L4-DNA Replication Flashcards
Describe the structure of DNA.
1’ carbon is attached to a nitrogenous base by a glycosidic linkage. The base can be a purine or pyrimidine. 2’ carbon is connected to only a hydrogen. The 5’ carbon is attached to a phosphate group.
Why does DNA have 3’ and 5’ ends?
Phosphodiester linkages connect the 3’ end of one nucleotide to a 5’ end of another. Hence there will always be a 5’ phosphate end and 3’ hydroxyl end in every strand of DNA.
Describe the central dogma of molecular biology.
DNA->RNA->protein
DNA –(transcription)->RNA-(translation)->protein
How does DNA fit into a prokaryotic cell using supercoiling?
Supercoiling twists DNA and puts DNA molecule under torsion (can be positive/negative or overwound/underwound) so that it takes up less space. Two classes of topoisomerases help supercoil and undwind the DNA. Class 1-Cuts one strand. Class 2 (gyrase)-Cuts two strands
What are transposable elements?
Segments of DNA that can move from one site on a DNA molecule to another site (either on same molecule or on a different DNA molecule). They are not found as separate molecules and are inserted into other types of DNA molecules. In general they play important roles in genetic variation.
Describe the genome of E. coli (size of its genome, organization, coding vs. non-coding DNA)
- • 4.5-5.5 Mbp. May enconde up to 4225 different proteins
- • Many genes involved in the same process are clustered (ex. Lac operon), others are not
- • After removing bacteriophage lambda, only 0.5% of genome consists of noncoding, repetitive sequences. The majority (88%) accounts for genes. 10% encode tRNAs and rRNAs.
- • Proteins that are coded for are usually around 300 amino acids
Compare and contrast plasmid replication to chromosomal replication.
Similarities-initiation at an origin of replication, bidirectional replication, theta intermediate 5’ -> 3’.
Differences-some small plasmids have unidirectional replication, plasmid replication occurs in 1/10th or less time of total cell division (occurs quicker), some plasmids replicate by a rolling circle mechanism.
How do R plasmids and virulence plasmids confer their properties on a host cell?
They give their host cells beneficial properties such as antibiotic resistance/multiple resistance or the abilities of 1)the pathogen to attach to and colonize specific host tissue and 2)production of toxins, enzymes and other molecules that cause damage to the host.
Why is DNA replication considered semi-conservative?
After replication, one strand is a parental/template strand and one strand is a new strand. (Compare to conservative where new DNA is completely new and based on a stationary parent/template or dispersive where new DNA is interspersed among parental DNA).
Define DNA polymerase, primase, and a primer.
- • Polymerase-enzyme that synthesizes or repairs new strand of DNA in a 5’ to 3’ direction, antiparallel to template DNA
- • Primase-RNA-polymerizing enzyme that makes a short RNA primer for DNA polymerases to build off of
- • Primer-short nucleic acid molecule to which DNA polymerase can attach the first nucleotide, often a short stretch of RNA
How is ds DNA unwound?
DNA helicase unwinds dsDNA using energy from ATP to expose short single stranded regions. Separates strains in advance of replication fork and causes positive supercoils that DNA gyrase travels ahead to cancel out.
Differentiate between the leading and lagging strand.
Leading strand-continuously synthesized from 5’ P042- to 3’ OH-. Requires only one primer.
Lagging strand- DNA synthesis occurs discontinuously because there is no 3’-OH at the replication fork. Requires multiple primers.
How are the fragments of the lagging strand joined together?
DNA pol II synthesizes strand until it reaches a previous Okazaki fragment. Pol I removes the RNA primer and replaces it with DNA. DNA ligases makes the last phosphodiester bond between the replaced primer region and the recently created strand.
Explain how bidirectional replication allows for shorter generation times in bacteria.
Strand is synthesized in two directions at once allowing for quicker DNA replication and shorter generation time. When E. coli is at optimum conditions, there are multiple replication forks.
How is PCR similar and different from DNA replication?
Similarities-DNA polymerase copies DNA, need for primers
Differences-does not replicate entire DNA strand, only a portion, DNA primers used instead of RNA primers, used for amplification rather than copying, varying temperatures in cycles
