Chapter 2 Review: Buffers, Hydrocarbons, Isomers, Functional Groups, and Chemical Bonds

Buffers and Blood pH Regulation

Buffers help maintain an organism’s internal solutions at a near-base or neutral pH.
Key components in the blood buffering system involve carbon dioxide (CO₂), carbonic acid (H₂CO₃), bicarbonate (HCO₃⁻), hydrogen ions (H⁺), and water (H₂O).
Buffer reaction (conceptual): the system moderates pH by shifting between CO₂/H₂O, H₂CO₃, and HCO₃⁻/H⁺ depending on metabolic activity.
Chemical equilibrium for the bicarbonate buffer (classic representation):
CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons H^+ + HCO_3^-
Physiological pH range: approximately 7.35–7.45; the body works to keep pH within this narrow window (near neutral).
Diagram interpretation (as described in the transcript):
- Blue arrows depict raising pH as more CO₂ is produced.
- Purple arrows depict lowering pH as more bicarbonate is created.
Important notes and clarifications:
- In physiology, increasing CO₂ typically shifts the equilibrium to the right, increasing H⁺ and lowering pH; buffering involves the bicarbonate system adjusting concentrations of H₂CO₃ and HCO₃⁻ to resist pH change.
- The buffer system acts quickly to minimize pH fluctuations due to metabolic activities, respiration, and other processes.
Related concepts and implications:
- Buffer capacity depends on the concentrations of the weak acid (H₂CO₃) and conjugate base (HCO₃⁻).
- pH homeostasis is critical for enzyme activity, membrane potential, and overall metabolic regulation.
Related equation (general buffering context, not explicitly shown in transcript):
pH = pKa + \log{10}\left(\frac{[A^-]}{[HA]}\right)
where [A⁻] is the conjugate base concentration and [HA] is the weak acid concentration.

Hydrocarbons

Definition: Hydrocarbons are organic molecules composed only of carbon and hydrogen.
Examples and notation:
- Methane: CH₄ (as a representative hydrocarbon).
- General structural hints from the transcript show hydrocarbon chains such as H–C–H and H–C–C–C–H.
Bonding and energy:
- Covalent bonds between carbon and hydrogen (C–H) and carbon–carbon (C–C) store chemical energy.
- This energy is released when these molecules are burned (combustion).
Real-world relevance:
- Burning hydrocarbons heats homes and powers cars, highlighting their role as energy sources.
Combustion example (stoichiometric representation):
CH4 + 2\,O2 \rightarrow CO2 + 2\,H2O
(general combustion reaction for methane; energy release is implied.)

Isomers

Isomers are compounds with the same molecular formula but different structural arrangements or spatial orientations.

(a) Structural isomers

Examples given: Butane vs isobutane.
- Both have the formula C₄H₁₀ but differ in carbon skeleton connectivity (straight-chain vs branched).
Concept: Different connectivity leads to different physical and chemical properties despite identical molecular formulas.

(b) Geometric isomers (cis/trans)

Example: 2-butene exists as:
- cis-2-butene: the two substituent groups (e.g., methyl groups) are on the same side of the C=C bond.
- trans-2-butene: the two substituent groups are on opposite sides of the C=C bond.
Key point: Restricted rotation around a double bond creates distinct cis and trans forms with different physical properties.

Definition: Non-superimposable mirror-image isomers.
Example students may encounter: L- and D- isomers; often designated as left- (L) and right- (D) handed.
Relevance: Enantiomers can have different biological activities due to chiral specificity in enzymes and receptors.

Functional Groups

Functional Groups: Groups of atoms within a molecule that confer consistent, characteristic properties and reactivity.
Each of the four major macromolecules (carbohydrates, lipids, proteins, nucleic acids) has its own characteristic functional groups.
Common functional groups highlighted in the transcript (and their basic properties):
- Hydroxyl group
- Structure: {ROH}
- Properties: Polar; participates in hydrogen bonding; increases solubility in water.
- Methyl group
- Structure: {R-CH_3}
- Properties: Generally nonpolar; hydrophobic; commonly modifies the properties of molecules.
- Carbonyl group
- Structure: {R-CO-R'}
- Properties: Polar; part of aldehydes and ketones; influences reactivity and polarity.
- Carboxyl group
- Structure: {R-COOH}
- Properties: Acidic; can ionize to release H⁺; common in fatty acids and amino acids.
- Amino group
- Structure: {R-NH_2}
- Properties: Basic; can accept H⁺ to form {R-NH_3^+}; key component of amino acids.
- Phosphate group
- Structure: typically a phosphate ester, e.g., {R-PO4^{2-}} or related forms (e.g., {R-PO3H_2} in some contexts).
- Properties: Often acidic (can release H⁺); critical in energy transfer (ATP), nucleotides, and regulation.
- Sulfhydryl group
- Structure: {R-SH}
- Properties: Polar; forms disulfide bonds (R–S–S–R) contributing to protein structure and folding.
Practical takeaway: Functional groups determine how molecules interact with others (e.g., hydrogen bonding, ionization, polarity) and influence solubility, reactivity, and biological roles.

Atoms, Isotopes, Ions and Bond Types (LRNR Activity Summary)

The activity focuses on identifying and matching common bond types:
- Ionic bond
- Definition: Attraction between an anion and a cation.
- Polar covalent bond
- Definition: A covalent bond in which electrons are shared unequally, leading to partial charges on atoms.
- Nonpolar covalent bond
- Definition: A covalent bond in which electrons are shared equally.
- Hydrogen bond
- Definition: A hydrogen atom covalently bonded to an electronegative atom is weakly attracted to another electronegative atom.
Quick match references from the transcript:
- Chemical bond in which two atoms share electrons equally → Nonpolar covalent bond
- Attraction between an anion and a cation → Ionic bond
- Bond in which a hydrogen atom covalently bonded to an electronegative atom is weakly attracted to a second electronegative atom → Hydrogen bond
- Chemical bond in which two atoms share electrons, but one atom has a stronger attraction than the other → Polar covalent bond
Context: These bond types underpin the behavior of molecules, their polarity, solubility, and interactions within biological systems.

Quick Conceptual Synthesis

Buffers keep pH within a narrow, biologically important range by balancing CO₂/H₂O/H₂CO₃/HCO₃⁻ and H⁺.
Hydrocarbons store chemical energy in covalent bonds and release it upon combustion to power tangible energy uses.
Isomerism (structural, geometric, and enantiomeric) explains why molecules with the same formula can behave very differently in biological systems and industry.
Functional groups define the identifiable chemistry of macromolecules, governing reactivity, polarity, acid-base behavior, and interactions such as hydrogen bonding and disulfide formation.
Bond types (ionic, polar covalent, nonpolar covalent, hydrogen bonds) describe how atoms share or transfer electrons and how molecules recognize and interact with each other in chemical and biological contexts.

Notes on context and realism:

The buffer diagram described in the transcript indicates the dynamic between CO₂ production and bicarbonate formation, with blue and purple arrows representing pH changes. In physiology, increased CO₂ typically lowers pH, while buffering with bicarbonate and related species helps stabilize pH.
The functional group table in the transcript lists several groups and their roles (acidic vs basic, polarity, ability to engage in hydrogen bonding), which are central to understanding organic chemistry and biochemistry.

Key equations and formulas included:

Bicarbonate buffering equilibrium:
CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons H^+ + HCO_3^-
Henderson–Hasselbalch (buffer equation):
pH = pKa + \log{10}\left(\frac{[A^-]}{[HA]}\right)
Methane combustion (example of hydrocarbon energy release):
CH4 + 2\,O2 \rightarrow CO2 + 2\,H2O
Representative bond-type identifications (from the LRNR activity): nonpolar covalent, polar covalent, ionic, hydrogen bonds (defined above).

End of notes for this transcript excerpt.