Cell Structure and Function Study Guide Test 1 I Different Mechanisms 1 Protein synthesis A Amino acids are linked by the formation of a covalent peptide bond that joins the carboxyl group of one amino acid with the amino acid of the next B Occurs on the ribosome C Catalyzed by a peptidyl transferase protein part of the ribosome D Establishes a chemical structural asymmetry found in all proteins E Eliminate H2O A All enzymes have a special binding site on its surface called the active site that cradles the counters of its substrate molecule B Binding site usually consists of a cavity in the protein surface formed 2 Protein Binding by a particular arrangement of amino acids C Many enzymes have two binding sites a One recognizes substrates b One recognizes regulatory molecules D Dimer two identical folding polypeptide chains form a symmetrical complex of two protein subunits held together by interactions between two identical binding sites E Ligand is also called the substrate and it binds to the active site on the protein a The active site on an enzyme binds 2 substrate molecules to encourage a reaction between them b A ligand must fit precisely into the proteins binding site like a hand into a glove so that a large number of noncovalent bonds can be formed between the protein and ligand c The two substrates have to bind many many times before the precise orientation occurs and the reaction can occur d Only a very small amount of those collision will be hard enough to provide enough force in order for reactions to occur e When substrate is in active site the enzyme strains the substrate forcing it through a transition state f Straining of the molecule is what catalyzes the reaction F Proteins are able to bind selectively because of the formation of a set of weak noncovalent bonds G Binding sites allow a protein to interact with specific ligands 3 Feedback Inhibition a type of control occurs when a molecule other than a substrate binds to an enzyme at a special regulatory site alters the rate at which substrates are converted to products A Enzyme acting early in a reaction pathway is inhibited by a late product of that pathway B Whenever large quantities of the final product begin to accumulate the product binds to an earlier enzyme and slows down its catalytic reaction C Can work instantaneously and is known as a negative regulation a Prevents enzyme from acting D Regulatory molecule has a shape that is totally different from the shape of the enzymes preferred substrate a Termed allotter means other protein molecules that can adopt two or more slightly different conformations and by a shift from one to another their activity can be regulated b Enzymes of this kind have two different binding sites one that recognizes substrates and one that recognizes regulatory molecules E The binding of an inhibitor at one site on the protein causes the protein to shift top a conformation in which its active site located elsewhere in the protein becomes less accommodating to the substrate molecule F Triggers a conformational change G Think of the process as B X Y Z EVENTUALLY THERE WILL BE SUBSTANTIAL BUILDUP OF Z THE CELL SHUTS DOWN PATHWAY WHEN ENOUGH IS BUILT UP A SNALL PORTION OF Z FEEDS BACK TO B AND SHUTS DOWN ENZYME THAT CATALYZES REACTION IN THE BEGINNING WHEN Z GETS LOW REACTION SEQUENCE WILL START UP AGAIN 4 Protein phosphorylation can either stimulate protein activity or inhibit it A Covalent addition of a phosphate group to a side chain of a protein catalyzed by a protein kinase Phosphorylation usually alters the activity or properties of the proteins in some way B Can cause a major conformational change which can in turn affect the binding of ligands elsewhere on the protein surface thus altering the proteins activity C Used in eukaryotic cells D Addition and removal of phosphate groups from specific proteins often occurs in response to signals that specify some changes in a cells state E Protein kinase adds a phosphate group to a target molecule phosphate group comes from current currency model when phosphate is put on the enzyme is turned on F Dephosphorylation taking a phosphate off G Protein phosphatase off enzyme takes phosphate off and enzyme is turned off H The more rapidly the cycle of taking a phosphate off and putting a phosphate on the faster the concentration of a phosphorylated protein can change in response to a sudden stimulus that increase its rate of phosphorylation I Keeping the cycle turning costs energy because one molecule of ATP if hydrolyzed with each turn of the cycle by the cell F GDP turns the cell off II Cellular Respiration 1 Glycolysis J Regulation of protein activity of phosphate addition and removal enzymatically transferred from ATP to the protein A Another way to regulate protein activity by the addition and removal 5 GTP hydrolysis of phosphate groups B Regulation of protein activity by the phosphate is part of the guanine nucleotide either GTP or GDP that is bound tightly to the protein C GTP binding proteins are in their active conformations with GTP bound the protein itself hydrolyzes this GTP to GDP releasing a phosphate and flips to an inactive conformation D This process is reversible active conformation is regained by dissociation of the GDP followed by the binding of a fresh molecule of GTP E GTP turns the cell on often stimulated in response to a signal received A Small amounts of ATP are generated in the cytosol B When glucose is converted into pyruvate only two molecules of ATP are produced per glucose molecule C Does not require oxygen involves the breakdown of glucose into two molecules of pyruvic acid D SUMMARY a Two ATP molecules are used to phosphorylate and activate the 6 carbon glucose this means a phosphate is taken from ATP which becomes ADP and added to the glucose molecule b An enzyme cuts the molecule apart producing two 3 carbon molecules of pyruvate c Two hydrogen atoms are removed by NAD to form 2 NADH d Four ATP molecules are produced by substrate level phosphorylation e Net yield of ATP is 2 2 are produced and 2 are used f Products 2NADH 2ATP and pyruvate most reduced compound formed also 2H2O are released A Occurs in the mitochondrial matrix needs oxygen B Generates a pool of chemical energy ATP NADH FADH2 from the oxidation of pyruvate end product of glycolysis C Pyruvate loses CO2 to form acetyl CoA D Acetyl CoA is oxidized to carbon dioxide when coenzyme A is released chemical energy is released and captured in the