IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon A. Acid/Base properties 1. carboxyl group is proton donor ! weak acid 2. amino group is proton acceptor ! weak base
3. At physiological pH: H3N+-C -COO- B. Ca is tetrahedral and bonded to 4 different groups 1. L configuration for all natural amino acids (few exceptions) 2. 20 different R groups C. Classification based on R-group - know one example from each 1. Aliphatic-hydrophobic 2. Aromatic-hydrophobic 3. Polar Uncharged-hydrophilic 4. Acidic-hydrophilic 5. B a s i c - hydrophilic V. Polypeptides and Proteins A. Peptide Bond 1. join amino group of one amino acid with carboxyl group of another by forming and amide bond between them ! Peptide Bond 2. C-N bond has partial double bond character B. Peptides and Polypeptides 1. Peptides contain relatively few amino acids linked by peptide bonds: dipeptide, tripeptide, tetrapeptide, …. 2. Polypeptide contains many amino acids and if there are very many amino acids one can call it protein C. Proteins have molecular weights > several thousand and have 3-4 levels of structure 1. Primary Structure (1°) sequence of amino acids connected by peptide bonds 2. Secondary Structure (2°) local conformation of peptide bond backbone stabilized by H-bonds: -helix: intrachain H-bonds & -sheet: interchain H-bonds 3. Tertiary Structure (3°): The complete 3-dimensional structure described by the way the polypeptide chain folds back on itself; stabilized by interactions (bonds) between the amino acid R-groups. Hydrophobic Bonds & van der Walls Interactions – most important 4. Quaternary Structure (4°): only some proteins have 4° structure which is the association of more than one polypeptide Complex Polymer Monomer Simple Polymer (Macromolecule) Monosaccharide Polysaccharide Oligosaccharide (Sugar) (Complex Carbohydrate) Nucleotide Oligonucleotide Nucleic Acid Polypeptide Amino Acid Peptide Protein
An Overview of Protein Functions
Table 5.1 Describing Macromolecular Structure α carbon α-Amino Acids
Amino group Carboxyl group
At low pH pH ~7 at high pH
H
H
+ + H + O - H + O - H O H N C C H N C C H N C C 3 OH + H+ 3 O + H+ 2 O R R R +1 Charge 0 Charge -1 Charge Stereochemistry -- Tetrahedral α-Carbon
L-Alanine D-Alanine O O O O C α-Carbon C
N N C C
C C 20 Different Amino Acids Are Found in Proteins
1-Letter Name 3-Letter 1-Letter Name 3-Letter
A Alanine A M Methionine Met
C Cysteine Cys N Asparagine Asn
D Aspartic Acid Asp P Proline Pro
E Glutamic Acid Glu Q Glutamine Gln
F Phenylalanine Phe R Arginine Arg
I Isoleucine Ile V Valine Val
K Lysine Lys W Tryptophan Trp
L Leucine Leu Y Tyrosine Tyr Fig. 5.16a: Non-polar, hydrophobic aliphatic and aromatic amino acids often cluster together and are found in the interior of proteins
Nonpolar side chains; hydrophobic Side chain
Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I)
Methionine Phenylalanine Tryptophan Proline (Met or M) (Phe or F) (Trp or W) (Pro or P) Fig. 5.16b: Polar uncharged side chains; hydrophilic
Serine Threonine Cysteine (Ser or S) (Thr or T) (Cys or C)
Tyrosine Asparagine Glutamine (Tyr or Y) (Asn or N) (Gln or Q) Fig. 5.16b: Amino Acids with Hydroxyl Groups in their Sidechains (S, T, Y)
These amino acids can also be modified by phosphorylation (addition of phosphate to the hydroxyl group) O- - Side chain-O-H Side chain-O-P-O O Fig. 5.16b: Amino Acids with Hydroxyl Groups in their Sidechains (S, T, Y)
O-PO3 O-PO3
These amino acids can also be modified by phosphorylation (addition of phosphate to the hydroxyl group) O- - Side chain-O-H Side chain-O-P-O O Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H) Note: similar size and shape but different chemical properties
Asparagine (Asn) N Aspartic Acid (Asp) D
Glutamine (Gln) Q Glutamic Acid (Glu) E Aromatic side chains (F,W,Y)
Tyrosine (Tyr) Y Phenylalanine (Phe) F Tryptophan (Trp) W
Ring system in side chain absorbs ultra-violet (UV) light giving us a way of measuring protein concentration
Note similar size and shape of Tyr and Phe (only difference is extra –OH group in Tyr making it more hydrophilic) Special cases:
Glycine is the smallest amino acid and its small side chain can fit into small spaces in protein Glycine (Gly) G
The sulfhydryl group (-S-H) of two cysteines can react to form a covalent disulfide bridge (-S-S-) Cysteine (Cys) C
The side chain of proline is covalently linked back to the α-amino group. This limits the rotation of the side chain and introduces kinks in proteins Proline (Pro) P Amino Acids Whose Structures You Need to Know
Alanine (Ala) Aliphatic hydrophobic
Phenylalanine (Phe) Aromatic hydrophobic
Serine (Ser) Polar uncharged
Lysine (Lys) Aspartic Acid (Asp) Basic Acidic Fig. 5.17: Peptide Bonds Link Amino Acids
Peptide bond
New peptide bond forming
Side chains
Back- bone
Amino end Peptide Carboxyl end (N-terminus) bond (C-terminus)
Peptide Bond: How proteins (polypeptides) are made from amino acids?
H H H H H2O O + O H O + O H3N C C N C C - H3N C C N C C - OH H O O H R1 R2 R1 R2 Amide bond Lone electron pair on N forms second bond O O- O + C C N C C C N C or C C N C H H H The Peptide Bond group is Polar and Planar (the atoms lie on a plane) δ- O The bond is shared between the O and N in δ+ π Cα C N Cα the Peptide Bond Group. Thus, each C=O and H C=N bond behaves like a double bond, and there is no rotation around the bonds connecting these atoms. Furthermore, all of the atoms of the peptide bonding group lie on a plane. Peptide Bond: Structural characteristics
O H Peptide Bonds C C N free rotation is not possible α around C-O and C-N bonds. Cα N C Cα Rotation is possible around H O the single bonds to the Cα’s
Planar Peptide Bond groups joined at Cα’s
Side Chain
Main Chain
Amino Terminus Carboxy Terminus Aspartame a.k.a. NutraSweet - Is a Dipeptide
AspartylAlanineMethylEster, a dipeptide. It is shown in two orientations to demonstrate the 120° bond angles between 120° between the atoms of the peptide bond, and the fact that all of these atoms lie on a plane. Secondary Structure: Local folding of the polypeptide backbone
1.5 Å
Hydrogen Bond
3.6 residues/turn 5.4 Å Hydrogen Bond .5 Å Fig. 5.18: Tertiary Structure Describes overall fold of polypeptide backbone
β-sheet
α-helices
Folding puts some amino acid side chains (Hydrophobic) in interior and some (Hydrophilic) on exterior surface of protein Different functional groups on surface give local sites distinct shapes and specific properties Fig. 5.20: What Bonds Stabilize Tertiary Structure?
1. Hydrophobic and van derWaals Interactions: Packing (clustering) of hydrophobic side chains into interior away from water, keeping most hydrophilic side chains on
surface.
2. Hydrogen bonds of secondary structure elements
3. Ionic interactions between oppositely charged side chains
4. Some proteins are also stabilized by disulfide bonds between pairs of cysteine side chains Fig. 5.21: The Four Levels of Protein Structure
Primary Secondary Tertiary Quaternary Structure Structure Structure Structure
β pleated sheet + H3N Amino end Examples of amino acid subunits
α helix Level of Type of Bond Structure
Between peptide bond groups
Hydrophobic Bond most important + others Fig. 5.22: Changing A Proteins’s Amino Acid Sequence Can Change Its Shape
Secondary Primary Quaternary Function Red Blood Structure and Tertiary Structure Cell Shape Structures 1 Normal Molecules do not hemoglobin associate with one 2 another; each carries 3 oxygen. 4 5 α subunit 6 β β 10 µm 7 α Normal hemoglobin β
1 Exposed Sickle-cell Molecules crystallize hydrophobic hemoglobin into a fiber; capacity 2 region to carry oxygen is 3 reduced. 4 5 α 6 β 10 µm 7 β subunit α β Sickle-cell hemoglobin Fig. 5.23: Amino Acid (primary structure) Sequence Determines Shape increase temperature, change pH, Anfinsen add chemical agents that experiment disrupt hydrogen bonds, ionic bonds (1965) and disulfide bridges Denaturation (Unfolding)
Folding (spontaneous) Normal protein Renaturation Denatured protein (Biologically active) (Biologically inactive) Proteins Form a Variety of Shapes and Sizes
http://www.sci.sdsu.edu/TFrey/ProtStructClass/ Quaternary Structure: Some proteins form stable oligomeric structures containing two or more polypeptides
Antibodies
Hemoglobin Photosynthetic Reaction Center (membrane protein) http://www.sci.sdsu.edu/TFrey/ProtStructClass/ Membrane Proteins: Some are a single polypeptide others have Quaternary Structure
Bacteriorhodopsin Bacterial Photosynthetic Porin Reaction Center (membrane protein) http://www.sci.sdsu.edu/TFrey/ProtStructClass/ Cofactors: Some proteins bind ions and/or organic molecules to help them fulfill their function
Hemoglobin Myoglobin http://www.sci.sdsu.edu/TFrey/ProtStructClass/ Molecules that interact stably have complementary shapes (fit like a lock-and-key or a hand in a glove) so that they can make lots of weak intermolecular bonds