Chapter 10
This repeating structural unit of eukaryotic chromatin consists of DNA wrapped around eight histone proteins.
What is a nucleosome?
This is the direction in which DNA polymerase synthesizes new DNA strands.
What is 5' to 3'?
This three-letter DNA sequence in bacteria, located about 10 base pairs upstream of the transcription start site, has the consensus sequence TATAAT and is where DNA unwinds.
What is the -10 box (or Pribnow box)?
This three-nucleotide sequence on mRNA specifies which amino acid should be added to the growing polypeptide chain.
What is a codon?
If a DNA template strand reads 3'-TACGGGCAT-5', the mRNA transcribed from it would be this sequence.
What is 5'-AUGCCCGUA-3'?
This type of chromatin is loosely packed and transcriptionally active, while heterochromatin is densely packed and silent.
What is euchromatin?
This bacterial protein binds to DnaA boxes at the origin of replication (oriC) and causes the AT-rich region to separate, initiating DNA replication.
What is DnaA protein?
This subunit of bacterial RNA polymerase holoenzyme recognizes and binds to the promoter, then is released after transcription begins.
What is the sigma (σ) factor?
The start codon AUG codes for this amino acid in eukaryotes (or formylmethionine in bacteria).
What is methionine?
A researcher observes that a gene region has heavily methylated DNA and deacetylated histones. Based on chromatin modifications, you would predict the gene is in this state of transcriptional activity.
What is transcriptionally inactive (or silenced, or heterochromatin)?
These four core histone proteins make up the octamer around which DNA wraps in a nucleosome.
What are H2A, H2B, H3, and H4?
These short DNA segments, named after their discoverer, are formed on the lagging strand during discontinuous replication.
What are Okazaki fragments?
This modified guanosine structure is added to the 5' end of eukaryotic mRNA to protect it from degradation and help ribosomes bind.
What is the 7-methylguanosine cap (or 5' cap)?
This region on bacterial mRNA, also called the Shine-Dalgarno sequence, is located in the 5' UTR and serves as the ribosome binding site.
What is the ribosomal binding site (RBS)?
During DNA replication, if DNA polymerase I is non-functional, this specific problem would occur, particularly affecting the lagging strand which has multiple instances compared to the leading strand's single instance.
What is RNA primers not being removed and replaced with DNA (or gaps remaining between Okazaki fragments)?
This enzyme creates negative supercoils in bacterial DNA using ATP and is a target for antibiotics like ciprofloxacin because it doesn't affect eukaryotic cells.
What is DNA gyrase (or DNA topoisomerase II)?
This enzyme in bacteria has 5' to 3' exonuclease activity to remove RNA primers and 5' to 3' polymerase activity to replace them with DNA, while DNA Pol III does the main synthesis work.
What is DNA polymerase I?
This large RNA-protein complex, composed of snRNPs, recognizes splice sites at intron-exon boundaries and catalyzes the removal of introns from pre-mRNA through two transesterification reactions.
What is the spliceosome?
According to the wobble rules, the third position of a codon can tolerate certain mismatches, allowing a single tRNA to recognize multiple codons; tRNAs that recognize the same amino acid but have different anticodons are called this.
What are isoacceptor tRNAs?
A eukaryotic gene undergoes alternative splicing where sometimes exon 2 is skipped. If the normal protein is 300 amino acids and exon 2 codes for 45 amino acids, but skipping it causes a frameshift that introduces a stop codon 20 amino acids later, the alternatively spliced protein would be this many amino acids long (assuming exon 2 starts at amino acid 100).
WORTH DOUBLE POINTS
What is 120 amino acids? (100 from before exon 2 + 20 amino acids after the frameshift before stop codon)
This chemical modification adds acetyl groups to histone tails, neutralizing positive charges and causing chromatin to open for transcription, while the opposite process condenses chromatin and silences genes.
What is histone acetylation (or what are histone acetyltransferases/HATs)?
This ribonucleoprotein enzyme solves the end-replication problem in eukaryotic chromosomes by using its internal RNA template to add repetitive DNA sequences to the 3' overhang, preventing chromosome shortening with each cell division.
What is telomerase?
This general transcription factor has both helicase activity to unwind DNA at the transcription start site and kinase activity to phosphorylate the CTD of RNA polymerase II, triggering the transition from initiation to elongation.
What is TFIIH?
In eukaryotic translation initiation, the small ribosomal subunit binds to the 5' cap and scans for the start codon following these rules: the start codon must be AUG, must have a guanine at the +4 position, and must have this type of nucleotide (either adenine or guanine) at the -3 position. These rules, which determine optimal translation initiation efficiency in eukaryotes, are named after this researcher.
What are Kozak's rules (or who is Marilyn Kozak)?
OR
What is the Kozak consensus sequence?
A pharmaceutical company wants to produce human insulin in E. coli bacteria. Since the human insulin gene contains introns and bacteria cannot process them, requires a 5' cap and poly-A tail for stability that bacteria don't add, and bacteria use the Shine-Dalgarno sequence instead of the 5' cap for ribosome binding, name the two major types of molecules they would need to use to create a functional bacterial expression system.
What is cDNA (complementary DNA made from mature mRNA, which lacks introns) and a bacterial expression vector with a Shine-Dalgarno sequence?
OR
What is reverse transcriptase to make cDNA from mRNA, and a plasmid with bacterial promoter/RBS?