Learning Module 7: Proteins

Vocabulary flashcards covering amino acid structure, protein organization levels, functional protein classes, post-translational modifications, and related biochemical concepts from Module 7.

Alpha Carbon ($\alpha$-carbon)

The central carbon atom of an amino acid to which an amino group, a carboxyl group, a hydrogen atom, and a variable side chain ($\text{R}$ group) are bonded.

Peptide Bond

A covalent bond formed through a dehydration synthesis reaction that links the carboxyl group of one amino acid to the amino group of an incoming amino acid.

Peptide Backbone

The continuous chain of carbon, oxygen, and nitrogen atoms formed by repeating peptide bonds, from which amino acid side chains branch off.

Primary Structure

The unique linear sequence of amino acids in a polypeptide chain, held together strictly by covalent peptide bonds.

Secondary Structure

Local folding motifs within a polypeptide, primarily the $\alpha$-helix and $\beta$-pleated sheet, stabilized by hydrogen bonds between backbone atoms.

Alpha Helix ($\alpha$-helix)

A helical secondary structure motif featuring $3.6$ amino acid residues per turn, stabilized by hydrogen bonds between the carbonyl oxygen and amino hydrogen of the peptide backbone.

Beta-Pleated Sheet ($\beta$-pleated sheet)

A secondary structure formed when parallel or antiparallel $\beta$-strands are bound together in pleats by hydrogen bonds across the peptide backbone.

Tertiary Structure

The overall three-dimensional conformation of a single polypeptide chain, created by interactions among side chains ($\text{R}$ groups) including hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide linkages.

Quaternary Structure

The overall protein organization resulting from the association and interaction of multiple individual polypeptide subunits.

Denaturation

The process in which environmental changes such as extreme temperature, altered pH, or chemical exposure disrupt a protein's three-dimensional shape and function without breaking its primary sequence.

Catabolic Enzymes

Enzymes that catalyze breakdown reactions to digest nutrients into smaller monomeric units.

Anabolic Enzymes

Enzymes that construct complex molecules from simpler substrate molecules.

Hormones

Chemical-signaling molecules, such as insulin or thyroxine, secreted by endocrine cells to regulate specific physiological processes such as growth, metabolism, and reproduction.

Structural Proteins

Proteins such as actin, tubulin, and keratin that construct cellular and physical structures like the cytoskeleton.

Essential Amino Acids

The 9 amino acids (in humans) that cannot be synthesized by the body and must be supplied through the diet.

N-Terminal

The free amino group terminus located at the start of a polypeptide chain.

C-Terminal

The free carboxyl group terminus located at the end of a polypeptide chain.

Titin

The largest known protein to date, located in skeletal and cardiac muscle, containing up to $34{,}350$ amino acids in a single chain.

Heavy Chain (H-2K)

The 346-amino-acid integral membrane protein of the mouse class I histocompatibility molecule, consisting of three extracellular domains ($\text{N}$, $\text{C1}$, $\text{C2}$), a transmembrane domain, and a cytoplasmic domain.

Beta-2 Microglobulin ($\beta_2\text{-microglobulin}$)

A 99-amino-acid peripheral membrane protein that noncovalently associates with the heavy chain of class I histocompatibility molecules via hydrogen bonds.

Glycoproteins

Proteins that contain short, branched carbohydrate chains covalently attached to specific amino acid residues.

N-Linked Glycosylation

The post-translational modification in which a carbohydrate chain is covalently linked to the asparagine ($\text{N}$) residue of a protein.

Kinases

Enzymes that catalyze the addition of phosphate groups to target protein residues (such as tyrosine) to control protein function.

Phosphatases

Enzymes that catalyze the removal of phosphate groups from protein residues to regulate protein function.

Circular Proteins

Proteins produced by some bacteria, plants, and animals (excluding humans) where internal peptides are removed and free ends are linked into a ring, providing high resistance to peptidase degradation.

Inteins

Internal protein segments ('protein introns') that are removed post-translationally before the remaining segments are spliced together.

Exteins

The remaining N-terminal and C-terminal polypeptide segments ('protein exons') that are ligated together via peptide bonds after an intein is excised.

Chaperones

Helper proteins that assist target proteins during the folding process by preventing polypeptide aggregation.

Sickle-Cell Anemia

A genetic disorder caused by a single point mutation replacing glutamic acid with valine at position 6 of the hemoglobin $\beta$-chain, causing hemoglobin molecules to form long fibers that deform red blood cells into crescent shapes.

William Warrick Cardozo

The researcher who demonstrated that sickle-cell anemia is an inherited disorder passed down from parents to offspring.

Cytochrome c

A highly conserved mitochondrial protein with a heme prosthetic group involved in cellular respiration, featuring 37 invariant amino acids out of 104 across all sequenced organisms.

Papain

A proteinase that cleaves specific sites on the long heavy chain of membrane proteins to release their extracellular domains for experimental analysis.

Tyrosine (vs. Phenylalanine)

An amino acid that differs structurally from phenylalanine by the covalent addition of a single hydroxyl group ($\text{OH}$) on its aromatic ring.

Disulfide bonds

covalent linkages formed between the sulfhydryl groups of cysteine residues in proteins, stabilizing their three-dimensional structures.

Side chain

of an amino acid that is not part of the backbone and determines its unique properties and interactions

Polar

refers to amino acids with side chains that have partial positive and negative charges, enabling them to form hydrogen bonds and interact with water.

Nonpolar

refers to amino acids with side chains that are hydrophobic and lack charge, making them less interactive with water and more likely to associate with other nonpolar substances.

R-Group

the variable side chain of an amino acid that defines its chemical properties and behavior in proteins.

What class of molecule is required to hydrolyze (break) the peptide bond in a real peptide?

Enzymes

4 bonds that contribute to the tertiary structure of a protein

disulfide linkages, hydrogen bonds, ionic bonds, hydrophobic interactions

In an oily environment, where would you expect to find the hydrophilic domains of a protein?

In the inside

Do all proteins require quaternary structure to be functional?

No, only some proteins require quaternary structure to be functional.