1. Gene expression refers to the processes that result in the production of functional protein. Gene expression can be controlled at the levels of transcription, processing (splicing in eukaryotes), translation, mRNA stability, and protein stability. Tissue-specific gene expression is essential for multcellular, differentiated organisms.
2. Transcription factors, as noted previously, are proteins that bind to DNA and affect the transcription of genes located near where they bind. Common DNA-binding structures are found in the diverse set of transcription factors that are know. They include motifs (motifs - structural features) for helix-turn-helix, homeodomains, leucine zippers, and zinc fingers.
3. Leucine zipper structures are found in adjacent alpha helices and contain regions with leucine residues appearing about every 7 amino acids. The leucine interact with each other to hold the strands together and in doing so allow other portions of the helix to bind DNA properly.
4. Zinc fingers are structures with cysteine residues that hold zinc ions and create a finger-like structure that can stick into the DNA helix.
5. Proteins that bind to specific DNA sequences must "read" the sequence of bases inside the helix, usually by inserting a region into the major groove of the DNA and "checking" the hydrogen bonding molecules inside. Since different base pairs have unique hydrogen bonding orientations, the proteins that find and bind to specific base sequences.
6. Control of gene expression is also essential for prokaryotic organisms to be able to respond properly to their environments. For example, E. coli prefers glucose for energy, but must be able to use other sugars, like lactose, when they are available.
7. An operon is a prokaryotic system for organizing genes all under the same transcriptional control. Genes on the same operon in prokaryotes are all synthesized on the same mRNA. mRNAs containing multiple gene coding sequences are referred to as polycistronic.
8. The lactose operon consists of three linked structural genes that encode enzymes of lactose utilization, plus adjacent regulatory sites. The three enzymes --z, y, and a--encode beta-galactosidase, beta-galactoside permease (a transport protein), and thiogalactoside transacetylase (an enzyme of still unknown metabolic function), respectively.
9. Transcription of the lac operon commences at a promoter (lacP) before lacZ and transcribes a 5,200 nucleotide messenger RNA molecule (mRNA), ending at a terminator beyond lacA.
10. X-Gal is a synthetic substance used to study lac operon expression. X-Gal has the useful property that it turns blue when acted on by beta-galactosidase, giving a measure of how much the operon has been induced by the amount of blue color produced.
11. Negative transcriptional regulation of the lac operon is accomplished by a protein known as the lac repressor. It binds the operon's operator region and inhibits transcription.
12. In the absence of inducer molecules, the lac repressor tightly binds to the operator and inhibits transcription of the operon. When inducer molecules are present, they bind to the lac repressor and change its shape and reduce its ability to bind the operator, thus allowing the RNA polymerase to bind the promoter and start transcription.
13. The promoter sequence of the lac operon differs somewhat from the ideal consensus sequence of an E. coli promoter. Consequently, in the absence of positive acting elements, the lac promoter does not function well on its own. A protein that acts positively to help activate the lac operon is the CRP (cAMP Receptor Protein). (more on this next time)
This course in general biochemistry is intended to integrate information about metabolic pathways with respiration (respiratory control) and initiate the student into a microscopic world where blueprints are made of deoxyribonucleic acids, factories operate using enzymes, and the exchange rate is in ATPs rather than Yens or Euros. Beyond explaining terms, and iterating reactions and metabolic pathways, this course strives to establish that the same principles that govern the behavior of the world around us also govern the transactions inside this microscopic world of the living cell. And by studying and applying these principles, we begin to understand cellular and bodily processes that include sensory mechanisms.
1. Lipids, Membranes and Transport
2. Electron Transport, Oxidative Phosphorylation and Mitochondrial 3. Transport Systems
3. Lipid Metabolism
4. Nucleotide Metabolism
5. DNA Replication