Section Week 3. Junaid Malek, M.D.

Transcription

1 Section Week 3 Junaid Malek, M.D.

2 Biological Polymers DA 4 monomers (building blocks), limited structure (double-helix) RA 4 monomers, greater flexibility, multiple structures Proteins 20 Amino Acids, greatest variety of possible structures

3 Proteins 4 major functions Structural Enzymatic Carriers Regulatory

4 Amino Acids: Components Major components include amine group, carboxylate group and the side chain Remember that 19 of 20 amino acids are chiral Amine and carboxylate groups participate in peptide linkages

5 Amino Acids: Structure Important to memorize structures, 3-letter and 1-letter codes for the exam

6 The Peptide Bond 3 alanine + 3 serine peptide (amide) bond in alanylserine

7 Double bond property of a peptide bond The reason why a peptide bond is not capable of rotating Rotation also restricted by R groups 2 2

8 cis vs. trans nomenclature 2 R R' 2 R R' Trans: The α-carbons are on opposite sides Cis: The α-carbons are on the same side

9 Why is trans favored over cis? Trans configuration favored due to less steric hindrance between R side-chain and peptide backbone eavily favored Trans Cis

10 Glycine nly achiral amino acid Adds flexibility to any polypeptide chain Less steric hindrance

11 Proline The only exception to the cis vs. trans rule Because the nitrogen contains two substituents, both cis and trans contain steric strain. Therefore, they exist in nearly equal proportions. Slightly favored C Trans Cis C

12 Cysteine Sulfur-containing amino acid Capable of undergoing reductionoxidation reactions Don t need to know specifics of red-ox reactions Just know that two distinct states exist that are not spontaneously interconvertable Disulfide bonds are important for protein folding

13 istidine Can act as an acid or a base ote that pka is near physiological p

14 Draw the following oligopeptide at p=7 Lys-Phe-Met-Arg Arg Phe S + 3 Lys Met

15 Draw the following oligopeptide at p=7 Gln-Ile-Glu-Thr Ile Thr Gln - Glu

16 Circle the ydrophobic Groups Put a square around the alcohol group Arg Phe Ile Thr S Lys Met Gln Glu

17 More Questions Phe 2 + Arg 2 Ile Thr S Lys Met Gln Glu Are these oligopeptides chiral? Yes Which of the two peptides interacts best with DA? Why? The peptide on the left, because it has two positively charged groups that can interact with negatively charged DA

18 More Questions ow many different pentapeptides can one make using the amino acids Gly, is, Cys, Ile, Try? 5!=5x4x3x2x1=120 Which peptide would you expect to be more soluble in water, one rich in aspartate and lysine or one rich in valine and alanine? Aspartate and lysine have side-chains capable of -bonding while valine and alanine do not

19 Protein Structure Primary Structure Tertiary Structure Secondary Structure Quaternary Structure

20 Primary Structure Linear sequence of amino acids bonded by peptide bonds o folding or side-chain interaction By convention, written from -terminus to C-terminus As with DA and RA, directionality matters! The primary sequence of amino acids will determine how the protein folds

21 Secondary Structure Local structures adopted by contiguous amino acids α-helix elical corkscrew structure that is typically right-handed due to chirality of amino acids Carbonyl groups all point in same direction β-pleated sheet Form sheet-like structures represented by arrows. rigin of arrow indicates amino terminus while arrowhead indicates carboxyl terminus. Carbonyl groups point in alternating directions

22 α-helix: Myoglobin

23 β-sheet: Superoxide Dismutase

24 α-helix and β-sheet: Acetylcholinesterase

25 Tertiary Structure Folding of a single polypeptide chain Forms due to interactions among R-groups and secondary structures Allows for amino acids far away on the primary chain to lie in close proximity to one another All information allowing a protein to form tertiary structure can be found in the primary sequence

26 Quaternary structure Interaction between multiple tertiary structures (from distinct polypeptide chains) Classic example is hemoglobin

27 Why does a protein fold? Anfinsen experiment: does a primary structure determine protein folding? A protein (Ribonuclease A) was denatured using urea and reduced to break disulfide bonds between cysteine residues bservation made that when urea was removed, the denatured polypeptide chain folded back into a compact structure When protein oxidized, regained 90% of original function

28 Protein folding In a second experiment, the denatured polypeptide chain was first oxidized before removing urea Result was a non-functional protein trapped in a non-native conformation by incorrect pairing of disulfide bonds These bonds prevented the protein from achieving its native structure

29 The Anfinsen Experiment: Conclusion Given that we prevent premature oxidation (and hence incorrect disulfide bridging), the protein will find its lowest energy conformation Thus, all information for proper protein folding can be found in its primary sequence! This is in turn determined by RA sequence, which is determined by DA sequence We can therefore conclude that all complex protein folding can be determined by the sequence of just 4 different base pairs!!!

30 What drives protein folding? Thermodynamics! ydrogen bonding along the backbone ydrogen bonds of the R groups with each other or with the backbone Ionic interactions between the R groups Van der Waal s interactions between R groups Disulfide bridges between cysteine residues

31 The ydrophobic Effect Tendency for non-polar substance to interact with each other rather than with water This leads to burial of non-polar sidechains within the interior of a protein as it collapses to form a globular structure Driven by the energetically unfavorable situation of having water molecules organized and surrounding a non-polar molecule Driven also to a lesser extent by Van der Waal s forces

32 Question: Protein Folding Segments of proteins that connect successive regions of secondary structures are referred to as turns or bends. These are often rich in glycine and proline residues. Why? Glycine is found in bends because of its small size Proline constrains the conformation a polypeptide chain can adopt, thus it is often the initiator of bends

33 Question: -bonding and Secondary structure Indicate whether the following amino acids can form -bonds to participate in the formation of α-helices or β-sheets Arginine Glutamate Glycine Phenlyalanine Proline Threonine

34 Question: Amino acid interactions Indicate the strongest interaction that can form between the side chains of the following amino acid pairs: Pro-Leu Van der Waal s Arg-Thr ydrogen bonding Ile-Val Van der Waal s

35 Question: Amino acid interactions More amino acid pairs: Tyr-Phe Van der Waal s Arg-Asp Ionic Cys-Met Van der Waal s

36 Question: Amino acid interactions More amino acid pairs: Gly-Ala Van der Waal s is-glu Ionic Cys-Cys Disulfide bond

37 Gibbs Free Energy

38 Gibbs Free Energy If ΔG is negative, the process is favored (energy is released) Two components of free energy are enthalpy () and entropy (S) If Δ is negative, the reaction (or system) is exothermic If Δ is positive, the reaction is endothermic Remember your Second Law of Thermodynamics (the entropy of the universe is always increasing)

39 What can we say about Δ and ΔS? Δ ΔS Reaction (-) (+) Spontaneous (+) (-) on-spontaneous (-) (-) (+) (+) Temperature dependent Temperature dependent

40 Gibbs Free Energy We can relate Keq and free energy using the equation ΔG =-RTlnKeq R=Equilibrium constant T=Temp (Kelvin) At equilibrium, there is a relationship between the chemical equilibrium and the change in free energy (ΔG) that occurs as a result of the chemical reaction. The change in free energy is related to the natural log of the equilibrium constant. If ΔG is negative, the process is favored (energy is released)