Genome Organization
True or false: Telomeres contribute to organized segregation during mitosis.
False (centromeres do this; telomeres are at the end of chromosomes and protect them from degradation)
List the three basic steps of transcription.
Initiation, elongation, termination
True or false: Bacteria have three types of RNA polymerases, RNA Pol I, RNA Pol II, and RNA Pol III.
False
Both core and ____ promoters are necessary for transcription in eukaryotes.
Proximal
True or false: DNA supercoiling is one way transcription is regulated in bacteria.
True
Histone acetylation results in ___________ (euchromatin, heterochromatin), where nucleosomes are packed _________ (tightly, loosely) and transcription is ___________ (upregulated, downregulated).
Euchromatin, loosely, upregulated
Name the polymerase used in eukaryotes to transcribe protein-coding genes.
RNA Pol II
Bacteria contain _____, which is a group of multiple linked genes that share one promoter.
Operons
Which of these is NOT one mechanism of eukaryotic transcription regulation that bacteria LACK?
Histone modifications, distal regulatory elements, multiple polymerase types, transcription factors
Transcription factors
When tryptophan is abundant, the trp operon is _______ (activated, repressed).
Repressed
Describe what a nucleosome consists of.
DNA wrapped around a nucleosome core/histone octamer (2x H2A, 2x H2B, H3, H4)
This domain of RNA Pol II consists of multiple repeats of a heptapeptide sequence and undergoes phosphorylation to regulate the transition between different steps of eukaryotic transcription.
C-terminal domain (CTD)
The core RNA polymerase complex plus the σ subunit makes up the ________.
Holoenzyme
Give 1 example of a disease caused by mutations in a transcriptional regulatory element.
β-thalassemia, hemophilia, hereditary persistence of fetal hemoglobin, δ-thalassemia, X-linked deafness, asthma and allergies, Beckwith–Wiedemann syndrome, α-thalassemia
Describe the conditions (stimuli) required for the lac operon to be ON, or transcriptionally active.
Absence of glucose, presence of lactose
State the role of H2A, H2B, H3, and H4. (they are all kind of the same).
Assemble to form the histone octamer, the core of the nucleosome, to help compact eukaryotic DNA.
Name one possible function of lncRNAs (long noncoding RNAs).
Get processed into small RNAs (e.g. miRNAs), bind proteins to affect their behavior, hybridize with sense RNA to cause alternative splicing or generate siRNAs, affect transcription of other genes
Explain the role of the σ subunit.
Increase affinity of the complex to promoters by recognizing their consensus sequences, stabilizing the initiation complex for transcription initiation.
Give 3 examples of types of distal regulatory elements in eukaryotes.
Silencers, insulators, locus control regions, enhancers
Identify the mistake in this explanation: The lac operon has multiple components. The operator is a protein that binds the lac operon to turn transcription off. The activator is a protein that binds the lac operon to turn transcription on.
The operator is not a protein; it’s a sequence of DNA that the repressor (encoded by lacI) binds.
Two part question: Name one protein that packs bacterial DNA and whether they are DNA-bending or DNA-bridging.
IHF - DNA-bending
HU - DNA-bending
H-NS - DNA-bridging
SMC - DNA-bridging
Describe the mediator and its role in eukaryotic transcription.
Multi-protein complex that acts as a bridge between TFs bound to regulatory sequences and RNA polymerase. Facilitates RNA polymerase recruitment to the promoter and subsequently transcription initiation
Name and briefly describe the two main termination mechanisms in bacteria.
Rho-dependent termination - Rho protein binds the rut sequence and causes RNA polymerase to dissociate
Intrinsic/sequence-dependent/rho-independent termination - Sequence in the RNA transcript forms a hairpin structure, causing the RNA Pol to pause and the RNA to be released
This region controls the expression of multiple globin genes during different stages of erythroid cell development and contains DNase I hypersensitive sites that mark areas accessible to transcription factors.
β-globin locus
Which of these describes a mechanism of the ara operon?
1. The same protein serves as both an activator and a repressor. 2. Ribosome stalling on the leader sequence of its mRNA transcript allows transcription to continue. 3. Transcription is regulated by both a dissociable repressor and an activator.
The same protein serves as both an activator and a repressor.