Flashcards in Molecular Bio Deck (45):
Do beta linkages project up or down?
Up! "It's better to B up"
What bond is formed between the bars of DNA
Hydrogen. They need to be relatively weak so that the DNa can come apart for replication.
Which carbon does the aromatic bad attach to on the ribose?
Which carbon does the phosphate attach to on the ribose?
DNA is a ____ hand double helix
Which DNA pairs increase Tm the most?
What stabilizes the bases of DNA?
Van der waals forces and hydrophobic interactions between bases
What special enzyme do prokaryotes have to pack DNA more tightly?
DNA gyrase breaks and supercoils prokaryotic DNA to create a dsDna supercoil.
What is nucleosome?
Histone (positive charge) wrapped with DNa (negatively charged)
DNAs exterior backbone is mostly ____ acidic and histones are mostly _____
DNA exterior is acidic, histones are basic
Which type of DNA stains darker and what does this mean? And lighter?
Heterochromatin stains darker because it is more densely packed.
Euchromatin is loosely packed and stains lighter. These regions undergo more frequent transcription.
Do prokaryotes have telomeres?
No especially not because they typically have circular DNA.
What are intergenic regions and what are some examples?
Non-coding regions of DNA. Transposons and tandem repeats are examples
DNA replication is ____conservative
What must happen before DNA polymerase can do its job?
Primase (an RNA polymerase) lays down 8-12 nucleotides of daughter DNA so that DNA polymerase can bind.
DNA is synthesized in what direction?
5' -> 3'
What is the difference between DNA pol III and pol I?
Pol III is very rapid and accurate because it has proofreading ability in the way of 3' -> 5' exonuclease activity.
Pol I is much slower so it does the first 400 bps or so and removes the primer before pol III comes in. It does have repair activity which III does not, however.
DNA pol I and III are found in which organisms?
What is a nonsense mutation?
Premature stop codon
What is the difference between ribose and deoxyribose?
Ribose has an OH on the 2' carbon of the pentose
What is more stable--RNA or DNA?
DNA because it is lacking the reactive hydroxyl on the 2' carbon that can act as a nucleophile.
What is the only coding type of RNA?
Eukaryotic DNA is _____cistronic and prokaryotic DNA is _____cistronic. What does this mean?
Eukaryotic DNA is monocistronic. Prokaryotic is poly cistronic.
Monocistronic means one gene, one protein. Polycistronic can make many different proteins from one gene.
Do eukaryotes process their mRNA? Do prokaryotes?
Eukaryotes process mRNA with 5' cap and 3' poly A tail. Prokaryotes do nothing.
What is the energetic driving force for both DNA and RNA polymerization?
The removal and subsequent hydrolysis of the high energy pyrophopshate from each nucleotide being added.
Is transcription a lower fidelity process than replication? Why or why not?
Yes because RNA polymerase doesn't have exonuclease activity.
What is the final and crucial subunit of the prokaryotic RNA polymerase for transcription?
What is a pribnow box?
Bacterial promoter between -35 and -10
Where dos transcription occur in prokaryotes? And eukaryotes? What is the significance of this?
Since prokaryotes have no nucleus, transcription (and translation) occur in the cytoplasm and can thus occur simultaneously.
Eukaryotic transcription occurs in the nucleus and translation in the cytoplasm (not simultaneous).
What is a primary difference between modification of prokaryotic and eukaryotic mRNA?
Prokaryotic mRNA does NOT HAVE INTRONS! And thus do not need to undergo splicing.
What types of RNA do RNA pol I,II, and III TRANSCRIBE?
RNA pol I transcribes rRNA
RNA pol II transcribes mRNA
RNA pol III transcribes tRNA
What process drives peptide bond formation?
Amino acid activation which makes an aminoacyl-tRNA formed by 2 high energy pyrophopshate bonds that are hydrolyzed.
The nitrogen of one amino acid will nucleophilic attack the carbonyl of the aminoacyl-tRNA of this amino acid and tRNA will be the leaving group.
What is the name of the prokaryotic ribosome?
What is the name of the eukaryotic ribosome?
Which ribosomal subunit has the ribozymic activity?
What is the Shine-Dalgarno sequence?
A ribosome binding site in mRNA (similar to a promoter) to initiate translation in prokaryotes. Just upstream of the start codon.
What is the start codon and what amino acid does it
AUG, codes for Methionine
What are the 3 stop codons?
UAA, UAG, and UGA
What is the eukaryotic version of the shine-dealgarno sequence?
5' UTR helps initiate translation sometimes called the kozak sequence.
Methylation generally turns ___ gene expression.
What is genomic imprinting?
Epigenetic modification of DNA usually by methylation to silence one copy of a gene. Consistent through a persons lifetime but can change in the germ line.
What are inducible enzymes?
Catabolic enzymes activated by an abundance of their own substrate.
What is the TATA box?
An upstream binding site that binds tbp which recruits transcription complex proteins.
Where are enhancers?
Can be either upstream OR downstream of promoters. Help increase transcription.