Proteins. Amino Acids. Chapter 3. Molecular Diagnostics Fundamentals, Methods and Clinical Applications Second Edition 2/5/2013

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1 Proteins Chapter 3 Amino Acids Nonpolar Alanine, Ala, A Isoleucine, Ile, I Leucine, Leu, L Methionine, Met, M Phenylalanine, Phe, F Tryptophan,Trp, W Valine, Val, V Negatively Charged (Acidic) Aspartic acid, Asp, D Glutamic acid, Glu, E Polar Asparagine, Asn, N Cysteine, Cys, C Glutamine, Gln, Q Glycine, Gly, G Proline, Pro, P Serine, Ser, S Threonine, Thr, T Tyrosine, Tyr, Y Positively Charged (Basic) Arginine, Arg, R Histidine, His, H Lysine, Lys, K 1

2 Amino Acids At ph 7, most of the carboxyl groups of the amino acids are ionized and the amino groups are not. The ionization can switch between the amino and carboxyl groups, making the amino acids zwitterions at physiological ph. pk1 = positive; pk2 negative At the ph where an amino acid is neutral, its positive and negative charges are in balance. This is the pi value. Amino Acids Amino acids are joined together by C C Nlinkages or peptide bonds to make proteins. At one end of the peptide will be an amino group (the amino terminal, or NH2 end), and at the opposite terminus of the peptide will be a carboxyl group (the car boxy terminal, or COOH end). 2

3 Extracellular domains (charged, glycosylated) Amino Acids Cell membrane Intracellular domains (hydrophilic) Transmembrane domains (hydrophobic) Amino acid content determines protein structure and function. A single protein can have separate domains with different properties Protein Structure Primary: amino acid sequence The sequence of amino acids in a protein determines the nature and activity of that protein. The single amino acid substitution that produces hemoglobin S in sickle cell anemia is a well known example. Replacement of a soluble glutamine residue with a hydrophobic valine at the sixth residue changes the nature of the protein so that it packs aberrantly in corpuscles and drastically alters cell shape. 3

4 Secondary: intrachain folding. Interactions between amino acid side chains fold a protein into predictable configurations. beta pleated sheets alpha helices Protein Structure Specialized secondary structures can identify functions of proteins. Zinc finger motifs are domains frequently found in proteins that bind to DNA. These structures consist of two beta sheets followed by an alpha helix with a stabilizing zinc atom. Leucine zipper, also found in transcription factors. The conserved sequence has a leucine or other hydrophobic residue at each seventh position for approximately 30 amino acids arranged in an alpha helical conformation such that the leucine side chains radiate outwardly to facilitate association with other peptides of similar structure. Because other amino acids besides leucine can participate in this interaction, the term basic zipper, or bzip, has been used to describe this type of protein structure. Zinc finger motif of the Sp1 protein, a eukaryotic transcription regulator. 4

5 Helix loop helix consisting of basic amino acids that bind consensus DNA sequences ( CANNTG) of target genes. This structure is sometimes confused with the helix turn helix. The helix turn helix is two alpha helices connected by a short sequence of amino acids, a structure that can easily fit into the major groove of DNA. The lambda repressor, a transcription factor of the bacteriophage lambda, has a helix turn helix motif. Protein Structure Tertiary: further folding, If a protein loses its tertiary structure, it is denatured. Mutations in DNA that substitute different amino acids in the primary structure can also alter tertiary structure. Proteins can also be denatured by heat (e.g., the albumin in egg white) or by conformations forced on innocuous peptides by infectious prions. Aggregations of prion induced aberrantly folded proteins cause transmissible spongiform encephalopathies, such as Creutzfeldt Jakob disease and bovine spongiform encephalitis (mad cow disease). 5

6 Protein Structure Quaternary: protein protein interaction for function. Monomers form multimers. Dimer Trimer Tetramer Conjugated proteins do have components other than amino acids. The nonprotein component of a conjugated protein is the non protein prosthetic group. Lipoproteins lipid Glycoproteins carbohydrate Metalloproteins metal atoms One of the most familiar examples of a conjugated protein is hemoglobin. Hemoglobin is a tetramer, having four Fe 2+ containing heme groups, one covalently attached to each monomer. Protein Function Enzymes Transport Storage Motility Structural Defense Regulatory Enzymes and transport, defense, and regulatory proteins are usually globular, making them soluble and allowing them to diffuse freely across membranes. Structural and motility proteins are fibrous and insoluble. 6

7 A gene is defined as the ordered sequence of nucleotides on a chromosome that encodes a specific functional product. Gene A gene is the fundamental physical and functional unit of inheritance. An ordered sequence of nucleotides on a chromosome that encodes a specific functional product Central Dogma of the Transfer of Biological Information DNA RNA protein Nucleic acid sequence must be translated into an amino acid sequence. 7

8 Solving the Genetic Code Four nucleotides are sufficient to code for 20 amino acids. 4 1 = 4, 4 2 = 16, 4 3 = 64, 4 4 = 256 George Gamow Solving the Genetic Code Synthetic RNAs UUUUUUUUU = phe phe phe GGGGGGGGG = gly gly gly CCCCCCCCC = pro pro pro AAAAAAAAA = lys lys lys Marshall Nirenberg and Johann Matthaei 8

9 Solving the Genetic Code Synthetic RNAs of defined sequence UCUCUC = ser leu ser leu Gobind Khorana The Genetic Code Three nucleotides = 1 codon = 1 amino acid Wobble is also used to describe movement of the base in the third position of the triplet to form novel pairing between the carrier trna and the mrna template during protein translation. 9

10 mrna: template Ribosomes: peptidyl transferase trna: adaptors trna charging, a reaction catalyzed by 20 aminoacyl trna synthetases. The Protein Translation Mg++ dependent charging reaction Anticodon stem trna CCA terminus T stem D stem Acceptor end T loop D loop Variable loop Anticodon loop 1. amino acid + ATP aminoacyl-amp + PPi 2. aminoacyl-amp + trna aminoacyl-trna + AMP The product of the reaction is an ester bond between the 3' hydroxyl of the terminal adenine of the trna and the carboxyl group of the amino acid. Protein Translation Aminoacyl-tRNA synthetases specifically attach amino acids to trnas. Only the appropriate trna and amino acid will fit into its cognate synthetase 10

11 The fidelity of translation is determined by the anticodon (the three bases complementary to the amino acid codon) of the trna as an adaptor between mrna and the growing protein. If amino acids are attached to trnas carrying anti codons to UAG, UAA, or UGA, the peptide chain will continue to grow instead of terminating at the stop codon. These trnas are called suppressor trnas, as they can suppress point mutations (single base pair changes) that generate stop codons within a protein coding sequence. Protein Translation Prokaryotes - 70S ribosomes 30S subunit (1 million daltons) is composed of a 16S ribosomal RNA (rrna) and 21 ribosomal proteins. 50S subunit (1.8 million daltons) is composed of a 5S rrna, a 23S rrna, and 34 ribosomal proteins. Eukaryotes - 80S ribosomes 40S small subunit (1.3 million daltons) 18S rrna and about 30 ribosomal proteins 60S subunit (2.7 million daltons). a 5S rrna, a 5.8S rrna, a 28S rrna, and about 40 ribosomal proteins. 11

12 Protein Translation Protein synthesis in the ribosome almost always starts with methionine in eukaryotes and N-formylmethionine in bacteria, mitochondria, andchloroplasts. trna Met or trna fmet is situated in the peptidyl site (P site) of the functional ribosome. All other trnas bind to an adjacent site, the aminoacyl site (A site) of the ribosome. Protein Translation The first peptide bond is formed between the amino acids in the A and P sites by transfer of the N-formylmethionyl group of the first amino acid to the amino group of the second amino acid, generating a dipeptidyl-trna in the A site. catalyzed peptidyl transferase. After formation of the peptide bond, the ribosome moves, shifting the dipeptidyltrna from the A site to the P site with the release of the empty trna from a third position, the E site, of the ribosome. 12

13 During translation, the growing polypeptide begins to fold into its mature conformation. This process is assisted by molecular chaperones. Chaperones apparently protect the growing unfinished polypeptides until they can be safely folded into mature protein. Chaperone Protein Translation: Termination Termination of the amino acid chain is signaled by one of three nonsense, or termination, codons (UAA, UAG, or UGA), which are not charged with an amino acid. Termination, or release, factors trigger hydrolysis of the finished polypeptide from the final trna. In eukaryotes, termination codon mediated binding of polypeptide chain release factors (erf1 and erf3) triggers hydrolysis of peptidyl trna at the ribosomal peptidyl transferase center. 13

14 Summary Proteins are made of combinations of 20 amino acids. Protein structure and function depend on the amino acid content and organization. A gene is defined, in part, by an open reading frame that contains the genetic code. In the genetic code, three nucleotides code for each amino acid. Proteins are translated from mrna by peptidyl transferase activity in the ribosome, using trna as adaptors. 14