BIOL 111 DNA and Transcription

What are nucleic acids?

Polymers of nucleotides that contain a nitrogenous base, a phosphate group, and a sugar molecule

What bond joins nucleic acids?

A phosphodiester bond

What groups do DNA and RNA include, respectively?

H (deoxy-) and OH (ribonuc-)

How does ribose chemically behave?

It has extra oxygen groups and is more soluble in water, which makes it more reactive but less stable

What are the functions of RNA?

It can act as a messenger (mRNA), can behave as an enzyme, and has a high turn over

How does deoxyribose chemically behave?

It has less oxygens and is more stable overall

What is the function of DNA?

Long term storage of genetic information

What are the two types of nitrogenous bases?

Purine (double ring) and pyrimidine (single ring) bases

What are the two purine bases?

Guanine and adenine

What are the three pyrimidine bases?

Thymine, cytosine, and uracil

What is special about cytosine?

It can deaminate into uracil and form mutations

Between thymine and uracil, which is more stable and costs more to make?

Thymine

What kind of bond attaches nucleotide bases?

Hydrogen bonds

Why do guanine and cytosine have a stronger bond than adenine and thymine?

Because of a 3rd hydrogen bond

What is significant about the 1928 Griffith experiment?

only the removal of DNA from a virus removed the ability for that virulent genetic memory to be transferred to non-virulent strains

What is central dogma?

a framework for how genetic info is stored, expressed, and used to build proteins

What are the steps of central dogma?

DNA encodes RNA through transcription to build proteins through translation

What are the functions of the major groove?

it is large and info rich and can be read by proteins without having to unwind the helix because of its size

What are the functions of the minor groove?

it is smaller and more uniform, which is good for structural stabilization and drug binding, but makes it harder to get into

About how many bases are there for a complete turn of a DNA strand?

10 bases

What is chargaff’s rule?

that the number of A’s to T’s and G’s to C’s always equal each other

What stabilizes the double helix formation?

hydrogen bonds between bases, and base stacking that is driven by van der waals forces and hydrophobic effects

Between the backbone of a helix structure and the bases inside it, which is hydrophobic and which is hydrophilic?

hydrophobic bases and hydrophilic backbone

What enzyme is involved in DNA replication?

DNA polymerase

What do errors in the transcription process create?

mutations

What is transcription?

DNA is split into a template strand and used for the synthesis of an RNA transcript

What directions do DNA and RNA move in, respectively?

DNA 5’ to 3’ and RNA 3’ to 5’

What is the exception to transcription occurring indiscriminately?

house-keeping genes

What is the rule about transcription occurring discriminately?

genes encode information in the presence of a relevant molecule

What is the promoter?

the regions where RNA polymerase and associated proteins bind to a DNA sequence to define the trasncriptional start site

What is the terminator?

the area where RNA polymerase disengages and the transcript is released

Where do the promotors and terminators lie in relation to the TSS (transcription start site)?

the promoter is before the TSS and the terminator is after the TSS

What two systems bind to increase the rate of transcription?

enhancer sequences and transcriptional activator proteins

What is the function of general transcription factors?

they build up next to the promoter sequence to create the transcription bubble

What are the three stages of transcription?

initiation, elongation, and termination

What is initation?

the interplay of various proteins binding to DNA to allow transcription to start and is when the transcription bubble forms

What is elongation?

when RNA is built inside the transcription bubble

What enzyme is building the RNA transcript?

RNA polymerase in prokaryotes and RNA polymerase II in eukaryotes

What direction is the RNA polymerase moving along the DNA template strand?

3’ to 5’ direction

In what direction is the RNA transcript being built?

5’ to 3’ direction

What determines when RNA polymerase will transcribe a particular gene?

only when regulatory proteins/signals allow it to bind to the promotor

What signals control regulators and the activation of RNA polymerase transcription?

environmental and cellular signals that happen only when the gene’s product is needed

What is rho-dependent termination?

recognizing a specific tho protein that unwinds the DNA-RNA hybrid to release RNA polymerase and the RNA transcript

What is rho-independent termination?

termination triggered by specific termination sequences (terminators) in DNA

What is polycistronic mRNA?

a single mRNA that contains multiple protein-coding regions and can be translated into different proteins

In eukaryotes, what helps the ribosome recognize mRNA?

the addition of a 5’ cap linked to the 5’ end of the primary transcript by a 3-phosphate bridge

What is polyadenlyation?

the addition of a polyA tail added to the 3’ end of an mRNA molecule

What is polyadenylation used for?

stability, exporting the mRNA into the cytoplasm, and efficiently translating into proteins

What is RNA splicing?

removing extra, noncoding regions called introns to produce a mature RNA

What are introns?

non-coding regions of a gene

What are exons?

protein-coding regions of a gene

What is the function of the spliceosome?

splicing the nucleus to remove introns at splice sites

What is alternative splicing?

one gene can produce different RNAs by including or excluding different exons from the final RNA sequence

What is the difference with polymerase between prokaryotes and eukaryotes?

1 polymerase vs polymerase I, II, and III

What is the difference in initiation between prokaryotes and eukaryotes?

Initiation at promoters vs initiation at promoters + pre-initation complex forms + enhancers regulate promoter activity

What is the difference in RNA processing between prokaryotes and eukaryotes?

mRNAs are polycistronic and transcription directly yields mRNA vs 5’ capping, splicing, and 3’ polyA tail

Is transcription coupled between prokaryotes and eukaryotes?

Transcription and translation happen at same time vs transcription in nucleus and translation in cytoplasm