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Chapter 4

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Ingo Ensminger

Chapter 4. pg153-154  Enzymes are not only regulated by the binding of small molecules  Regulation a protein activity by protein phosphorylation; attaching a phosphate group covalently to one of it’s amino acids side chains  Each phosphate group carries two negative charges, the enzyme-catalyzed addition of phosphate group to a protein can cause major conformation change (by attracting a cluster of positively charged amino acid side chains.)  This conformational change has an affect on the binding of ligands elsewhere on the protein structure thus altering the protein’s activity  Removal of the phosphate group by a second enzyme returns the protein to its original conformation and restores its initial activity  Protein phosphorylation is a reversible process and it controls the activity of many types of protein in eukaryotic cells  More than one third of the 10,000 or so proteins in a typical mammalian cell appear to be phosphorylated at any minute  The addition and removal of phosphate groups from specific proteins often occurs in response to signals that specify some change in the cell’s state  Protein phosphorylation involves the enzyme catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on serine, threonine or tyrosine side chain of the protein, this reaction is catalyzed by a protein kinase  The removal of a phosphate group is catalyzed by a protein phosphatase  Phosphorylation can either stimulate protein activity or inhibit it, depending on the protein involved and the site at which it is being phosphorylated  Cells contain hundreds of different protein kinases each responsible for phosphorlysing a different protein or set of proteins  Many different protein phosphatases, many are highly specific (one or a few proteins) while others act on a broad range of proteins  The state of phosphorylation of a protein at any moment in time and thus its activity depends on the relative activity of the protein kinase and phosphatase that acts on it  Adding a phosphate group to a particular side chain of the protein and then removing it later in the cycle; this allows proteins to switch rapidly from one state to another  The more rapidly the cycle is turning the faster the concentration of a phosphorylated group can change in response to a sudden stimulus that increases its rate of phosphorylation.  Keeping the cycle turning costs energy because one molecule of ATP is hydrolyzed with each turn of the cycle  PG 153 GTP-binding proteins are also regulated by the cyclic gain and loss of a phosphate group, AND nucleotide hydrolysis allows motor proteins to produce large movements in cells Chapter 7 pg-254-260  The ribosome is a ribozyme  The ribosome is one of the largest and most complex structures in the cell, composed of two-thirds RNA and one-third protein  The structure strongly confirms that the rRNAs (not the proteins) are responsible for the ribosome’s overall structure and its ability to choreograph protein synthesis  The rRNAs are folded into highly compact, precise three-dimensional structures that form the core of the ribosomes  The ribosomal proteins are generally located on the surface of the ribosome, where they fill gaps and crevices of the folded RNA  The main role of the ribosomal proteins seems to be to fold and stabilize the RNA core, while permitting the changes in the rRNA conformation that are necessary for this RNA to catalyze efficient protein synthesis  The three tRNA binding sites (A, P and E) on the ribosome formed primarily by the rRNAs  The catalytic site for the peptide bond formation is formed by the 23S RNA of the large subunit; the nearest amino acid is located too far away to make contact with the incoming amino-acyl tRNA or with the growing polypeptide chain  This catalytic site in the RNA based peptidyl transferase is similar to that found in protein enzymes; it is highly structured pocket that precisely orients the two reactants, the elongating polypeptide and the charged RNA thereby greatly increasing the probability of a productive reaction  RNA molecules that possess catalytic activity are called ribozymes  The site at which protein synthesis begins on an mRNA is crucial because it sets the reading frame for the whole length of the message  An error of one nucleotide either way at this stage will cause every subsequent codon message to be misread, resulting in a nonfunctional protein with a garbled sequence of amino acids  The initiation step is also important because it is the last point at which the cell can decide whether the mRNA is to be translated; the rate of initiation thus determines the rate at which the protein is synthesized from the RNA  The translation of an mRNA begins with the codon AUG  A special tRNA is required to initiate translation called the initiator tRNA always carries the amino acid methionine (or a modified form called formyl methionine, in bacteria) so that all the newly made proteins have methionine as the first amino acid at their N-terminal end, the end of the protein that is synthesized first  The methionine (initiator) is usually removed later by a specific protease.  The initiator tRNA is distinct from the tRNA that usually carries methionine  In eukaryotes, the initiator tRNA is first loaded to the small ribosomal subunit along with additional proteins called translation initiation factors  Only the charged initiator tRNA is capable of binding tightly to the P-site of the small ribosomal subunit  Next, the loaded ribosomal subunit binds to the 5’ end of an mRNA molecule which is signaled by the cap that is present on the eukaryotic mRNA  The small ribosomal subunit then moves forward (5’  3’) along the mRNA searching for the first AUG. When this AUG is encountered, several initiation factors dissociate from the small ribosomal subunit to make way for the large ribosomal subunit to assemble and complete the ribosome. Because the initiator tRNA is bound to the P-site, protein synthesis is ready to begin with the addition of the next charged tRNA to the A-site  The mechanism for selecting a start codon is different in bacteria  Bacterial mRNAs have no 5’ caps to tell the ribosome where to begin searching for the start of translation, instead they have specific ribosome binding sequences (up to 6 nucleotides long) that are located a few nucleotides upstream of the AUGs at which translation begins  A prokaryotic ribosome can readily bind directly to a start codon that lies in the interior of an mRNA, as long as the ribosome binding site precedes it be several nucleotides  Such ribosome-binding sequences are necessary in bacteria, as prokaryotic mRNAs are often polycistronic, that is, they encode several different proteins, each of which is translated from the same mRNA molecule.  The end of the protein-coding message in both prokaryotes and eukaryotes is signaled by stop codons- UAA, UAG, UGA.  The stop codons are not recogniz
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