Exam 2: Fundamentals of Gene Structure, Gene Expression, and Human Genome Organization

What are the different natural ways in which proteins are chemically modified in cells and why do they need to be modified?

What roles do snRNA, snoRNA and scaRNA have in RNA maturation? Do any of them participate in other functions?

Which, if any, of the following statements are false? a) During translation, the individual codons of an mRNA are "read" by transient hydrogen bonding to a complementary anticodon sequence on a transfer RNA. b) According to their anticodon, transfer RNAs usually have a specific amino acid attached to their 3' end. c) When the anticodon of a tRNA binds to a codon with a suitably complementary sequence, the amino acid is released and becomes part of a polypeptide. d) Translation terminates at an in-frame termination codon (UAA, UAG, or UGA in the universal genetic code) because for these codons, there are no transfer RNAs with a complementary anticodon sequence.

With respect to expression of an RNA gene, which, if any, of the following statements are false?

Fill in the blanks below. More than half of our genome is composed of families of highly repetitive DNA sequences. Close to 15% of these are composed of tandem repeats of short sequences that are found predominantly at or close to ____1____ and in other regions of ____2____ heterochromatin (which includes much of the long arm of the ___3____ chromosome, and much of the short arms of the five acrocentric chromosomes). The remaining 85% or so of the highly repetitive DNA is made up of interspersed repetitive DNA sequences that are scattered across the genome and belong to families of ____4____ repeats. Only a small fraction of the ____4____ repeats are based on DNA ____4___ (which transpose by a ___5___-and-paste mechanism). The great majority are ____6____ repeats, some of which can actively transpose by a ___7___-and-paste mechanism (which involves using a _____8____ ____9_____ to make cDNA copies of RNA transcripts, with the copies integrating elsewhere in the genome).

Fill in the blanks below. Two important RNA processing events lead to specialized end sequences in most human mRNAs: ____1____ at the 5' end, and ____2____ at the 3' end. The altered sequences protect the RNA from attack by cellular ____3_____ and confer a measure of stability. In ____1____ the most distinctive change is a specialized end nucleotide, ____4_____ _____5______, that is joined to its neighbor using a distinctive ____6______ bond. In this case, the ____7____ carbon atom of the end nucleotide is joined to the ____7_____ carbon atom of its neighbor. In ____2______ a sequence of about 200 ____8____ is enzymatically added to the 3' end by a dedicated enzyme called _____9_____ ____10______.

Exon shuffling has been thought to have occurred periodically during the evolution of me. What advantages might it have, and how might it have arisen?

Which, if any, of the following statements is false?

Regarding exons, which, if any, of the following statements is correct?

Fill in the blanks below. During evolution duplication of a gene produces two copies. The sequence of one copy may continue to be conserved (because it remains subject to ____1_____ ____2____; the other copy is free to mutate. The latter will most likely acquire deleterious mutations and degenerate to become a ____3_____. If duplication occurs at the genome level, the ______3______ will often be located close to the parent gene. It may contain copies of the full length sequence of the parent gene (including the promoter, exons, and introns), and is known as a ____4_____ _____3______ . Sometimes, however, the duplication involves making a cDNA copy of an mRNA after which the cDNA copy integrates into a new locus that is often very distant from the parent gene. Because the cDNA copy lacks promoter sequences, it is usually not expressed and will acquire inactivating mutations and degenerates. This type of _____3____ is known as a _____5____ ___3_____ or a ____6_____. Sometimes, the cDNA copy integrates close to a promoter sequence and is expressed, and if so, on rare occasions, the expression of this gene copy becomes an asset to the cell so that it becomes subject to ____1____ ____2____ and is a conserved functional gene. Such a cDNA copy is known as a ____7____.

Regarding polypeptide structure, which, if any of the following statements is incorrect.

In addition to coding sequence, which is generally very highly conserved, what additional percentage of our genome is highly to moderately conserved?

Following the completion of the Human Genome Project the ENCODE Project was developed as a major follow-up project. What were the aims, and what the outcome?

In what ways are the transcription and processing of our mitochondrial genes rather different from that of most of our nuclear genes?

Regarding the structures of amino acids, which, if any, of the following statements is incorrect?

Nearly half of our genome is composed of transposon repeats, some of which can actively transpose, occasionally causing disease by inserting into or close to genes, (causing gene inactivation or inappropriate expression of oncogenes). Many of them work by making copies that transpose and so can increase in copy number, and so there is a need to limit the number of actively transposing sequences in case they overwhelm the genome. Two types of small RNAs act to limit the spread of transposons. What are these RNAs and where do they work?

During evolution, as multicellular organisms became ever more complex, there has been a relentless drive to duplicate DNA sequences. As a result, our genome contains many examples of duplicated exons, duplicated genes, plus duplications of large chromosomal regions. What kinds of advantages might DNA duplication events confer that could enable ever greater functional complexity?

Which, if any, of the following statements are false?

Explain what is meant by a functional pseudogene and illustrate your answer with an example.

Roughly what percentage of our genome is made up of transposon repeats?