Module 1: Basic Chemistry in Biology — Atom Structure and Bonds

Flashcards covering atom structure, elements, molecules, isotopes, bonds, water properties, acids/bases, pH, and buffers.

What subatomic particles compose atoms and what are their charges?

Protons (positive), neutrons (neutral), and electrons (negative).

Where do electrons reside relative to the nucleus, and how many electrons can each orbital hold?

Electrons occupy space around the nucleus; each orbital can hold 2 electrons.

How are electron shells organized and what are the capacities of the first three shells?

Electron shells are levels around the nucleus: 1st shell holds 2 electrons, 2nd shell holds 8, 3rd shell holds up to 18.

What is a valence shell and what does its electron count determine?

The outermost shell; its electron count determines reactivity. A full valence shell is stable and nonreactive.

What is an element and which four major elements make up about 96% of the body?

An element is a substance that cannot be divided into different substances and is composed of one type of atom. The four major elements are Oxygen (O), Nitrogen (N), Hydrogen (H), and Carbon (C).

Name the major minerals in the body.

Calcium (Ca), Potassium (K), Sulfur (S), Sodium (Na), Magnesium (Mg), Phosphorus (P).

Name trace elements essential for health.

Iron (Fe), Zinc (Zn), Copper (Cu), Manganese (Mn), Fluoride (F).

Define a molecule and give two examples.

A molecule is made of two or more atoms. Examples: H2O (2 Hydrogen, 1 Oxygen) and O2 (two Oxygen atoms).

Define a compound and describe its relationship to molecules.

A compound is a combination of two or more different elements. All compounds are molecules, but not all molecules are compounds; e.g., water is both a molecule and a compound, CO2 is a molecule and a compound.

What is an isotope?

Atoms with the same number of protons but different mass numbers (varying neutrons); same element, different neutrons; some isotopes emit radioisotopes.

What forms chemical bonds between atoms, and what are the possible ways electrons can participate in bonding?

Chemical bonds form to fill outer energy levels; electrons can be shared, donated, or borrowed to form molecules or compounds.

Describe ionic bonds and how ions form.

Ionic bonds form when one atom donates an electron to another. The donor becomes a cation (positive, e.g., Na+); the acceptor becomes an anion (negative, e.g., Cl-); opposite charges attract.

What are cations and anions?

Cations are positively charged ions; anions are negatively charged ions.

Describe covalent bonds.

formed when atoms share electrons; energy levels overlap; no ions are formed; bonds can be single, double, or triple and are generally strong.

How are single, double, and triple covalent bonds represented, and what does a bar indicate?

Single, double, or triple bonds correspond to sharing one, two, or three pairs of electrons. A bar is used to denote each shared pair (e.g., H–H, O=O).

What is a hydrogen bond and why is it important?

A weak attraction between a hydrogen atom and another electronegative atom (O or N). It’s crucial for water's properties, surface tension, and the shaping of proteins and DNA.

What is the significance of water in the body?

Water makes up about two-thirds of body weight; it’s a great solvent, participates in reactions (dehydration synthesis and hydrolysis), and has a high heat capacity.

What is the difference between hydrophilic and hydrophobic molecules?

Hydrophilic (polar) molecules mix with water (e.g., ions, glucose). Hydrophobic (nonpolar) molecules do not mix with water (e.g., fats, oils, cholesterol, triglycerides).

Define acids, bases, and pH in simple terms.

Acids dissociate to release H+ ions; strong acids dissociate completely (e.g., HCl); weak acids dissociate partially (e.g., H2CO3). Bases dissociate to release OH– ions; strong bases dissociate completely (e.g., NaOH); weak bases partially (e.g., NH3 in water). The pH scale measures free H+ relative to OH–; 7 is neutral; below 7 is acidic; above 7 is basic.

What is a neutralization reaction?

When an acid and a base react to form water and a salt, effectively neutralizing each other.

What is a pH scale and what do the values indicate?

A logarithmic scale measuring the concentration of free hydrogen ions vs. hydroxide ions; 7 is neutral; below is acidic; above is basic.

What is a buffer and what is its role in the body?

A system that stabilizes pH by binding or releasing hydrogen ions; many buffers help maintain body pH within a narrow range.

What are dehydration synthesis and hydrolysis?

Dehydration synthesis joins monomers by removing water; hydrolysis breaks bonds by adding water; both are common in aqueous (water-containing) reactions.

What happens to ionic compounds in water in terms of electrolytes?

Ionic compounds dissociate in water into ions, forming electrolytes that can conduct electricity.

What is an atom’s valence and why is it important?

Valence refers to the outer shell electron count and determines bonding behavior and reactivity.

What is an ion, and how does it differ from a neutral atom?

An ion has a net electrical charge due to gain or loss of electrons; a neutral atom has equal numbers of protons and electrons.

Give carbon isotope examples and how they differ.

Isotopes such as 12C, 13C, 14C differ in neutron numbers (6 protons each; 12C has 6 neutrons, 13C has 7 neutrons, 14C has 8 neutrons).