A Chemical Look at Proteins: Workhorses of the Cell A A Life ciences 1a Lecture otes et 4 pring 2006 Prof. Daniel Kahne Life requires chemistry 2 amino acid monomer and it is proteins that make the chemistry happen. 1
Lectures 6-8: The Molecular Basis of Translation Proteins: The Workhorses of Biology a. A chemical look at proteins i. Introduction to proteins and amino acids ii. Conformational peculiarities of peptide bonds iii. tructures and properties of the twenty natural amino acids iv. A closer look at four special amino acids -- Gly, Pro, Cys, and is. v. Collaborations between amino acids in proteins b. Protein structure i. The four levels of structure ii. A closer look at secondary structure c. Protein folding: i. Anfinsen s experiment ii. Thermodynamic forces involved in protein structures. iii. Thermodynamics of protein folding iv. The Levinthal paradox (the kinetics of protein folding) v. Molecular chaperones Lecture eadings Alberts pp. 55-56, 74-75; McMurry Chapter 18 A polymer is built of repeating monomer units. Biological (atural) Polymers P 2 nucleotide monomer P P C 3 P C 3 P nucleic acid polymer sugar monomer polysaccharide DA is the information carrier of life; along with A it provides instructions to make proteins. ugars are important in energy storage and have other functions that are not well understood. 2
Proteins: Amino acid polymers 2 amino acid monomer protein polymer Proteins have the most diverse shapes of the biological polymers. Proteins are comprised of a wider variety of monomers and has a more varied charge distribution. The different shapes combined with different properties allow proteins to have an incredible range of different functions. ome important functions of proteins Tubulin - cytoskeletal tructural proteins: emoglobin - 0 2 carrier air, skin, eyes, muscle, silk Carriers: espiration and metabolism DA polymerase Bcr-Abl - signal transduction Enzymatic Digestion, blood clotting, replication, transcription, translation egulatory: Coordinate events within and between cells 3
Crystal structure of DA with P53 protein bound The structural variability of DA is limited. Proteins can adopt many structures; predicting what a protein will look like from its sequence is hard. Protein 3D structure depends on primary sequence 3 Lys er Ala Phe Amino acid sequence Folded polypeptide chain Question: What happens if you change a single amino acid in the primary sequence? 4
mall changes at the amino acid level can affect structure: ickle Cell Anemia C is Leu Thr Pro Glu emoglobin: elical, globular structure ormal ed Blood Cells Glutamate at 6 position ormally forms tetramer C is Leu Thr Pro Val ickle -emoglobin: Valine at 6 position Quaternary structure clumps together ickle Cell ed Blood Cells Parts of an amino acid 2 α amino acid building block: amine (basic) carboxylic acid (acidic) α-carbon is tetrahedral groups distinguish amino acids 5
Amino acids with groups are chiral 2 2 L - enantiomer D - enantiomer The building blocks of proteins are chiral. When we string them together the protein is chiral. A review of chirality L - carvone D - carvone caraway spearmint 6
A peptide bond connects two amino acids + 2 2 ' ' amino acid amino acid peptide bond + 2 A protein contains many peptide bonds (from 40 to well over 1000s). Peptide bonds play a role in the shape of a protein. Bonding in ethylene C C Ethylene contains one double bond. A double bond is made up of a σ and a π bond. π bonding orbitals of ethylene 7
Peptide bonds are planar like ethylene Ethylene contains a carbon-carbon double bond that is not free to rotate. flat twist breaks one bond The peptide bond is typically drawn as a single bond, implying that it is free to rotate. owever, it is known that it can not. Why not? flat twisted amide Peptide Bonds have partial double bonds : 60% 40% We can draw more than one Lewis dot structure without changing the position of the atoms. We call these structures resonance structures. esonance structures are drawn using DUBLE- EADED arrows. This notation is reserved strictly for resonance 8
A peptide bond is flat and polar ' δ+ ' dipole (separated charge) These resonance structures together represent the structure of a peptide bond. ne resonance form makes it easy to see that peptide bonds are flat and have strong dipoles. Dipoles are important for the shape and function of a protein. δ- Geometric isomerism around amide bonds Trans: The α-carbons are on opposite sides (strongly favored for all amino acids except one) Cis: The α-carbons are on the same side 9
Partial double bond character of the peptide bond constrains the polypeptide conformation but... ' '' ''' groups play a major role in the particular three dimensional structure that forms. Acidic 2 C C 2 C C 2 C C Polar 2 C C 2 C C 2 C C 2 C C C 2 C Aspartic Acid Asp D C 2 C 2 C Glutamic Acid Glu E C 2 C 2 Aspargine Asn C 2 C 2 C 2 Glutamine Gln Q C C 3 Threonine Thr T C 2 erine er C 2 Cysteine Cys C 2 2 C C C 3 Alanine Ala A C C C 2 C C 3 C 3 Leucine Leu L 2 onpolar 2 C C C C 3 C C C C 3 C 2 C 3 C 3 Valine Val V Isoleucine Ile I 2 20 natural amino acids C C C 2 C 2 C 3 Methionine Met M Important for Peptide hape 2 C C Glycine Gly G C Proline Pro P 2 2 Basic C C C 2 istidine is C C C 2 Phenylalanine Phe F 2 Cyclic 2 C C C 2 C 2 C 2 C 2 2 Lysine Lys K C C C 2 Tyrosine Tyr Y 2 2 C C C 2 C 2 C 2 C 2 Arginine Arg C C C 2 Tryptophan Trp W 10
pk a values for amino acids with ionizing side chains acid conjugate base pk a Aspartic Acid Asp 3.9-4.0 Glutamic Acid Glu 4.3-4.5 istidine is 6.0-7.0 Cysteine Cys 9.0-9.5 Tyrosine Tyr 10.0-10.3 Lysine Lys 3 2 10.4-11.1 Arginine Arg 2 2 2 12.0 erine er 13.0 Distribution of the amino acids in ature Amino Acid Frequency in proteins (%) Leucine Alanine Glycine erine Valine Glutamic acid Threonine Arginine Lysine Aspartic acid Isoleucine Proline Asparagine Glutamine Phenylalanine Tyrosine Methionine istidine Cysteine Tryptophan 9.0 8.3 7.2 6.9 6.6 6.2 5.8 5.7 5.7 5.3 5.2 5.1 4.4 4.0 3.9 3.2 2.4 2.2 1.7 1.3 Increasing Frequency 11
Four special amino acids 2 C 2 2 glycine proline cysteine histidine Glycine: The mallest Amino Acid 2 First amino acid discovered in 1820 from gelatin. = hydrogen educed steric hindrance: can adopt a wider range of peptide conformations compared to other amino acids. 12
Trans Proline Cis eavily favored C lightly favored In proline, the trans isomer is only slightly favored over the cis isomer. Thus, proline can readily adopt the cis conformation. C Cysteine and Cystine cysteine cystine Disulfide bonds constrain protein conformation 13
Disulfide Bonds and Perms educe Curl xidize What is pk a? + K a = pk a = - log K a K a = p 7.5 4.5 pk a = - log [ + ] = p 7 6.5 6 5.5 5 Titration Curve of istidine 4 1 1.2 1.4 1.6 1.8 2 Volume of Base (ml) 14
istidine can shuffle between forms 2 slight increase in physiological p (more basic) slight decrease in physiological p (more acidic) 2 ydrolysis of a peptide bond chymotrypsin acrosin Factor X ' Uncatalyzed rate 7-400 years + 2 + 2 ' Enzymes make the rate of reactions go faster. 15
Amino acids cooperate in catalysis Asp 102 er is chymotrypsin er 195 is 57 The catalytic triad: serine, histidine, and aspartic acid work together to cleave amide bonds Asp The aspartate -bonds to the histidine side chain, perturbing its pka and making it more basic. This makes it easier for histidine to remove a proton from serine during the reaction. Take home messages Proteins are polymers of amino acids. Amino acids are connected through peptide bonds. The nature of the peptide bond constrains the shape of the polymer. onbonded interactions between side chains also constrain the shape of the peptide backbone. There are twenty amino acids, each containing unique side chains. Amino acids can work in concert in a polypeptide chain to generate new functions. Question: ow does a straight chain polymer of amino acids fold?? 16