Protein Structure, Function & Synthesis

Vocabulary flashcards reviewing key concepts, definitions, and structures covered in the lecture on protein structure, function, translation, and sorting.

Amino Acids

Building blocks or monomers of proteins consisting of an alpha carbon, carboxyl group, amino group, hydrogen, and an R group or side chain.

R Group (Side Chain)

The variable component of an amino acid that determines its unique characteristics, such as interaction with water, acidity or basicity, and polarity.

Peptide Bonds

Covalent bonds that join amino acids together through a dehydration reaction that removes a water molecule, forming short bonds that limit rotation.

Primary Structure

The linear sequence of amino acids in a protein where R groups alternate positions on adjacent amino acids.

Secondary Structure

Protein structure resulting from hydrogen bonding along the polypeptide backbone, forming common structures such as alpha helices and beta sheets.

Alpha Helix

A common secondary structure where each carbonyl group in the backbone forms a hydrogen bond with an amide group four amino acids away.

Beta Sheet

A common secondary structure formed by hydrogen bonds between carbonyl groups in one part of a polypeptide and amide groups in another, which can be pleated and parallel or antiparallel.

Tertiary Structure

The overall three-dimensional folded shape of a polypeptide chain, governed by noncovalent interactions.

Quaternary Structure

Structure resulting from multiple protein subunits joining together to form a fully functional protein complex.

Central Dogma

The core principle describing the flow of genetic information in cells from DNA to RNA via transcription, and from RNA to protein via translation.

Ribosomes

Cellular structures composed of proteins and ribosomal RNA (rRNA) with a large and small subunit that read mRNA in the $5'$ to $3'$ direction to synthesize proteins.

Reading Frame

The specific position where the ribosome begins reading mRNA in sequential sets of 3 nucleotides (codons), starting with the codon for methionine.

A Site

The ribosomal binding site that accepts an incoming aminoacyl tRNA.

P Site

The ribosomal site where peptide bond formation occurs between adjacent amino acids.

E Site

The ribosomal site from which uncharged tRNAs exit the ribosome.

Transfer RNA (tRNA)

Molecules that carry specific amino acids to the ribosome, containing an anticodon loop that base pairs with codons on mRNA and a $3'$ sequence ending in $5' \text{-CCA-} 3'$ where the amino acid attaches.

Aminoacyl tRNA Synthetase

An enzyme that attaches a specific amino acid to the $3'$ end of its corresponding uncharged tRNA, producing a charged tRNA.

Shine-Dalgarno Sequence

A specific mRNA sequence ($5' \text{-AGGAGGU-} 3'$) in prokaryotes to which the ribosome binds, initiating translation at the first downstream AUG start codon.

Signal-Recognition Particle (SRP)

A complex that binds to a signal sequence at the amino-terminal end of a growing polypeptide chain and halts translation while targeting the ribosome to the ER membrane.

Signal-Anchor Sequence

A sequence in transmembrane proteins that threads through an ER channel until encountered, causing the ER channel to release the protein into the membrane.