Chemistry Foundations for Anatomy & Physiology: Study Notes

Chemistry Comes Alive: Foundations for Anatomy & Physiology

Introduction: The Role of Chemistry in Human Biology

Understanding basic chemistry is essential for grasping the mechanisms of the human body, the nature of disease, and the principles behind medical treatments. This section introduces the importance of chemical principles in anatomy and physiology.

• Chemistry explains how the body functions at the molecular level.

• Disorders and treatments often involve chemical changes or interventions.

• Biological molecules are central to physiological processes.

Goals for Chapter 2

• Understand the chemical makeup of the body.

• Describe atomic structure and chemical properties, including covalent and ionic bonding.

• Use the periodic table to predict bonding behavior of elements.

• Explain hydrogen bonding and its impact on water and biological molecules.

• Define acids, bases, and pH.

• Describe buffers and their role in maintaining pH stability, especially in blood.

• Write and interpret the bicarbonate buffer system and its physiological implications.

• Understand the structure, function, and reactions of the four major types of organic molecules: carbohydrates, lipids, proteins, and nucleic acids.

• Describe DNA replication.

• Identify factors affecting the rate of chemical reactions.

• Explain protein denaturation and its causes.

Atomic Structure and Elements

Structure of the Atom

Atoms are the fundamental units of matter, composed of three major subatomic particles:

• Proton: Positively charged, located in the nucleus.

• Neutron: No charge (neutral), located in the nucleus.

• Electron: Negatively charged, orbits the nucleus.

The number of protons determines the element's identity. For example, hydrogen has 1 proton, helium has 2, etc.

Major Elements of the Human Body

The human body is primarily composed of four elements:

• Oxygen (O): Essential for energy production and found in water and organic molecules.

• Carbon (C): Backbone of organic molecules.

• Hydrogen (H): Involved in acid-base balance and present in all organic molecules.

• Nitrogen (N): Key component of amino acids and proteins.

Lesser elements (e.g., calcium, phosphorus, potassium) are also important and will be introduced as the course progresses.

Concentration of Solutions

Solutions are described by their concentration, which can be expressed as percent (parts per 100) or molarity (moles per liter, M).

• Mole: The amount of substance containing $6 \times 10^{23}$ particles (Avogadro's number).

• Atomic or molecular weight is the sum of the atomic weights of all atoms in a molecule, measured in grams per mole.

Chemical Bonds and Molecular Structure

Types of Chemical Bonds

Atoms combine to form molecules through chemical bonds:

• Ionic Bonds: Formed when electrons are transferred from one atom to another, creating ions (charged particles). Occur between atoms with nearly full or empty outer shells.

• Covalent Bonds: Formed when atoms share electrons. Occur between atoms with half-filled outer shells.

• Hydrogen Bonds: Weak attractions between partially charged regions of molecules, especially important in water and biological molecules.

Electronegativity and Polar Molecules

Some atoms (e.g., oxygen) attract shared electrons more strongly, creating polar molecules with partial charges. This leads to hydrogen bonding, which is crucial for water's properties.

Properties of Water

Unique Properties Due to Hydrogen Bonding

• High heat capacity: Absorbs and releases heat slowly.

• High heat of vaporization: Requires much energy to change from liquid to gas.

• Solvent properties: Dissolves ionic substances and forms hydration layers around charged molecules.

• Reactivity: Participates in hydrolysis and dehydration synthesis reactions.

• Cushioning: Protects organs (e.g., cerebrospinal fluid).

Acids, Bases, and pH

Definitions

• Acids: Proton donors; release $H^+$ ions. Example: $\text{HCl} \rightarrow H^+ + Cl^-$

• Bases: Proton acceptors; release $OH^-$ ions. Example: $\text{NaOH} \rightarrow Na^+ + OH^-$

pH Scale

The pH scale measures hydrogen ion concentration:

• Acidic: pH 0–6.99 (high $H^+$ concentration)

• Neutral: pH 7.00 (equal $H^+$ and $OH^-$)

• Alkaline (Basic): pH 7.01–14 (low $H^+$ concentration)

Most body fluids are slightly basic (blood pH ≈ 7.4). Deviations can be life-threatening.

Buffers and the Bicarbonate Buffer System

Buffers resist changes in pH by absorbing or releasing $H^+$ ions. The major buffer in blood is the bicarbonate buffer system:

• Equation: $H_2O + CO_2 \rightleftharpoons H_2CO_3 \rightleftharpoons H^+ + HCO_3^-$

• This system helps maintain blood pH and is influenced by breathing and metabolic activity.

Organic Compounds in the Body

Carbohydrates

Carbohydrates are the major energy source and building blocks in plants and animals.

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., sucrose, lactose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

Lipids

Lipids are diverse molecules with roles in energy storage, cell membranes, and signaling.

• Neutral fats (triglycerides): Three fatty acids bonded to glycerol.

• Phospholipids: Two fatty acids and a phosphate group; major component of cell membranes.

• Steroids: Four interlocking hydrocarbon rings; includes cholesterol and hormones.

Proteins

Proteins are macromolecules made of amino acids, essential for structure and function.

• Amino acids: Building blocks containing an amino group and a carboxyl group.

• Peptide bonds: Link amino acids via dehydration synthesis.

• Levels of organization:

  • Primary: Amino acid sequence

  • Secondary: Alpha helices and beta sheets (hydrogen bonding)

  • Tertiary: Folding of secondary structures

  • Quaternary: Multiple polypeptide chains

• Fibrous proteins: Structural (e.g., collagen, keratin)

• Globular proteins: Functional (e.g., enzymes, antibodies)

Enzymes and Chemical Reactions

Enzymes are biological catalysts that speed up chemical reactions without being consumed.

• Factors affecting reaction rate: Temperature, concentration, and catalysts.

• Enzyme activity depends on shape and can be affected by pH and temperature.

• Denaturation: Loss of protein structure and function due to extreme conditions.

Nucleic Acids

Nucleic acids store and transmit genetic information.

• DNA (Deoxyribonucleic Acid): Double-stranded helix, found in the nucleus, encodes genetic instructions.

• RNA (Ribonucleic Acid): Single-stranded, involved in protein synthesis (mRNA, tRNA, rRNA).

• Nucleotide: Composed of a nitrogenous base, pentose sugar, and phosphate group.

Adenosine Triphosphate (ATP)

ATP is the cell's primary energy carrier.

• Structure: Adenine base, ribose sugar, three phosphate groups.

• ATP hydrolysis releases energy for cellular work.

• Related molecules: AMP (adenosine monophosphate), ADP (adenosine diphosphate).

HTML Table: Major Elements of the Human Body

Element	Symbol	Role in the Body
Oxygen	O	Energy production, water, organic molecules
Carbon	C	Backbone of organic molecules
Hydrogen	H	Acid-base balance, organic molecules
Nitrogen	N	Amino acids, proteins

Key Equations

• Bicarbonate Buffer System:

$H_2O + CO_2 \rightleftharpoons H_2CO_3 \rightleftharpoons H^+ + HCO_3^-$

• Acid Dissociation:

$\text{HCl} \rightarrow H^+ + Cl^-$

• Base Dissociation:

$\text{NaOH} \rightarrow Na^+ + OH^-$

• Avogadro's Number:

$6 \times 10^{23}$

Summary

• Chemistry underpins all physiological processes.

• Understanding atomic structure, chemical bonds, and molecular interactions is essential for studying anatomy and physiology.

• Water, acids, bases, buffers, and organic molecules are central to maintaining homeostasis and supporting life.