BIO 13 Study Guide: Biochemistry, Cells, Proteins, and Nucleic Acids

Vocabulary flashcards generated from BIO 13 lecture content covering cell biology, chemistry basics, functional groups, protein folding structures, gel electrophoresis, and nucleic acids.

Self-sustaining System

A characteristic of living organisms under NASA's definition, meaning it does not require an agent or chemist present to keep its biological processes going in an appropriate environment.

Prokaryotic Cell

A cell type defined by the absence of a membrane-bound nucleus and containing DNA in a circular chromosome, cytoplasm, cell wall, and ribosomes.

Eukaryotic Cell

A larger cell type containing membrane-bound organelles, linear chromosomes inside a distinct nucleus, mitochondria, and an endomembrane system.

Mass Number

The combined total number of protons and neutrons within an atom's nucleus.

Atomic Number

The total number of protons in an atom's nucleus, which equals the number of electrons in a neutral atom.

Orbital

A region within an atom that can hold up to $1$ pair of electrons ($2$ electrons total).

Valence Shell

The outermost electron shell of an atom.

Valence Electrons

The total number of electrons present in an atom's valence shell.

Valence Number

The number of unpaired electrons in an atom's valence shell, which determines how many covalent bonds that atom can form.

Covalent Bond

A chemical bond formed by the sharing of two unpaired valence electrons between two atoms.

Electronegativity

A characteristic of an element measuring how strongly an atom pulls on electrons in a covalent bond.

Nonpolar Covalent Bond

A covalent bond formed between atoms with little to no difference in electronegativity, resulting in equal sharing of electrons and no stable partial charges.

Polar Covalent Bond

A covalent bond formed between atoms with a small difference in electronegativity, where electrons are shared unequally and spend more time near the higher electronegativity atom, creating stable partial charges.

Ionic Bond

A bond created by the electrostatic attraction between oppositely charged ions, resulting from a very large difference in electronegativity where electrons are fully transferred.

Hydrogen Bond

An electrostatic attraction between a partially positive hydrogen atom and a partially negative atom (such as oxygen or nitrogen).

London Dispersion Forces

Weak, fluctuating electrostatic attractions between nonpolar molecules caused by small, temporary dipoles created by electron movement; also known as van der Waals forces.

Hydrophilic

Refers to polar or ionic molecules that readily interact with and dissolve in water through hydrogen bonding.

Hydrophobic

Refers to nonpolar molecules that do not dissolve in water and are pushed together in aqueous environments to maximize the water's hydrogen-bonding network.

Physiological pH

The biological pH range of typical cellular environments, defined as $7.0$ to $7.4$.

Carboxyl Group

An acidic functional group ($-COOH$) that donates/releases an $H^+$ ion into solution, becoming negatively charged.

Amino Group

A basic functional group ($-NH_2$) that accepts/gains an $H^+$ ion from the environment at physiological pH, becoming positively charged ($-NH_3^+$).

Amide

A functional group composed of a carbonyl group bonded to an amine group that does not accept protons at physiological pH and remains polar uncharged.

Condensation Reaction

A chemical reaction that links monomers together into a polymer chain through the loss/formation of a water molecule, requiring and storing energy; also called a dehydration reaction.

Hydrolysis Reaction

A chemical reaction that breaks polymers apart into individual monomers by splitting a water molecule, releasing energy.

Peptide Bond

The covalent bond that links two amino acids together between the carbonyl carbon of one amino acid and the amino nitrogen of another.

N-terminus

The start of a polypeptide chain, characterized by a free amino group.

C-terminus

The end of a polypeptide chain, characterized by a free carboxyl group.

Primary Structure

The linear sequence and order of amino acids in a polypeptide chain from N-terminus to C-terminus, held together by covalent peptide bonds.

Secondary Structure

Local, repeating 3D patterns of the peptide backbone (such as alpha-helices and beta-pleated sheets) maintained by hydrogen bonding between partial charges on backbone atoms.

Tertiary Structure

The overall global 3D structure of a single folded polypeptide chain, maintained primarily by interactions among amino acid side chains (R groups), including hydrogen bonds, ionic bonds, hydrophobic effects, and disulfide bonds.

Quaternary Structure

The overall 3D arrangement and interaction between two or more distinct polypeptide chain subunits in a functional protein complex.

Molecular Chaperones

Specialized proteins in cells that assist newly synthesized or unfolding proteins to fold into their lowest energy, functional 3D structures.

Prions

Infectious misfolded proteins that cause normal copies of the protein to also misfold and aggregate into toxic fibrils and plaques.

SDS-PAGE

Polyacrylamide Gel Electrophoresis utilizing sodium dodecyl sulfate to denature proteins and coat them in uniform negative charges, allowing them to be separated along a gel matrix based strictly on relative size.

Phosphodiester Linkage

The covalent bond that links adjacent nucleotides together in a nucleic acid chain between the pentose sugar of one nucleotide and the phosphate group of the next.

Antiparallel Strands

The structural arrangement of two complementary strands of DNA running alongside each other in opposite directions, one running $5'$ to $3'$ and the other $3'$ to $5'$.

Stem-Loop Structure

A common secondary structure in single-stranded RNA formed when complementary base pairing occurs between antiparallel regions on the same strand to form a double-helical stem, leaving an unpaired loop region.