Figure 4-1 General structural formula for α-amino acids.
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1 Figure 4-1 General structural formula for α-amino acids. Voet Biochemistry 3e Page 65
2 Figure 4-2 Zwitterionic form of the α-amino acids that occur at physiological ph values. Voet Biochemistry 3e Page 65
3 Figure 4-3 Condensation of two α-amino acids to form a dipeptide. Voet Biochemistry 3e Page 68
4 Figure 4-4a Structure of phenylalanine. (a) Ball and stick form. Voet Biochemistry 3e Page 69
5 Figure 4-4b Structure of phenylalanine. (b) Space-filling model. Voet Biochemistry 3e Page 69
6 Figure 4-5 Structure of cystine. Voet Biochemistry 3e Page 69
7 Figure 4-8 The tetrapeptide Ala-Tyr-Asp-Gly. Voet Biochemistry 3e Page 71
8 Figure 4-9 Greek lettering scheme used to identify the atoms in the glutamyl and lysyl R groups. Voet Biochemistry 3e Page 71
9 Vast Majority Figure 8-1 The trans-peptide group. Voet Biochemistry 3e Page 220
10 Highly Un-favored Figure 8-2 The cis-peptide group. Voet Biochemistry 3e Page 220
11 Voet Biochemistry 3e Page 220 Figure 8-3 A polypeptide chain in its fully extended conformation showing the planarity of each of its peptide groups.
12 Figure 8-4 The torsional degrees of freedom in a peptide unit. Voet Biochemistry 3e Page 221
13 Steric Clash Figure 8-5 Conformations of ethane. Voet Biochemistry 3e Page 221
14 How would the energetic barrier vary if the side chains were changed to something other than hydrogen? Voet Biochemistry 3e
15 amide hydrogen carbonyl oxygen Voet Biochemistry 3e Page 221 The two angles are -60 deg (phi) and 30 deg (psi) Figure 8-6 Steric interference between adjacent residues.
16 Conformation Map or Ramachandran diagram Voet Biochemistry 3e A plot of the phi and psi angles that are allowed based on the van der Waals radii chosein
17 ~75% of the angles are not allowed Pleated sheets Some helices Figure 8-7 The Ramachandran diagram. Voet Biochemistry 3e Page 222
18 Obtained from high resolution crystal structures Figure 8-8 Conformation angles in proteins. Voet Biochemistry 3e Page 222
19 Outer limit Normally allowed Figure 8-9 The Ramachandran diagram of Gly residues in a polypeptide chain. Voet Biochemistry 3e Page 223
20 What does this say about glycine as a side chain in proteins? Voet Biochemistry 3e
21 P = pitch; N = number of repeating units per turn Figure 8-10 Examples of helices. ribbon Voet Biochemistry 3e Page 223
22 Notice the glue that holds this structure together Characteristics Phi = -57 deg Psi = -47 deg N = 3/6 res/turn Pitch = 5.4 A Voet Biochemistry 3e Page 224 Figure 8-11 The right-handed α helix.
23 Which atoms form the hydrogen bonds depicted in this figure? Figure 8-11 The right-handed α helix. Voet Biochemistry 3e Page 224
24 Voet Biochemistry 3e Page 225 Figure 8-12 Stereo, space-filling representation of an α helical segment of sperm whale myoglobin (its E. helix) as determined by X-ray crystal structure analysis.
25 The alpha helix Voet Biochemistry 3e A common secondary structure in both fibrous and globular protein Average length in globular protein is ~12 residues a length of 18 A Helicases as long as 53 residues have been observed
26 Protein helical nomenclature Voet Biochemistry 3e Two numbers are involved The first number is the number of residues per helical turn (n) The second number is the number of atoms, including H, in the ring that is closed by the hydrogen bond (m) In the case of the alpha helix it would be called helix
27 Figure 8-13 The hydrogen bonding pattern of several polypeptide helices. Voet Biochemistry 3e Page 225
28 Voet Biochemistry 3e Page 226 Figure 8-14 Comparison of the two polypeptide helices that occasionally occur in proteins with the commonly occurring α helix.
29 Figure 8-15 The polyproline II helix. Voet Biochemistry 3e Page 227
30 Figure 8-16a β pleated sheets. (a) The antiparallel β pleated sheets. Voet Biochemistry 3e Page 227
31 Figure 8-16b β pleated sheets. (b) The parallel β pleated sheets. Voet Biochemistry 3e Page 227
32 Hydrogen bonding Alternating sides for side chains Voet Biochemistry 3e Page 228 Figure 8-17 A two-stranded β antiparallel pleated sheet drawn to emphasize its pleated appearance.
33 Properties of beta sheets Voet Biochemistry 3e Beta sheets are common structural motifs in proteins In globular protein they are 2-15 strands in size, 6 being the average size Have an aggregate width of ~25 A Parallel beta sheets of <5 are rare
34 Voet Biochemistry 3e Page 228 Figure 8-18 Stereo, space-filling representation of the 6- stranded antiparallel β pleated sheet in jack bean concanavalin A as determined by crystal X-ray analysis.
35 Voet Biochemistry 3e Page 229 Figure 8-19a Polypeptide chain folding in proteins illustrating the right-handed twist of β sheets. (a) Bovine carboxypeptidase A.
36 Example of a beta barrel cylindrical structure Voet Biochemistry 3e Page 229 Figure 8-19b Polypeptide chain folding in proteins illustrating the right-handed twist of β sheets. (b) Chicken muscle triose phosphate isomerase.
37 Figure 8-20 Connections between adjacent polypeptide strands in β pleated sheets. Voet Biochemistry 3e Page 229
38 Preferred right hand twisting of beta sheet favors right handed crossover Voet Biochemistry 3e Page 230 Figure 8-21 Origin of a right-handed crossover connection.
39 Around half of globular protein structure is alpha helices and beta sheets Voet Biochemistry 3e The other half is mostly coil or loop formation
40 Linkage between residues 2 and 3 is flipped Figure 8-22 Reverse turns in polypeptide chains. Voet Biochemistry 3e Page 230
41 Coiled-coil structure although irregular is not random coil Voet Biochemistry 3e
42 Fibrous proteins have highly elongated structures with secondary structure being the dominating feature Voet Biochemistry 3e Structure not well resolved by X-ray crystallography
43 keratin Nonpolar residues Voet Biochemistry 3e Page 233 Figure 8-27a The two-stranded coiled coil. (a) View down the coil axis showing the interactions between the nonpolar edges of the α helices.
44 keratin Red hydrophobic strip Voet Biochemistry 3e Page 233 Figure 8-27b The two-stranded coiled coil. (b) Side view in which the polypeptide back bone is represented by skeletal (left) and space-filling (right) forms.
45 Collagen component of connective tissue Voet Biochemistry 3e Has great tensile strength and is one of the most abundant proteins in vertebrates
46 ~33 Gly, 15-30% Pro and Hyp (4-hydroxypropyl) Every 3rd residue is Gly for packing reasons Voet Biochemistry 3e Page 234 Figure 8-28 The amino acid sequence at the C-terminal end of the triple helical region of the bovine α1(i) collagen chain.
47 Figure 8-29 The triple helix of collagen. Voet Biochemistry 3e Page 235
48 Staggered conformation Voet Biochemistry 3e Page 236 Figure 8-30c X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly) 10 in which the fifth Gly is replaced by Ala. (c) A schematic diagram.
49 Fibrils are covalently cross-linked Figure 8-31 Electron micrograph of collagen fibrils from skin. Voet Biochemistry 3e Page 237
50 Globular proteins compact more sphere-like structures Voet Biochemistry 3e Enzymes generally are part of this group of proteins, as well as transport and receptor proteins
51 Figure 8-35 X-Ray diffraction photograph of a single crystal of sperm whale myoglobin. Voet Biochemistry 3e Page 240
52 For comparison Figure 8-24 X-Ray diffraction photograph of a fiber of Bombyx mori silk. Voet Biochemistry 3e Page 231
53 Voet Biochemistry 3e Page 244 Figure 8-39a Representations of the X-ray structure of sperm whale myoglobin. (a) The protein and its bound heme are drawn in stick form.
54 Voet Biochemistry 3e Page 244 Figure 8-39b Representations of the X-ray structure of sperm whale myoglobin. (b) A diagram in which the protein is represented by its computer-generated C α backbone.
55 Voet Biochemistry 3e Page 244 Figure 8-39c Representations of the X-ray structure of sperm whale myoglobin. (c) A computer-generated cartoon drawing in an orientation similar to that of Part b.
56 Side Chain Location Varies with Polarity Voet Biochemistry 3e Nonpolar residues occur generally in the interior of a protein away from the the aqueous solvent (Val, Leu, Ile, Met, Phe) Charges polar residues are on the surface of the protein (Arg, His, Lys, Asp, Glu) Uncharged polar groups are usually on the surface, but can also be found in the interior. (Ser, Thr, Asn, Gln, Tyr, Trp)
57 Voet Biochemistry 3e Page 247 Figure 8-43a The H helix of sperm whale myoglobin. (a) A helical wheel representation in which the side chain positions about the α helix are projected down the helix axis onto a plane.
58 exterior interior White main chain Purple polar side chains Brown nonpolar side chains Voet Biochemistry 3e Page 247 Figure 8-44 A space-filling model of an antiparallel β sheet from concanavalin A.
59 Figure 8-56 A GRASP diagram of human growth hormone. Voet Biochemistry 3e Page 258
60 Elements of Protein Structure Voet Biochemistry 3e Primary Structure amino acid sequence of polypeptide chain Seconday Structure examples such as beta sheet and alpha helix Tertiary Structure three dimensional structure. Consists of various protein domains Quaternary Structure arrangement of several subunits example of hemoglobin
61 Figure 8-63 The quaternary structure of hemoglobin. Voet Biochemistry 3e Page 266
62 Table 8-4 (top) Structural Bioinformatics Websites (URLs). Voet Biochemistry 3e Page 256
63 Table 8-4 (middle) Structural Bioinformatics Websites (URLs). Voet Biochemistry 3e Page 256
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