Lecture Three: Protein Structure contd….
[Chapter 2 – Berg, Tymoczko & Stryer]
(Figures in Red are for the 7th Edition)
 Primary Structure
 The _____________ (and disulphides)
 Secondary Structure
 Local sequence conformation
 Particularly repeating units
 -helix
 -pleated sheet
 DEFINITION
 The Tertiary Structure of a Protein
 The spatial arrangement of amino acids usually far
apart from each other in the linear sequence
 Myoglobin (Figure 2-48 pages 47) (2-43, page 46)
and Concanavalin A
 These are example proteins consisting of ______
______________ chains
 Each has a specific structure
 DEFINITION
 The Native Structure of a Protein
 The three dimensional structure of a protein when in a
_______________________
 (Figure 6-3, page 166) (6-3, page 183)
 Ribonuclease A (RNase A)
 The structure of RNase A comprises -helices and -Sheets
 124 amino acids
 ________ 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
 Christian Anfinsen’s Experiments
 Background to Experiment
 In a solution of either Urea (8M) or Guanidine
Hydrochloride (6M) proteins lose their _______________
 Proteins Denature
 Unfolded protein - Random Coil
 -Mercaptoethanol is a _______________ which breaks
disulphide bonds
 Experiment One
 Figure 2-58, page 51 (2-53, page 49)
 Dissolve RNase A in a solution of -Mercaptoethanol and
8M Urea
 Result: The RNase A completely loses enzyme
activity
 Denatured RNase A
 Then remove the -Mercaptoethanol and 8M Urea
 Involves a procedure called _________
 Oxidise the cysteine residues to _______ 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
 The Primary Structure of a protein dictates its
Tertiary Structure
 Experiment Two
 Figure 2-58 & Figure 2-59, pages 51 & 52 (2-53, p.49, 2-54, p.50)
 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  1%
 Now add trace amounts of -Mercaptoethanol
 The disulphide bonds can _________
 Result: After ~10 hours RNase A completely regains
its enzymatic activity
 ________________ has driven the protein to its
native structure
 Further Significant Conclusion
 The thermodynamically most stable structure of
RNase A is its ______________
 Also true for all proteins
 Footnote:
 Anfinsen obtained the 1972 Nobel Prize for Chemistry for
his work with RNase A
 DEFINITION
 The Quaternary Structure of a Protein
 The spatial arrangement in a protein made up from
more than one polypeptide chain
 Each chain is called a _________ of the protein
 They are referred to by either Greek or Alphabetic
letters
 Haemoglobin (Look also at Figure 2-54, page 50) (2-49, p.48)
 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 2 2 configuration
 Reasons for quaternary structure
 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 _____________
____________
 This is through the allosteric effect
 A change in one subunit induces a change in
another
 DEFINITION
 Protein Conformation
 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 ______________ in its native
conformation
 Protein folding
 The principal factor governing protein folding is the
burying of ____________ side chains
 This forms the Protein Core
 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
 Summary of Lecture Three:
 The Tertiary Structure of a protein is the conformation
adopted by a single polypeptide chain
 The Quaternary Structure of a protein is the
conformation adopted by a protein containing more than
one polypeptide chain
 Protein folding buries hydrophobic residues
 The Protein Core
 Proteins fold via the formation of stable partially correct
secondary structure intermediate stages