BMB 251 1st EditionExam # 4 Study Guide Lectures: 25-31Lecture 25 (September 7)Problem Set Seven Review/AnswersDifferent Points of Control of Gene ExpressionInside the Nucleus CytoplasmTranscriptional (main control point) TranslationalRNA Processing mRNA DegradationRNA Transport and Relocation Protein Activity- DNA binding proteins are able to sense patterns in nucleotide sequences on the major groove of the DNA. This does not disrupt base-pairing- Most DNA binding proteins recognize specific sequences through the major groove of DNA because there is more differentiation in the patterns of sequences, which are more distinguishable than on the minor groove.- DNA binding domains:o Helix-Turn-Helix: two alpha helices are connected by a short chain of amino acids (which create the “turn”)o Zinc finger: the core is composed of zinc atom(s), attached to either two alpha helices or one alpha helix and one beta sheeto Leucine zipper: two alpha helices are joined together to create a coiled-coil  dimerization: Y-shaped structure o Helix-Loop-Helix: two alpha helices of different sizes are attached by a polypeptide loop- Dimerization of DNA binding proteins creates many binding options. While it is greatly specific, italso allows for many partners to be joined together and increases the options of binding partners- When too much tryptophan is present in the cell, it will bind with the repressor and put it into itsactive form. This then blocks sigma factor from binding and transcribing new tryptophan. When the cell begins to need more tryptophan, they will not bind to the repressor, keeping it inactive and allowing sigma factor to bind and begin transcription- Prokaryotes have multiple sigma factors because they can all transcribe a certain part of DNA; this allows prokaryotes to create many different variations of proteins from a single gene because the sigma factors all bind at different promoter regions. This gives prokaryotes their polycistronic nature- In eukaryotes, an activator refers to a protein that binds near the promoter and helps transcription to begin. A repressor binds on or within the promoter region, blocking the eTFs andtherefore stopping the process of transcription- Bacteria do not have introns, and an advantage of splicing one large pre-mRNA into smaller mature mRNAs is that it gives genes multiple options of protein creation from one single transcribed gene- mRNAs are destroyed through mRNA degradation controlLecture 25 (Monday March 30)- Cell differentiation depends on gene control/expression, not changes in the actual nucleotide sequenceo Cell types in multicellular organisms come from synthesis of different RNA and proteins (structural proteins of chromosome, DNA/RNA polymerase, ribosomal proteins, etc.)- There are many regulations where gene expression can be controlled from the process of creating a protein from a geneo Transcriptional control (most prominent): controls when/ how often a gene is transcribedo RNA processing control: controls splicing and processing of RNA transcriptso RNA transport and localization control: selecting which mRNA is exported out of nucleus and where in the cytosol it will be localizedo Translational control: selecting which mRNA in cytosol are translated by ribosomeo mRNA degradation control: selectively destabilizing certain mRNA o Protein activity control: selectively activating, inactivating, degrading or locating specific proteins after they have been synthesized- Gene regulatory proteins: turn genes on or off by binding noncovalently to the major and minor grooves of DNA- Many Gene regulatory proteins contain one or another of a small set of DNA-binding structural motifs (allow DNA and protein to fit together perfectly)o Helix-Turn-Helix: constructed from two alpha helices connected by a short, extended chain of amino acids (create “turn”) Recognition helix: the more C-terminal helix, which fits into the major groove of DNA Part of polypeptide outside of H-T-H domain also makes important contacts withDNA, helping to “fine-tune” the interaction N-terminal alpha helix functions primarily as a structural component that helps to position the recognition helix Many bind as symmetric dimers to DNA sequences composed of two very similar“half-sites” (two copies of recognition helix separated by exactly one turn of DNA helix) Composed solely of amino acidso Zinc fingers: includes one or more zinc atoms as its structural components Two types: 1. Occur in proteins which activate rRNA synthesis: zinc holds alpha helix and beta sheet together- Usually found in clusters where each has their alpha helix interacting and forming an almost continuous stretch along the major groove- Strong and specific DNA-protein interaction is built up through repeatingbasic structural units 2. Occur in large family of intracellular receptor proteins: two alpha helices are packed together with zinc atoms - Usually form dimers that allow one of the two alpha helices of each subunit to interact with major groove of DNA **Both use zinc as structural component and alpha helix to interact with the major groove of DNAo Beta sheets: two stranded beta sheet, with amino acid side chains extending from sheet toward DNA, reads info on major groove (instead of alpha helix seen in previous motifs)o Few DNA-binding proteins use peptide loops to read nucleotide sequences, instead of alpha helices and beta sheets (Ex. P53 recognizes nucleotide pairs from both major and minor groove using these loops)o Leucine zipper motif: two alpha helices (one from each monomer) are joined together toform a short coiled-coil  combines portion of proteins responsible for dimerization andDNA binding Helices held together by hydrophobic interactions of amino side chains (usually on leucines) which extend from one side of each helix  Creates Y-shaped structure of alpha helices, which allow their side chains to interact with the major groove Heterodimerization: example of combinatorial control, in which combinations of different proteins, rather than individual proteins, control a cell process o Helix-Loop-Helix motif: short alpha helix connected by a loop to a second, larger alpha helix Flexibility of loop allows one helix to fold back and pack against the otherLecture 26 (Wednesday April 1)- Activators: DNA binding proteins that bind NEAR the promoter in order to enhance RNA polymerase binding- Repressors: DNA binding proteins