Chemistry of the Cell: Elements, Molecules, and Macromolecules

Practice flashcards covering Chapter 2: Chemistry of the Cell, including atomic structure, chemical bonds, pH, solutions, and macromolecules.

What is an atom and what are its main structural components?

An atom is a single unit of matter with a dense, positively charged nucleus containing protons and neutrons, surrounded by electron shells containing negatively charged electrons.

What are the electrical charges and masses in daltons of protons, neutrons, and electrons?

Protons have a $+$ charge and a mass of $1\, \text{dalton}$; neutrons have no charge ($\text{N/A}$) and a mass of $1\, \text{dalton}$; electrons have a $-$ charge and a mass of $0\, \text{daltons}$.

What is the chemical definition of an element?

An element is a substance that cannot be broken down by chemical reactions, consisting of a collection of atoms with identical properties.

How do atomic number and atomic mass differ?

Atomic number is the number of protons in an atom's nucleus, which is always identical for all atoms of an element. Atomic mass is the mass of the atom, equal to the number of protons plus the number of neutrons in the nucleus.

According to Table 2.1, what are the atomic numbers, mass numbers, and covalent bond counts for the six key elements in living organisms?

Hydrogen ($\text{H}$): Atomic Number $1$, Mass Number $1$, Covalent Bonds $1$. Carbon ($\text{C}$): Atomic Number $6$, Mass Number $12$, Covalent Bonds $4$. Nitrogen ($\text{N}$): Atomic Number $7$, Mass Number $14$, Covalent Bonds $3$. Oxygen ($\text{O}$): Atomic Number $8$, Mass Number $16$, Covalent Bonds $2$. Phosphorus ($\text{P}$): Atomic Number $15$, Mass Number $31$, Covalent Bonds $3$. Sulfur ($\text{S}$): Atomic Number $16$, Mass Number $32$, Covalent Bonds $2$.

What are the three main types of chemical bonds and their relative strengths?

1. Covalent bonds: Strong bonds found in water, atmospheric gases, and organic molecules. 2. Ionic bonds: Strong bonds found in salts and ionic compounds. 3. Hydrogen bonds: Weak bonds that hold together larger biological molecules and facilitate water dissolving substances.

What is an ionic bond, and how do anions and cations differ?

An ionic bond is a strong bond formed when one non-electronegative atom donates its electron(s) to another more highly electronegative atom. An ion is a charged atom or molecule; an anion is negatively charged ($-$) and a cation is positively charged ($+$).

What defines a covalent bond and an organic molecule?

A covalent bond is a strong chemical bond formed when two atoms share their outermost electrons. An organic molecule consists of both Carbon ($\text{C}$) and Hydrogen ($\text{H}$) and contains $\text{C-C}$ bonds.

What causes a polar covalent bond to form, and which electronegative elements commonly form them with Hydrogen?

A polar covalent bond forms when one atom has a higher electronegativity (stronger pull on shared electrons) than the other, resulting in partial charges ($\delta-$ and $\delta+$). Elements such as Oxygen ($\text{O}$), Nitrogen ($\text{N}$), and Sulfur ($\text{S}$) have high electronegativity and frequently form polar covalent bonds with Hydrogen ($\text{H}$).

What characterises nonpolar covalent bonds and nonpolar molecules?

Nonpolar covalent bonds occur between atoms with similar electronegativity values that share electrons evenly, such as $\text{C-H}$ bonds or any element bonded to itself. Examples of nonpolar molecules include hydrocarbons and small gases like $\text{O}_2$ and $\text{CO}_2$.

What are hydrogen bonds and where do they function in biological systems?

Hydrogen bonds are weak bonds formed due to the partial positive charge ($\delta+$) of Hydrogen atoms and partial negative charges ($\delta-$) on atoms in other molecules. They occur between water molecules, between water and other polar molecules, and hold together large macromolecules like proteins and DNA.

What do the terms hydrophilic, hydrophobic, and amphipathic mean?

Hydrophilic substances attract water ('water-loving') and readily dissolve in water (e.g., polar molecules and ionic compounds). Hydrophobic substances repel water ('water-fearing') and do not dissolve in water (e.g., nonpolar molecules). Amphipathic molecules possess both hydrophilic and hydrophobic regions.

What structural feature makes a phospholipid amphipathic?

A phospholipid consists of a hydrophilic ('water-loving') polar head group and hydrophobic ('water-fearing') nonpolar fatty acid tails.

How is pH defined mathematically and how does it relate to hydrogen ion concentration?

pH is defined as $\text{pH} = -\log[\text{H}^+]$. Lower pH values have higher $\text{H}^+$ concentrations and are more acidic, while higher pH values have lower $\text{H}^+$ concentrations and are more basic. A pH of $7$ is neutral.

What are the four major classes of macromolecules, their subunits, and primary functions as outlined in Table 2.3?

1. Carbohydrates: Monosaccharide subunits; structural component of cell walls and storage products. 2. Lipids: Varying subunits; important component of cell membranes. 3. Proteins: Amino acid subunits; enzyme catalysts and structural portion of many cell components. 4. Nucleic acids: Nucleotide subunits (Deoxyribonucleotides in DNA carry genetic info; Ribonucleotides in RNA function in protein synthesis).

What is the relationship between monomers, polymerization, and polymers?

Monomers are single subunit molecules that undergo polymerization to form long, repeating chains called polymers.

How are carbohydrates classified, and what are specific examples of monosaccharides, disaccharides, and polysaccharides?

Monosaccharides (monomers) include Glucose, Mannose, Galactose, and Fructose. Disaccharides include Sucrose and Lactose. Polysaccharides (polymers) include Cellulose (non-branching), Glycogen (branching), and Dextran (branching).

How are triglycerides synthesized from glycerol and fatty acids?

Triglycerides (fats) are synthesized through dehydration synthesis, combining $1\, \text{glycerol}$ molecule with $3\, \text{fatty acid}$ chains and producing $3\, \text{H}_2\text{O}$ as byproducts.

What subunits make up proteins, and what percentage of a cell's dry mass do proteins comprise?

Proteins are made up of amino acid monomers and account for approximately $50\%$ of the dry mass of cells.

What are the structural components of an amino acid?

An amino acid features a central Carbon atom bonded to a Hydrogen, a positively charged Amino group ($\text{H}-\text{N}^+-\text{H}_2$ at neutral pH), a negatively charged Carboxyl group ($\text{C}=\text{O},\text{O}^-$ at neutral pH), and a variable Side chain ($\text{R}$ group).

What components make up a nucleotide, and how do DNA and RNA differ?

A nucleotide consists of a phosphate group, a pentose sugar, and a nitrogenous base. DNA contains deoxyribose sugar and nitrogenous bases Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). RNA contains ribose sugar and nitrogenous bases Adenine (A), Guanine (G), Cytosine (C), and Uracil (U).

What is the direction of genetic information flow according to the central dogma?

Information flows from $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$.