General Biology Study Notes: Biomolecules, Cell Theory, and Chemical Foundations

Proteins: Structure and Function

Overview of Proteins

Proteins are essential macromolecules composed of amino acids, performing a wide variety of functions in living organisms. Their structure determines their function, and they exhibit remarkable diversity in form and activity.

• Amino acids are the building blocks of proteins. Each amino acid has a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R-group).

• The R-group determines the chemical reactivity and solubility of the amino acid.

• Amino acids are linked by peptide bonds (C-N covalent bonds) formed via dehydration reactions.

• Proteins are polymers of amino acids, and the sequence of amino acids is called the primary structure.

Levels of Protein Structure

• Primary structure: The unique sequence of amino acids in a polypeptide, stabilized by peptide bonds.

• Secondary structure: Local folding patterns such as alpha helices and beta-pleated sheets, stabilized by hydrogen bonds between backbone groups.

• Tertiary structure: The overall three-dimensional shape of a polypeptide, resulting from interactions among R-groups and between R-groups and the backbone.

• Quaternary structure: The arrangement of multiple polypeptide subunits in a protein, stabilized by various interactions.

Types of R-group Interactions in Tertiary and Quaternary Structure

• Hydrogen bonding

• Hydrophobic interactions

• Van der Waals interactions

• Covalent bonding (e.g., disulfide bridges)

• Ionic bonding

Protein Folding and Function

• Protein folding is crucial for function; misfolded proteins can lead to loss of function or disease.

• Molecular chaperones assist in proper protein folding (e.g., heat shock proteins).

• Proteins are dynamic and may change shape in response to binding or environmental changes.

Protein Functions

• Catalysis: Enzymes speed up chemical reactions.

• Structure: Provide support and shape to cells and tissues.

• Movement: Motor proteins move cells or molecules within cells.

• Signaling: Transmit signals between cells.

• Transport: Move substances across membranes or within organisms.

• Defense: Antibodies and other proteins protect against pathogens.

Carbohydrates: Structure and Function

Overview of Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically with the formula (CH2O)n. They serve as energy sources, structural components, and are involved in cell recognition.

• Monosaccharides: Simple sugars (e.g., glucose) that vary in carbon number, carbonyl group position (aldose or ketose), and spatial arrangement of atoms.

• Disaccharides: Two monosaccharides linked by a glycosidic bond (formed via condensation reaction).

• Polysaccharides: Polymers of monosaccharides (e.g., starch, glycogen, cellulose, chitin).

Functions of Carbohydrates

• Energy storage: Starch (plants) and glycogen (animals) store glucose for later use.

• Structural support: Cellulose (plants), chitin (fungi and arthropods), and peptidoglycan (bacteria) provide rigidity to cell walls.

• Cell identity: Glycoproteins and glycolipids on cell surfaces are involved in cell recognition and signaling.

Table: Major Polysaccharides and Their Functions

Polysaccharide	Organism	Function
Starch	Plants	Energy storage
Glycogen	Animals	Energy storage
Cellulose	Plants	Structural support (cell wall)
Chitin	Fungi, Arthropods	Structural support (cell wall, exoskeleton)
Peptidoglycan	Bacteria	Structural support (cell wall)

Lipids: Structure and Function

Overview of Lipids

Lipids are hydrophobic, carbon-containing molecules that are insoluble in water due to their high proportion of nonpolar C-H bonds. They serve as energy storage, structural components of membranes, and signaling molecules.

• Fats (triglycerides): Composed of glycerol and three fatty acids, joined by ester linkages. Used for energy storage.

• Phospholipids: Contain a glycerol backbone, two fatty acids, and a phosphate group. Major component of cell membranes, forming bilayers due to their amphipathic nature (hydrophilic head, hydrophobic tails).

• Steroids: Characterized by a four-ring structure. Examples include cholesterol and hormones (e.g., estrogen, testosterone).

Saturated vs. Unsaturated Fatty Acids

• Saturated fatty acids: No double bonds between carbons; solid at room temperature.

• Unsaturated fatty acids: One or more double bonds; liquid at room temperature due to kinks in the hydrocarbon chain.

Phospholipid Bilayer and Membrane Permeability

• Phospholipids spontaneously form bilayers in water, creating a selective barrier (plasma membrane).

• Membrane permeability depends on fatty acid saturation, tail length, and presence of cholesterol.

• Small, nonpolar molecules cross membranes easily; large or charged molecules cross less readily.

Cell Theory and the Nature of Life

Cell Theory

The cell theory is a fundamental concept in biology, stating that all living organisms are composed of cells, and all cells arise from pre-existing cells.

• Cells are the basic unit of life, separated from the environment by a plasma membrane.

• All cells share a common ancestry.

• Cell division is the process by which cells replicate.

Genetic Information and the Central Dogma

• Genetic information is stored in DNA, organized into genes located on chromosomes.

• The central dogma of molecular biology: DNA is transcribed into RNA, which is translated into protein.

• Proteins carry out most cellular functions.

Evolution and Natural Selection

• Species are related by common ancestry and change over time through evolution.

• Natural selection acts on heritable variation, leading to adaptation and speciation.

• Fitness: The ability of an individual to produce viable offspring relative to others.

• Adaptation: Traits that increase fitness in a particular environment.

Chemical Foundations of Life

Atoms, Elements, and Molecules

• Atoms consist of protons, neutrons, and electrons.

• Elements are defined by the number of protons (atomic number).

• Isotopes are atoms of the same element with different numbers of neutrons.

• Electrons occupy energy levels (shells); the outermost shell determines chemical reactivity.

Chemical Bonds

• Covalent bonds: Atoms share electron pairs.

• Ionic bonds: Electrons are transferred from one atom to another, creating charged ions.

• Hydrogen bonds: Weak attractions between a hydrogen atom with a partial positive charge and an electronegative atom (e.g., oxygen, nitrogen).

• Van der Waals interactions: Weak attractions due to transient dipoles.

Properties of Water

• Water is polar, forming hydrogen bonds that give rise to unique properties:

  • High cohesion and adhesion

  • High specific heat and heat of vaporization

  • Excellent solvent for polar and ionic substances

  • Less dense as a solid (ice floats)

  • Surface tension

Acids, Bases, and pH

• Acids donate protons (H+), bases accept protons.

• The pH scale measures the concentration of H+ ions: $pH = -\log[H^+]$

• Buffers help maintain stable pH in biological systems.

Chemical Reactions and Energy

• Chemical reactions involve breaking and forming bonds, transforming reactants into products.

• Potential energy: Stored energy due to position or structure.

• Kinetic energy: Energy of motion.

• First law of thermodynamics: Energy is conserved.

• Second law: Entropy (disorder) increases in spontaneous processes.

Functional Groups in Organic Molecules

• Common functional groups: hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), sulfhydryl (-SH).

• Functional groups confer specific chemical properties and reactivity to organic molecules.

Summary Table: Types of Biological Molecules

Class	Monomer	Polymer	Main Functions
Proteins	Amino acids	Polypeptides	Catalysis, structure, transport, signaling, defense
Carbohydrates	Monosaccharides	Polysaccharides	Energy storage, structure, cell identity
Lipids	Fatty acids, glycerol	Not true polymers	Energy storage, membranes, signaling
Nucleic acids	Nucleotides	DNA, RNA	Information storage and transfer

Additional info: Some explanations and examples have been expanded for clarity and completeness based on standard General Biology curriculum.