DNA & Replication
What are the 3 secondary forms of DNA and which is most common and stable?
What is A-DNA, B-DNA, and Z-DNA; B-DNA is most common and stable.
DNA is more stable due to deoxyribose containing only one alcohol group which is used to polymerize DNA. Ribose has two alcohol groups, causing it to hydrolyze in slightly basic conditions, which is the typical cell environment (pH ~7-7.4).
Triplets of DNA and mRNA provide instructions on which amino should be added to the protein product. What are these triplets called?
What types of genes are typically under little to no regulation as they are always expressed?
What are housekeeping genes or constitutive genes.
What is the major difference between bacterial gene regulation and eukaryotic gene regulation?
Because there are more steps in gene expression within eukaryotes, there are more points at which regulation can take place.
What forces keep two DNA strands bonded to each other? What forces occur between adjacent nucleotides, keeping the DNA strand stable?
What is hydrogen bonding between DNA strands (between base pairs) and pi-stacking between adjacent nucleotides (involving Van der Waals force and electrostatic interactions).
What 3 components are found in genes of both prokaryotes and eukaryotes?
What is promoter, RNA-coding region, and terminator sequence.
What 3 processes occur in mRNA processing and in what order?
What are addition of 5' methylguanine cap, addition of 3' poly-A tail, and mRNA splicing.
What type of gene regulation is used by bacteria (between epigenetic regulation, transcription regulation, mRNA processing regulation, translation regulation, and post-translation regulation)? What is their primary mechanism?
What is transcription regulation. Their primary mechanism is the use of operons which contain a regulatory gene just upstream that codes for a regulatory protein that serves as an "ON" or "OFF" switch.
- Chromatin remodeling complexes reposition histones.
- Histone tails can be acetylated/deacetylated.
- Histone tails can be methylated/demethylated.
- DNA can be methylated/demethylated.
What is the term for the mechanisms used to fix damaged DNA? What type of repair is used when DNA polymerase inserts an incorrect nucleotide?
What is DNA Damage Response (DDR); mismatch repair
What two consensus sequences are identified and bound by RNA polymerase in prokaryotes?
What type of intron is spliced by the spliceosome between Group I introns, Group II introns, Nuclear pre-mRNA introns, and Transfer RNA introns?
What are Nuclear pre-mRNA introns.
Provide an example of a common DNA binding domain. Where do they most likely bind to DNA?
What is:
- Helix-turn-helix
- Zinc finger
- Leucine zipper
Tend to bind to major groove.
Describe chromatin immunoprecipitation.
DNA binding proteins (like histones) are covalently linked to DNA.
Cell is lysed.
DNA is cut up.
Protein-linked DNA is isolated using antibodies.
Links are broken.
DNA is sequenced.
What is:
- PCR or qPCR (amplify DNA for detection, sequencing, cloning, etc.)
- DNA cloning (amplify DNA and potentially its protein product)
- Sequencing (read the sequence of nucleotides in DNA of interest)
Rho-dependent termination - Rho factor binds to Rut site on mRNA and moves towards RNA polymerase like a guided missile. When it reaches, the mRNA is pried off the DNA and RNA polymerase via helicase activity.
Rho-independent - use intrinsic terminators; within the mRNA transcript are inverted repeats that are complimentary to each other. They form secondary structure that forces the transcript off DNA and RNA polymerase.
What macromolecules are spliceosomes composed of and which contains the active enzymatic site?
What are proteins (small nuclear ribonucleoprotein particles or snRNPs) and small nuclear RNA (snRNA); the snRNA contain the active site, specifically U2 and U6.
Although bacteria primarily rely on operons, what is another form of gene regulation in bacteria?
Antisense RNA - can bind to mRNA to prevent translation.
Riboswitch - regulatory molecules can bind to mRNA secondary structure (the riboswitch); it changes shape and blocks the ribosome binding site.
Ribozymes - similar to riboswitch but in this case, binding of the regulatory molecule causes the mRNA to gain enzymatic activity and self-cleave.
Of the basal transcription apparatus, which protein complex is most commonly a target of transcription regulation?
The mediator complex.
What are origin/replication licensing and firing? When in the cell cycle do they occur?
Origin licensing occurs when pre-recognition complex assembles at origin of replication (G1). Origin firing occurs when the complex is activated by an active Cdk (complex then becomes active helicase) and occurs at the beginning of S phase.
What is the most common consensus sequence found in the promoter of eukaryotic genes, and what proteins bind to it?
What is the TATA box; TATA-binding protein (TBP), which is part of TFIID, binds to the TATA box.
What is codon degeneracy/redundancy?
Multiple codons may code for the same amino acid. These codons have different nucleotides in the 3rd codon position. This allows for certain DNA or RNA mutations to occur without changing the protein sequence (silent mutations; a type of point mutation or single nucleotide substitution).
The arg operon (produces amino acid arginine) is normally on as it is not ubiquitously present. When arginine becomes abundant, it binds to an ArgR repressor protein to shut off the operon. What type of operon is this?
What is a negative repressible operon.
How can T-cells increase translation of many proteins when engaging a pathogen?
By increasing materials necessary for translation such as initiation factors.