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Atoms, Molecules, and Bonds: Foundations of Chemistry in Anatomy & Physiology

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Atoms, Molecules, and Bonds

Introduction to Chemistry in Anatomy & Physiology

Chemistry is fundamental to understanding physiological processes in the human body. All biological functions, from muscle contraction to nerve signaling, are based on chemical interactions. This section introduces the basic chemical principles essential for Anatomy & Physiology students.

2.1 Matter and Energy

Matter: Definition and States

  • Matter is anything that has mass and occupies space. It can be seen, smelled, and/or felt.

  • States of matter include:

    • Solid: Definite shape and volume.

    • Liquid: Changeable shape, definite volume.

    • Gas: Changeable shape and volume.

Energy: Forms and Properties

  • Energy is the capacity to do work or put matter into motion.

  • Energy exists in two main forms:

    • Kinetic energy: Energy in action.

    • Potential energy: Stored (inactive) energy.

  • Energy can be transformed from potential to kinetic energy (e.g., stored energy released as movement).

Types of Energy in Biological Systems

  • Chemical energy: Stored in bonds of chemical substances.

  • Electrical energy: Results from movement of charged particles.

  • Mechanical energy: Directly involved in moving matter.

  • Radiant (electromagnetic) energy: Travels in waves (e.g., heat, visible light, ultraviolet light, X-rays).

Energy Conversion

  • Energy may be converted from one form to another (e.g., electrical energy to light energy in a lamp).

  • Energy conversion is inefficient; some energy is always lost as heat.

2.2 Atoms and Elements

Elements: The Building Blocks of Matter

  • Elements are substances that cannot be broken down into simpler substances by ordinary chemical methods.

  • Four elements make up 96% of the human body: Oxygen (O), Carbon (C), Hydrogen (H), and Nitrogen (N).

  • The periodic table lists all known elements (currently 118, with 92 occurring naturally).

Periodic table of the elements

Major, Lesser, and Trace Elements in the Human Body

The human body is composed of major, lesser, and trace elements, each with specific biological functions.

Element

Symbol

Approx. % Body Mass

Functions

Oxygen

O

65.0

Component of organic/inorganic molecules; needed for ATP production

Carbon

C

18.5

Component of all organic molecules

Hydrogen

H

9.5

Component of organic molecules; influences pH

Nitrogen

N

3.3

Component of proteins and nucleic acids

Calcium

Ca

1.5

Bone/teeth structure; muscle contraction; nerve impulses; blood clotting

Phosphorus

P

1.0

Bones/teeth; nucleic acids; ATP; phospholipids

Potassium

K

0.4

Major cation in cells; nerve impulses; muscle contraction

Sulfur

S

0.3

Component of proteins

Sodium

Na

0.2

Major cation in extracellular fluids; water balance; nerve impulses

Chlorine

Cl

0.2

Major anion in extracellular fluids

Magnesium

Mg

0.1

Bone; metabolic reactions

Iodine

I

<0.01

Thyroid hormone production

Iron

Fe

<0.01

Hemoglobin; enzymes

Additional info: Trace elements such as zinc, copper, and selenium are required in minute amounts and are often enzyme cofactors.

Atoms: Structure and Subatomic Particles

  • Atoms are the smallest units of an element that retain its properties.

  • Composed of three subatomic particles:

    • Protons (p+): Positive charge, 1 atomic mass unit (amu), located in nucleus.

    • Neutrons (n0): No charge, 1 amu, located in nucleus.

    • Electrons (e-): Negative charge, negligible mass, orbit nucleus.

Particle

Charge

Mass (amu)

Located in Nucleus?

Proton

+1

1

Yes

Neutron

0

1

Yes

Electron

-1

~0

No

Atomic Models

  • Planetary model: Electrons depicted in fixed orbits around nucleus (outdated).

  • Orbital model: Electrons occupy regions of probability (electron cloud) around nucleus (current model).

Two models of the structure of an atom

Electron Distribution and Chemical Properties

  • Chemical behavior depends on the number of electrons in the outermost shell (valence shell).

  • Atoms with unpaired electrons in the valence shell are more reactive.

Atomic structure of the three smallest atoms

Identifying Elements: Atomic Number, Mass Number, and Isotopes

  • Atomic number: Number of protons in the nucleus (also equals number of electrons in a neutral atom).

  • Mass number: Total number of protons and neutrons in the nucleus.

  • Isotopes: Atoms of the same element with different numbers of neutrons (same atomic number, different mass number).

Atomic number and atomic mass explanation Isotopes of hydrogen

Radioisotopes and Their Uses

  • Radioisotopes are unstable isotopes that decay, emitting energy (radioactivity).

  • Used in biological research and medicine (e.g., PET scans for cancer detection).

  • Radioactivity can damage living tissue but is also used therapeutically to destroy cancer cells.

PET scan showing cancerous throat tissue

2.3 Combining Matter: Molecules and Compounds

Molecules and Compounds

  • Molecule: Two or more atoms bonded together (can be the same or different elements).

  • Compound: A molecule containing two or more different kinds of atoms (e.g., H2O, NaCl).

  • Molecules with only one type of atom are not compounds (e.g., O2).

Emergent properties of a compound: sodium and chlorine form sodium chloride

Example: Sodium (Na, a reactive metal) and chlorine (Cl, a poisonous gas) combine to form sodium chloride (NaCl, table salt), which is safe and essential for life.

Concept Check

Review and answer questions related to atomic structure, elements, and chemical bonds to reinforce your understanding of these foundational concepts.

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