DNA & RNA, Transcription & Translation Flashcards
What does the enzyme RNA Polymerase I make?
rRNA (18S, 28S, 5.8S)
What does the enzyme RNA Polymerase II make?
mRNA, snRNA, miRNA, & IncRNA
What does the enzyme RNA Polymerase III make?
tRNA, 5S RNA, U6snRNA, & 7SK RNA
DNA and RNA grow in which direction?
5’ to 3’
Which bases are pyrimidines?
Cytosine & Thymine
Which bases are purines?
Adenine & Guanine
What is alpha-amanitin?
An inhibitor of eukaryotic RNA polymerase II
What is rifampicin?
An inhibitor of RNA polymerase; blocks RNA exit channel
What are the basic components of an nucleotide?
A pentose sugar, a purine or pyrimidine nitrogenous base attached to the 1’ carbon, and 1, 2, or 3 phosphates attached to the 5’ carbon. A DNA nucleotide has an OH group on the 3’ carbon of the pentose sugar. RNA has OH groups on both the 2’ and 3’ carbons.
Order from most soluble to least soluble: purines, pyrimidines, bases, nucleosides, nucleotides,
Pyrimidines > purines > nucleotides > nucleosides > bases
What is the central dogma of biological information transfer?
DNA replicates to make more DNA. DNA undergoes transcription to make RNA. RNA undergoes translation to make proteins.
Describe Gout and Lesch-Nyhan
Gout and Lesch-Nyhan are a failure to dissolve purines and purine byproducts in tissues. Purines are least soluble of all building blocks.
Identify the chemistry in the phosphodiester linkage of DNA and RNA polynucleotide strands.
Phosphate group on the 5’ carbon binds with the OH on the 3’ carbon
Describe the important experiments that helped to establish DNA as the genetic material
Avery, McCloud, and McCarty showed, using virulent and non-virulent bacteria, that DNA is the transforming material → aka, the genetic material.
Chargaff showed that % purines = % pyrimidines and that %G=%C, and %A = %T.
Rosalind Franklin and Maurice Wilkins used x-ray diffraction to show helical structure and 3.4 nm repeat.
Watson and Crick put together the double helix structure.
What are some nucleotides that are not in DNA or RNA?
cAMP, cGMP, NAD, Coenzyme A
What is the difference between a nucleoside and a nucleotide?
A nucleoside is a the pentose sugar plus a base. Adding phosphate groups makes it a nucleotide.
What is the complementary RNA strand of this DNA strand: 5’ AGCCTGTAGC 3’
5’ GCUACAGGCU 3’
How many Hydrogen bonds does one G-C bond make? One A-T bond?
A G-C bond makes three H bonds. An A-T bond makes two H bonds.
What are four conditions that will increase the melting temperature (stability) of DNA?
High salt concentration, high G-C concentration, longer strand, neutral pH.
What kinds of DNA are circular versus linear?
Mitochondrial and bacterial DNA
Where does methylation of DNA most commonly occur?
Methylation of Cytosine attached to 5’ carbon when this cytosine is adjacent to and just upstream of a guanine.
What is deamination of DNA and what are its consequences?
Deamination is the removal of an amino group and replacement of an Oxygen usually at a base. 5-Methylcytosine can be deaminated to become Thymine. There is now a 50/50 chance of making an mutagenic “correction.” Correction mechanism does not know whether C or T is the mutated base.
What is depurination and what are its consequences?
Purine bases are subject to attack by water, resulting in depurination: a break between the sugar and base.
What is UV Cross-linking and what are its consequences?
UV waves can cause two adjacent thymines to cross-link with one another.
What is oxidative damage and what are its consequences?
Hydroxyl radicals are generated by ATP production can cause OH groups to be attached to bases. Can cause downstream issues of DNA replication or transcription.
What are three classes of RNA in human cells and what are examples of them?
- Structural RNA ( rRNA, tRNA, snRNA small nuclear, and snoRNA small nucleolar)
- Regulatory RNA (control gene expression) = miRNA, siRNA (small interfering)
- Information-containing RNA = mRNA
What do topoisomerases do?
Relax supercoils in DNA
How does puromycin work?
Puromycin is a nucleotide analogue that mimics the tRNA acceptor region, allowing peptide transfer and termination. Puromycin will bind the ribosome and react with growing peptide chain to terminate translation (example of mimicry in antibiotics).
How can DNA replication be bidirectional if both strands must grow in the 5’ to 3’ direction?
There is a leading strand that grows continuously and a lagging strand that grows in Okazaki fragments.
What is the end-replication problem?
There is a progressive shortening of chromosomal ends during rounds of DNA replication. The leading strand can be synthesized to the very end but the lagging strand cannot be.
What do origin binding proteins do during DNA replication?
They recognized initiation sites on the DNA which are usually A-T rich. There are many many initiation sites on one DNA strand.
What do helicases do during DNA replication?
Unwind the double-stranded DNA
What do single-strand binding proteins do during DNA replication?
They bind to the single-stranded DNA to keep them from winding together again
What does primase do during DNA replication?
Creates an RNA primer for the replication of DNA
What does DNA Polymerase I do during DNA replication?
Removes RNA primer and replaces it with DNA. Is “distributive,” meaning it can come off easily and it does not use a sliding clamp.
What does DNA Polymerase III do during DNA replication?
Moves with a sliding clamp to make complementary new DNA strand.
What does DNA ligase do during DNA replication?
Ligates DNA fragments.
What does the sliding clamp do during DNA replication?
Allows DNA Polymerase III to stay clamped onto strand and slides in the 5’ to 3’ direction of new strand.
What does gyrase do during DNA replication?
Gyrase is a topoisomerase inhibited by quinolones. Found mostly in prokaryotic cells.
What does telomerase do during DNA replication?
Telomerase is a reverse transcriptase that elongates telomeres by using RNA templates to add DNA segments to ends of telomeres. This prevents the end-replication problem.