Post-translational Modifications and 3D Structure

What are the five stages of protein synthesis?

1. Activation of amino acids, 2. Initiation of translation, 3. Elongation, 4. Termination and ribosome recycling, 5. Folding and post-translational processing.

What occurs during the activation stage of protein synthesis?

Amino acids are aminoacylated onto tRNA.

What defines the termination stage of protein synthesis?

The process continues until a STOP codon is reached, followed by the dissociation of mRNA and protein, and ribosome recycling.

List three common post-translational modifications.

Enzymatic removal of the formyl group or Met, acetylation of the N-terminal residue, and removal of signal sequences.

Why might a protein undergo post-translational modification?

To achieve its fully active conformation or to activate an enzyme by removing specific sequences.

What is the biochemical convention for naming atoms in amino acids?

Start from the alpha-carbon and proceed down the R-group.

How are amino acids classified based on their R substituents?

Nonpolar aliphatic, aromatic, polar uncharged, positively charged (basic), and negatively charged (acidic).

Which amino acids absorb UV light at 270-280 nm?

Tryptophan (Trp) and Tyrosine (Tyr), with Phenylalanine (Phe) to a lesser extent.

Which amino acid is capable of forming disulfide bonds to stabilize protein structure?

Cysteine.

What characterizes the R groups of positively charged (basic) amino acids at pH 7?

They are hydrophilic and contain primary amino, guanidinium, or imidazole groups.

What characterizes the R groups of negatively charged (acidic) amino acids at pH 7?

They possess a net negative charge and contain a second carboxyl group.

What is a peptide?

A small condensation product of amino acids linked by substituted amide linkages, typically with a molecular weight less than 10 kDa.

What is a residue in the context of protein structure?

An amino acid that has been incorporated into a peptide or protein chain.

What is the function of isoprenyl groups like farnesyl pyrophosphate in proteins?

They help anchor proteins into cell membranes.

How do uncommon amino acids typically arise in proteins?

They are usually not incorporated by ribosomes but arise through post-translational modifications.

What are conjugated proteins?

Proteins that contain additional functional groups beyond the 20 standard amino acids.

Are post-translational modifications always permanent?

No, some modifications are transient and reversible.

What is the role of the hydroxyl group in Tyrosine?

It can form hydrogen bonds.

What is the primary chemical nature of nonpolar, aliphatic R groups?

They are hydrophobic.

What happens to the ribosome during the termination stage?

It is recycled for future use in protein synthesis.

What is the result of removing a sequence from a protein during post-translational processing?

It can serve to activate an enzyme.

What are the three primary characteristics of the peptide bond due to resonance?

It is less reactive than esters, quite rigid and nearly planar, and exhibits a large dipole moment in the trans configuration.

Which bonds in a polypeptide chain allow for free rotation?

The bonds connected to the alpha carbon, specifically the N-Calpha bond (phi) and the Calpha-carbonyl carbon bond (psi).

What does a Ramachandran plot display?

The distribution of phi and psi dihedral angles found in a protein, identifying favorable and unfavorable backbone conformations.

What is the primary stabilizing force for alpha helices?

Hydrogen bonds between the backbone amides and carbonyl oxygen groups located four amino acids away.

What is the typical geometry of an alpha helix?

A right-handed helix with 3.6 residues per turn and a rise of 5.4 angstroms per turn.

How are side chains oriented in an alpha helix?

They point outward and are roughly perpendicular to the helical axis.

What structural feature allows alpha helices to fit into the major groove of dsDNA?

An outer diameter of 10-12 angstroms.

What stabilizes the structure of beta sheets?

Hydrogen bonds between backbone amides and carbonyl oxygens of adjacent segments.

How are side chains oriented in a beta sheet?

They protrude from the sheet, alternating in an up and down direction.

What is the difference between parallel and antiparallel beta sheets?

In parallel sheets, H-bonded strands run in the same direction; in antiparallel sheets, they run in opposite directions.

What is the 'native fold' of a protein?

The specific three-dimensional conformation a protein adopts in aqueous solution to fulfill its biological function.

What is the hydrophobic effect's role in protein folding?

It increases net entropy by releasing water molecules from the structured solvation layer as hydrophobic amino acids are buried in the interior.

What are the four major favorable interactions that stabilize protein structure?

Hydrophobic effect, hydrogen bonds, London dispersion forces, and electrostatic interactions (salt bridges).

How are fibrous proteins typically characterized?

They are typically insoluble and composed of a single type of secondary structure.

What is the definition of quaternary structure?

The spontaneous assembly of individual polypeptide subunits into a larger functional cluster.

What is the difference between a cofactor, coenzyme, and prosthetic group?

A cofactor is a general term for non-amino acid components; a coenzyme is an organic cofactor; a prosthetic group is a cofactor covalently attached to the protein.

What is a protein domain?

An independently stable region of a protein that can sometimes undergo movements as a single entity.

What is a protein motif?

A simple combination of a few secondary structure elements that may be associated with a specific function.

Where are hydrophilic amino acid residues typically located in soluble proteins?

On the surface of the protein.

What are 'conformations' in the context of protein structure?

Structural states that can be achieved without breaking covalent bonds, primarily through rotations about bonds.

What is the 'random coil' in protein secondary structure?

An irregular arrangement of the polypeptide chain that does not form regular secondary structures like helices or sheets.

Why is the peptide bond considered a resonance hybrid?

Because the electrons are delocalized between the carbonyl oxygen and the amide nitrogen, preventing rotation.

What is the significance of conserved amino acids in proteins?

They often indicate critical functional regions such as active sites, metal binding sites, or fold-determining residues.

What is the cost of protein folding?

There is a decrease in conformational entropy when the protein is constrained into one specific native fold.