Unit 1.2 Introduction to Cell Biochemistry Flashcards

Matter has mass and occupies space, existing in solid, liquid, gas, or plasma states.
An element is a basic substance composed of one type of atom that cannot be broken down into other substances with different properties.
There are $92$ naturally occurring elements. Six elements account for $95\%$ of the body weight of organisms: Carbon ( $C$ ), Hydrogen ( $H$ ), Nitrogen ( $N$ ), Oxygen ( $O$ ), Phosphorus ( $P$ ), and Sulfur ( $S$ ).

Subatomic particles:
- Protons: Positively charged, located in the central nucleus.
- Neutrons: Uncharged, located in the central nucleus; slightly heavier than protons.
- Electrons: Negatively charged, orbiting in shells around the nucleus; very low, negligible mass.
Atoms are typically electrically neutral.
Atomic Number: Equal to the number of protons.
Mass Number: Equal to the number of protons plus neutrons.
Electron Orbitals and Shells:
- Each orbital holds up to $2$ electrons.
- Valence electrons reside in the outermost shell (valence shell) and determine chemical reactivity.
- Octet Rule: The outermost shell is most stable with $8$ electrons (or $2$ electrons if the atom has only $1$ shell). Unfilled valence shells render an atom reactive.

Molecule: A discrete, neutral group of two or more atoms held together primarily by covalent bonds (e.g., $H_2$ , $O_2$ , $H_2O$ , $CO_2$ ).
Compound: A pure substance composed of two or more different elements in a fixed ratio (e.g., $H_2O$ , $CO_2$ , $NaCl$ , $C_6H_{12}O_6$ ).
- $H_2$ is a molecule but not a compound.
- $H_2O$ is both a molecule and a compound.
- $NaCl$ is a compound but not a molecule.
Relative bond strength in biological systems: Covalent bonds > Ionic bonds > Hydrogen bonds > Van der Waals interactions.

Electronegativity ( $\Delta\text{EN}$ ): The ability of an atom to attract shared electrons in a chemical bond.
- Nonpolar Covalent Bond (\Delta\text{EN} < 0.4 - 0.5): Electrons are shared equally between atoms (e.g., $H_2$ , $O_2$ , $CH_4$ ).
- Polar Covalent Bond ( $\Delta\text{EN} = 0.5 - 1.7$ ): Electrons are shared unequally, giving the more electronegative atom a partial negative charge ( $\delta^-$ ) and the other a partial positive charge ( $\delta^+$ ) (e.g., $H_2O$ ).
- Ionic Bond (\Delta\text{EN} > 1.7): One or more electrons are completely transferred, creating charged ions (anions with negative charge, cations with positive charge) (e.g., $NaCl$ ).
- Hydrogen Bond: A weak attraction between a $\delta^+$ hydrogen atom and a $\delta^-$ atom of a different molecule or functional group. Individually weak, but collectively strong.

Water ( $H_2O$ ) is a polar molecule with asymmetrical, bent geometry and polar covalent bonds, enabling extensive intermolecular hydrogen bonding.
Hydrophilic: Molecules with partial or full ionic charges that interact readily with water and dissolve.
Hydrophobic: Nonpolar molecules lacking partial charges that do not interact with water and are insoluble.

Macromolecules are large organic molecules with a carbon backbone bound to hydrogen and specific functional groups (clusters of atoms imparting distinct properties).
Monomers are joined together or broken down via specific enzymatic reactions:
- Dehydration Synthesis (Condensation): Monomers join via covalent bonds with the removal of a water molecule ( $H_2O$ ).
- Hydrolysis: Polymers are broken into monomers through the addition of a water molecule ( $H_2O$ ).

Four Classes of Biomolecules:
- Carbohydrates: Monosaccharide (subunit) $\rightarrow$ Polysaccharide (polymer).
- Lipids: Glycerol and fatty acids (subunits) $\rightarrow$ Does not form true polymers.
- Proteins: Amino acids (subunit) $\rightarrow$ Polypeptide (polymer).
- Nucleic Acids: Nucleotide (subunit) $\rightarrow$ DNA, RNA (polymer).