Molecular Genetics Flashcards
Origin of replication
location on the chromosome where replication begins
Bidirectional
DNA replication proceeds in both directions simultaneously from the origin
Semi-conservative
each of the newly formed daughter helices is made up of one old strand paired with one new strand
Semi-discontinuous
one strand (the leading strand) is synthesized continuously and the other strand (the lagging strand) is synthesized in Okazaki fragments (i.e., discontinuous)
DNA replication start to finish
DNA replication begins at an origin of replication. Helicase unzips the double-helix. Immediately, single strand binding proteins coat the individual strands and prevent them from re-annealing. Simultaneously both strands are fed through a replication complex that contains all of the proteins necessary for replication. Because DNA polymerase can only add to an existing 3’ OH group, primase (an RNA polymerase) first constructs short RNA primers on both strands. Two DNA polymerase molecules then begin building new complementary DNA strands. In doing so, they must “read” (i.e., move along the strand) in the 3’ to 5’ direction and are therefore building the new strands in the 5’ to 3’ direction. The sliding clamp is a protein that helps keep the DNA polymerase tightly associated with the strand. Because both enzymes must move along the strand in the 3’ to 5’ direction, they will be moving in opposite directions. If this continued indefinitely the two enzymes would move farther and farther apart. Instead, all enzymes and proteins remain closely associated with the replication fork in what is often called the “replication complex.” As a result, the enzyme working on the lagging strand must copy short segments downstream, release from the strand, move upstream, and copy another short segment downstream—and then repeat. This also means that while the leading strand requires only a single primer, the lagging strand requires multiple primers—one for each these short segments called Okasaki fragments. After this initial replication step, the enzyme RNase H removes all RNA primers. DNA polymerase then fills in the gaps. However, DNA polymerase functions only to add nucleotides to existing 3’ OH functional groups. Therefore, although it can add a nucleotide to fill the last missing base pair in a gap, it cannot connect that last nucleotide to its downstream neighbor. This functionality is performed by DNA ligase. DNA ligase creates the last necessary phosphodiester bond creating a completed strand.
How does the lengths of replicated DNA strands compare to the original? Why?
The replicated strand is always slightly shorter. The DNA polymerases require an existing 3’ hydroxyl group to which they can add their first nucleotide—they cannot set down a nucleotide with a free 5’ end. For this reason, an RNA primer must be placed at the 5’ end of any DNA strand. Later in the process all primers are removed and the gaps are filled in by DNA polymerase and DNA ligase. At the 5’ end, however, there will still be no existing 3’ hydroxyl group and so DNA polymerase cannot replace that section of primer. As a result, every time a chromosome is replicated the new daughter strands will be slightly shorter than the parent strands—by an amount exactly equal to the RNA primers that were in place on both ends of the chromosome
What are telomeres and why are they important?
Long sections of repetitive DNA nucleotides found on both ends of chromosomes. Act as a buffer-region of non-coding DNA so that length loss does not affect the coding region. Buffer lasts for about 50 replication cycles
What is telomerase?
enzyme that adds length to the telomeres
Why is telomerase turned off in mature somatic cells?
Built-in destruction clock that helps to prevent uncontrolled cell division
DNA polymerase reads from _ ‘to _’
3’–5’, meaning creates 5’-3-
What are the different mechanisms for DNA repair?
Proofreading
Mismatch repair
Base excision
Nucleotide excision
what is an endonuclease?
enzyme that cleaves the phosphodiester bond of a polynucleotide chain
what are restriction endonucleases
enzymes that cleave at specific nucleotide sequences.
Incomplete dominance
if red+blue, = purple
Complete dominance
all of the dominant ie red
Co-dominant
both red and blue show up
phenotype
what trait physically appears as
genotype
what traits alleles consist of
what are mutations
mistakes in DNA
where do large scale mutations take place
chromosomal level
inversion
two genes on same chromosome switch places
translocation
gene on one chromosome swapped with one on another
mutagen
chemical/physical substance/event that can cause genetic mutations
where are reactive oxygen species produced. examples? what effects might they have? what prevents them?
mitochondria. O2-, H202. they can be bad because they can react with DNA and cause damage such as double strand breaks or base modification (bases changed/swapped). antioxidants help prevent oxidative stress (when ROS gets too high)