Protein Structure and Function: Peptides and peptide bond 1

Flashcards for Protein Structure and Function: Peptides and peptide bond 1

Peptide Bond

A chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water.

Peptide Sequence

The order in which amino acid residues, connected by peptide bonds, are present in the peptide or protein.

Peptide

A molecule of water is eliminated for each peptide bond formed, and the resulting product is termed this.

Amino acid residue

The remaining portion of the amino acid in the peptide.

N-terminal and C-terminal ends

These ends of the peptide are available for further reaction.

Condensation reaction

The reaction that forms peptide bonds, catalyzed by the ribosome.

tRNA

Molecules which transport amino acids to the ribosome during peptide bond formation.

Linus Pauling and Robert Corey

He analyzed the geometry and dimensions of peptide bonds in crystal structures.

10%

The C-N bond length in a peptide bond is shorter than found in usual amines by this percentage.

40%

Due to resonance with the C=O group, the C-N bond has some double bond character with this percentage.

Peptide bond

The rigidity of this reduces the degrees of freedom during folding.

Torsion Angles   

The three main torsion angles of a polypeptide backbone: phi (φ), Cα-N; psi (ψ), C=O to Cα; and omega (ω), peptide bond.

Omega (ω)

The planarity of the peptide bond restricts this torsion angle to 180° (trans) in nearly all the main chain peptide bonds.

Omega (ω)

In rare cases, this torsion angle = 0° for a cis peptide bond which usually involves proline.

Trans

The peptide bond is nearly always in this configuration because it is more favorable over cis.

Cis

Steric hindrance between functional groups attached to Cα atoms are greater in this configuration.

Proline

The cyclic nature of its side chain allows both the cis and trans configurations to have nearly equivalent energies. Thus, it is found in the cis configuration.

Hydrolysis

In aqueous solution, formation of a peptide bond is not favored thermodynamically (ΔG ≈ 10 kJ/mol at room temperature), instead, the reverse reaction, this, of a peptide bond, is favored.

Polypeptide Nomenclature

The convention is always to represent the N-terminus on the left and the C-terminus on the right.

Peptide naming convention

Lists the individual AA’s in order starting at the N-terminus with the name of every AA ending in –yl, except for the C-terminal AA, which takes its full name.

Oligopeptides

Short peptides of a few residues.

Polypeptides

Longer chain peptides.

Proteins

Very long chain polypeptides (>10,000 daltons) folded into regular structures.

Polypeptide and Protein

Refers simply to a chain of amino acids, while the term refers to the chain of amino acids after it folds properly and is (in some cases) modified. It may consist of more than one polypeptide chain.

Molecular weight of an average AA mol. wt. in a protein is about 128

Used to describe an amino aicd when referring to the abundance in known proteins.

Residues

Estimate the number of these in a protein by dividing the molecular weight by 110.

Peptide Sequences

The number of unique sequences possibilities is enormous, organisms typically rely on 30,000 to 35,000 sequences, so necessary function will determine which sequence are constructed!

Amino acids

joined together by peptide bonds, in proteins (or polypeptides) have different properties determined by their R group side chains: acidic, basic, neutral, hydrophobic, etc.

Folding

The amino acid side-chains direct this of the nascent polypeptide into a function protein and stabilize its final conformation.

Conjugated proteins

Contain permanently associated chemical components – non–amino acid part.

Prosthetic group

Chemical components – non–amino acid part of conjugated proteins.

Lipoproteins

Contain Lipids.

Glycoproteins

Contain sugars.

Metalloproteins

Contain specific metals.

Salting out

Lower solubility of proteins in salt to selectively precipitate proteins.

Dialysis

Use semipermeable membrane to separate proteins from small solutes.

Chromatography

Separates based on binding affinity, eluted by high concentration of salt or ligand.

Gel filtration chromatography

Separates based on size; large proteins emerge from the column before small proteins do.

Chromatography

Separates based on net electric charge, pH and concentration of free salt ions affect protein affinity.

Electrophoresis

Visualize and characterize purified proteins.

Proteases

Catalyze hydrolytic cleavage of peptide bonds.

Mass Spectrometry

Provides Information on Molecular Mass, Amino Acid Sequence, and Entire Proteomes with high accuracy.

Tandem MS (MS/MS)

Two mass filters in tandem; first sorts peptides produced by cleavage; second measures m/z ratios of charged fragments.

Consensus sequence

Reflects most common amino acid at each position.

Homologs

Homologous proteins, members of protein families.

Paralogs

Homologs in same species.

Orthologs

Homologs in different species.