IV. -Amino Acids: carboxyl and amino groups bonded to -Carbo n
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. Aromat ic - h y drophobic
3. Polar Uncharged-hydrophilic 4. A c i d i c-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
Monomer Simple Polymer Complex Polymer (Macromolecule)
Monosaccharide (Sugar)
Oligosaccharide Polysaccharide
(Complex Carbohydrate)
Nucleotide Oligonucleotide Nucleic Acid
Amino Acid Peptid e Polypeptide
Protein
Table 5.1
An Overview of Protein Functions
Describing Macromolecular Structure
Amino group Carboxyl group
α carbon α-Amino Acids
H3N C C O OH
+
R
H
H3N C C O O
+
R
H
H2N C C O O
R
H
- H+ + H+
- H+ + H+
+1 Charge 0 Charge -1 Charge
At low pH pH ~7 at high pH
Stereochemistry -- Tetrahedral α-Carbon
L-Alanine D-Alanine
α-Carbon C
C
C
O O
N
C
C
C
O O
N
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
G Glycine G S Serine Set
H Histidine H T Threonine Thr
I Isoleucine Ile V Valine Val
K Lysine Lys W Tryptophan Trp
L Leucine Leu Y Tyrosine Tyr
20 Different Amino Acids Are Found in Proteins
Nonpolar side chains; hydrophobic Side chain
Glycine (Gly or G)
Alanine (Ala or A)
Valine (Val or V)
Leucine (Leu or L)
Isoleucine (Ile or I)
Methionine (Met or M)
Phenylalanine (Phe or F)
Tryptophan (Trp or W)
Proline (Pro or P)
Fig. 5.16a: Non-polar, hydrophobic aliphatic and aromatic amino acids often cluster together and are found in the interior of proteins
Fig. 5.16b: Polar uncharged side chains; hydrophilic
Serine (Ser or S)
Threonine (Thr or T)
Cysteine (Cys or C)
Tyrosine (Tyr or Y)
Asparagine (Asn or N)
Glutamine (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)
Side chain-O-H Side chain-O-P-O- O
O-
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)
Side chain-O-H Side chain-O-P-O- O
O-
O-PO3 O-PO3
Aspartic acid (Asp or D)
Glutamic acid (Glu or E)
Lysine (Lys or K)
Arginine (Arg or R)
Histidine (His or H)
Note: similar size and shape
but different chemical properties
Glutamine (Gln) Q Glutamic Acid (Glu) E
Asparagine (Asn) N Aspartic Acid (Asp) D
Aromatic side chains (F,W,Y)
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)
Tyrosine (Tyr) Y Phenylalanine (Phe) F Tryptophan (Trp) W
Special cases:
Glycine is the smallest amino acid and its small side chain can fit into small spaces in protein
Glycine (Gly) G
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
The sulfhydryl group (-S-H) of two cysteines can react to form a covalent
disulfide bridge (-S-S-) Cysteine (Cys) C
Alanine (Ala) Aliphatic hydrophobic
Phenylalanine (Phe) Aromatic hydrophobic
Serine (Ser) Polar uncharged
Aspartic Acid (Asp) Acidic
Lysine (Lys) Basic
Amino Acids Whose Structures You Need to Know
Fig. 5.17: Peptide Bonds Link Amino Acids
Peptide bond
New peptide bond forming
Side chains
Back- bone
Amino end (N-terminus)
Peptide bond
Carboxyl end (C-terminus)
Peptide Bond: How proteins (polypeptides) are made from amino acids?
The π bond is shared between the O and N in the Peptide Bond Group. Thus, each C=O and 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.
H3N C C O OH
+
R1
H
N C C O O-
R2
H
H
H
H2O
N C C O O-
R2
H
H3N C C O +
R1
H
Amide bond
C C N C O
H
H
Lone electron pair on N forms second bond
C C N C O -
+ C C N C
O
H H or
The Peptide Bond group is Polar and Planar
(the atoms lie on a plane)
Cα C N Cα O
H
δ-
δ+
Main Chain
Side Chain
Amino Terminus Carboxy Terminus
Peptide Bond: Structural characteristics
Cα Cα C
C Cα N
N
H
H O
O
Planar Peptide Bond groups joined at Cα’s
Peptide Bonds free rotation is not possible around C-O and C-N bonds. Rotation is possible around the single bonds to the Cα’s
AspartylAlanineMethylEster, a dipeptide. It is shown in two orientations to demonstrate the
120° bond angles between between the atoms of the peptide bond, and the fact that all of these
atoms lie on a plane.
120°
Aspartame a.k.a. NutraSweet - Is a Dipeptide
.5 Å
Secondary Structure: Local folding of the polypeptide backbone
1.5 Å
Hydrogen Bond
3.6 residues/turn 5.4 Å Hydrogen
Bond
Fig. 5.18: Tertiary Structure Describes overall fold of polypeptide backbone
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
β-sheet
α-helices
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 Structure
Secondary Structure
Tertiary Structure
β pleated sheet
Examples of amino acid subunits
+H3N Amino end
α helix
Quaternary Structure
Level of Structure
Type of Bond
Hydrophobic Bond most important + others
Between peptide bond groups
Primary Structure
Secondary and Tertiary Structures
Quaternary Structure Function Red Blood
Cell Shape
β subunit
β subunit β
β
α
α
Exposed hydrophobic region
Molecules do not associate with one another; each carries oxygen.
Molecules crystallize into a fiber; capacity to carry oxygen is reduced.
Sickle-cell hemoglobin
Normal hemoglobin
10 µm
10 µm
Sick
le-c
ell h
emog
lobi
n N
orm
al h
emog
lobi
n 1 2 3 4 5 6 7
1 2 3 4 5 6 7
β
β α
α
Fig. 5.22: Changing A Proteins’s Amino Acid Sequence Can Change Its Shape
Normal protein Denatured protein
Denaturation
Renaturation
Fig. 5.23: Amino Acid (primary structure) Sequence Determines Shape
(Biologically active) (Biologically inactive)
increase temperature, change pH, add chemical agents that disrupt hydrogen bonds,
ionic bonds and disulfide bridges
(Unfolding)
Folding (spontaneous)
Anfinsen experiment (1965)
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
Hemoglobin Photosynthetic Reaction Center (membrane protein)
Antibodies
http://www.sci.sdsu.edu/TFrey/ProtStructClass/
Photosynthetic Reaction Center (membrane protein)
Membrane Proteins: Some are a single polypeptide others have Quaternary Structure
Bacteriorhodopsin Bacterial Porin
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
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