Protein Structure and Analysis lect 3

Flashcards about protein structure and analysis techniques.

Nature of the Amide Bond

The nitrogen dominates into the carbon nitrogen bond, resulting in a delocalized structure and a partially double-bonded nature, restricting free rotation and creating a flat molecule.

Amides vs Amines

Amides have a carbonyl next to the nitrogen and do not protonate the nitrogen, thus not behaving as a nucleophile or a base.

Artificial Peptide Synthesis

Using DCC to activate the carboxylic acid.

Protecting Groups in Peptide Synthesis

Complex chemistry using protecting groups to react two functional parts, two amino acids at a time.

Automated Peptide Synthesizers

Done in the solid state using microbeads as a support, allowing for washing off reagents while retaining the desired peptide.

Use of Short Peptide

Short peptide sequences widely used in biology, particularly for biological signaling and are also found in secretions.

Forensic Proteomics and Fingerprint Analysis

Analyzing the fingerprint's biological components, such as proteins and peptides, to provide a unique biological fingerprint for forensic analysis.

Primary Structure of Protein

Consists of the residue sequence, the order the amino acids are put in from nitrogen to carbon.

Secondary Structure of Protein

Regular structural motifs based around the amino acid backbone, determined by hydrogen bonds between the amide chains.

Tertiary Structure of Protein

The way the protein folds into complex three-dimensional structures.

Quaternary Structure of Protein

When different proteins come together to form a discrete molecular machine.

Secondary Structure Determination

Determined by hydrogen bonds between the amide chains.

Ramachandran Principle

The most likely confirmations for a polypeptide chain include alpha helices, beta strands, and turns.

Alpha Helix

An amino acid chain arranged in a helix with hydrogen bonds along the chain between the amide bonds.

Amino Acids Promoting Alpha Helices

Methionine, alanine, leucine, glutamic acid (glue).

Beta Sheets

Long chains of relatively straight conformations that stack next to each other with hydrogen bonding between different parts of the chain.

Amino Acids Promoting Beta Sheets

Bulky aromatic residues and branched amino acids.

Other Secondary Structures

Turns, beta turns, elongated helices, triple helices, and random coils.

Tertiary Structure Stabilisation

The interactions largely between the side groups, including hydrogen bonding, hydrophobic effect, charged group interactions, pi stacking, and direct covalent bonds (disulfide bridges).

Disulfide Bonds

Two sulfur groups can bond forming disulfide bonds in a protein from cysteine.

Sulfur Bonds in Conditioners

Conditioners breaks the bonds while it's in there, and once you rinse it out, the bonds reform in the shape you want your hair

Quaternary Structure Formation

Multiple polypeptide chains come together by intermolecular forces between the chains.

Insulin

A hormone with two polypeptide chains.

Cytochrome C

Vital for respiration and has five different polypeptides.

Time to Get Single Crystal for XRD

Weeks or months to vary concentration salts, ligands, precipitants, surfactants, temperature, organic solvents just trying to get a single crystal.

Gel Electrophoresis

The most common, easiest way of protein and peptide analysis where charged molecules move between a cathode and anode.

Polyacrylamide Gel Electrophoresis

A hydrophilic gel like a jelly, were the sample is introduced and an electric field is applied and separated by weight.

Sodium Dodecyl Sulfate (SDS)

Forms micelles around the protein, giving it an overall negative charge for separation.

AI in Predict Protein Structure

Can predict the exact protein structure that will result from the amino acid residues.

Crystal

A large lump of solid matter with a repeat unit cell