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Homework 1 Due 9/10/11
Question 1

See SwethaAkella

Question 2

Wikipedia:Ricin is a toxic protein derived from the castor bean plant. Amounts as small as a grain of rice can kill a human, being that its LD 50 is 22 ug/kg. Its toxicity is due to the fact that it inhibits protein synthesis (it is a ribosome inactivating protein, RIP), and for this reason symptoms take time to reveal themselves. Ricin's genome has been sequenced and documented in papers such as Chan AP et al.  Draft genome sequence of the oilseed species Ricinus communis.  Nat Biotechnol. 2010 Aug 22..

Ricin's sequence can be found at Genbank:P02879.1

Question 3

Okayasu H, Sutter R, Czerkinsky C, Ogra PL.  Mucosal immunity and poliovirus vaccines: Impact on wild poliovirus infection and transmission.  Vaccine. 2011 Sep 3.

Question 4

A cis-acting sequence signal is a piece of DNA or RNA that regulates a gene within itself. They can often act as binding sites for trans-acting factors.

    • TATA box: This is a sequence found in the promoter region of genes in archaea and eukarya and is considered to be a signal for binding of transcription factors or histones. Wikipedia:TATA_box
    • SOS box: A sequence in the promoter of some genes where the LexA repressor binds to stop transcription if there is no DNA damage. Wikipedia:SOS_box
    • CAAT box: This is a sequence of nucleotides with the GGCCAATCT sequence that appears 75-80 bp upstream of a given gene's transcription site. It signals an RNA transcription factor. It seems to be make sure that a gene is transcribed in the right quantities. Wikipedia:CAAT_box
    • Pribnow Box: It is a sequence of 6 nucleotides, TATAAT, which is required for bacterial transcription. It is an A,T rich sequence that serves a similar purpose to the TATA box. Wikipedia:Pribnow_Box

Gene Function

Enzyme Commission numbers are a way of classifying enzymes based on the reactions they catalyze. They specify reactions rather than the enzymes themselves, so that enzymes that catalyze the same reactions have the same nymbers. Each code is made of the letters 'EC' and then four numbers separated by periods, which narrow down the classification of the enzyme sequentially. For example, EC 1 indicates oxidoreductases, EC 2 indicates transferases. BRENDA is used as a database for EC numbers. (Wikipedia:EC_numbers)

Reactome on the other hand is a database of biological pathways, and each deals with a different organism. It breaks down the processes into molecular events with input and output, or substrates and products. (Wikipedia:Reactome)

Whereas EC numbers deal with individual enzyme-catalyzed reactions, Reactome presents the pathways on a whole, within which one can choose reactions to find based on EC numbers.

Representations of Protein Structure

Electrostatic surface models visualize the electric potential on protein surfaces by color coding different potentials.

The space filling model visualizes the protein by representing molecules as spheres.

While they both show the structures of proteins, they focus on different sets of information about them. Abalone, PyMOL, and QMOL are programs used for molecular mechanics modeling.

(Wikipedia:List_of_Software_for_Molecular_Mechanics_Modeling, Wikipedia:PyMOL)


Genome sequencing is a process that determines the full DNA sequence of an organism. It can include any or all of chromosomal DNA, mitochondrial DNA, and chloroplast DNA. (Wikipedia:Full_genome_sequencing)

Metagenomics on the other hand is study of metagenomes, genetic material derived from environmental samples. It is a new field, and allows scientists to study organisms in their own environments. (Wikipedia:Metagenomics)

Databases such as BLAST, MEGAN, and MG-RAST provide genome sequences of specific organisms and can also compare a specific sequence to that of a given organizm's genome. Currently, Nanopore is one of the methods used for genome sequencing, whether the organism is grown in lab or taken from natural environments.

RNA Structure

RNA folding software begins with a given sequence, and predicts the conformation of that protein whereas RNA design software goes in the other direction, starting with a structure and working backwards to derive the sequence that would give the desired structure.

An example of RNA folding software is BARNACLE, a python library that uses probability to sample RNA structures that match a given sequence. There is also other software like FARNA and iFoldRNA.


Computational Biology

Systems Biology refers to the trend in bioscience research to focus on interactions in biological systems as an interdisciplinary study. It studies interactions between biological systems, and the relationship between function and behavior of the same systems. (Wikipedia:Systems_Biology)

Molecular BioPhysics is another interdisciplinary field that aims to study biomolecular systems and use molecular structure and dynamic behavior to explain biological function. (Wikipedia:Molecular_Biophysics)

Both fields' goals are to study biological systems, but systems biology approaches it in terms of function and behavioral interactions, whereas molecular biophysics focuses on the physical structure and interactions of systems. Programs used in both fields of study are BioSens, BALSA, and BIOCHAM.

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