Lecture 2 The Principal Aspects of Protein Structure Flashcards
What kind of bond joins amino acids?
Proteins consist of joined amino acids
- They are joined by a peptide bond (Also called an Amide Bond)
- ATP is required to produce a peptide bond
What is a polypeptide?
Many joined amino acids are called a Polypeptide
- Amino acids in a polypeptide are called amino acid residues
- A protein consists of one or more polypeptide chains
How are residues read?
A polypeptide chain has direction
- The order of residues is read from the N Terminal to the Carboxyl (C-) [Acid] Terminal
- The residue order of a protein is called its sequence
- This sequence is unique to that protein
What are the parts of a polypeptide chain?
The polypeptide chain has a regular repeating part
- This region is called the main chain
- The main chain atoms are - N H Cα Hα C O (Also referred to as the backbone of a polypeptide)
- The variable region of a polypeptide are the side chains of the amino acids
What are the features of the peptide bond?
- partial double bond characteristics, which shortens the C-N bond from a single bond towards double bond length
- double bond means the peptide group is rigid
- It acts as a stabiliser
- The peptide bond is in the Trans conformation (trans across peptide bond)
- The H of the amino group is nearly always trans to the O of the carbonyl group
- Only proline can allow Cis conformation bonding
- Found in the chain as Xaa-Pro = where Xaa is any other amino acid
- The side chains of all the other amino acids would clash were they to be in the cis conformation
What are some characteristics of protein structure, use an example.
The residue sequence is unique to that protein
-Proven by Sanger in 1953/ He used insulin in his studies
Eg. - Cysteine residues have a highly reactive SH group
- In an oxidising environment cysteines can pair to form Disulphide bonds
In what ways can the structure of a protein be described?
The Primary Structure of a Protein: The amino acid sequence (and disulphides if any)
The Secondary Structure of a Protein: The spatial arrangement of amino acids near to one another in the linear sequence
- Proteins can contain regular repeating units (Proposed by Pauling and Corey in 1951)
Two repeating structures were proposed: - The α-helix - The β -pleated sheet
What is the α helix structure and what are its characteristics??
- The first repeating structure proposed hence α -The structure is a regular tight coil
- The structure has an axis central to the coil
- There is a 100o rotation about the axis from one residue to the next
- 3.6 residues per turn
- For main chain atoms it is ~ 5Å diameter
- The distance along the axis from one residue to the next is 1.5Å = This is called the rise per residue of the helix
- The PITCH of a helix = Number of residues per turn x Rise: = 3.6 x 1.5 = 5.4Å
- The hydrogen bonding pattern in an α-helix is very specific
- The Carbonyl Oxygen of residue (i) is bonded to the Hydrogen of an amide in residue (i+4)
- Myoglobin is a protein whose secondary structure consists primarily of a-helices
What is the β-pleated structure and what are its characteristics?
- The second type of repeating structure proposed
- Comprised of strands of polypeptide - Known as β-strands
- The residues are almost fully extended in the strands
- Two forms of β-pleated sheet exist: -antiparallel -strands in the sheet run in opposing directions to each other
- parallel -strands run in the same direction to each other
- Antiparallel sheets are slightly more stable than parallel sheets
- The hydrogen bonding is slightly distorted in parallel sheets but is not in antiparallel sheets
- The distance from Cα to Cα for a β-strand in an antiparallel conformation is 3.5Å
- Concanavalin A is a protein whose secondary structure consists primarily of β-pleated sheets
- Beta sheets are often twisted rather than flat
- Sharp turns are found within proteins to keep them as compact and globular structures = These are known as β-turns
- Usually four residues and often glycine is in the third position
What is another type of secondary structure Eg. Collagen Helix?
THE COLLAGEN HELIX:
- Collagen is the most abundant animal protein
- Around 1000 residues in a collagen chain
- Nearly every third residue is glycine
- The collagen helix has a rise ~2.9Å and three residues per turn
- The Pitch = 3 x ~2.9 = ~8.7Å
- Different from the α-helix
- In the collagen structure three helices wind around each other
- Glycine always packs on the inside of the triple helices
- Steric hindrance bars any other amino acids from being on the inside of the collagen triple helix
- Hydrogen bonding within the triple helix are between strands
What is another type of secondary structure Eg. 3 (10) helix ?
3(10) HELIX
- Three residues involved linearly in the chain
- Ten atoms from a Hydrogen bond donor to its Hydrogen bond acceptor
