Study Guide: Chemical Elements, Atomic Structure, Chemical Bonds, and Water Properties in Biology

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Major Topic: Matter Consists of Chemical Elements in Pure Form and in Combinations Called Compounds

Elements and Compounds

All matter is composed of chemical elements, which can exist alone or combined as compounds. Understanding the nature of elements and compounds is fundamental to biology.

Element: A substance that cannot be broken down into simpler substances by chemical means. There are 92 naturally occurring elements, each represented by a chemical symbol (e.g., O for oxygen).
Compound: A substance formed by the chemical combination of two or more elements in fixed ratios (e.g., , sodium chloride).

The Elements of Life

Only a subset of elements are essential for life, and these are required for healthy living and reproduction.

20-25% of all elements are essential for organisms.
Essential elements are similar among living organisms but vary in number (humans need 25, plants need 17).
Oxygen, carbon, hydrogen, and nitrogen make up about 96% of the human body. The remaining 4% includes calcium, phosphorus, potassium, and sulfur.
Trace elements are required in minute amounts but are vital for proper biological function (e.g., iron, iodine).

Evolution of Tolerance to Toxic Elements

Some elements are toxic to organisms, but certain species have evolved mechanisms to tolerate or detoxify them.

Examples of toxic elements: arsenic (lethal to humans).
Some plants (e.g., sunflowers) can tolerate and accumulate toxic elements like lead, zinc, and heavy metals, which can be used for environmental detoxification.

Major Topic: Structure of Atoms

Subatomic Particles

Atoms are composed of smaller particles called subatomic particles, which determine their chemical properties.

Electron: Negatively charged particle.
Proton: Positively charged particle.
Neutron: Neutral particle.
Protons and neutrons are located in the atomic nucleus; electrons orbit in a cloud around the nucleus.
Neutron and proton mass are nearly identical ( g or 1 dalton); electron mass is about that of a proton.
Dalton: Unit of measurement for atomic and molecular mass.

Atomic Number and Atomic Mass

Atoms of different elements have unique numbers of subatomic particles.

Atomic number: Number of protons in an atom, usually shown as a subscript on the left side of the element symbol.
Atoms are electrically neutral if they have equal numbers of protons and electrons.
Mass number: Total number of protons and neutrons, shown as a superscript on the left side of the symbol.
To find the number of neutrons: .

Isotopes

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

Isotopes have different mass numbers but behave similarly in chemical reactions.
Example: Carbon-12 (6 neutrons, most common), Carbon-13 (7 neutrons), Carbon-14 (8 neutrons, radioactive).
Radioactive isotope: Decays spontaneously, emitting energy and particles, and can transform into another element.
Applications: Used as tracers in biology (e.g., PET scans), but can be hazardous (e.g., nuclear fallout).

Major Topic: The Energy Levels of Elements

Energy Levels and Electron Shells

Electrons in atoms occupy specific energy levels, which influence chemical behavior.

Energy: The ability to cause change.
Electrons have potential energy based on their distance from the nucleus; farther electrons have higher potential energy.
Electrons occupy shells; the first shell holds up to 2 electrons, the second up to 8.
Atoms with complete outer shells are chemically inert.

Electron Distribution and Chemical Properties

The arrangement of electrons in shells determines an atom's chemical properties and reactivity.

Atoms tend to fill their outermost shell (valence shell).
Elements with the same number of valence electrons have similar chemical properties.
Atoms with incomplete valence shells are reactive and form chemical bonds.

Major Topic: The Formation and Function of Molecules Depend on Chemical Bonding Between Atoms

Covalent Bonds

Covalent bonds form when atoms share pairs of valence electrons, creating molecules.

Single bond: One pair of electrons shared (represented by a single line).
Double bond: Two pairs of electrons shared (represented by two lines).
Electronegativity: An atom's ability to attract electrons in a covalent bond.
If atoms have equal electronegativity, electrons are shared equally (nonpolar covalent bond).
If atoms have unequal electronegativity, electrons are shared unequally (polar covalent bond), resulting in partial charges.
Example: In water (), oxygen is more electronegative than hydrogen, so electrons are closer to oxygen, giving it a partial negative charge.

Ionic Bonds

Ionic bonds form when electrons are transferred from one atom to another, creating charged ions.

Cation: Positively charged ion (loses electrons).
Anion: Negatively charged ion (gains electrons).
Ionic bond: Attraction between oppositely charged ions.
Example: Sodium (Na) transfers an electron to chlorine (Cl), forming Na+ and Cl-, which combine to make NaCl (table salt).
Compounds formed by ionic bonds are called salts.

Weak Chemical Interactions

Weak bonds play important roles in biological molecules, affecting their structure and function.

Hydrogen bond: Weak bond between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.
Van der Waals interactions: Weak attractions due to transient asymmetrical electron distributions in molecules.
Weak bonds help biological molecules maintain their shape and interact with each other.

Molecular Shape and Function

The shape of a molecule is crucial for its biological function.

Molecular shape determines how molecules recognize and respond to each other.
Biological molecules interact through weak bonds only if their shapes are complementary.
Molecules with similar shapes often have similar biological functions.

Major Topic: Chemical Reactions Make and Break Chemical Bonds

Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, transforming reactants into products.

Reactants: Starting materials in a chemical reaction.
Products: Resulting materials after the reaction.
Example: Photosynthesis converts carbon dioxide and water into glucose and oxygen.
Law of conservation of mass: The total amount of matter remains constant during a chemical reaction.
Chemical equilibrium: When the forward and reverse reactions occur at the same rate.

Major Topic: Properties of Water and Their Biological Importance

Cohesion of Water Molecules

Water molecules are held together by hydrogen bonds, resulting in unique properties essential for life.

Cohesion: Water molecules stick to each other due to hydrogen bonding.
Adhesion: Water molecules stick to other substances (e.g., cell walls).
Surface tension: Difficulty in breaking the surface of a liquid due to cohesive forces.

Moderation of Temperature by Water

Water moderates temperature due to its high specific heat and heat of vaporization.

Kinetic energy: Energy of motion; temperature measures average kinetic energy of molecules.
Calorie: Amount of heat needed to raise the temperature of 1 gram of water by 1 degree Celsius.
Specific heat: Amount of heat required to change the temperature of 1 gram of a substance by 1 degree Celsius.
Water has a high specific heat (1 cal/g/°C), so it resists temperature changes.
Heat of vaporization: Amount of heat needed to convert 1 gram of liquid to gas.
Evaporative cooling: As water evaporates, the surface cools because the fastest (highest energy) molecules leave.

Floating of Ice on Liquid Water

Ice is less dense than liquid water, allowing it to float and providing important ecological benefits.

Water expands as it freezes, making ice less dense than liquid water.
This property insulates aquatic environments, allowing life to persist under ice.

Water: The Solvent of Life

Water's polarity makes it an excellent solvent, capable of dissolving many substances essential for biological processes.

Solution: Homogeneous mixture of substances.
Solvent: The dissolving agent (water in aqueous solutions).
Solute: The substance being dissolved.
Hydration shell: Water molecules surround and separate ions or polar molecules.

Hydrophilic and Hydrophobic Substances

Substances interact with water differently based on their chemical nature.

Hydrophilic: Substances that have an affinity for water (usually polar or ionic).
Hydrophobic: Substances that repel water (usually nonpolar).
Some hydrophilic substances do not dissolve but can absorb water (e.g., cotton).

Solute Concentration in Aqueous Solutions

Concentration of solutes in water is measured in moles, which is important for chemical reactions in biology.

Molecular mass: Sum of the masses of all atoms in a molecule.
Mole: molecules (Avogadro's number).

Acids, Bases, and pH

Acids and bases affect the concentration of hydrogen ions in solution, which is measured by pH.

Acid: Substance that increases hydrogen ion () concentration.
Base: Substance that reduces hydrogen ion concentration, often by increasing hydroxide ions ().
Water dissociates into and ions.
pH is defined as .
At 25°C, M.
Acidic solutions have higher ; basic solutions have higher .
Buffer: Substance that minimizes changes in pH by accepting or donating hydrogen ions.

Acidification: A Threat to Our Oceans

Increasing atmospheric CO2 leads to ocean acidification, which threatens marine life.

CO2 dissolves in seawater, forming carbonic acid and lowering pH.
Ocean pH has dropped by 0.1 units over the past 200 years due to increased CO2 emissions.