NamBagPP2

Matter and Elements

Introduction to Chemistry in Biology

Chemistry is fundamental to understanding biological processes, as all living things are composed of matter and energy. Matter consists of elements, which are the basic building blocks of all substances.

• Chemistry: The study of matter and energy.

• Matter: Anything that has mass and occupies space; composed of elements.

• Energy: The power to do work.

• Elements: Fundamental (pure) forms of matter that cannot be broken down into simpler substances.

• Periodic Table: A chart listing all known elements in order of increasing atomic number.

Atoms: The Smallest Functional Units

Atomic Structure

Atoms are the smallest units of an element that retain its properties. They consist of a central nucleus and surrounding shells.

• Nucleus: Contains protons (positive charge, have mass) and neutrons (no charge, have mass).

• Shells: Surround the nucleus and contain electrons (negative charge, very small mass).

Atomic Symbol: One or two letters representing an element (e.g., Na for sodium, O for oxygen).

Atomic Number: Number of protons in the nucleus; unique for each element.

Atomic Mass: Approximately equal to the number of protons plus neutrons.

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

Isotopes and Radioisotopes

Isotopes

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different atomic masses.

• Stable Isotopes: Do not change over time.

• Radioisotopes: Unstable isotopes that emit energy (radiation) and can be used in scientific and medical applications.

Applications: Carbon-14 dating for ancient biological materials, diagnostic imaging, cancer treatment, and power supply for implants.

Additional info: Carbon-14 is not used for dating fossils directly; it is used for dating biological materials less than 100,000 years old.

Free Radicals

Unpaired Electrons and Biological Impact

Free radicals are atoms or molecules with one or more unpaired electrons, making them highly reactive.

• Can damage proteins and DNA.

• May accelerate cellular aging.

Molecules and Chemical Bonds

Formation of Molecules

Molecules are stable associations between two or more atoms, which may be of the same or different elements.

• Examples: Oxygen molecule (O2), Water (H2O), Table salt (NaCl).

Types of Chemical Bonds

Atoms interact to fill their outermost electron shells, forming chemical bonds that hold them together.

• Covalent Bonds: Atoms share electrons; very strong bonds.

• Ionic Bonds: Attraction between oppositely charged ions.

• Hydrogen Bonds: Weak attractions between polar molecules.

Bond Type	Description	Examples
Covalent	Atoms share electrons to fill outer shells	H2, O2, H2O
Ionic	Attraction between oppositely charged ions	NaCl
Hydrogen	Weak attraction between polar molecules	Between water molecules

Covalent Bonds

• Nonpolar Covalent Bonds: Electrons shared equally (e.g., H2, O2, CH4).

• Polar Covalent Bonds: Electrons not shared equally (e.g., H2O).

Ionic Bonds

• Ion: Electrically charged atom or molecule.

• Cation: Positively charged ion (loses electrons).

• Anion: Negatively charged ion (gains electrons).

• Example: Na+ and Cl- form NaCl.

Hydrogen Bonds

• Occur between polar molecules with uneven charge distribution.

• Important for the properties of water and biological molecules.

Elements Essential for Life

Major Elements in Living Organisms

Although nearly 100 elements occur naturally, about 99% of body weight consists of six elements:

• Oxygen (O)

• Carbon (C)

• Hydrogen (H)

• Nitrogen (N)

• Calcium (Ca)

• Phosphorus (P)

Element	Symbol	Function in Life
Oxygen	O	Component of water, essential for respiration
Carbon	C	Backbone of organic molecules
Hydrogen	H	Component of water and organic molecules
Nitrogen	N	Component of proteins and nucleic acids
Calcium	Ca	Constituent of bone, essential for muscle contraction
Phosphorus	P	Component of nucleic acids and energy storage molecules

Water: The Biological Solvent

Properties of Water

Water is vital for life due to its unique properties:

• Excellent solvent for polar molecules and ions.

• Liquid at body temperature, facilitating transport.

• Absorbs and holds heat energy, helping regulate body temperature.

• Participates in essential chemical reactions.

Hydrophilic and Hydrophobic Substances

• Hydrophilic: Polar molecules attracted to water; dissolve easily.

• Hydrophobic: Nonpolar molecules; do not interact or dissolve in water.

Water in the Body

• About 60% of body weight is water.

• Main constituent of intracellular and extracellular spaces.

Water and Temperature Regulation

• Absorbs heat with only modest temperature increase.

• Evaporative cooling helps the body lose excess heat.

Water in Chemical Reactions

• Synthesis: Produces water molecules (e.g., dehydration synthesis).

• Breakdown: Consumes water molecules (e.g., hydrolysis).

Acids, Bases, and pH

Hydrogen Ions and pH

Hydrogen ions (H+) are crucial for many biological processes. The concentration of H+ in solution determines its acidity or alkalinity, measured by the pH scale.

• Acid: Molecule that donates H+; increases H+ concentration.

• Base: Molecule that accepts H+; decreases H+ concentration.

• pH Scale: Ranges from 0 (acidic) to 14 (basic); pH 7 is neutral.

$\text{pH} = -\log_{10}[\text{H}^+]$

• Higher [H+] = lower pH (more acidic).

• Lower [H+] = higher pH (more basic).

Buffers

• Minimize changes in pH.

• Help maintain stable pH in body fluids.

• Carbonic acid and bicarbonate are important buffer pairs.

$\text{HCO}_3^- + \text{H}^+ \rightleftharpoons \text{H}_2\text{CO}_3$

Organic Molecules

Carbon-Based Molecules

Organic molecules are made primarily of carbon and hydrogen, often with other elements. Carbon's ability to form four covalent bonds allows for complex structures.

• Can form single, double, or triple bonds.

• Can create linear, branched, or ring-shaped molecules.

Types of Organic Molecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Macromolecules: Synthesis and Breakdown

Dehydration Synthesis and Hydrolysis

• Dehydration Synthesis: Removes water to link monomers into polymers; requires energy.

• Hydrolysis: Adds water to break polymers into monomers; releases energy.

Carbohydrates

Structure and Function

Carbohydrates are used for energy and structural support. General formula: Cn(H2O)n.

• Energy source for most organisms.

• Structural support (e.g., cellulose in plants).

Types of Carbohydrates

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

• Disaccharides: Two monosaccharides linked (e.g., sucrose, maltose, lactose).

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

Lipids

Structure and Function

Lipids are hydrophobic molecules important for energy storage, cell membrane structure, and hormones.

• Triglycerides: Glycerol + 3 fatty acids; energy storage.

• Phospholipids: Glycerol + 2 fatty acids + phosphate; main component of cell membranes.

• Steroids: Four carbon rings; includes cholesterol and hormones (estrogen, testosterone).

Proteins

Structure and Function

Proteins are polymers of amino acids, joined by peptide bonds. Their function depends on their structure.

• Amino Acids: 20 types; each has an amino end, carboxyl end, and R group.

• Peptide Bond: Joins amino acids via dehydration synthesis.

• Polypeptide: Chain of 3-100 amino acids.

• Protein: Polypeptide longer than 100 amino acids with complex structure and function.

Levels of Protein Structure

• Primary: Amino acid sequence; stabilized by peptide bonds.

• Secondary: Alpha helix or beta pleated sheets; stabilized by hydrogen bonds.

• Tertiary: Three-dimensional shape; stabilized by covalent, ionic, hydrophobic, and hydrogen bonds.

• Quaternary: Two or more polypeptide chains joined.

Denaturation

• Permanently disrupts protein structure.

• Caused by high temperature or pH changes.

• Leads to loss of biological function.

Enzymes

Biological Catalysts

Enzymes are proteins that speed up chemical reactions without being consumed. They are essential for life and homeostasis.

• Shape and activity depend on temperature, pH, ion concentration, and inhibitors.

Nucleic Acids

Genetic Information Storage

Nucleic acids are polymers of nucleotides, storing and transmitting genetic information.

• DNA (Deoxyribonucleic Acid): Double-stranded; contains deoxyribose and bases (adenine, guanine, cytosine, thymine).

• RNA (Ribonucleic Acid): Single-stranded; contains ribose and bases (adenine, guanine, cytosine, uracil).

Information Flow: DNA → RNA → Proteins

Nucleotide Structure

• Five-carbon sugar (deoxyribose or ribose)

• Nitrogenous base

• Phosphate group

ATP: The Energy Carrier

Adenosine triphosphate (ATP) is the universal energy source for cells. Energy is stored in the bonds between phosphate groups.

$\text{ATP} \rightarrow \text{ADP} + P_i + \text{energy}$

ATP can be replenished by reattaching phosphate using energy from cellular reactions:

$\text{ADP} + P_i + \text{energy} \rightarrow \text{ATP}$

Additional info: These foundational chemistry concepts are essential for understanding the molecular basis of anatomy and physiology, including cellular structure, metabolism, and genetic inheritance.