Biochemistry Exam 4

• inducible enzymes are typically associated with catabolic pathways
• constitutive enzymes are typically associated with anabolic pathways
• inducible systems involve molecules that are the end products of catabolic biosynthetic pathways
• in inducible systems, the presence of the starting product in the environment induces and regulates gene expression
• repressible systems involve molecules that are end products of anabolic pathways
• in repressible systems, the abundance of end products in the environment represses and regulates gene expression and helps to conserve energy
• it is possible for a system to utilize both positive and negative regulation
• genes encoding for enzymes with similar functions are organized in clusters with their regulatory sequences. These clusters are known as operons
• regulatory regions are located upstream from the operon
• activator binding site is before the promoter and recruits polymerase
• repressor binding site is after the promoter region and blocks polymerase
• activators and repressors are trans-acting, whereas their binding sites are cis-acting
• the lac operon has 3 structural genes: lacZ, lacY, and LacA
• the lac repressor is a tetramer with two functional units that can act in different ways depending on what other operator sequence it binds to
• common H-bonding side chains include asparagine, glutamate, glutamine, lysine, and argenine
• DNA binding by the lac repressor occurs due to hydrogen binding and hydrophobic interactions
• CAP only works in the presence of cAMP
• in the absence of glucose, cAMP levels increase, resulting in the formation of a CAP-cAMP complex, which binds to the CAP site of the promoter, stimulating transcription
• the CAP-cAMP complex constitutes positive control
• when tryptophan is present, the repressor and tryptophan complex attain new conformation and then binds to the operator, repressing transcription
• the attenuator is inactive when tryptophan levels are low
• the attenuator is active when tryptophan levels are high
• in the absence of tryptophan, an inactive repressor is made and cannot bind to the operator
• in the presence of tryptophan, it binds to the repressor, causing an allosteric transition to occur
• riboswitches bind with small ligands which causes conformational change and induces the secondary RNA domain and creates the appropriate terminator structure
• in bacteria, regulation is linked to metabolic need, whereas in eukaryotes there are several levels to regulation
• in bacterial gene regulation, transcription and translation occur in the cytoplasm, and RNA is degraded quickly
• chromatin's compact structure inhibits access to DNA proteins and affects transcription
• changes in chromatin conformation can cause it to change from opened to closed due to the histone composition
• chromatin remodeling involves repositioning or removal of nucleosomes on DNA by chromatin remodeling complexes
• repositioned nucleosomes make chromosome regions more accessible to transcription factors and RNA polymerase
• DNA methylation occurs most commonly at the 5 position cytosine and the cytosine of CG doublets in DNA
• DNA polymerases are involved in nuclear genome DNA replication
• eukaryotes have multiple origins of replication on each chromosome
• transcription and translation are separated by time and space in eukaryotes
• general transcription factors are required at every polymerase II promoter
• initiation of transcription is signaled by phosphorylation of the polymerase C-terminus
• DNA can bend to bring a promoter closer to an enhancer
• chromatin remodeling can occur with a coactivator that has HAT activity or a corepressor with HDAC activity
• RNA is susceptible to decay by exoribonicleases