General Biology I: Study Guide – Chemistry of Life, Proteins, and Nucleic Acids

Chemistry of Life

What Does It Mean to Be Alive?

All living organisms share five fundamental characteristics that distinguish them from non-living matter.

• Cells: All organisms are made up of membrane-bound cells.

• Replication: All organisms can reproduce.

• Information: Organisms store hereditary information in genes and respond to environmental information.

• Energy: Organisms acquire and use energy (e.g., ATP).

• Evolution: Populations of organisms change over time.

Minimal requirements for life:

• Cell membrane and cytosol

• Storage of information (DNA)

• Ability to make fuel (ATP)

• Ability to copy information for reproduction

• Genetic variation/mutations for adaptation

Chemical Components of Cells

Cells are composed of various chemical elements and compounds, which interact through chemical bonds to form the structures and molecules necessary for life.

• Electron shells: Electrons occupy shells around the nucleus. The first shell is full with 2 electrons; other shells stabilize with 8 electrons (Octet rule).

• Valence electrons: Electrons in the outermost shell determine reactivity and bonding.

Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules. The main types are:

• Ionic bond: Transfer of electrons from one atom to another, forming ions. Cation is positively charged (lost electrons), Anion is negatively charged (gained electrons).

• Covalent bond: Sharing of electrons between atoms. Can be nonpolar (equal sharing) or polar (unequal sharing).

• Hydrogen bond: Weak attraction between a hydrogen atom and an electronegative atom (e.g., oxygen, nitrogen).

Key Elements of Life

Six key elements are essential for life: Hydrogen (H), Oxygen (O), Carbon (C), Nitrogen (N), Phosphorus (P), and Sulfur (S).

• Valence electrons in the outermost shell are crucial for chemical reactivity.

• Stable states for all elements: Achieved by filling electron shells.

• Noble gases: Already have stable electron configurations and are generally unreactive.

Types of Bonds and Electronegativity

• Ionic bonds: Transfer of electrons (metal + nonmetal, cation/anion).

• Covalent bonds: Sharing electrons (between nonmetals; polar vs. nonpolar).

• Hydrogen bonds: Weak attractions between polar molecules (e.g., water).

• Electronegativity trend: Increases left → right, bottom → top on the periodic table. Oxygen is one of the most electronegative elements.

Polarity and Water Properties

Polarity refers to the distribution of electrical charge across a molecule. Water is polar, which gives it unique properties:

• Cohesion & surface tension

• Adhesion to polar surfaces

• Liquid water denser than ice

• High heat capacity & heat of vaporization

• Universal solvent for polar/hydrogen bonding molecules

Functional Groups & Proteins

Functional Groups

Functional groups are specific groups of atoms within molecules that confer particular chemical properties.

• Hydroxyl (-OH): Polar

• Phosphate: Negative charges, store energy

• Sulfhydryl (-SH): Forms disulfide bonds (important in protein structure)

• Amino (-NH2): Acts as a base

• Carboxyl (-COOH): Acts as an acid

• Methyl (-CH3): Stable, nonpolar

Acids & Bases

• Acid: Donates H+; carboxyl becomes COO-

• Base: Accepts H+; amino becomes NH3+

• pH: High pH = fewer H+ = basic

Proteins

Proteins are polymers of amino acids and perform a wide variety of functions in cells.

• 20 different amino acids, differing in R-groups (side chains)

• R-groups determine properties: nonpolar (hydrophobic), polar (hydrophilic), charged (interact with ions)

Protein Structure Hierarchy

• Primary: Amino acid sequence

• Secondary: α-helix, β-sheet (hydrogen bonds along backbone)

• Tertiary: 3D folding (hydrogen, ionic, hydrophobic, van der Waals, disulfide bonds)

• Quaternary: Multiple polypeptides forming one protein

Disulfide bonds (cysteine) add stability.

Structure-function relationship: Protein shape determines function (enzymes, receptors, antibodies, etc.).

Proteins & Nucleic Acids

Functions of Proteins

• Enzymes (catalysts)

• Hormones (signal molecules)

• Transcription factors

• Hemoglobin (oxygen transport)

• Motor proteins (cargo transport)

• Antibodies (immune defense)

• Structural proteins (muscles, cytoskeleton)

• Transport proteins and receptors

Amino Acids & Functional Groups

• Building blocks of proteins = amino acids

• Functional groups:

  • Hydroxyl (-OH): polar

  • Phosphate: negative charges, store energy

  • Sulfhydryl (-SH): forms disulfide bonds (cysteine)

  • Amino (-NH2): acts as a base

  • Carboxyl (-COOH): acts as an acid

  • Methyl (-CH3): stable, nonpolar

Key point: The R group (side chain) makes each amino acid unique.

Peptide Bonds & Polypeptides

• Peptide bond: Joins amino acids together (dehydration/condensation reaction, not hydrolysis).

• Backbone characteristics:

  • R-group orientation: Allows side chain interactions

  • Directionality: N-terminus → C-terminus

  • Flexibility: Bonds can rotate, allowing folding

Levels of Protein Structure

• Primary: Sequence of amino acids

• Secondary: Local folding (α-helices, β-pleated sheets, stabilized by hydrogen bonds)

• Tertiary: Overall 3D shape (interactions: hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals, disulfide bonds)

• Quaternary: Multiple polypeptides forming one protein

Structure → Function: Protein's shape determines its function (enzymes, receptors, antibodies, etc.).

Nucleic Acids

Central Dogma

The central dogma of molecular biology describes the flow of genetic information:

• DNA → RNA → Protein

• Replication: DNA copies itself

• Transcription: DNA → RNA

• Translation: RNA → protein

Overview

• Types: DNA & RNA

• Monomers: Nucleotides

• Functions:

  • DNA: Stores and transmits hereditary information

  • RNA: Translates DNA into proteins

Nucleotides & Nucleosides

• Nucleotide = sugar + nitrogenous base + phosphate group

• Nucleoside = sugar + base (no phosphate)

• Sugars:

  • DNA = deoxyribose (H at 2' carbon)

  • RNA = ribose (OH at 2' carbon)

Nitrogenous Bases

• Purines (2 rings): Adenine (A), Guanine (G)

• Pyrimidines (1 ring): Cytosine (C), Thymine (T, only DNA), Uracil (U, only RNA)

DNA & RNA Differences

• DNA: A, T, G, C

• RNA: A, U, G, C

• DNA = millions of nucleotides; RNA = thousands

Nucleic Acid Structure

• Backbone: Alternating sugar + phosphate

• Ends: 5' phosphate, 3' OH

• Always read 5' → 3'

Table: Comparison of DNA and RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Strands	Double-stranded	Single-stranded
Function	Genetic information storage	Protein synthesis, gene regulation

Key Equations

• pH calculation: $pH = -\log[H^+]$

• ATP hydrolysis: $ATP + H_2O \rightarrow ADP + P_i + \text{energy}$

Additional info:

• Protein folding is critical for function; misfolding can cause diseases (e.g., prions).

• Water's polarity and hydrogen bonding are essential for life-supporting properties.