Lecture 4: Macromolecules II: Proteins and Nucleic Acids

Vocabulary practice flashcards covering structural features, folding levels, biological functions, and degradation of proteins as well as structure and composition of nucleic acids from Bio93 Lecture 4.

Polymer

A long molecule built from similar subunits (monomers) linked together by covalent bonds.

Polypeptide

A polymer consisting of amino acid monomers joined by covalent peptide bonds in a specific sequence, extending from an amino end ($\text{N-terminus}$) to a carboxyl end ($\text{C-terminus}$).

Enzymatic proteins

Proteins that selectively accelerate chemical reactions, such as digestive enzymes catalyzing the hydrolysis of bonds in food molecules.

Storage proteins

Proteins dedicated to storing amino acids; examples include casein in milk for mammal offspring, ovalbumin in egg whites, and protein reserves inside plant seeds.

Defensive proteins

Proteins that protect organisms against disease; for example, antibodies binding to viruses and bacteria to neutralize and mark them for destruction.

Transport proteins

Proteins that carry substances throughout an organism or across membranes, such as hemoglobin delivering oxygen in vertebrate blood or membrane channels facilitating solute transit.

Hormonal proteins

Signaling proteins that coordinate an organism's physiological activities; for instance, insulin secreted by the pancreas to stimulate tissue glucose uptake.

Receptor proteins

Proteins embedded in cell membranes that mediate cellular responses to chemical stimuli by detecting and binding signaling molecules.

Contractile and motor proteins

Proteins that generate cellular and organismal movement, such as actin and myosin in muscle contraction, or motor proteins driving the undulations of cilia and flagella.

Structural proteins

Proteins that provide physical architecture and support, such as keratin in hair and horns, silk fibers in spider webs, and collagen and elastin in connective tissues.

Amino acid

An organic monomer of proteins composed of a central $\alpha\text{ carbon}$ bonded to a hydrogen atom, an amino group ($-\text{NH}_2$ or $\text{H}_3\text{N}^+$), a carboxyl group ($-\text{COOH}$ or ionized $-\text{COO}^-$), and a variable side chain ($\text{R group}$).

Peptide bond

A covalent linkage formed between the carboxyl carbon of one amino acid and the amino nitrogen of another via a dehydration reaction releasing a water molecule ($\text{H}_2\text{O}$).

Primary structure

The linear sequence of amino acids in a polypeptide chain, encoded genetically, which ultimately determines the higher-order folding and function of a protein.

Secondary structure

Repetitive folding patterns within a polypeptide stabilized by hydrogen bonds between atoms of the polypeptide backbone ($\text{N-H}\cdots\text{O=C}$), characteristic of $\alpha\text{ helices}$ (coils) and $\beta\text{ pleated sheets}$ (folds).

Tertiary structure

The overall 3D conformation of a single polypeptide, stabilized by interactions among variable amino acid $\text{R groups}$, including hydrogen bonds, ionic bonds, hydrophobic/van der Waals interactions, and covalent disulfide bridges.

Disulfide bridge

A strong covalent link formed between the sulfhydryl groups ($-\text{SH}$) of two cysteine monomers within a polypeptide, providing structural stability to tertiary folding.

Quaternary structure

The overall multi-subunit protein architecture formed and stabilized by the aggregation of two or more individual polypeptide chains interacting via their $\text{R groups}$, as seen in transthyretin or collagen.

Sickle-cell anemia

A genetic disease resulting from a single nucleotide substitution in DNA and mRNA that replaces a normal glutamic acid (Glu) at position 6 with valine (Val) in the $\beta\text{ subunit}$ of hemoglobin, causing abnormal hemoglobin fibers and sickled red blood cells.

Denaturation

The loss of a protein's native three-dimensional conformation caused by disrupting environmental conditions—such as altered $\text{pH}$, high salt concentration, or elevated temperature—which inactivates its biological function.

Chaperone protein

A protein complex found throughout the cell that assists nascent or stress-damaged polypeptides to fold or refold properly by offering an isolated, sheltered microenvironment.

Ubiquitin

A small regulatory polypeptide that binds to misfolded, aberrant, or unneeded proteins, serving as a molecular tag known as the "kiss of death" that directs them to the proteasome for destruction.

Proteasome

A large cellular protein complex that recognizes ubiquitin-tagged misfolded or damaged proteins and uses proteases to hydrolyze them into short peptide fragments for amino acid recycling.

Multiple myeloma

A hematologic cancer originating in bone marrow plasma cells ($\text{B cells}$) that produces high volumes of aberrant, misfolded proteins, creating an extreme dependency on proteasomal degradation for cell survival.

Carfilzomib

A proteasome inhibitor used in multiple myeloma therapy to prevent degradation of damaged proteins, causing them to accumulate and initiate programmed cell death (apoptosis).

Nucleotide

The monomeric subunit of nucleic acids consisting of three parts: a five-carbon pentose sugar, a nitrogenous base, and one or more phosphate groups.

Phosphodiester linkage

The covalent bond that bridges the pentose sugar of one nucleotide to the phosphate group of an adjacent nucleotide via a dehydration reaction, establishing the sugar-phosphate backbone of a nucleic acid.

Deoxyribose

The five-carbon pentose sugar found in DNA nucleotides, characterized by having a hydrogen atom ($-\text{H}$) rather than a hydroxyl group ($-\text{OH}$) at its $2'$ carbon position.

Pyrimidines

A family of nitrogenous bases characterized by a single six-membered ring; includes cytosine ($\text{C}$), thymine ($\text{T}$, in DNA), and uracil ($\text{U}$, in RNA).

Purines

A family of nitrogenous bases featuring a six-membered ring fused to a five-membered ring; includes adenine ($\text{A}$) and guanine ($\text{G}$).

Complementary base pairing

The specific pairing rule governed by hydrogen bonds in double-stranded DNA, where adenine binds to thymine ($\text{A-T}$) through $2\text{ hydrogen bonds}$ and guanine binds to cytosine ($\text{G-C}$) through $3\text{ hydrogen bonds}$.