2.1 Atoms and Molecules
5 min read•august 22, 2024
Atoms and molecules form the foundation of life's chemistry. They're the building blocks that create everything from DNA to proteins. Understanding their structure and interactions is key to grasping how living things work at the most basic level.
This section dives into atomic structure, chemical bonds, and carbon's role in biology. It sets the stage for exploring more complex biological molecules and processes throughout the rest of the chapter on the chemistry of life.
Atomic Structure and Subatomic Particles
Composition and Charges of Subatomic Particles
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- Atoms are the fundamental unit of matter composed of protons, neutrons, and electrons
- Protons have a positive charge, neutrons have no charge, and electrons have a negative charge
- The charges of these subatomic particles balance each other out in a neutral atom
- In an ion, the number of protons and electrons is unequal, resulting in a net positive (cation) or negative (anion) charge (sodium ion Na+, chloride ion Cl-)
Atomic Number, Mass Number, and Electron Configuration
- The number of protons in an atom's nucleus determines the element's identity and is called the atomic number
- For example, carbon always has 6 protons, while oxygen has 8 protons
- The mass number is the sum of the number of protons and neutrons in an atom's nucleus
- Isotopes of an element have the same number of protons but differ in their number of neutrons (carbon-12, carbon-13, carbon-14)
- Electrons occupy specific energy levels (shells) around the nucleus, with each level having a maximum number of electrons it can hold
- The arrangement of electrons in these shells is known as the electron configuration
- The electron configuration determines an atom's chemical properties and bonding behavior (reactivity, valency)
Formation of Chemical Bonds
Octet Rule and Electron Sharing
- Chemical bonds form when atoms share or transfer electrons to achieve a more stable electron configuration
- The octet rule states that atoms tend to form bonds that allow them to have eight electrons in their outermost shell (valence shell)
- This configuration resembles the stable electron arrangement of noble gases (helium, neon, argon)
- Atoms with incomplete outer shells will form bonds to achieve a complete octet (hydrogen, carbon, oxygen)
- Molecules are formed when two or more atoms bond together through covalent or ionic bonds
- The type of bond formed depends on the electronegativity difference between the atoms involved
Electronegativity and Bond Formation
- Electronegativity is the ability of an atom to attract electrons in a chemical bond
- Atoms with high electronegativity (oxygen, nitrogen) tend to gain electrons, while atoms with low electronegativity (metals) tend to lose electrons
- The electronegativity difference between atoms determines the type of bond formed
- Large differences result in ionic bonds, while small differences lead to covalent bonds
- The unequal sharing of electrons in a covalent bond due to electronegativity differences creates polar covalent bonds (water molecule H2O)
Ionic vs Covalent Bonds in Biology
Ionic Bonds and Compounds
- Ionic bonds form when there is a large electronegativity difference between atoms, resulting in the complete transfer of electrons from one atom to another
- In an ionic bond, the atom that loses electrons becomes a positively charged cation, while the atom that gains electrons becomes a negatively charged anion
- For example, in sodium chloride (NaCl), sodium loses one electron to become Na+, while chlorine gains one electron to become Cl-
- Ionic compounds, such as sodium chloride (NaCl) and calcium phosphate (Ca3(PO4)2), are held together by the electrostatic attraction between oppositely charged ions
- Ionic compounds have high melting points, are soluble in water, and conduct electricity when dissolved or molten
Covalent Bonds and Molecules
- Covalent bonds form when there is a small electronegativity difference between atoms, resulting in the sharing of electrons between atoms
- In a covalent bond, the shared electrons are attracted to the nuclei of both atoms, forming a stable molecule
- Covalent bonds can be single (H2), double (O2), or triple (N2), depending on the number of electron pairs shared between the atoms
- Most biological molecules, such as proteins, carbohydrates, and nucleic acids, are held together by covalent bonds
- These molecules are essential for life processes, including energy storage (glucose), information storage (DNA), and catalysis (enzymes)
- Covalent bonds can be polar or nonpolar, depending on the electronegativity difference between the atoms involved
- Polar molecules (water) have uneven charge distribution and can form hydrogen bonds, while nonpolar molecules (lipids) have even charge distribution and are hydrophobic
Carbon's Importance in Biological Molecules
Carbon's Unique Properties
- Carbon is the most important element in forming complex biological molecules due to its unique properties and versatility in bonding
- Carbon has four valence electrons, allowing it to form stable covalent bonds with up to four other atoms, including other carbon atoms
- This property enables carbon to form a wide variety of molecular structures, such as chains (fatty acids), rings (glucose), and branched structures (amino acids)
- Carbon can form single, double, or triple bonds, further increasing the diversity of carbon-based molecules
- Double bonds (C=C) are found in unsaturated fatty acids and some vitamins (vitamin A), while triple bonds (C≡C) are less common in biological molecules
Diversity of Carbon-Based Biological Molecules
- The ability of carbon to form stable covalent bonds with other elements, such as hydrogen, oxygen, nitrogen, and sulfur, allows for the formation of key biological molecules
- Carbohydrates (glucose, cellulose) are composed of carbon, hydrogen, and oxygen and serve as energy sources and structural components
- Lipids (triglycerides, phospholipids) are primarily made of carbon and hydrogen and function in energy storage and cell membrane structure
- Proteins (enzymes, antibodies) contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur, and play crucial roles in catalysis, transport, and immune response
- Nucleic acids (DNA, RNA) are made of carbon, hydrogen, oxygen, nitrogen, and phosphorus and store and transmit genetic information
- The presence of carbon-based molecules is a defining characteristic of life on Earth, and the study of these molecules is central to the field of biochemistry
- Understanding the structure and function of carbon-based biological molecules is essential for fields such as medicine, biotechnology, and agriculture