Ch 11t molgen

Ch 11t molgen - Chapter 11 Transcription Initiation...

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Chapter 11: Transcription Initiation Molecular Genetics Lecture Outline Tech Note 11.1: X-ray crystallography . You will see a lot of this over the next 20 years as disease- related genes from the human genome are examined for potential drug-binding sites to produce new disease-curing drugs. The biggest hurdle is the initial one: producing highly pure protein in large quantities suitable for crystalization. The crystal diffracts X-rays in similar trajectories and creates a spot pattern on X-ray film. This pattern can be interpreted to reveal the exact location of every atom, or at least the location of protein secondary structures. Tougher to do with big proteins. Nuclear magnetic resonance (NMR) is used mostly with H nuclei and allows one to figure out what other atoms are connected to or adjacent to each H atom in the molecule. Basically, a nucleus can shift its orientation between two phases, with one orientation having a lower energy level than the other. NMR measures the energy difference between these orientations. The exact energy difference is influenced by the chemical environment around the atom, and this difference from a standard energy difference is called the chemical shift. Advantages to NMR: no crystals needed. Disadvantage: only works on small proteins. DNA-binding in Nature: Table 11.1: It may seem like DNA and RNA binding to proteins is a pretty arcane topic, but look at all the manifestations in this table. Fig. 11.7: Proteins bind to DNA especially upstream of the gene at the promoter. They can promote, or sometimes inhibit, transcription. Table 11.2: Just to let you know what "motifs" are, and that there is a great variety of them. A motif is commonly occurring sequence or functional unit that could be found in many proteins or domains. Fig. 11.2: helix-turn-helix DNA-binding motif. Can you see the recognition helix? 2 nd alpha helix What does it do? Makes vital contact inside the major groove, which allows the DNA sequence to be read Why is the geometry of the "turn" section important? Allows the recognition helix to exactly fit inside the major groove Fig. 11.3: Another helix-turn-helix -- the homeodomain. What are homeodomain proteins? Binds to homeotic gene promoters Fig. 11.4: Zinc fingers. Which part binds the major groove? Alpha helix What do the other parts do? Helps in the positioning within the groove What do the two cys and two his R-groups do? Attach the B- sheet and the alpha helix to the zinc atom What is the advantage of having a multi-fingered DNA-binding domain (Fig. 11.5)? a lot more transcriptional control TBP domain is one example of a DNA-binding domain that (1) binds via a beta-sheet, not an alpha helix, and (2) binds the minor groove. Unusual. Fig. 11.12:
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Ch 11t molgen - Chapter 11 Transcription Initiation...

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