Lecture 3 The Principal Aspects of Protein Structure II Flashcards
What are the three basic structures of a protein?
Primary Structure:
-The amino acids(polypeptide chain) (and disulphides)
Secondary Structure:
- Local sequence conformation
- Particularly repeating units
- α-helix
- β-pleated sheet
The Tertiary Structure of a Protein:
- The spatial arrangement of amino acids usually far
apart from each other in the linear sequence
+Quaternary structure does not exist for all proteins
What are some example proteins consisting of a single polypeptide chain?
- Myoglobin and Concanavalin A
- These are example proteins consisting of single polypeptide chains
- Each has a specific structure
Whats the definition of the native structure of a protein?
- The Native Structure of a Protein
- The three dimensional structure of a protein when in a physiological environment.
What is the structure of Ribonuclease A (RNase A) ?
- The structure of RNase A comprises α-helices and β-Sheets
- 124 amino acids
- four disulphide bonds
In the native structure the correct arrangement is: - 26-84 40-95 58-110 67-72
- RNase A hydrolyses RNA
- Experiments with RNase A determined the key
factors involved in producing a native structure
What background theory did Christian Anfinsen use for his experiment?
- Christian Anfinsen’s Experiments
Background to Experiment: - In a solution of either Urea (8M) or Guanidine
Hydrochloride (6M) proteins lose their native structures - Proteins Denature
- Unfolded protein - Random Coil
-Mercaptoethanol is a reducing agent which breaks
disulphide bonds
What was the first of Christian Anfinsen’s experiment and what results did it produce?
-Dissolve RNase A in a solution of β-Mercaptoethanol and 8M Urea = Result: The RNase A completely loses enzyme activity
- Denatured RNase A
- Then remove the β-Mercaptoethanol and 8M Urea
- Involves a procedure called Dialysis
- Oxidise the cysteine residues to reform disulphide bonds = Result: The RNase A spontaneously regains all its enzyme activity
- Renatured RNase A
+Significant Conclusion
- The amino acid sequence of RNase A provides the
information needed to specify its native structure
- THIS IS TRUE FOR ALL PROTEINS (IMPORTANT)
- The Primary Structure of a protein dictates its
Tertiary Structure
What was the second of Christian Anfinsen’s experiment and what results did it produce?
- Denatured RNase A
- Initially remove ONLY the -Mercaptoethanol but RETAIN the 8M Urea = Result: RNase A slowly regains ~1% enzymatic activity
+Reason: There is only one correct arrangement of
disulphides but 105 different combinations - 1/105 approx.= 1%
-Now add trace amounts of β-Mercaptoethanol - The disulphide bonds can rearrange = Result: After ~10 hours RNase A completely regains
its enzymatic activity - thermodynamics has driven the protein to its
native structure
+ Further Significant Conclusion: - The thermodynamically most stable structure of
RNase A is its native structure - Also true for all proteins
What the quaternary structure?
-definition: The spatial arrangement in a protein made up from more than one polypeptide chain
- Each chain is called a subunit of the protein
- They are referred to by either Greek or Alphabetic
letters
What is an example protein with a quaternary structure?
- Haemoglobin is an example protein with quaternary
structure - It has FOUR separate polypeptide chains
- Two identical alpha subunits
- Two identical beta subunits
- The structure is an α(2)β(2) configuration
Why does the quaternary structure exist?
-Enables smaller quantities of genetic material to create
larger proteins and structures
- Example: Viruses use 60 repeats of a four subunit
structure to produce a highly symmetric coat
- Quaternary structure is excellent for regulating protein function
- This is through the allosteric effect
- A change in one subunit induces a change in
another
What is protein conformation ?
-definition: The three-dimensional arrangement of a proteins atoms in its structure
- Protein conformation is independent of the
number of chains in the protein
- A protein is not always in its native
conformation
Protein folding:
- The principal factor governing protein folding is the
burying of hydrophobic side chains
- This forms the Protein Core
- Proteins fold via the formation of stable partially correct secondary structure intermediate stages
Explain Levinthal’s paradox.
Levinthal’s Paradox:
- Levinthal calculated that a protein containing 100
residues would take 1.6 x 1027 YEARS to fold to a
native structure by using random chance at getting
the correct structure
- RNase A folds in seconds to its native structure
Conclusion: Proteins do not fold via a random pathway
Answer: Proteins fold to their native structures via the formation of stable partially correct secondary structure features as intermediate stages in the folding process
= This results in proteins taking only seconds to form their native structures
