Amino Acids, Peptides and proteins

What is an oligomeric protein?

If the polypeptides are identical

What is a protomer?

The two identical subunits in an oligomeric protein

What are conjugated proteins?

Proteins that contain chemical components in addition to amino acids.

What is 4-hydroxyl proline?

A derivative of proline commonly found in collagen

What is y carboxy glutamate?

Found in blood crossing portien prothrombin

What is desmosine?

Found in elastine

What is ornithine and citrulline?

key intermediates of the biosynthesis of arginine and in the urea cycle.

What are the covalent peptide bond constraints there structure of a protein?

• In a polypeptide the α carbons of adjacent amino acid residues are separated by three covalent bonds, arranged as Cα-C-N-Cα

• X ray diffraction studies indicated that the 6 atoms (Cα-C-N-Cα + oxygen bound to carbonium +hydrogen bound to nitrogen) of this

  peptide group lie in a single plane.

• The oxygen has a partial negative charge and the nitrogen a partial positive charge, setting up a small dipole.

• Therefore, due to the planarity of this peptide group and the partial double-bond character, the peptide C-N bonds cannot rotate freely.

• The peptide bond is rigid and planar

How is the peptide bond is rigid and planar?

• The peptide conformation is defined by three dihedral angles called Φ (Phi), Ψ (Psi), Ω (Omega) reflecting the rotation about each of the three repeating bonds in the peptide backbone.

• A dihedral angle is the angle of intersection between two planes

What is the secondary structure - alpha helix?

• A α helix is generated when a single polypeptide chain twists around on itself to form a rigid cylinder. A Hydrogen bond forms between every fourth peptide bond, linking the C=0 of one peptide bond to the N-H of another. Note that all of the N -H groups point up whereas the C=O point down. This gives polarity to the helix.

• The right-handed helices are the most common.

• The R groups are on the outside of the helix

• A turn every 3.6 residues

What are the destabilising factors of alpha helix?

• Negatively (Asp, Glu) and positively (Lys, Arg) charged AA destabilise the structure.

• The shape of some polar uncharged AA (Asn,Glm,Ser, Thr and Cys) destabilise the structure)

• Proline: destablising kink

• Gly: too high flexibility.

• Alanine has the greatest tendency to form α helices

What is the secondary structure - beta strands and sheets?

• In the β sheet adjacent peptide chains run in opposite (parallel) directions. The hydrogen bond forms between peptides in different strands.

• Hydrogen bonding is stronger in antiparallel β sheets because the

  C=O and N-H groups are better aligned.

• Flexible loops and turns link region of secondary structure: Pro, Thr, Ser and Gly are common residues here

What are beta turns?

• β turns are common in globular proteins, as this structure allow some amino acid residues to form turns and loops and assume a very compact structure.

• β turns are the connecting elements that link successive runs of a helix or β conformation.

• Gly and Pro residues often occur in β turns, the former because it is

  small and flexible, the latter because peptide bonds involving the

  imino nitrogen of proline can assume readily the right configurati

What is circular dichroism spectroscopy?

• Any form of structural asymmetry in a molecule

gives rise to differences in absorption of polarized

light.

• Measurement of this difference is called circular

dichroism spectroscopy.

• Since the circular dichroism spectroscopy curves are different for α and β helices and unstructured proteins, the CD spectrum can give an estimate of the fraction of the protein made by the two common secondary structures.

What are fibrous proteins?

have polypeptides chains arranged in long strands or sheets

What are globular proteins?

have polypeptide chains arranged into a spherical or globular shape

What are membrane proteins?

have polypeptide chains embedded in hydrophobic lipid membranes

What are intrinsically disordered proteins?

have polypeptide chains lacking stable tertiary structures

What is alpha keratin?

• The fundamental structure is a repeating element of a secondary structure, for example α helices.

• All fibrous proteins are insoluble in water, a property conferred by the high concentration of hydrophobic AA both in the interior and in the surface of the protein.

• α Keratin is made of two α helices oriented in parallel and wrapped around each other in a super twisted coiled coil.

• The cross - links stabilising the quaternary structure are dislufite bonds that confer strength to

What is collagen?

• The fundamental structure is a repeating element of a secondary structure, α helices.

• As a protein fundamental to confer strength, collagen is abundant in connective tissues, such as cartilages and bones.

• 3 helically intertwined α helices.

• Genetic mutations in the genes encoding collagen give rise to

• Osteogenesis Imperfecta and Marfan syndrom

What is silk fibroin?

• The protein of silk, fibroin is produced by spiders.

•Its polypeptide chains are predominant in β

conformation

• Silk does not stretch because the β conformation is highly extended. The structure is flexible because the sheets are kept together by weak interactions

What are globular proteins?

• Globular proteins are roughly spherical in shape and might have

several types of secondary structures folded together .

• They are often soluble as the hydrophobic residues are hidden

inside whereas hydrophilic stick outside.

• Most enzymes such as chymotrypsin and lysozyme and regulatory proteins are globular proteins.

• Other examples of globular proteins:

• Proteins transporting ions and molecules such as

hemoglobin

• Proteins important to defend us against pathogens:

antibodies and

cytokines

• Proteins implicated in muscle contraction:

actin, myosin

What is myoglobin?

• The function of myoglobin is to store oxygen and facilitate oxygen diffusion in rapidly contracting muscle.

• it’s a single polypeptide chain with a single iron protoporphyrin or Heme group.

• The backbone of myoglobin is α helices and β turns.

• The molecule is so compact that the interior has room only for four molecules of water

What is the graphical representation of oxygen binding to haeme?

• Y is the fraction of myoglobin bound to oxygen

• [L] is the concentration of the ligand, oxygen

• Kd is the dissociation constant

• The reaction can be formulated as P+L = PL, where P is a protein, L a ligand and PL the protein-ligand.

• Kd= [P] [L]/ [PL]

What is a haemoglobin?

• Hemoglobin is made of two an and two B polypeptides.

• Hemoglobin subunits are structurally related to myoglobin and carry oxygen in the blood of animals.

• Hemoglobin transitions between two major conformations: T state and R state.

• Oxygen can bind to hemoglobin in both states, but it has more affinity for the R state.

• When there is no oxygen bound the most stable conformation is the T state.

• When oxygen binds to the T state, it triggers a conformational change to the R state.

How is protein structure determined by x ray crystallography?

Steps required:

• protein purification

• Crystallize the protein

• Collected diffraction data

• Calculate electron density

• Fit known amino acids residues into density