritional value.

Enzyms in bread making

Amylase breaks down starch → sugars → yeast makes CO2 → bread rises.

Cellulosic Ethanol (biofuel)

Made from agricultural waste like corn stalks.

Advantage: Doesn’t compete with food crops.

Disadvantage: Harder to ferment → less efficient fuel production (for now).

Allosteric Site

a region on a protein, distinct from the active site, where molecules can bind and alter the protein's shape and function

Enzyme regulation

• Enzymes can be activated or inhibited depending on cellular needs.

•  Allosteric Site: A regulatory site different from the active site.

•  Molecules bind here to turn enzyme on or off.

• Some enzymes have multiple active sites and regulatory sites.

Competitive inhibition

• Enzyme inhibition

•  Inhibitor mimics substrate and binds to the active site, blocking it.

Non-competitive (allosteric) inhibition

• Inhibitor binds to allosteric site, changes enzyme shape.

• Enzyme inhibition

Allosteric activation

Activator binds to allosteric site, stabilizes active form of enzyme.

Allosteric Inhibition

Inhibitor binds to allosteric site, stabilizes inactive form.

Feedback inhibition

• Final product of a pathway inhibits an earlier enzyme (negative feedback).

Factors that impact Enzyme activity

• pH: Each enzyme has an optimal pH (e.g., pepsin at pH 2, amylase at pH ~6.5).

• Temperature: Most human enzymes work best at ~37°C.

• Substrate Concentration: More substrate increases reaction speed until all enzymes are saturated.

General cell functions

Ingest food, excrete waste, and may move

Organelles

Specialized structures working together for cell function

Animal cell

• Shape: Circular

• Key Structures:

  • Nucleus: Nuclear envelope, nuclear pore, chromatin, nucleolus

  • Endoplasmic Reticulum: Rough (with ribosomes) & Smooth

  • Other Organelles: Mitochondria, ribosomes, Golgi apparatus, lysosomes, centrioles, microtubules, vacuoles

  • Cytoplasm enclosed by plasma membrane

Plant cell

• Shape: Rectangular

• Includes:

  • Nucleus (with nucleolus), mitochondria, chloroplasts (with thylakoids), chromoplast, lysosomes

  • Ribosomes (free & polyribosomes), vacuole (large), Golgi apparatus, microtubules, rough & smooth ER, plasmodesmata

Cell membrane function

• Separates cytoplasm from the environment

• Controls chemical entry/exit

• Maintains internal chemical balance

Phospholipid structure

• Head: Hydrophilic, polar, phosphate group — water-attracting

• Tail: Hydrophobic, non-polar, fatty-acid chains — water-repelling

Membrane arrangment

• Bilayer: Tails face inward, heads face water

• Fluid-Mosaic Model:

  • Lipids, proteins, cholesterol = flexible and dynamic membrane

  • Proteins/cholesterol can move within membrane

Cholesterol in cell membrane

• Stabilizes membrane

• Keeps it fluid at low temp, stabilizes at high temp

Integral proteins (cell membrane)

Channels for molecule/ion transport

Glycoproteins (Cell membrane)

Receptor sites, cell adhesion

Selective permeability

Controls what passes through the membrane

Passive transport

• No energy required

Diffusion

• passive transport

• Molecules move high → low concentration

• Affected by: state of matter, temperature, molecule size

Osmosis

• Passive transport

• Water diffusion across a selectively permeable membrane

• Water moves to area with higher solute (less water)

• Types of solutions:

  • Isotonic: Equal solute; no net water movement

  • Hypertonic: Higher solute outside; water exits cell

  • Hypotonic: Lower solute outside; water enters cell

Osmometer

• measures osmosis

• Measures direction of water flow

• Water in = hypertonic solution

• Water out = hypotonic solution

Facilitated diffusion

• Passive transport

• Used for large molecules

• Molecules use transport proteins to move across membrane

• Still along concentration gradient (no energy used)

• Highly specific — proteins recognize size, shape, charge

Active transport

• Required energy/ATP

• Moves substances against concentration gradient (low → high)

• Uses transport proteins + ATP

• Maintains homeostasis

  • Stores nutrients

  • Removes waste

Steps for active transport

• Ion binds to transport protein

• ATP moves ion across

• Ion released inside cell

Active vs. Passive transport

Vesicle transport

Transport for large molecules

Endocytosis

• Part of Vesicle transport

• brings materials into cell

Phagocytosis

• Vesicle transport and Endocytosis

• cell eats solids

• ex: bacteria

Pinocytosis

• Vesicle transport and Endocytosis

• cell drinks fluid

Receptor-Mediated Endocytosis (RME)

• Vesicle transport and Endocytosis

• Specific molecules bind to receptors

• Vesicle forms and carries them into cell

• Ex: Cholesterol uptake

  • Too much cholesterol → plaque buildup → heart disease

Exocytosis

Uses vesicles to remove waste or secrete substances