Atoms, Elements, and Chemical Bonds: Foundations of General Biology

Atoms, Elements, and Chemical Bonds

Introduction

This section introduces the basic chemical principles essential for understanding biological systems, including the structure of atoms, the nature of elements, and the formation of molecules through chemical bonds.

Hypotheses and Mimicry in Biology

Hypothesis for Bright Colored Butterfly Wings

• Mimicry of poisonous species: Non-poisonous butterflies may evolve bright colors to resemble poisonous ones, deterring predators.

• Color as a warning: Bright colors signal toxicity to potential predators.

• Color attracting mates: Bright coloration can serve as a mating flag, aiding in reproduction.

• Camouflage: Some species use coloration to blend into their environment.

Example of Mimicry

• A black and yellow moth mimicking the colors of a wasp.

Scientific Method Application

• Prediction: If coloration is a mating flag, then brightly colored males should attract more mates.

• Test: Paint some butterflies dark and some bright; observe mating success.

• Conclusion: Females prefer the bright color even after the smell of paint on the males' wings fades.

Elements and Atoms

Elements

• Element: A substance that cannot be broken down into simpler substances by chemical processes.

• There are 94 naturally occurring elements; 25 are found in living things.

• Four elements are found in 96% of living things: carbon, hydrogen, oxygen, and nitrogen.

Element	Symbol	Role in Living Things
Carbon	C	Backbone of organic molecules
Hydrogen	H	Component of water and organic molecules
Oxygen	O	Essential for respiration, water
Nitrogen	N	Component of proteins and nucleic acids

Atoms

• The smallest portion of an element that retains its properties.

• The word "atom" comes from the Greek for "indivisible."

Components of Atoms

• Protons: Positively charged particles in the nucleus; mass = 1 amu (atomic mass unit) or 1 dalton.

• Neutrons: Neutral particles in the nucleus; mass = 1 amu or dalton.

• Electrons: Negatively charged particles; very small mass; located in orbitals around the nucleus.

Atomic Number and Mass

• Atomic number: Number of protons in an atom; defines the element.

• Atomic mass: Number of protons plus neutrons.

• Example: Sulfur (S) has atomic number 16 and atomic mass 34. Number of neutrons = 34 - 16 = 18.

Isotopes

• Atoms of the same element with different numbers of neutrons.

• Example: Hydrogen has three isotopes: $^1H$, $^2H$, $^3H$.

• Isotopes have the same atomic number but different atomic masses.

Electrons and Orbitals

Electrons

• Very small mass; negative charge (-e).

• Located in orbitals around the nucleus.

• In a neutral atom, the number of electrons equals the number of protons.

Electron Shells and Orbitals

• Electrons occupy energy levels called shells, which contain orbitals.

• K shell: Closest to the nucleus; contains one orbital (2 electrons).

• L shell: Next shell; contains four orbitals (8 electrons).

• Orbitals fill in a specific order: 1s, 2s, 2p, 3s, 3p, etc.

• Valence shell: The outermost shell containing electrons; determines chemical reactivity.

Valence Electrons

• Electrons in the outermost shell.

• Important for forming chemical bonds.

• Example: Oxygen (atomic number 8) has 6 valence electrons in the L shell.

Molecules and Chemical Bonds

Molecules

• Two or more atoms bonded together.

• Types:

  • Consisting of the same element (e.g., $H_2$)

  • Consisting of different elements (e.g., $H_2O$)

Covalent Bonds

• Formed when atoms share pairs of electrons.

• Single covalent bond: Sharing one pair of electrons (e.g., $H-H$).

• Double covalent bond: Sharing two pairs of electrons (e.g., $O=O$).

• Triple covalent bond: Sharing three pairs of electrons (e.g., $N  N$).

• Nonpolar covalent bond: Electrons are shared equally between atoms.

• Polar covalent bond: Electrons are shared unequally due to differences in electronegativity.

Electronegativity

• The tendency of an atom to attract electrons in a chemical bond.

• Important for determining bond polarity.

• To determine bond type, subtract the electronegativity values of the two atoms:

$\text{Electronegativity difference} = |\text{Electronegativity}_1 - \text{Electronegativity}_2|$

• If the difference is less than 0.5, the bond is nonpolar covalent (equal sharing).

• If the difference is greater, the bond is polar covalent (unequal sharing).

Examples

• Molecule of Hydrogen ($H_2$): Two hydrogen atoms share electrons equally, forming a nonpolar covalent bond.

• Molecule of Oxygen ($O_2$): Two oxygen atoms share two pairs of electrons (double bond).

• Molecule of Nitrogen ($N_2$): Two nitrogen atoms share three pairs of electrons (triple bond).

• Methane ($CH_4$): Carbon shares electrons with four hydrogens; all valence spots are filled.

Summary Table: Types of Covalent Bonds

Bond Type	Number of Shared Electron Pairs	Example
Single	1	$H_2$
Double	2	$O_2$
Triple	3	$N_2$

Additional info: The notes also reference the importance of electronegativity in biological molecules, as it affects molecular interactions and properties such as solubility and reactivity.