BIOL 130 Module 5

Protein Structure, Function, and Synthesis

Amino acid

The building blocks of proteins

Peptide bond

A covalent bond between amino acids

Primary structure

A linear sequence of amino acids that form a polypeptide chain and determines the secondary, tertiary, and quaternary structure of proteins

Secondary structure

Describes the conformation of proteins of the polypeptide chain. Results from hydrogen bonding between neighbouring amino acids of the polypeptide backbone and can form an alpha helix or beta sheet

Alpha helix

Forms due to hydrogen bonds to the fourth amino acid neighbour above and below in the spiral and let molecules that are not nearby in the main structure to interact with one another

Beta sheet

Segments of the polypeptide lying side by side in a folding conformation. Sheets can be parallel or antiparallel

Tertiary structure

Described the conformation of the entire protein in a 3D shape and determines the functional form of the protein. This structure is determined by the spatial distribution of hydrophobic and hydrophilic R groups and chemical interactions between the R groups

Quaternary structure

The spatial arrangement of subunits. The polypeptide chains in each subunit can be identical or non-identical

Translation

A sequence of bases in mRNA used to specify the order of amino acids added to the polypeptide chain

mRNA

Primary transcript developed during transcription

Ribosomes

Protein factories where translation occurs. Ribosomes consist of a large subunit and a small subunit

A site

Space in the ribosome where aminoacyl tRNA enters

P site

Space in the ribosome where the growing polypeptide chain is held

E site

Space in the ribosome where empty tRNA exits the ribosome

Codon

Nucleotide combinations that code for the amino acid placement

Anticodon

Complementary sequence of three nucleotides pairs with the codon to deliver the correct amino acid

Reading frame

Dividing a nucleotide sequence of an RNA or DNA molecule into codons that direct protein synthesis

Transfer RNA

A physical adapter between mRNA and the amino acid sequence that pairs anticodons with a complementary codon on the mRNA

Aminoacyl tRNA synthetases

tRNA with an amino acid attached to be added to the growing polypeptide chain

Genetic code

64 codons specify 20 amino acids that are read from 5’ to 3’

Start codon

Initiates translation (AUG)

Stop codon

Terminates translation (UAA, UAG, UGA)

Translation initiation

The small ribosomal subunit and initiation factors scan the mRNA for the start codon

Translation elongation

Aminoacyl tRNA enters the A site and base pairs with the next codon. The ribosome shifts one codon to the right leaving an uncharged tRNA in the E site, peptide bearing tRNA in the P site, and the A site is free for the next charged tRNA

Translation termination

A protein release factor binds to the A site at the stop codon and the polypeptide chain is complete

Initiation factors

Proteins that bind to ribosomes and help assemble the translation initiation complex

Release factors

Proteins that terminate protein synthesis by recognizing stop codons and releasing the polypeptide chain from the ribosome

Shine-Dalgarno sequence

The initiation complex is formed at one or more internal sequences present in the mRNA in prokaryotic translation. There is no 5’ cap or mRNA molecules

Polycistronic mRNA

Primary transcripts contain information for more that one gene in prokaryotes

Gene regulation

Not all genes are expressed in the cell at the same time

Protein translational modifications

Changes made to the protein after translation

Protein sorting

The cell delivers newly synthesized proteins to their correct intercellular or extracellular destination based on specific signal sequences

Protein sorting - No signal

Stay in cytosol

Protein sorting - Amino terminal signal

To chloroplast or mitochondria

Protein sorting - Integral signal

To nucleus

Signal recognition particle (SRP)

Binds to the specific amino terminal signal and transports proteins to the endoplasmic reticulum