A&p Book Notes

Chapter 2: Atoms, Ions, & Molecules

Atomic Structure

The body is composed of matter, which is anything that has mass and occupies space. All matter is composed of atoms, the smallest particle that exhibits the chemical properties of an element. There are 92 naturally occurring elements organized in the periodic table, grouped into major, minor, and trace elements based on their percentage by weight in the human body.

Major Elements:

Almost 99% of body weight comprises:

  • Oxygen (O): Essential for respiration, vital in water (H2O)

  • Carbon (C): The backbone of organic molecules, essential component of carbohydrates, proteins, lipids, and nucleic acids

  • Hydrogen (H): Integral part of water and organic molecules, involved in energy transfer

  • Nitrogen (N): A major component of amino acids and nucleic acids, critical for protein synthesis

  • Calcium (Ca): Important for bone structure, muscle contraction, and neurotransmitter release

  • Phosphorus (P): A critical component of DNA, RNA, and ATP; important for energy transfer and storage

Minor Elements:

Comprise less than 1% of body weight:

  • Sulfur (S): Found in amino acids, important for protein structure

  • Potassium (K): Essential for nerve transmission and muscle function

  • Sodium (Na): Crucial for maintaining osmotic balance and nerve impulse conduction

  • Chlorine (Cl): Important for forming gastric acid (HCl) and fluid balance

  • Magnesium (Mg): Required for numerous enzyme-catalyzed reactions and DNA synthesis

  • Iron (Fe): Key component of hemoglobin, necessary for oxygen transport

Components of an Atom

Atoms consist of three subatomic particles:

  • Protons: Positively charged particles located in the nucleus, contribute to the atomic mass. The number of protons defines the atomic number of an element.

  • Neutrons: Neutral particles, have a mass similar to protons, also found in the nucleus. The number of neutrons can vary, leading to different isotopes of an element.

  • Electrons: Negatively charged particles, much lighter than protons, located in orbitals around the nucleus. The number of electrons in a neutral atom equals the number of protons.

Atomic Mass and Atomic Number

The atomic mass is expressed in atomic mass units (amu) or daltons, reflecting the total number of protons and neutrons in the atom's nucleus. The atomic number, which is located above the element's chemical symbol in the periodic table, indicates the number of protons. Elements are arranged by increasing atomic number, and as a result, the atomic mass typically increases as well.

Subatomic Particles Count

  • The atomic number defines the number of protons.

  • Neutrons are determined by subtracting the atomic number from the atomic mass, allowing for the identification of specific isotopes.

  • Atoms are chemically neutral when the number of protons equals the number of electrons.

Electron Shells and Isotopes

Electron shells have specific energy levels and capacities:

  • 1st shell: Holds a maximum of 2 electrons.

  • 2nd and subsequent shells: Can hold up to 8 electrons each, following the octet rule for stable configurations.

Isotopes

Isotopes are atoms of the same element with the same number of protons but a different number of neutrons, which results in different atomic masses.

  • Radioisotopes: These are unstable isotopes that decay over time, releasing radiation in the form of particles or electromagnetic waves, a process that can be used in medical imaging and cancer treatment.

Chemical Stability

The periodic table is organized vertically by the number of electrons in the outer (valence) shell. A complete outer shell leads to chemical stability, often fulfilling the octet rule where atoms will gain, lose, or share electrons to achieve full valence shells.

Ions & Ionic Compounds

Chemical Compounds

Chemical compounds form stable associations between two or more elements in fixed ratios. Compounds can be classified as either ionic (formed by transfer of electrons) or molecular (formed by sharing of electrons).

Ions Explained

Ions are charged atoms formed through the loss or gain of electrons:

  • Cations: Positively charged ions that donate electrons.

  • Anions: Negatively charged ions that accept electrons.

Ions function as electrolytes, essential for various biological processes, including muscle contractions and nerve impulses.

Ionic Bonds

Cations and anions bond together through ionic bonds, typically forming salts, which dissociate into ions in solutions and conduct electricity.

Covalent Bonds

Atoms can achieve stability by sharing electrons, resulting in covalent bonds that form molecules.

  • Molecular formulas indicate the quantity and types of atoms (e.g., H2CO3 for carbonic acid).

  • Structural Formula: Illustrates the arrangement of atoms and the types of bonds within a molecule.

Isomers

Isomers are molecules that have the same molecular formula but different spatial arrangements of atoms. Examples include glucose and galactose, which have different functional properties due to their structural differences.

Covalent Bonds Types

Covalent bonds can be single, double, or triple, depending on the number of shared pairs of electrons between atoms, influencing the molecule's shape and reactivity.

Carbon Skeletons

Carbon skeletons form the backbone of organic molecules, which can be linear (straight chains), branched, or cyclic (rings). The ability of carbon to form four covalent bonds allows for a vast array of complex organic structures.

Electronegativity and Bond Types

Understanding BondingElectronegativity refers to the ability of an atom to attract electrons in a bond. The type of bond formed between atoms depends on the difference in electronegativity:

  • Nonpolar covalent bonds: Equal sharing of electrons between identical atoms.

  • Polar covalent bonds: Unequal sharing occurs in bonds between atoms with different electronegativities, resulting in partial charges.

Electronegativity Trends

Electronegativity increases from left to right across a period and decreases from top to bottom of a group in the periodic table, influencing the nature of bonds formed.

Properties of Water

Molecular Structure

Water (H2O) is a polar molecule, comprised of one oxygen atom bonded to two hydrogen atoms. The polar nature enables water to form hydrogen bonds with adjacent molecules, vital for many biochemical processes.

Physical Properties of Water

  • Cohesion: Attraction between water molecules due to hydrogen bonds, leading to high surface tension.

  • Adhesion: Water's attraction to other substances, important for processes like capillary action.

  • Surface Tension: Causes water to behave as a stretched elastic surface, enabling small objects to float.

  • High Specific Heat: Water has a high specific heat, meaning that significant energy is required to change its temperature; most energy breaks hydrogen bonds before increasing kinetic energy, aiding in temperature regulation in organisms.

Solubility and Mixtures

Solutions and Mixtures

Water is referred to as a universal solvent because it allows many substances to dissolve, making it crucial for biological reactions. Types of mixtures include:

  • Suspensions: Particles that settle unless mixed.

  • Colloids: Particles that remain dispersed but can appear cloudy.

  • Solutions: Homogeneous mixtures where solutes are dissolved, and not visible.

Hydrophilic and Hydrophobic

Hydrophilic substances (polar molecules and ions) dissolve in water, while hydrophobic substances (nonpolar molecules) do not dissolve, affecting how substances interact in biological systems.

Acids, Bases, and pH

Acids and Bases

  • Acids: Substances that increase H+ concentration in a solution, leading to lower pH values.

  • Bases: Increase OH- concentration or decrease H+ concentration, raising pH values.

  • pH Scale: Measures acidity/basicity from 0 to 14, with 7 being neutral.

Buffers

Buffers are substances that help maintain stable pH levels by accepting or donating H+, crucial in biological systems to ensure enzymatic and metabolic processes function correctly.

Biological Macromolecules

General Characteristics

Biological macromolecules typically contain carbon, hydrogen, and oxygen, and may also include nitrogen, phosphorus, or sulfur. They consist of repeating units, known as polymers made up of monomers.

Lipids

Lipids include triglycerides, phospholipids, and steroids (e.g., cholesterol).

  • Functions of Lipids: Energy storage, forming cell membranes, signaling molecules in hormonal functions.

  • Fatty Acids: Can be saturated (single bonds, solid at room temperature) or unsaturated (double bonds, liquid at room temperature).

Carbohydrates

Carbohydrates consist of monosaccharides (simple sugars), disaccharides, and polysaccharides.

  • Glycogen: The storage form of glucose, primarily found in the liver and muscles, used for energy when needed.

Nucleic Acids

Classes of nucleic acids include DNA and RNA.

  • DNA: Double-stranded, carries genetic information, has deoxyribose sugar and thymine.

  • RNA: Single-stranded, involved in protein synthesis, contains uracil instead of thymine.

  • ATP: The primary energy currency of the cell, consists of adenine, ribose, and three phosphate groups.

Proteins

Proteins are made up of amino acids linked by peptide bonds.

  • Protein Structure: Exists at multiple levels - primary (sequence of amino acids), secondary (formation of alpha-helices and beta-sheets), tertiary (3D shape), and quaternary (multiple polypeptide chains).

  • Diverse Roles of Proteins: Functions include transport, catalysis (as enzymes), structural support, immune protection, and regulation of cellular activities.

Cohesion and Adhesion

Cohesion refers to the attraction between molecules of the same substance. In water, cohesion is primarily due to hydrogen bonding, which causes water molecules to be attracted to one another. This phenomenon contributes to water's high surface tension, allowing it to resist external force and enabling small objects to float on its surface. Cohesion is crucial in various biological processes, such as the movement of water in plants, where it helps pull water up from roots to leaves through the xylem.

Cohesion has high heat of vaporization and specific high heat

Adhesion, on the other hand, is the attraction between molecules of different substances. This is also influenced by hydrogen bonding in the case of water. Adhesion allows water to cling to other surfaces, which is essential for processes like capillary action. In plants, adhesion helps water molecules adhere to the walls of the xylem vessels, aiding in the upward movement of water and nutrients against gravity. Adhesion is also vital in maintaining moisture on surfaces and in the formation of menisci in liquids when they interact with solid boundaries.

Water readily dissolves other polar molecules

Readily dissolves table salts via adhesion

Both cohesion and adhesion are essential for proper water transport in biological systems and contribute to various physical properties of water that support life.

Temperature significantly impacts both cohesion and adhesion. At higher temperatures, the energy of water molecules increases, which can weaken hydrogen bonds, reducing cohesion and consequently lower surface tension. This reduction may affect small objects' ability to float. In contrast, cooler temperatures enhance hydrogen bonding, increasing cohesion and surface tension. Similarly, adhesion can vary with temperature; warmer water may spread less on surfaces due to decreased adhesive forces, while cooler temperatures can promote stronger adhesion, aiding in processes like capillary action.

Water's ability to dissolve other molecules is a key aspect of its adhesive properties. This capability arises because water is a polar molecule, meaning it has regions of positive and negative charge. When water encounters other polar molecules or ionic compounds, the positive end of water molecules (hydrogens) is attracted to negative ions or regions, while the negative end (oxygen) is attracted to positive ions or regions.

This interaction allows water to effectively surround and interact with solute molecules, facilitating their dissociation and dissolution. Therefore, the adhesive property of water enables it to interact and form solutions with a variety of substances, making it an excellent solvent, often referred to as the "universal solvent." This characteristic is vital for many biochemical processes in living organisms.

Water's high heat of vaporization and high specific heat are primarily related to cohesion due to the strong hydrogen bonds between water molecules.

  • High Heat of Vaporization: This property refers to the amount of energy required to convert water from a liquid to a vapor state. The strong cohesive forces of hydrogen bonds need to be broken before water molecules can escape into the gas phase, which is why it requires a significant amount of heat energy for vaporization. This characteristic is vital in regulating temperature in both the environment and living organisms, as it prevents overheating by allowing for effective cooling through evaporation.

  • High Specific Heat: This indicates that water can absorb a lot of heat energy without experiencing a significant rise in temperature. The cohesive hydrogen bonds help water molecules maintain their arrangement, allowing them to absorb energy while minimizing temperature fluctuation. This property is crucial for maintaining stable temperatures in aquatic environments and for the metabolism in organisms, as it protects cells from extreme temperature changes.

In contrast, adhesion involves the attraction between water and different substances, influencing processes such as capillary action, but it does not directly relate to the energy needed to change the state of water or stabilize its temperature.