Fundamentals of Biochemistry: Atoms, Water, and Macromolecules

Atoms to Organisms & Macromolecules

Levels of Organization

Biological systems are organized in a hierarchical manner, from the smallest units to the most complex.

• Organism: An individual living entity.

• System: Groups of organs working together.

• Organ: Structures composed of tissues performing specific functions.

• Tissue: Groups of similar cells performing a function.

• Cell: Basic unit of life.

• Organelle: Specialized structures within cells.

• Compound: Chemical combination of elements.

• Element: Pure substance consisting of one type of atom.

• Atom/element: Non-living, smallest unit of matter.

• Electron, proton, neutron: Subatomic particles.

Definitions: Matter, Energy, Atom, Element, Electron, Proton, Neutron

Understanding the basic building blocks of matter is essential in biology.

• Matter: Anything that occupies space and has mass.

• Energy: Anything that does work; does not occupy space or have mass.

• Atom: Smallest unit of matter; made of electron, proton, and neutron.

• Element: Purest form of matter; periodic table of elements; tells you what something is made of.

• Electron: Negative subatomic particle found in energy levels surrounding the nucleus of an atom; determines chemistry of atoms.

• Proton: Positively charged subatomic particle found in nucleus of atom; determines what element it is.

• Neutron: Neutrally charged subatomic particle found in nucleus of atom; adds to mass and varies in number.

Most Common Elements in Living Things: CHON

Living organisms are primarily composed of four elements.

• Carbon (C)

• Hydrogen (H)

• Oxygen (O)

• Nitrogen (N)

Other Essential Elements

Besides CHON, living organisms require other elements for proper function.

• Na+ (Sodium)

• K+ (Potassium)

• Cl- (Chloride)

• Ca2+ (Calcium)

Drawing Atoms: Electron Energy Levels

Electrons are arranged in energy levels around the nucleus. The first energy level holds up to 2 electrons, the second and third up to 8 each. The outermost electrons are called valence electrons and are involved in chemical bonding.

• Atoms share or transfer electrons to fill their outer energy levels.

• Hydrogen has only one electron and needs one more to fill its first shell.

Life Based on Carbon

Carbon is the backbone of organic molecules due to its ability to form four covalent bonds.

• Carbon can bond to itself, make rings, and has 4 places to bond to other atoms.

• This allows it to make a variety of different large molecules: proteins, lipids, carbohydrates, and nucleic acids.

Chemical Bonds: Types and Examples

Chemical bonds are attractions between atoms that hold compounds together.

• Chemical bonds are internal (within 1 compound) and external (between two compounds).

• Bonds are divided into ionic (charge attractions, + to -) and covalent (sharing electrons between atoms).

• Covalent is further divided into polar covalent (unequal sharing of electrons, leads to slight charges) and nonpolar covalent (equal sharing, no charge).

Functional Groups: Polarity and Properties

Functional groups are specific groups of atoms within molecules that determine their chemical properties.

Functional Group Name	Formula	Properties
Hydroxyl	HO-	Polar (✓); hydrophilic
Carbonyl	C=O	Polar (✓); hydrophilic
Carboxyl	R-COOH	Polar/acid (✓); hydrophilic
Amino	R-NH2	Polar (✓); hydrophilic
Phosphate	PO43-	Polar (✓); hydrophilic
Methyl	H3C-	Nonpolar; no charge; hydrophobic

Hydrophilic means water-loving since it carries a charge; hydrophobic means it hates water due to no charges on the compound/functional group.

Water

Importance of Water

All living things need water to survive. Water is essential for metabolism, transport, and maintaining homeostasis.

Polar Covalent Bonds vs. Weak Hydrogen Bonds in Water

Water molecules are held together by polar covalent bonds and interact with each other via weak hydrogen bonds.

• Polar covalent bonds occur between H atoms and O atom in one water molecule.

• Oxygen keeps the electron longer, giving it a slight negative charge ($ext{O}^{ ext{δ}-}$) and H a slight positive charge ($ext{H}^{ ext{δ}+}$).

• This polarity allows water molecules to form hydrogen bonds with each other.

• Hydrogen bonds are weak attractions between the slightly positive H of one molecule and the slightly negative O of another.

Cohesion and Surface Tension

Cohesion is the attraction between water molecules due to hydrogen bonding, leading to surface tension.

• Cohesion allows water molecules to stick together.

• Surface tension provides strength for the surface of water, allowing organisms to walk on water or larvae to develop at the top of water.

Adhesion of Water

Adhesion is the attraction of water molecules to other substances, important for transport in plants and animals.

• Adhesion allows water to stick to the inside of transport tubes in plants or blood vessels in animals.

• It enables water to travel up against gravity (capillary action).

Dipole and Solvent Properties of Water

Water's dipole nature makes it an excellent solvent for charged and polar substances, facilitating metabolism and transport.

• Solvent: Water dissolves substances with charges, distributing them evenly.

• Nonpolar substances do not dissolve easily in water.

• Water surrounds charged or polar molecules, allowing them to be transported in living systems.

Macromolecules

Four Major Macromolecules

Living things are made up of four major types of macromolecules.

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids

Universal Monomers of Macromolecules

Each macromolecule is made up of specific universal monomers.

• Carbohydrates: Monosaccharides (simple sugars)

• Lipids: Fatty acids + Glycerol

• Nucleic acids: Nucleotides

• Proteins: Amino acids

Universal vs. Species-Specific Monomers

Universal monomers are interchangeable building blocks for all organisms, while species-specific monomers are unique to certain species.

• Universal monomers allow organisms to build their own macromolecules for growth.

• Species-specific monomers indicate macromolecules are unique to a species (e.g., chicken muscle protein vs. human muscle protein).

Condensation and Hydrolysis

Macromolecules are assembled and broken down by condensation and hydrolysis reactions.

• Condensation: Small molecules are assembled into large ones; water is produced.

• Hydrolysis: Water is used to break down macromolecules into their monomers.

Carbohydrates: Size, Function, and Examples

Carbohydrates are simple sugars used for quick energy and structural purposes.

• Monosaccharides: Simple sugars; formula: $C_nH_{2n}O_n$

• Pentose (5-carbon) monomers: Deoxyribose, ribose

• Hexose (6-carbon) monomers: Glucose (from photosynthesis), fructose (from fruit), galactose (from milk)

Examples of Monosaccharides:

• Glucose

• Fructose

• Galactose

Additional info: Disaccharides and polysaccharides are formed by condensation reactions between monosaccharides, resulting in larger carbohydrate molecules such as sucrose, starch, and cellulose.