14 - Eukaryotic Genes

Question 1

basic structure of eukaryotic vs prokaryotic cell with respect to gene expression

Answer 1

• Prokaryotic genes are usually under the control of operons.
• In eukaryotes, there are no operons but there are many other methods of gene control such as chromatin remodeling, RNA breakdown, miRNA inhibition, protein tagging by ubiquotin.

Question 2

structure of eukaryotic endomembrane system with respect to gene expression

Answer 2

• Transcription happens in the nucleus which makes a pre-mRNA molecule
• the pre-mRNA molecules gets fixed in the nucleus to form the mRNA molecule befor it is sent off to the cytoplam
• in the cytoplam ribosomes translates the mRNA

Question 3

structure of eukaryotic promoters/enhancers

Answer 3

• Promoter - contains a TATA box, a sequence about 25 bp upstream of the start point.
• Promoter proximal reagion - contains regulatory sequnces called promoter proximal elements. regulatory proteins that bind to promoter proximal elements my stimulated or inhibit the rate of transcription initiation.
• Enhancer - is located further upstream the promoter proximal reagion. regulatory proteins binding to regulatory sequenes within an enhancer also stimulate or inhibit the rate of transcription initiation.

Question 4

mechanism of translation initiation in euks

Answer 4

• general transcription factors bind to the promoter in the area of the TATA box
• These factors recruit the enzyme RNA polymerase II, and orient the enzyme to start transcription at the correct place.
• This combination forms the transcription initiation complex. On its own, this complex brings about only a low rate of transcription initiation, which leads to just a few mRNA transcripts.
• Activators are regulatory proteins that control the expression of one or more genes. They bind to the promoter proximal elements to stimulate transcription initiation so many more transcripts are synthesized in a given time.
• Activators binding at the enhancer greatly increase transcription rates. A coactivator (also called a mediator), a large multiprotein complex, forms a bridge between the activators at the enhancer and the proteins at the promoter and promoter proximal region, causing the DNA to form a loop. The interactions between the activators at the enhancer, the coactivator, the proteins at the promoter, and the RNA polymerase greatly stimulate transcription up to its maximal rate.

Question 5

protein motifs common in DNA binding proteins

Answer 5

• A highly specialized region in a protein produced by the three-dimentional arrangement of amino acid chains within and between domains
• Helix-turn-helix
  
  • A helix-turn-helix motif is part of a protein bound to DNA. One of the alpha-helices binds to base pairs in the major groove of the DNA. A looped region of the protein—the
    turn—connects to a second alpha-helix that helps hold the first helix in place.
• Zinc finger
  
  • are parts of proteins named for their resemblance to fingers projecting from a protein, and the presence of a bound zinc atom. Zinc fingers bind to specific base pairs in the grooves of DNA.
• Leucine Zipper
  
  • Leucine zipper proteins are dimers, with each monomer consisting of
    alpha-helical segments. Hydrophobic interactions between leucine residues within the leucine zipper motif hold the two monomers together. Other alpha-helices bind to DNA base pairs in the major groove.

Question 6

which gene expression components cross the nuclear membrane to get from where they are made to where they function

Answer 6

• mRNA must cross the nucleus in order to be translated.
• Proteins translated in the cytosol but that function in the nucleus must also cross the nucleus to get back in.
• snRNA never crosses the nucleus BUT the protein component of snRNP’s DO need to cross the membrane.
• tRNA must cross nucleus since it works in the cytosol
• and rRNA (same deal)

Question 7

various stages of gene expression subject to regulation

Answer 7

• Transcriptional regulation,
• post-transcriptional,
• translational,
• post-translational.

Question 8

how organisms express different genes in each different tissue

Answer 8

• Different genes can be expressed in a number of different ways. Different protein factors binding to the promoter and enhancer in eukaryotes can have an effect on which genes are expressed. Another method of expressing different genes in different tissue is by alternative splicing, a procces in which different exons are cut out of pre-mRNA’s during splicing. This gives rise to multiple different proteins from the same strand of mRNA.
• Note that during alternative spicing, introns are always cut out, but different exons being cut out is what differentiates the expression of genes

Question 9

the advantages to alternative splicing

Answer 9

• Alternative splicing allows organisms to produce many proteins from the same DNA gene by splicing out different combinations of exons. This is very useful in order to provide organisms with the potential to greatly increase their diversity and control gene expression, while at the same time reducing the need for multiple RNA’s to be transcribed (saves energy)
• In one example, Drosophilia can make thousands of proteins from one mRNA strand

Question 10

mechanism of action of miRNA

Answer 10

• miRNA is transcribed as a single stranded RNA that complementary base pairs with itself after transcription in order to make a loop structure. The top of the loop is clipped off by “dicer” resulting in a double stranded RNA. One strand of this RNA is then digested by an enzyme, while the other strand base pairs with the complementary strand of mRNA, thereby stopping translation of that mRNA.
• miRNA’s have been thought to be related to cancer since they can control the expression of various genes, and if they were to function incorrectly, they could potentially stop the translation of important genes.

Question 11

mechanism of targeting proteins to cellular organelles

Answer 11

• Proteins are targeted to specific organelles by “tags” that exist on the final protein structure. These tags are in the coding sequence of the original DNA and are removed from the protein once that protein gets to where it needs to be. Proteins that are Nucleus-bound do not have their tags removed since the nucleus dissolves during mitosis + meiosis

Question 12

mechanisms to regulate protein function after they are made

Answer 12

• Protein function can be regulated after translation by tagging these proteins for degradation (ubiquotin tags the proteins for digestion by a proteosome) and recycling them
• Another example of protein regulation is methylation, and acetylation of the protein as well as allosteric activation and cofactors.

Question 13

mechanism of ubiquitin/proteosome protein degradation

Answer 13

Ubuquitin tags proteins for degradation at which point they are “recycled” by a proteosome which breaks the protein down into its constituent amino-acids to be used again in the formation of another protein.

Question 14

In general, role of various types of RNA in gene expression

Answer 14

• Messenger RNA (mRNA) - an RNA molecule that serves as a template for protein synthesis
• precursor mRNA (pre-mRNA) - the primary transcript of a eukaryotic protein-coding gene, which is processed to form messenger RNA
• Transfer RNA (tRNA) - the RNA that brings amino acids to the ribosome for addition to the polypeptide chain
• Ribosomal RNA (rRNA) - the RNA component of ribosomes
• Micro RNAs (miRNAs) - small RNAs that regulate gene expression by binding to specific mRNAs and decreasing their translation.
• Short interfering RNAs (siRNAs) - small RNA molecules that regulate expression of certain genes by binding to their mRNA and reducing translation
• Small interfering RNA (siRNA) - a class of single-stranded RNAs that cause Na interference.
• Small Nuclear RNA (snRNA) - are found in small ribonucleoprotein particles (snRNPs) wich remove introns through splicing