Exam 5: Genomics, Proteomics, and Systems Biology

Neandertals are thought to be our closest evolutionary relatives, having diverged from humans 300,000 to 400,000 years ago, and their genome has been sequenced. Which statement about humans and Neandertals is false?

Next-generation DNA sequencing is not an acceptable method for detecting differences in gene expression during development. Which statement most likely describes the reason why?

In RNAi screens, siRNAs are incubated with cells in culture to assess functional consequences of the targeted gene. Which statement regarding siRNA and its action is true?

In 2010, scientists developed a series of overlapping oligonucleotides that extended a full 1.08 million base pairs and used it to develop the first complete organism using a synthetic genome. The newly created cells had normal growth and morphology. What organism did they generate in these groundbreaking experiments?

You have identified a unique 8-base sequence in the promoter of a gene that controls growth. Describe an experiment that may address whether this sequence is capable of directing transcription of other genes.

Why is it thought that regulatory elements occur in clusters?

If an organism has a 2 million base genome and 90% of it encodes proteins, and the average gene is 300 codons, how many genes does it have?

In the pathway through which epinephrine signals the breakdown of glycogen to glucose in muscle cells, there are at least six different proteins involved before glycogen phosphorylase acts to cleave a glucose off of glycogen. Additional administration of epinephrine will increase the pathway. In a cell line in which phosphorylase kinase is mutated, what will happen if epinephrine is used to treat the cells?

Which of the following would not necessarily be part of a cellular signaling network?

Bioinformatics is

Which of the following steps comes first in next-generation sequencing?

Remarkably, only _______% of the human genome corresponds to protein-coding sequences.

A more common name for the high-throughput DNA sequencing method of massively parallel sequencing is _______.

The human genome has more genes than plant genomes have.

You have a cell signaling cascade in which a cell signal initially targets and activates protein 1 which in turn activates protein 2 which then activates protein 3 and finally activates protein 4. You are given a cell line that never expresses protein 2, yet in every experiment in which you give the initiating signal, you get activation of protein 4. How could you explain these results?

An estimated 40% of the human genome encodes proteins that are related to proteins found in a number of other species. These proteins are involved in which cellular processes?

The first complete sequence of a cellular genome was of the bacterium _______.

Five percent of the genome is conserved among all mammals, yet only ~1% directly encodes proteins. What is the likely role for the remaining 4%?

From 2001 to 2014, the cost of sequencing an individual's genome has dropped from several million dollars to several _______ dollars.

An interesting observation that has arisen out of systems biology in the study of the genome and proteome is that humans have 21,000 genes, yet we have identified over 100,000 proteins. What are some of the contributors to this almost five-fold difference?