Peptides + primary structure

What is a peptide

A molecule containing amino acid residues joined by peptide bonds.

What is a peptide bond

A covalent amide bond formed between the carboxyl group of one amino acid and the amino group of another.

How is a peptide bond formed

By a condensation reaction between an amino group and a carboxyl group, with the net loss of water.

What is a dipeptide

A peptide containing two amino acid residues.

What is a tripeptide

A peptide containing three amino acid residues.

What is an oligopeptide

A relatively short chain of amino acid residues.

What is a polypeptide

A chain of amino acid residues joined by peptide bonds.

What is the N-terminus of a peptide

The end with the free amino group, unless modified.

What is the C-terminus of a peptide

The end with the free carboxyl group, unless modified.

In which direction are peptide sequences conventionally written

From the N-terminus to the C-terminus.

What is a terminal modification of a peptide

A chemical alteration of the N-terminus or C-terminus, such as acetylation, amidation, or esterification.

What is a Dalton (Da)

A unit of molecular mass equal to one-twelfth the mass of a carbon-12 atom, approximately equivalent numerically to one gram per mole.

What is relative molecular mass ((M_r))

The ratio of a molecule's mass to one-twelfth the mass of a carbon-12 atom; it has no units.

How do you determine the amino acid composition of a peptide

Identify which amino acids are present and how many of each occur.

How does amino acid composition differ from amino acid sequence

Composition gives the identities and amounts of residues, whereas sequence gives their specific order.

How can peptide sequence affect its net charge

The ionizable termini and side chains contribute charges according to their pKa values and the solution pH.

What is primary protein structure

The amino acid sequence, the number of polypeptide chains, and the disulfide-bond pattern.

Why is primary structure important

The amino acid sequence constrains higher levels of structure and therefore influences protein function.

How can a protein sequence be deduced from DNA

Translate the coding information using the correct reading frame and genetic code.

What is a limitation of predicting protein sequence from DNA alone

It does not automatically account for post-translational modifications.

What is mass spectrometry

An analytical technique that measures ions according to their mass-to-charge ratio.

How can tandem mass spectrometry (MS/MS) determine a protein sequence

A protein is cleaved into peptides, peptide ions are fragmented, and the fragment patterns are analyzed to infer the peptide sequences.

What is MALDI

Matrix-assisted laser desorption/ionization, a method used to ionize samples for mass spectrometry.

What is ESI

Electrospray ionization, a method that generates gas-phase ions from a solution for mass spectrometry.

How can mass spectrometry help characterize proteins

It can identify proteins, determine molecular mass, and detect cofactors, modifications, or metabolites.

What is amino acid composition analysis

A method in which a protein is hydrolyzed into amino acids and the resulting amino acids are identified and quantified.

What is a limitation of amino acid composition analysis

It does not reveal the order of the amino acids in the original sequence.

What is Sanger's method in protein sequencing

A method that labels the N-terminal amino acid so it can be identified after hydrolysis.

What is Edman degradation

A stepwise sequencing method that identifies and removes the N-terminal residue of a peptide while leaving the remainder available for further cycles.

Why are older protein-sequencing methods still useful

They can confirm protein identity, help characterize proteins when DNA sequence information is unavailable, and support other analytical methods.

What is a protein sequence alignment

An arrangement of two or more sequences that highlights matching residues and differences.

What is BLAST

Basic Local Alignment Search Tool, used to compare a sequence with sequences in a database.

What is a conserved residue

An amino acid that is retained at a corresponding position across related sequences.

What is a gap in a sequence alignment

A position inserted into an alignment to represent an insertion or deletion in evolutionary comparisons.

What is a signature sequence

A characteristic pattern of residues associated with a protein family or function.

What is a consensus sequence

A representation of the most common residues or permitted residue patterns at each position in an alignment.

What is a sequence logo

A visual representation of sequence conservation in which the height of symbols reflects how strongly residues are conserved.

What can protein sequence alignments reveal

Possible evolutionary relationships, conserved functional or structural residues, and similarities among protein families.

How can sequence conservation identify important residues

Residues that remain conserved across related proteins may be essential for folding, stability, binding, or catalytic function.