Biology: Atomic Structure, Chemical Bonds, and Microscopy Techniques

Chemistry

The study of interactions between atoms and molecules.

Atom

The smallest unit of matter that cannot be subdivided into smaller substances without losing its properties.

Molecule

A structure formed when atoms interact to combine.

Compound

A molecule that contains two or more kinds of atoms.

Water

A compound consisting of two atoms of hydrogen and one atom of oxygen (H2O).

Atomic number

The number of protons in the nucleus of an atom.

Atomic mass

The total number of protons and neutrons in an atom.

Electron shells

Arrangements of electrons corresponding to different energy levels.

Electron configuration

The arrangement of electrons in electron shells.

Innermost shell

The electron shell that can hold up to 2 electrons.

Second shell

The electron shell that can hold up to 8 electrons.

Third shell

The electron shell that can hold up to 8 electrons if it is the outermost shell.

Valence shell

The outermost shell of an atom that determines its reactivity with other atoms.

Valence

The number of missing or extra electrons in the outermost shell, representing the combining capacity of an atom.

Chemical bonds

Attractive forces formed by the valence electrons of combining atoms.

Hydrogen atom structure

An H atom contains a nucleus and one electron shell with one electron and one unfilled space.

Carbon atom structure

A C atom contains a nucleus and two electron shells, with 2 electrons in the innermost shell and 4 electrons in the outermost shell.

Nitrogen atom structure

An N atom contains a nucleus and two electron shells, with 2 electrons in the innermost shell.

Ionic Bond

An attraction between ions of opposite charge that holds them together to form a stable molecule. Weaker ionic bonds are important in biochemical reactions such as antigen-antibody reactions.

Covalent Bond

A bond formed by two atoms that share one or more pairs of electrons. Covalent bonds are stronger and more common in organisms than ionic bonds. They are very common and are responsible for holding together the atoms of most molecules in organisms.

Hydrogen Bond

A relatively weak bond in which a hydrogen atom that is covalently bonded to one oxygen or nitrogen atom is attracted to another oxygen or nitrogen atom. Hydrogen bonds do not bind atoms into molecules, but serve as bridges between different molecules or different portions of the same molecule, for example, within proteins and nucleic acids, to stabilize the structures.

Chemical Reaction

A process in which one or more substances (reactants) are transformed into one or more different substances (products) through the breaking and forming of chemical bonds.

Endergonic Reaction

A reaction that absorbs more energy than it releases.

Exergonic Reaction

A reaction that releases more energy than it absorbs.

Anabolism

The synthesis of molecules in a cell.

Catabolism

Includes the decomposition reactions in a cell.

Hydrogen Bonding in Water

A water molecule can form hydrogen bonds with up to four nearby water molecules.

Water Characteristics

Attributed to its polarity and hydrogen-bonding, including being an excellent temperature buffer and solvent.

Solutes in Solutions

Polar and ionic substances undergo dissociation in water, forming solutes in solutions.

Surface Tension

Created by the hydrogen bonding between water molecules.

Sodium Chloride in Water

Describes how water acts as a solvent for sodium chloride (NaCl).

Oxygen Atom Structure

The O atom contains a nucleus and two electron shells, with the nucleus depicted as a large filled red circle labeled O.

Outer Electron Shell

The outermost shell has two single electrons and two pairs of electrons depicted as filled black circles.

Carbohydrates

Cellular energy sources and components of cell structures.

Lipids

Nonpolar molecules that are insoluble in water, serving as primary structural components of cell membranes and energy storage.

Proteins

Polymers of amino acid building blocks that are essential for cell structure and function.

Nucleic Acids

Molecules that carry genetic information, including DNA and RNA.

Monosaccharides

The simplest form of carbohydrates, consisting of single sugar molecules.

Disaccharides

Carbohydrates formed from two monosaccharides.

Polysaccharides

Carbohydrates that are made up of long chains of monosaccharide units.

Fats

Lipids that contain glycerol and fatty acids.

Phospholipids

Lipids composed of glycerol, two fatty acids, and a phosphate group; they are amphipathic.

Steroids

A type of lipid characterized by a carbon skeleton with four fused rings; cholesterol is an example.

Amino Acids

Building blocks of proteins, with 20 different types available.

Denaturation

The process that leads to the loss of shapes and functions of proteins.

Enzymes

Proteins that speed up chemical reactions.

Transport Proteins

Proteins that move chemicals across membranes.

Receptor Proteins

Proteins embedded in the cell membrane that bind to specific external or internal signals.

Flagella

Structures that aid in the movement of cells.

Exotoxins

Some bacterial toxins that can be proteins.

Cytoskeleton-like Elements

Structural components of cells that provide support and shape.

Nucleotides

The building blocks of nucleic acids, consisting of a five-carbon sugar, a phosphate group, and a nitrogen-containing base.

Adenosine Triphosphate (ATP)

The principal energy-carrying molecule of all cells, storing energy in high-energy bonds.

Micrometers

Units of measurement for microorganisms, where 1 μm = 10^-6 m.

Nanometers

Units of measurement for microorganisms, where 1 nm = 10^-9 m.

Total Magnification

The product of the objective lens and ocular lens in a microscope.

Resolution

The ability of lenses to distinguish two points or fine detail and structure.

Limit of Resolution

The smallest distance at which two points can be distinguished, which is 0.2 μm (200 nm) for a compound light microscope.

Resolving Power

Calculated as λ/2NA, where λ is the wavelength and NA is the numerical aperture of the lens.

Refractive index

Measure of the light-bending ability of a medium.

Immersion oil

Used to keep light from refracting.

Fluorescence Microscopy

Uses UV (short wavelength) light source of illumination.

Fluorescent substances

Absorb UV light and emit longer wavelength (visible) light.

Fluorescent dyes

Used to stain cells that do not naturally fluoresce.

Fluorochrome

A fluorescent dye that can stain cells bright yellow, green, or orange against a dark field of view.

Fluorescent-antibody (FA) technique

Also known as immunofluorescence; uses antibodies specific for a type of microbial pathogen tagged with a fluorochrome.

Pathogenic microbe detection

Fluorescent antibodies adhere to the microbe, causing it to fluoresce when viewed with fluorescence microscopy.

Electron Microscopy

Uses electrons instead of light for imaging.

Transmission Electron Microscopy

A beam of electrons passes through ultrathin sections of a specimen.

Scanning Electron Microscopy

An electron gun produces a beam of electrons that scans the surface of an entire specimen.

Magnification of Transmission Electron Microscopy

10,000-10,000,000x.

Limit of resolution for Transmission Electron Microscopy

0.2 nm.

Magnification of Scanning Electron Microscopy

1000-500,000x.

Limit of resolution for Scanning Electron Microscopy

0.5 nm.

Simple stain

Highlights the entire microorganism to visualize cell shapes and structures.

Differential Stains

Used to distinguish between bacteria.

Special Stains

Used to distinguish parts of microorganisms.

Gram stain

Classifies bacteria into Gram-positive or Gram-negative.

Acid-fast stain

Used for the identification of Mycobacterium and Nocardia.

Examples of Special Stains

Capsule stain, Endospore stain, Flagella stain.