Untitled Quiz

Chapter 2: Chemical Principles

• This chapter covers the fundamental chemical principles essential for understanding microbiology.
• Objectives include exploring the structure of atoms, chemical bonding, reactions, important biological molecules (both inorganic and organic), and the role of chemistry in microbiology.
• Key vocabulary includes atom, molecules, electrons, neutrons, atomic number, atomic weight, element, isotopes, electron shell, energy levels, and valence.
• Chemistry is vital in microbiology as it underpins cellular structure and function. Many diseases have molecular-level effects.
• Understanding the infection process requires fundamental chemistry knowledge.
• Life on Earth relies on chemical reactions. Cell and tissue construction and function are part of this process and play a role in infection.
• The biological level of organization includes atoms, molecules, cells, tissues, organs, organ systems, and organisms.

Atomic Structure

• Elements consist of only one type of particle (atoms).
• Atoms contain subatomic particles: electrons, protons, and neutrons.
• Protons and neutrons are found in the atomic nucleus, which is the central part of the atom.
• Electrons orbit the nucleus in orbitals (3-D space).
• Electron energy refers to the energy levels within these orbitals.
• In a neutral atom, the number of electrons equals the number of protons.
• Electron shells (energy levels) have a limited capacity for electrons: the first shell holds 2, the second 8, and subsequent shells have increasing capacities.
• Chemical properties of an atom are largely determined by the valence electrons (the outermost ring).
• Atomic number is the fixed number of protons in the atomic nucleus (e.g., hydrogen (H) or oxygen (O)).
• Atomic weight is mostly the mass of protons plus neutrons (atomic mass unit (AMU) or Dalton), with the mass of electrons being negligible in comparison.

Chemical Elements

• Chemical elements are pure substances with atoms of the same number of protons.
• Each element has its own unique chemical symbol.
• Critical elements in living organisms include hydrogen, carbon nitrogen, and oxygen.
• Elements can have isotopes; these are atoms of the same element that have a different number of neutrons. This results in a different atomic weight, but the chemical behavior is similar.
• Radioactive isotopes are unstable and break down, emitting radiation, into other elements.

Chemical Bonds

• Atoms form molecules through chemical bonds.
• The objective of forming these bonds is to achieve a full valence shell.
• Bond energy is the energy needed to break a bond.
• Atoms form bonds in three ways: gaining, losing, or sharing electrons.
• Types of chemical bonds include:
  • Covalent bonds: atoms share electron pairs. This is a stronger type of bond compared to ionic bonds. Molecules are formed through these bonds.
  • Ionic bonds: atoms gain or lose electrons, becoming ions (with electric charges, either positive or negative).
  • Hydrogen bonds: weaker bonds formed by attraction between a partially negative charge and a hydrogen atom that is covalently bonded to oxygen or nitrogen.
• These bonds are crucial to the structures and properties of molecules in biological systems.

Chemical Reactions

• Chemical reactions involve the making or breaking of chemical bonds.
• The total number of atoms remains the same.
• Chemical reactions re-arrange atoms into new molecules with different properties.
• Reactions require energy (activation energy) to start.
• Different types of chemical reactions are seen in living systems, such as:
  • Synthesis reactions: when smaller molecules/particles combine to form a larger molecule
  • Decomposition reactions: larger molecules break down into smaller ones.
  • Exchange reactions: involve a combination of both synthesis and decomposition.
• Reactions can be classified as endothermic (absorbing energy) or exothermic (releasing energy).

Important Biological Molecules

• Organic compounds typically contain carbon and hydrogen atoms and are generally structurally complex. Examples are carbohydrates, lipids, proteins, nucleic acids and ATP
• Inorganic compounds usually lack carbon; they're typically small and simple molecules. Water is a key inorganic molecule.

Water

• Water is a vital inorganic molecule. It has special properties essential for life including its polarity.
• Hydrogen bonds between water molecules lead to unique physical and chemical properties crucial to life.
• Water's polarity makes it a good solvent.
• Water's properties affect chemical reactions within living organisms.

Inorganic Molecules: Acids, Bases, and Salts

• Acids: dissociate into H+ (protons) and anions.
• Bases: dissociate into OH- (hydroxide) ions.
• Salts: dissociate into cations and anions, neither of which is H+ or OH-.

Acid-Base Balance (pH)

• Maintaining a stable pH is essential for organisms.
• Changes in [H+ ] (hydrogen ion) concentration significantly impact enzyme activity and organism survival
• Optimal pH ranges for most organisms are around 6.5 - 8.5

Macromolecules

• Macromolecules are large molecules made up of repeating small units (monomers) bonded together through covalent bonds. Key examples include carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

• Carbohydrates are sugars and starches.
• They are composed of carbon, hydrogen, and oxygen.
• Monosaccharides (simple sugars) can contain from 3 to 7 carbons; important ones include glucose, ribose, and 2-deoxyribose.
• Disaccharides are formed by joining two monosaccharides through dehydration synthesis. Hydrolysis reactions break them apart.
• Polysaccharides are long chains of monosaccharides. Important examples include starch, glycogen, cellulose, and chitin.

Lipids

• Lipids include fats, oils, and other water-insoluble molecules.
• Key components of lipids include glycerol and fatty acids.
• Types include simple lipids (mono, di, and triglycerides - formed by dehydration synthesis from the molecule glycerol and 3 fatty acids), complex lipids (like phospholipids) and steroids.
• Saturated fatty acids contain only single C-C bonds.
• Unsaturated fatty acids have at least one C=C double bond. These can be cis or trans.
• Phospholipids are major components of cell membranes.

Proteins

• Proteins are made up of amino acids held together by peptide bonds.
• Amino acids have an amino group (-NH2), a carboxyl group (-COOH), and a variable side chain (R group).
• Proteins have different levels of structure: primary, secondary, tertiary, and quaternary.
• Conjugated proteins contain amino acids and other components like carbohydrates or lipids.

Nucleic Acids

• Nucleic acids are polymers of nucleotides.
• Nucleotides consist of a five-carbon sugar (either ribose or deoxyribose), a phosphate group, and a nitrogen-containing base.
• DNA (deoxyribonucleic acid) is essential for storing genetic information. It has a double helix structure with base pairs: adenine-thymine and guanine-cytosine.
• RNA (ribonucleic acid) is essential for protein synthesis. It is single-stranded and has uracil in place of thymine, with base pairs: adenine-uracil and guanine-cytosine

Adenosine Triphosphate (ATP)

• ATP is a crucial energy carrier molecule in cells.
• ATP stores energy released from chemical reactions.
• ATP releases energy by breaking off phosphate groups and releasing useful energy for cell work.