Chemistry Basics: Elements and Atoms

• Chemistry is the study of matter, while biochemistry focuses on the chemistry of living organisms
• Matter occupies space and has mass, existing as solids, liquids, or gases

Elements and Atoms

• An atom is the smallest particle of an element
• An element is a basic chemical substance composed of atoms
• Elements are represented by one or two-letter symbols on the Periodic Table
• There are 92 naturally occurring elements, with about 26 created in the laboratory
• Oxygen (O), carbon (C), hydrogen (H), and nitrogen (N) are the most abundant naturally occurring elements in the human body

Atomic Structure

• Atoms contain three subatomic particles: protons, neutrons, and electrons
• Protons are positively charged particles located in the nucleus with a mass of 1 atomic mass unit (amu)
• Neutrons are neutral particles in the nucleus with a mass of 1 amu
• Electrons are negatively charged particles that revolve around the nucleus and have negligible mass
• Atoms are neutral because they contain an equal number of protons and electrons
• The atomic number (A#) represents the number of protons in an atom's nucleus
• Atomic weight (AW) is approximately equal to the number of protons plus neutrons in the nucleus

Isotopes

• Isotopes are atoms of an element with the same atomic number but different atomic weights due to varying numbers of neutrons
• Some isotopes have stable nuclei, while others have unstable nuclei that break apart, releasing radioactive energy

Molecules and Compounds

• Molecules form when two or more atoms combine
• A molecular formula indicates the number and types of atoms in a molecule
• Molecules of an element result when atoms of the same element combine (e.g., O2, N2)
• Compounds form when atoms of different elements combine (e.g., H2O, C6H12O6)

Bonding of Atoms

• Electrons arrange themselves in orbits or shells around the nucleus
• The first shell holds up to 2 electrons, while the second and third shells can each hold up to 8 electrons
• Atoms react with each other to fill their outermost shell
• The outermost shell's electrons are valence electrons, and it is called the valence shell
• Atoms form bonds to fill their valence shell

Ionic Bonds

• Ions form when atoms gain or lose electrons to fill their valence shell
• Cations are positively charged ions, such as Na+
• Anions are negatively charged ions, such as Cl-
• Ionic bonds result from the attraction between oppositely charged ions
• Table salt (NaCl) is an example of a compound held together by ionic bonds

Covalent Bonds

• Covalent bonds occur when atoms share electrons equally
• Covalent bonds are very strong
• Molecular hydrogen (H2) and molecular oxygen (O2) are examples of covalent bonds
• Polar bonds are covalent bonds with unequal electron sharing
• Polar molecules have one end with a slight positive charge and the other with a slight negative charge
• H2O (water) is an example of a polar molecule

Hydrogen Bonds

• Hydrogen bonds are weak bonds between a hydrogen atom covalently bonded to another atom and another atom
• Hydrogen bonds are vital for interactions between water molecules and DNA chains
• Hydrogen bonds are easily broken and reformed

Chemical Reactions

• Chemical reactions occur when chemical bonds are formed, rearranged, or broken
• Synthesis reactions involve building bigger molecules from smaller building blocks, which is constructive and anabolic (e.g., monomers -> polymer)
• Decomposition reactions involve breaking a bigger molecule down into smaller components, which is destructive and catabolic (e.g., polymer -> monomers)
• Exchange reactions involve both degradation and synthesis
• Reversible Reactions: products can be changed back to reactants

Synthesis Reactions

• Synthesis involves the building of a large molecule from smaller building blocks (monomers)
• It includes constructive, anabolic reactions
• Bonds are formed which now hold chemical energy
• Water is usually removed from building blocks to form a bond (dehydration)

Degradation Reactions

• Degradation involves the breakdown of a polymer into individual monomers
• Includes breakdown, digestive, decomposition, and catabolic reactions
• Bonds are broken
• Energy is released when the bond is broken
• Water is required to break the bond (hydrolysis)

Acids, Bases, and Salts

• Electrolytes are charged particles (ions) crucial for muscle contraction, nerve impulses, and bone growth
• Electrolytes must be maintained within a narrow range in the blood and tissues for homeostasis
• When acids are dissolved in water, the ions dissociate into a hydrogen cation (H+) and an anion (negative ion)
• Bases dissociate (ionize) when dissolved in water to form a hydroxide anion (OH-) and a cation (positive ion)
• Salts dissociate into ions when dissolved in water, forming an anion and a cation

Acid and Base Concentrations

• The relative concentrations of hydrogen ions and hydroxyl ions determine the body's pH
• Physiologic pH is 7.4
• pH < 7.4 = acidosis (lethal below 7.0)
• pH > 7.4 = alkalosis (lethal above 7.8)
• Buffers prevent abrupt pH changes, usually weak acids, and function by donating H+ when needed and accepting H+ when in excess
• The carbonic acid (H2CO3) buffering system is an example

Chemical Constituents of Cells

• Living organisms are composed of both inorganic and organic matter

Inorganic Substances

• Inorganic substances are small compounds that do not contain carbon and hydrogen (Ex: water, oxygen, carbon dioxide, salts)
• Water is a polar molecule that demonstrates hydrogen bonding, making it an excellent solvent
• Polar substances and ionic compounds dissolve or break apart in water
• Water participates in chemical reactions such as dehydration (synthesis) and hydrolysis (decomposition)
• It acts as a temperature buffer and provides a cooling mechanism through high heat of vaporization
• Examples of inorganic salts includes bicarbonate ions (buffers), calcium ions (development and blood clotting), and potassium ions (cell membrane potential)

Organic Substances

• Organic substances contain carbon and hydrogen
• Small molecules (monomers) connect through covalent bonds to form macromolecules or polymers
• Water plays a role in the formation and breakage of bonds between monomers through dehydration synthesis and hydrolysis

Carbohydrates

• Carbohydrates (sugars) contain carbon, hydrogen, and oxygen in a 1:2:1 ratio
• Monosaccharides (glucose, fructose, galactose) are the building blocks (monomers) of carbohydrates
• Disaccharides (maltose, lactose, sucrose) consist of two monosaccharides
• Polysaccharides (starch, glycogen) are composed of many glucose molecules which function as energy storage

Lipids

• Lipids contain carbon, hydrogen, and oxygen, but less oxygen compared to carbohydrates
• Fats (triglycerides) are composed of glycerol and three fatty acids
  • Saturated fats feature single bonds between carbons, are solid, and mainly derive from animals
  • Unsaturated fats contain one or more double bonds, are liquids (oils), and mostly come from plants
• "Trans" fats are unsaturated fats solidified artificially and include margarine
• Phospholipids, consisting of a triglyceride with a phosphate group substitution, are essential for cell membranes
• Steroids, such as cholesterol, are composed of four interconnected carbon rings and affects cell membranes and chemical messengers (hormones)

Proteins

• Proteins are composed of amino acid monomers
• Amino acids contains an amino group, carboxyl group, and an R-group determining their type
• Amino acids create polymers through dehydration synthesis linked by peptide bonds
  • The amino acids chains varies:
  • peptide = 2-100 amino acids
  • polypeptide = 100-thousands of amino acids without a function
  • protein = 100-thousands of amino acids with a specific function
• Proteins helps to create structure (keratin), facilitate transport (hemoglobin), act as chemical messengers (hormones/neurotransmitters), and enable movement (actin/myosin)

Protein Structure

• Primary (1°) structure refers to the sequence of amino acids
• Secondary (2°) structure comes from twisting of the amino acid chain, and is a result of hydrogen bonding
• Tertiary (3°) structure comes from folding of the amino acid chain, which is a result of ionic bonds, disulfide bridges, and hydrophobic interactions
• Quaternary (4°) structure involves interactions between different amino acid chains
• Proteins must be in a complete 4 degree structure to be functional

Nucleic acids

• Nucleic acids are composed of nucleotide monomers
• There are three parts that makes up a nucleotide consisting of pentose sugar, nitrogenous base, and phosphate group

Types of Nucleic Acids

• DNA contains:
• deoxyribose sugar
• bases adenine (A), thymine (T), cytosine (C), and guanine (G)
• Double stranded strands are held together by hydrogen bonds a. A complements T (2 hydrogen bonds) b. C complements G (3 hydrogen bonds)
• Double helix (ladder is twisted)
  • Function = genetic material (i.e. genes, chromosomes) •It directs protein synthesis
• DNA contains all necessary information needed to sustain and reproduce life!
• RNA contains:
• ribose
• bases A,G,C, and uracil (replaces thymine)
• Single stranded
• It transports DNA code during protein synthesis