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Task 1

Please see Suhani Vora Homepage

Task 2

Here is a link to a short paragraph about the toxic protein ricin:

RicinBackground

Task 3

Review paper which summarizes what is currently known of the Polio virus and recent advances in our understanding of CNS invasion.

Mueller S, Wimmer E, Cello J.  Poliovirus and poliomyelitis: a tale of guts, brains, and an accidental event.  Virus Res. 2005 Aug;111(2):175-93.

Task 4

Part A

Descriptions of four different cis - acting sequence signals:

1. Internal Ribosome Entry Site - nucleotide sequence found with mRNA that forms a structure that can substitute for a 5' cap which is usually necessary for translation of a transcript. The IRES is capable of attracting a eukaryotic ribosome to initiate tranlsation. Primarily, viruses use IRESs to ensure translation of genes regardless of whether the host is actively translating genes. However, IRESs are also thought to be present in some mammalian genes that are involved in stress survival.[1]

2. Leader Peptide - a short peptide sequence that is translated at the start of a bacterial mRNA transcript which controls expression of downstream genes. In general, leader peptides control expression of genes in an operon that code for enzymes needed for amino acid synthesis. The peptide controls translation because it contains repeats of the amino acid which the downstream genes would be used to synthesize. Because transcription and translation are coupled in prokaryotes, a stalled ribosome can affect the formation of transcriptional terminator sequences in an RNA transcript - this allows a stall in translation to lead to transcription of a complete transcript and allows a leader peptide sequence to control the expression of genes. [2]

3. Selenocysteine Insertion Sequence - RNA element around 60 nucleotides long that directs cell machinery to incorporate the amino acid selenocysteine wherever the UGA stop codon is present in the transcript. The SECIS forms a stem-loop structure and is predominantly located right after the UGA codon in prokaryotes and in the 3' UTR in eukaryotic transcripts. [3]

4. TATA box - DNA sequence that is considered the core promoter element of the promoter region in archaea and eukaryotic genes. The sequence, usually 5'-TATAAA-3', facilitates binding of TATA binding protein which leads to further binding of remaining transcription factors necessary for activation of RNA Pol II and initiation of transcription. Most genes do not contain a TATA box, as the TATA box is not necessary for transcription. Alone, the TATA box and associated transcription factors lead to basal levels of transcription. [4]

Part B

Here is a table comparing various Computational Biology tools:

Concepts Bioinformatics ToolsSorted ascending Comparison of Tools
Computational Biology In the context of computational biology, Systems biology is an approach to understanding biological properties by using system wide data (acquired from techniques such as transcriptomics or proteomics) to improve hypothesized biological models. Systems biology tools include systems level simulatory programs such as COPASI and simBio. Molecular biophysics aims to understand biomolecular systems through the study of molecular/supramolecular structure, dynamics, and interactions; computational tools used to study molecular biophysics include GROMACS(molecular dynamics) and CHARMM force-field (macromolecular simulations).[13,14] While Systems biology uses comprehensive information to understand biological function, Molecular biophysics is a reductionist approach that uses individual molecular interactions and dynamics to understand biological function.
Gene Function Enzyme Commission Numbers are a system of naming enzymes according to their catalytic activities; enzyme commission numbers can be used to find structural and sequence information on UniProt (a protein information database) or the NCBI protein database while further information on enzyme nomenclature can be found on ENZYME. The Reactome Database is a database of biological pathways in; the largest Reactome focuses on human pathways including putative pathways predicted by computational models. Within Reactome, tools such as Small molecule Search and PathFinder allow users to find information on specific biological pathways. [5,6] The Reactome Database gives more general pathway level information that can lead to identification of enzymes involved in particular processes, while Enzyme Commission Numbers generally lead to more specific information about the particular proteins that exhibit a class of catalytic activity.
RNA Structure RNA folding software is used to predict secondary and tertiary structure, including formation of different motifs, from an RNA sequence; examples of folding programs are CentroidFold and BARNACLE. RNA design software can be used to take a particular structure or motif and design the optimal sequence that would form that fold; examples of design programs are CombFold and RNA Designer.[11,12] RNA folding software can be used to determine the fold/structural properties of an RNA sequence while RNA design software would be used to create a sequence that will fold into a desired structure.
Representations of Protein Structure Space-filling models are molecular models that show the approximate size and orientation in space of atoms relative to each other. Electrostatic surface models show the relative positions of models, but additionally show regions of high and low electrostatic potential via an overlay of color. Programs such as PyMOL, Jmol, and SPARTAN are used to generate these models.[7,8] Electrostatic surface models may be more useful if one is looking for electrostatic interactions within a molecule or between models while a Space-filling model model may be more useful for studying steric interactions.
Genomics Genome sequencing is a technique used to determine the entire DNA sequence of an organism (including its chromosome, mitochondria, and chloroplast specific DNA). Metagenomics is a method of studying the presence of various microbes within an environmental sample in order to gain information about the population. The Metagenomics-RAST (MG-RAST)server can be used to analyze metagenome data sets. [9,10] While metagenomics is used to study populations of microbes, genome sequencing is primarily used to study the individual genetic characteristics of a singular organism of any species.

[1-14] SuhaniVoraHomework1References

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