02 Gene Regulation and Epigentics

Question 1

What is a gene?

Answer 1

old definition: “a unit of inheritance”

2003: a complete chromosomal segment responsible for making a functional product
* deficit to this definition is that it does not include regulatory elements that govern expression of a gene (promoters, enhancers, repressors etc)

Question 2

polycistronic transcription in prokaryotes

Answer 2

• mRNA is co-linear with chromosome
  (generally, no introns)
• mRNA is mature for co-transcriptional translation as it is being synthesized
• why? no nucleus to block transcription

Question 3

monocistronic transcription in prokaryotes

Answer 3

• mature mRNA is not co-linear with chromosome
  (generally, contains introns)
• mRNA cannot be co-transcriptionally translated
• why? RNA must be exported out of the nucleus

Question 4

Describe transcription in Trypanosoma brucei, a parasitic protozoa

Answer 4

• the rare exception; also some nematodes)
• polycistronic transcription in a eukaryote
• transcript is broken AFTER transcription is completed

Question 5

What is the clinical relevance of the differences between prokaryotic and eukaryotic transcription?

Answer 5

prokaryotic (bacteria) and eukaryotic (host) genes have different structures

differences have ramifications for complexity of products and gene regulation

Question 6

homologs

Answer 6

“similar” genes

vauge, now in disfavor

Question 7

orthologs

Answer 7

• “same” gene found in two different species, derived from same progenitor gene; differences arose during speciation
• direct descendents
• often detectable similar across phylogenetic distances
• may retain similar structural elements (conformation) and function, even if sequences differ

ex: Rad51 gene in Babesia bovis is a true ortholog of the progenitor gene

Question 8

paralogs

Answer 8

multiple genes within a species, derived from orthologous gene through gene duplication

differ because of mutations, different selection pressures, and evolution after speciation

arise by duplication and subsequent evolution, often for alternative functions

Question 9

What non-templated information is found in eukaryotic mRNAs that is lacking from prokaryotic mRNAs?

Answer 9

• introns (immature mRNA)
• 7-methyl-gaunosine triphosphate cap at 5’ end of transcript
• polyadenylated structure at 3’ end of transcript

Question 10

During development isoforms of hemoglobin dominate, beginning with fetal hemoglobin. What is the relationship of the different hemoglobin subunits (alpha, beta, gamma) to one another? WhY/

Answer 10

paralogs

one original gene that has specialized over time

Question 11

What are some levels of regulation of gene expression at the level of transcription?

Answer 11

constitutive: always on (may not actually exist)
regulated: level modulated with need
silenced: always off (may not actually exist)

Question 12

regulated control of gene expression

Answer 12

level modulated with need often the only mechanism considered, but not the only one functioning

transcription factors, phosphorylation of RNA polymerase, ncRNA regulation

Question 13

Where in the process can gene expression be regulated?

How does it affect translation?

Answer 13

transcript abundance is ultimately controlled at MANY different levels, not just transcriptional activity

amount of protein end product that may accumulate is also regulated at MANY different levels, not just translational control

often there is little correlation between transcript levels and protein levels