Chemical Composition of Cells

Atoms, Bonds, and Organic Molecules

This section introduces the foundational chemical principles underlying cell structure and function, focusing on the types of atoms, chemical bonds, and molecules that are essential for life.

Learning Objectives

• Recognize the atomic bases for different types of bonds in biological molecules.

• Describe why carbon, hydrogen, nitrogen, and oxygen are the most abundant atoms in biological molecules.

Emergence of Life

Where Does "Life" Emerge?

Life emerges at a specific level of biological organization, where molecules interact to form complex structures capable of metabolism, growth, and reproduction.

• Biological organization progresses from atoms to molecules, organelles, cells, tissues, organs, and organisms.

• Cells are the basic unit of life, where chemical reactions occur in a controlled environment.

• Life is defined by the ability to maintain homeostasis, reproduce, and respond to stimuli.

A Chemical Connection to Biology

Why Are We Carbon-Based Lifeforms?

Cells are efficient incubators that maintain favorable conditions for chemical reactions essential to life. Most biological molecules inside cells are carbon-based, while the external environment is dominated by water.

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

• DNA, RNA, proteins, and lipids are all primarily composed of carbon-based molecules.

• Water is the main component outside and inside cells, but the functional molecules are carbon-based.

Key Definitions

• Matter: Anything that has mass and takes up space. Excludes energy forms like light and heat.

• Atom: The smallest unit of matter that retains the properties of an element. Composed of protons, neutrons, and electrons.

• Element: A substance consisting of a single type of atom that cannot be broken down by chemical reactions. Examples: carbon, hydrogen, oxygen, nitrogen.

• Molecule: Two or more atoms chemically bonded together. Examples: H2O, proteins, DNA.

• Compound: A molecule consisting of two or more different elements in a fixed ratio. Examples: NaCl, H2O.

Atomic Structure and Properties

Subatomic Particles

The properties of elements depend on the structure of their atoms, which are composed of subatomic particles.

• Protons: Positive charge, mass ≈ 1 Dalton (Da).

• Neutrons: No charge, mass ≈ 1 Dalton (Da).

• Electrons: Negative charge, negligible mass.

• The atomic number is defined by the number of protons in the nucleus.

• Electrons orbit the nucleus in shells; the arrangement of electrons determines chemical reactivity.

Periodic Table and Biological Elements

Elements Essential for Life

Out of the 92 naturally occurring elements, only a few are essential for life. Biological molecules are mostly made from carbon, hydrogen, oxygen, and nitrogen.

• These four elements make up approximately 96% of the mass of living organisms.

• Other important elements include phosphorus, sulfur, calcium, and magnesium.

Distribution of Elements

Earth's Crust vs. Human Body

The distribution of elements in the Earth's crust is different from that in the human body. Carbon, hydrogen, oxygen, and nitrogen are abundant in living organisms but not in the Earth's crust.

• These elements are important for biology because they form stable covalent bonds and are involved in key biological processes.

• Some elements are rare in the Earth's crust but essential for life.

Chemical Reactivity

Valence Electrons and Bond Formation

Chemical reactivity is determined by the arrangement of electrons in the outermost shell (valence shell) of an atom.

• Atoms with unpaired valence electrons are more reactive and tend to form bonds to achieve a full valence shell.

• Noble gases have full valence shells and are chemically inert.

• Atoms form chemical bonds to become more stable.

Types of Chemical Bonds in Biology

Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. They are the strongest and most common bonds in biological molecules.

• Nonpolar Covalent Bonds: Electrons are shared equally between atoms (e.g., H2, O2).

• Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

• Carbon forms four covalent bonds, allowing for complex molecular structures.

Ionic Bonds

Ionic bonds are formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Example: Sodium chloride (NaCl) is formed by the transfer of an electron from sodium to chlorine.

• Organic molecules can also form ionic bonds under certain conditions.

Hydrogen Bonds

Hydrogen bonds are weak interactions that occur when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom.

• Hydrogen bonds are crucial for the structure of DNA, proteins, and water.

• Although weak individually, they are strong in large numbers.

Van der Waals Interactions

These are weak attractions between molecules or parts of molecules that result from transient local partial charges.

• Important for the three-dimensional structure of macromolecules.

Functional Groups in Organic Molecules

Role and Examples

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

• Examples include hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), and phosphate (-PO4).

• Functional groups determine the reactivity and interactions of organic molecules.

Summary Table: Types of Chemical Bonds

Key Equations

• Atomic mass calculation:

• Compound ratio example:

Conclusion

Understanding the chemical composition of cells is fundamental to biology. The unique properties of carbon, hydrogen, oxygen, and nitrogen enable the formation of complex molecules necessary for life. Chemical bonds, especially covalent bonds, are essential for the structure and function of biological macromolecules.