1 Chapter 3: Protein ZHOU Yong Department of Biology Xinjiang Medical University

2 Teaching Requirements 1. Mastering: structure of amino acid and definition of peptide bond and peptide chain. 2. Understanding: molecular structures (four folding levels), types and function of protein.

3 Chapter 3: Protein A: Building Blocks - Amino Acids B: Peptides C: Secondary Structure D: Three-Dimensional Structure E: Enzymes

4 Section A: Building Blocks - Amino Acids An amino acid is defined as the molecule containing an amino group (NH 2 ), a carboxyl group (COOH) and an R group. It has the following general formula, R-CH(NH 2 )-COOH The R group differs among various amino acids. In a protein, the R group is also called a sidechain. the structure of tyrosine

5 There are over 300 naturally occurring amino acids on earth, but the number of different amino acids in proteins is only Acidic: aspartate, glutamate. In a neutral solution, the R group of an acidic amino acid may lose a proton and become negatively charged. 2. Basic: lysine, arginine, histidine. In a neutral solution, the R group of a basic amino acid may gain a proton and become positively charged. Interaction between positive and negative R groups may form a salt bridge, which is an important stabilizing force in proteins. 3. Aromatic: tyrosine, tryptophan, phenylalanine. Their R groups contain an aromatic ring. 4. Sulfur: cysteine, methionine. Their R groups contain a sulfur atom (S). The disulfide bond formed between two cysteine residues provides a strong force for stabilizing the globular structure. 5. Uncharged hydrophilic: serine, threonine, asparagine, glutamine. Their R groups are hydrophilic and capable of forming hydrogen bonds. 6. Inactive hydrophobic: glycine, alanine, valine, leucine, isoleucine. These amino acids are more likely to be buried in the protein interior. Their R groups do not form hydrogen bonds and rarely participate in chemical reactions. 7. Special structure: proline. In most amino acids, the R group and the amino group are not directly connected. Proline is the only exception among 20 amino acids found in protein. Due to this special feature, proline is often located at the turn of a peptide chain in the three-dimensional structure of a protein.

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9 Section B: Peptides The peptide is a chain of amino acids linked together by peptide bonds. Polypeptides usually refer to long peptides whereas oligopeptides are short peptides (< 10 amino acids). Proteins are made up of one or more polypeptides with more than 50 amino acids. Primary structure: The primary structure of a protein refers to its amino acid sequence. The amino acid in a peptide is also called a residue. Peptide bond: A peptide bond is the linkage between two amino acids, formed by the condensation reaction.

10 The amino acid sequence (primary structure) of RNase A.

11 Formation of the peptide bond by condensation reaction.

12 Section C: Secondary Structure 1.Hydrogen Bond

13 2. Alpha Helix An  helix has the following features: every 3.6 residues make one turn, the distance between two turns is 0.54 nm, the C=O (or N-H) of one turn is hydrogen bonded to N-H (or C=O) of the neighboring turn.

14 Amphipathic  helix

15 2. Beta Strand, Beta Sheet and Beta Barrel (1)Beta strand: In a  strand, the torsion angle of N-C  -C-N in the backbone is about 120 degrees. The following figure shows the conformation of an ideal  strand. Note that the sidechains of two neighboring residues project in the opposite direction from the backbone. Figure: An ideal  strand.

16 (2) Beta sheet A  sheet consists of two or more hydrogen bonded  strands. The two neighboring  strands may be parallel if they are aligned in the same direction from one terminus (N or C) to the other, or anti-parallel if they are aligned in the opposite direction.

17 (3) Beta barrel: A  barrel is a closed  sheet.

18 (4) Protein Motifs and Domains The motif is a characteristic domain structure consisting of two or more  helices or  strands. Common examples include coiled coil, helix-loop-helix, zinc finger, leucine zipper, etc. Many proteins also contain specific domains such as the SH2 domain.

19 (a) The domain organization. (b) The structure of the helix-loop-helix motif. Figure. The transcription factor MyoD.

20 Zinc Finger The zinc finger motif can be divided into three types: C 2 H 2 zinc finger: It is characterized by the sequence CX 2- 4 C....HX 2-4 H, where C = cysteine, H = histidine, X = any amino acid. In the 3D structure, two cysteine residues and two histidine residues interact with a zinc ion. C 4 zinc finger: Its consensus sequence is CX 2 CX 13 CX 2 CX CX 5 CX 9 CX 2 C. The first four cysteine residues bind to a zinc ion and the last four cysteine residues bind to another zinc ion. C 6 zinc finger: It has the consensus sequence CX 2 CX 6 CX 5- 6 CX 2 CX 6 C. The yeast's Gal4 contains such a motif where six cysteine residues interact with two zinc ions.

21 C 2 H 2 zinc finger: The structure of a zinc finger region of Sp1.

22 C 4 zinc finger: The complex of the ER's (estrogen receptor) zinc finger domain and DNA. In this figure, two ERs form a dimer. Each ER binds to two zinc ions.

23 C 6 zinc finger: Structure of Gal4's zinc finger. Like many other transcription factors, Gal4 form a dimer to interact with DNA. In each Gal4, six cysteine residues bind to two zinc ions.

24 Leucine Zipper: The structure of the AP-1/DNA complex. It contains a leucine zipper motif where two  helices look like a zipper with leucine residues (green color) lining on the inside of the zipper.

25 Section D: Three-Dimensional Structure The three-dimensional (3D) structure is also called the tertiary structure. If a protein molecule consists of more than one polypeptide, it also has the quaternary structure, which specifies the relative positions among the polypeptides (subunits) in a protein 3D structure of RNase A

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27 Section E: Enzymes 1. Classification 2. Catalytic mechanism 1. Classification: Based on catalyzed reactions, the nomenclature committee of the International Union of Biochemistry and Molecular Biology (IUBMB) recommended the following classification. (1) Oxidoreductases catalyze a variety of oxidation-reduction reactions. Common names include dehydrogenase, oxidase, reductase and catalase. (2) Transferases catalyze transfers of groups (acetyl, methyl, phosphate, etc.). Common names include acetyltransferase, methylase, protein kinase and polymerase. The first three subclasses play major roles in the regulation of cellular processes. The polymerase is essential for the synthesis of DNA and RNA. (3) Hydrolases catalyze hydrolysis reactions where a molecule is split into two or more smaller molecules by the addition of water.

28 1)Proteases splits protein molecules. Examples: HIV protease and caspase. HIV protease is essential for HIV replication. Caspase plays a major role in apoptosis. 2)Nucleases splits nucleic acids (DNA and RNA). Based on the substrate type, they are divided into RNase and DNase. 3)Phosphatase catalyzes dephosphorylation (removal of phosphate groups). 4) Lyases catalyze the cleavage of C-C, C-O, C-S and C-N bonds by means other than hydrolysis or oxidation. Common names include decarboxylase and aldolase. 5) Isomerases catalyze atomic rearrangements within a molecule. Examples include rotamase, protein disulfide isomerase (PDI), epimerase and racemase. 6) Ligases catalyze the reaction which joins two molecules. Examples include peptide synthase, aminoacyl-tRNA synthetase, DNA ligase and RNA ligase. Each enzyme is assigned an EC (Enzyme Commission) number. For example, the EC number of catalase is EC

29 2. Catalytic Mechanisms of Enzymes

30 REVIEW QUESTIONS Which of these statements about the polypeptides in cells is WRONG? A. They are a polymer of γ -amino acids linked by peptide bonds. B. The sequence of amino acids is determined by instructions on the cell’s DNA. C. They have an- NH 3 + group at one end of the polymer. D. They have a -COO − group at one end of the polymer. E. They are called proteins if they fold into a specific shape.

31 REVIEW QUESTIONS Which of the following statements is INCORRECT? A. Enzymes are made from proteins. B. One enzyme can facilitate the reaction of many different substrates. C. Enzymes sometimes use induced fits to break apart their substrates. D. Enzymes are not required for spontaneous reactions. E. Not all catalysts are enzymes.