General Biology Study Notes: Carbon Chemistry, Water Structure, and Solution Calculations

Problems While You Wait for Lecture

Molecular Mass and Molarity Calculations

Understanding molecular mass and molarity is essential for preparing solutions in biological experiments. These calculations are foundational for laboratory work and chemical analysis.

• Molecular Mass: The sum of the atomic masses of all atoms in a molecule, measured in daltons (Da) or atomic mass units (amu).

• Mole: A unit representing $6.02 \times 10^{23}$ molecules (Avogadro's number).

• Molarity (M): The concentration of a solution, defined as moles of solute per liter of solution.

• Example Calculation: For urea (CO(NH2)2): - Carbon (C): 12.01 Da - Oxygen (O): 16.00 Da - Nitrogen (N): 14.01 Da × 2 - Hydrogen (H): 1.01 Da × 4 Total molecular mass: $12.01 + 16.00 + (14.01 \times 2) + (1.01 \times 4) = 60.06$ Da To make a 1M solution: Dissolve 60.06 grams of urea in 1 liter of water. Number of molecules in 1M solution: $6.02 \times 10^{23}$ molecules per liter.

Lecture 4: Carbon Chemistry

Introduction to Carbon Chemistry

Carbon chemistry is the study of organic compounds, which are molecules containing carbon atoms. Carbon's ability to form four covalent bonds makes it uniquely versatile, allowing for a vast diversity of molecular structures essential for life.

• Organic Compounds: Molecules containing carbon, often bonded to hydrogen, oxygen, nitrogen, and other elements.

• Importance: Organic compounds include carbohydrates, proteins, lipids, and nucleic acids.

• Carbon Atom: Atomic number 6, four valence electrons, forms four covalent bonds.

Review: Structure of Water

Water Molecule Structure

Water (H2O) is a polar molecule with unique properties due to its molecular structure and hydrogen bonding.

• Polarity: Oxygen is more electronegative than hydrogen, creating a partial negative charge near oxygen and partial positive charges near hydrogens.

• Three-Dimensional Shape: Bent shape due to two lone pairs on oxygen, resulting in an angle of about 104.5° between hydrogen atoms.

• Structural Formula: Shows the arrangement of atoms and bonds in the molecule.

Hydrogen Bonding Between Water Molecules

Hydrogen bonds are weak attractions between the partially positive hydrogen atom of one water molecule and the partially negative oxygen atom of another.

• Covalent Bond: Strong bond formed by sharing electrons between atoms within a molecule.

• Hydrogen Bond: Weak bond formed by attraction between opposite charges on different molecules.

• Importance: Hydrogen bonding gives water its high cohesion, surface tension, and ability to dissolve many substances.

Elements in the Human Body

Major Elements and Their Abundance

The human body is composed primarily of a few key elements, each with specific roles in biological molecules.

Element	Symbol	Percentage of Body Mass
Oxygen	O	~65%
Carbon	C	~18%
Hydrogen	H	~10%
Nitrogen	N	~3%
Phosphorus	P	~1.5%
Sulfur	S	~0.3%
Other trace elements	-	<0.1%

Chemical Bonds and Isomerism

Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. Carbon forms single, double, or triple covalent bonds to fill its valence shell.

• Single Bond: Sharing one pair of electrons ($-$).

• Double Bond: Sharing two pairs of electrons ($=$).

• Triple Bond: Sharing three pairs of electrons ($\equiv$).

Isomers

Isomers are compounds with the same molecular formula but different structures, leading to different properties.

• Structural Isomers: Differ in the covalent arrangement of atoms.

• Cis-Trans Isomers: Differ in arrangement around a double bond.

• Enantiomers: Mirror-image isomers, important in biological activity.

• Example: Ibuprofen and albuterol have enantiomers with different biological effects.

Functional Groups in Organic Molecules

Key Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

Group	Structure	Properties	Example
Hydroxyl	-OH	Polar, forms hydrogen bonds, hydrophilic	Ethanol
Carbonyl	>C=O	Polar, found in sugars	Acetone (ketone), Propanal (aldehyde)
Carboxyl	-COOH	Acidic, can donate H+	Acetic acid
Amino	-NH2	Basic, can accept H+	Glycine
Sulfhydryl	-SH	Can form disulfide bonds, stabilizes proteins	Cysteine
Phosphate	-OPO32-	Contributes negative charge, energy transfer	ATP
Methyl	-CH3	Nonpolar, affects gene expression	5-Methyl cytosine

Solution Chemistry: pH and Ion Concentration

pH Scale and Ion Concentration

The pH scale measures the concentration of hydrogen ions in a solution, indicating its acidity or alkalinity.

• pH Definition: $\text{pH} = -\log[H^+]$

• Neutral Solution: $[H^+] = [OH^-] = 1 \times 10^{-7}$ M, pH = 7

• Acidic Solution: $[H^+] > [OH^-]$, pH < 7

• Alkaline Solution: $[OH^-] > [H^+]$, pH > 7

• Relationship: $[H^+][OH^-] = 1 \times 10^{-14}$ (at 25°C)

• Effect of Adding Acid: Increases $[H^+]$, decreases pH.

• Effect of Adding Base: Increases $[OH^-]$, increases pH.

pH Value	[H+] (M)	Solution Type
1-6	High	Acidic
7	Equal to [OH-]	Neutral
8-14	Low	Alkaline (Basic)

Examples and Applications

• Biological Relevance: Enzyme activity, cellular processes, and organism health depend on maintaining proper pH.

• Environmental Example: Fish require water with pH between 5.5 and 7.5 for survival.

Summary Table: Common Atoms in Organic Molecules (HONC 1234 Rule)

Element	Valence Electrons	Typical Bonds Formed
Hydrogen (H)	1	1
Oxygen (O)	2	2
Nitrogen (N)	3	3
Carbon (C)	4	4

Additional info:

• Some context and examples were inferred from standard General Biology curriculum and textbook conventions.

• Tables were reconstructed and expanded for clarity and completeness.