An Idea Blossoms
Complex Reality
Capturing Function
What's In A Name?
An Ancient Problem
100
What is the Central Dogma?
Information travels from DNA through RNA to protein
100
What is a pseudogene?
Pseudogenes are regions of the genome long considered fossils or past genes.
100
What does it mean to 'knock out' a gene and explain the importance of this genetic technique.
To 'knock out' a gene means to delete or disrupt the gene of interest so that it has been made inoperative. This technique is used to learn about the phenotypic function of a sequenced gene in an organism.
100
How did scientists working with yeast name genes?
They frequently combined three letters and a number. Ex. FZO1
100
What is the Semantic Web?
The Semantic Web is a development that hopes to improve standardization of online information. Hyperlinks take on a meaning beyond simple connection and represent standardized relationships between a pair of entities.
200
Who was the first to use the term 'gene'?
Wilhelm Johannsen
200
How is gene regulation different in bacteria versus mammalian systems and other higher eukaryotes?
In a bacterial system, there is a proximal relationship between transcription factors and genes with regulatory sequences of a particular gene directly upstream. In higher eukaryotes, genes can be regulated very far upstream by enhancers 50,000 base pairs away, even beyond adjacent genes. The looping and folding of the DNA brings distant spans into close spatial proximity.
200
Define DAG. What does DAG stand for?
Directed Acyclic Graph. This system captures more complexity than simple hierarchy by displaying more than one functional parent to the query.
200
Name two genes in the Notch gene signaling pathway.
See Figure 6.
200
What is the four-step process toward effective gene classification?
1. A gene is identified and named as precisely as possible 2. Brief descriptions of that gene are compiled 3. Standardized keywords are created to categorize genes 4. Those categories can be arranged into a hierarchy or another organizing template
300
What did Mendel show in his famous breeding experiments?
He showed that certain traits do not appear blended in offspring. However these traits are passed on as distinct, discrete entities. In addition, he showed that genotype dictates phenotype.
300
How has our advanced understanding of DNA complicated gene classification?
Alterations at the transcriptional level can lead to different gene products with various functions. Such alternations include alternative splicing, gene regulation, and epigenetic modifications.
300
Why is it more important to understand the detailed biochemistry of a gene's products versus its phenotypic effects?
A phenotypic effect doesn't capture function on the molecular level.
300
Provide an example where a similar gene in two different organisms has an alternate name.
lov-1 in round worms and PKD1 in humans.
300
Name a challenge in creating an ontology.
Tremendous amount of domain-specific knowledge is required.
400
What are the consequences of our expanding knowledge of the gene in the field of biology?
Due to thousands of gene products generated each month, we need to come up with new ways to analyze the data in an organized fashion. Databases need to be manually curated often in order to eliminate redundancy, to improve genetic research and reduce error.
400
What is the lac operon and what was the purpose of using STRING for the lacZ query?
The lac operon is used for lactose metabolism in E. coli and other bacteria. It consists of three structural genes (lacZ, lacY, lacA) which are regulated by a promoter, a terminator and operator adjacent to the genes. STRING showed how the lacZ gene interacted with other predicted functional partners.
400
What is a shortcoming to the DAG approach?
Some areas of a DAG (directed acyclic graph) can be much richer structurally than others because not all aspects of subcellular life are equally well studied.
400
How is the problem with unstandardized gene nomenclature remedied today? Provide an example.
Ex. The Life Science Identifiers is an organization which aims to make biological identifiers consistent and usable across different databases.
400
What is the WikiProteins project?
A community tagging system for proteins (i.e. the scientific community is responsible for protein annotation).
500
Explain the logic behind naming a gene amylase.
Genes named amylase are those involved in a hydrolysis reaction involved in breaking down starch.
500
Why is it difficult for scientists to classify non-genic material?
The function of non-gene transcribed material is unclear. So how do we classify these elements?
500
How can capturing the functions of proteins be challenging?
1. A single gene does not always yield a protein with a single function 2. Individual proteins are often comprised of different domains that might serve a discrete cellular need 3. An assemblage of proteins produced by two or three genes can be necessary to carry out a single identifiable function in a cell
500
Why is the lack of reliable central nomenclature standards becoming a more urgent concern in biology?
A universal way for scientists to classify and refer to genes is critical. Standardizing nomenclature will also eliminate redundancy of similar genes being named differently.
500
Surprise! Sing a song about systems biology or identify this protein: MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKA E
Growth factor receptor bound protein 2 [Mus musculus]
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