Core Principles and Macromolecules in Cell Biology

Chapter 2: The Chemistry of the Cell

Cell Theory

The cell theory is a foundational concept in biology, describing the properties and significance of cells in living organisms.

• All organisms consist of one or more cells.

• The cell is the basic unit of structure for all organisms.

• All cells arise only from pre-existing cells.

Carbon

Carbon is the backbone of organic molecules and is essential for the structure and function of cells.

• Importance: Forms stable covalent bonds, enabling complex organic molecules.

• Atomic Number: 6

• Common Bonds: Hydrogen, oxygen, nitrogen, sulfur, phosphorus

Covalent Bonds

Covalent bonds are strong chemical bonds formed by the sharing of electron pairs between atoms.

• Single: One pair of electrons shared

• Double: Two pairs shared

• Triple: Three pairs shared

Hydrocarbons

Hydrocarbons are organic molecules consisting entirely of hydrogen and carbon, often found in cell membranes.

• Found in: Lipid tails in membranes

• Characteristics: Nonpolar, hydrophobic

Polarity

Polarity refers to the uneven distribution of electrons in a molecule, resulting in partial charges.

• Key Point: Leads to important properties such as solubility and reactivity

Properties of Water

Water is vital for cellular processes due to its unique chemical and physical properties.

• Cohesion: Surface tension

• Temperature Stability: High specific heat

• Solvent: Dissolves polar molecules

• Density: Ice floats

• Reactivity: Participates in chemical reactions

Chapter 3: Macromolecules of the Cell

Proteins

Proteins are polymers of amino acids that perform a wide range of functions in cells.

• Functions: Enzymes, structure, transport, signaling

• Structure: Amino group, carboxyl group, R group

• Assembly: Peptide bonds via dehydration synthesis

Amino Acids

Amino acids are the building blocks of proteins, each with a unique side chain (R group).

• R Group: Side chain

• Categories: Nonpolar, polar, charged

Protein Ends

Proteins have two distinct ends, which determine their directionality and function.

• N-terminus: Amino end

Levels of Organization

Proteins have hierarchical levels of structure that determine their shape and function.

• Primary: Sequence of amino acids

• Secondary: Alpha helix, β-pleated sheet

• Tertiary: 3D folding (globular, fibrous, transmembrane)

• Quaternary: Multiple subunits

Stabilizing Bonds

Various chemical interactions stabilize protein structure.

• Hydrogen, van der Waals, hydrophobic, ionic, disulfide bonds

Covalent Modifications

Proteins can be modified after translation to regulate their function.

• Disulfide: Cysteines

• Lipids: Anchoring

• Phosphates: Regulation

• Sugars: Cell recognition

• Ubiquitin: Degradation

• Methyl/Acetyl: Gene regulation

Folding Aids

Chaperone proteins assist in proper protein folding.

• Chaperones: Prevent misfolding

Nucleic Acids

Nucleic acids store and transmit genetic information in cells.

• DNA: Double-stranded, deoxyribose, thymine

• RNA: Single-stranded, ribose, uracil

Nucleotides

• Components: Sugar, phosphate, base

• Purines: Adenine (A), Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

Bonds

• Phosphodiester: Backbone

• Hydrogen Bonds: Between bases

Base Pairing

• A-T, G-C

• Antiparallel: Opposite strand directions

• Semiconservative: Each new DNA has one old strand

Carbohydrates

Carbohydrates are energy sources and structural components in cells.

Types

• Monosaccharides: Simple sugars

• Polysaccharides: Chains (e.g., glycogen)

Assembly

• Bond: Glycosidic linkage

Glucose Formula

• $C_6H_{12}O_6$

Glycogen

• Function: Energy storage in animals

Lipids

Lipids are hydrophobic molecules with diverse functions in cells.

Classes

• Fatty acids, triglycerides, phospholipids, glycolipids, steroids

Fatty Acids

• Structure: Hydrocarbon chain + carboxyl group

• Saturated: No double bonds

• Unsaturated: One or more double bonds

• Trans Fats: Artificial, unhealthy

Triglycerides

• Function: Energy storage

Phospholipids

• Phosphoglycerides: Glycerol backbone

• Sphingolipids: Sphingosine backbone

Glycolipids

• Lipids with sugar groups

Steroids

• Function: Hormones, membrane fluidity

Chapter 4: Cells and Organelles

Origins of Cells

The endosymbiotic theory explains the origin of eukaryotic organelles.

• Key Point: Mitochondria and chloroplasts originated from symbiotic bacteria

Domains

Cells are classified into three domains based on genetic and structural differences.

• Bacteria

• Archaea

• Eukarya

Comparisons

The following table compares key features of prokaryotes, archaea, and eukaryotes.

Feature	Prokaryotes	Archaea	Eukaryotes
Nucleus	No	No	Yes
Membrane-bound organelles	No	No	Yes
Cell wall	Yes	Variable	Variable

Surface-to-Volume Ratio

Smaller cells have a higher surface-to-volume ratio, allowing more efficient exchange of materials.

Cell Structures

Major organelles and their functions:

• Nucleus: DNA storage

• Mitochondria: Energy production

• ER (Endoplasmic Reticulum): Protein/lipid synthesis

• Golgi: Processing and packaging

• Lysosomes: Digestion

• Cytoskeleton: Structure and transport

Transport

Cells move materials via several mechanisms.

• Endocytosis: Intake

• Exocytosis: Release

• Vesicle: Transport bubble

Deoxyribonucleotide

Deoxyribonucleotides are the building blocks of DNA.

• Base + deoxyribose sugar + phosphate

DNA vs RNA (3 Differences)

• Sugar type

• Base (T vs U)

• Structure (double vs single strand)

DNA Structure

• Sugars/phosphates: Backbone

• Bases: Interior

• Bonding: Hydrogen bonds (weak but specific)

Levels of DNA Organization

1. Double Helix

2. Nucleosome: DNA wrapped around histones

3. 30-nm Fiber

4. Scaffold Attachment

5. Chromosomes: Supercoiled during mitosis

Chromatin States

• Heterochromatin: Inactive, tightly packed

• Euchromatin: Active, loosely packed

Viruses, Viroids, Prions

Non-cellular infectious agents can affect living organisms in various ways.

• Viruses: Protein coat + nucleic acid

• Viroids: Infectious RNA

• Prions: Misfolded proteins causing disease