How does RF1 use mimicry to terminate the reaction once a stop codon is encountered during translati

7.3 Stop codons are not decoded by tRNAs. Rather, release factors (proteins) recognize different stop codon, occupy the A-site, and prevent further binding of tRNA.

http://www.pnas.org/content/93/11/5443.long

9.2 ATP is a molecule made up of 3 phosphate molecules and one nitrogenous base. There is a high energy bond between the 3rd and 2nd phosphate, which can be broken down into ADP + P this is a reversible reaction.

Okay that helps a lot  8)--the youtube video is very clear--but what about the other questions?

10.1 Explain experimental evidence to suggest that transcription factors overcome repressive chromatin structure.

Natural transcription factors overcome the repressive chromatin structure by forming non-covalent complexes on the DNA with other transcription factors. These cooperative complexes overcome the difficulties of single-molecule transcription factors, allowing specific, combinatorial control of a range of transcriptional targets.

11.1 Name one protein that is responsible for moving histones relative to DNA, and explain how this is important for liberating regulatory sequences.

Histones control gene expression by modulating the structure of chromatin and the accessibility of regulatory DNA sequences to transcriptional activators and repressors. Posttranslational modifications of histones have been proposed to establish a "code" that determines patterns of cellular gene expression. Acetylation of histones by histone acetyltransferases (the protein) stimulates gene expression by relaxing chromatin structure, allowing access of transcription factors to DNA, whereas deacetylation of histones by histone deacetylases promotes chromatin condensation and transcriptional repression.

11.5 What is the histone code and how is it epigenic?

The Histone Code is hypothesized to be a code consisting of covalent histone tail modifications. Together with other modifications such as DNA methylation, the code is part of the epigenetic code. While in one individual, the genetic code in each cell is the same, the epigenetic code is tissue and cell specific. Therefore it is epigenitic because modifications to histones depends on the tissue (histones in eye cell DNA will be different than histones in liver cell DNA - they will be modified differently).

That clears up a lot... but I just reread my lecture notes + read the text book and I still don't get:

9.4 Use lysozyme to illustrate two features of proteins: that they stabilize unfavorable intermidiate/transitional states, and they temporarily react with substrates in order to progress reactions toward completion?

9.4 Use lysozyme to illustrate two features of proteins: that they stabilize unfavorable intermidiate/transitional states, and they temporarily react with substrates in order to progress reactions toward completion?

Lysozymes are enzymes (proteins) used to degrade the peptidoglycans in bacteria. They temporarily react with substrates (peptidoglycan), break it down, which allows other reactions to occur towards completion. For instance, once you breakdown the cell wall, now you can get to the content within the cell which is enclosed by the cell wall. In addition, enzymes generally lower the activation energy by creating an environment in which the transition state is stabilized. So once peptidoglycan goes into the micro-environment of the enzyme, it can now be targeted by other molecules to attach its chemical makeup.

Makes sense?