Unit 3 Chapter 14: DNA and the Gene-Synthesis Repair Flashcards
What is was Fredrick Griffith’s experiment
- took 2 strains of pneumoccus bacteria (S strain and an R strain)
- injected the strains into mice
- S strain killed them causing pneumonia
- R strain did nothing
- Heat treated/dead S bacteria did nothing
- Mixture of Heat S and regular R killed the mice (analysis showed live S bacteria in the dead mice so something must have transformed from the dead S to the live R)
- led to the transforming principle
What is the transforming principle
bacteria are capable of transferring genetic information through a process known as transformation
Does DNA work in other organisms
yes, viruses too
What are bacteriophages
- viruses that infect bacteria cells
- most abundant thing ever
- host specific
- DNA is stored in the head, injected into bacteria through tail
- cell either replicates these viruses using the viral DNA that was injected releasing a ton of new ones (lytic) or DNA is replicated but so is the rest of the bacterial genome, it is stored and remains dormant until the conditions are right and viral replication is initiated which causes lysis of the cell (lysogenic)
What is the Hershey-Chase Experiment
- intention was to answer whether genes were protein or DNA
- used T2 Bacteriophage and e.coli
- knew that infections begin when T2 attaches to cell well and injects its own DNA into the bacteria which acts as a host for the virus
- after injection the viral capsid remains attached like an ghost
- T2 made up of protein and DNA, but which entered cell?
- important facts: protein contains S not P and DNA contains P not S
- grew T2 in the presence of radioactive P and S and allowed each set to infect e. coli
- if genes consist of DNA then protein should be found in the ghosts an DNA should be in the cell, but if they consist of protein only protein should be in the cells
- blended their samples to get rid of ghosts
- found that all protein was in ghosts and all DNA was in cells
- DNA was pronounced hereditary material
What is semi-conservative replication
the hypothesis that if the old DNA was separated each strand could be used as a template to create the daughter DNA so that the daughter would contain one old strand and one new one
What is conservative replication
the hypothesis that if the base strands temporarily faced outward so that complementary strands no longer faced inwards then they could serve as the template for an entirely new double helix (daughter DNA would have 2 completely new strands)
What is dispersive replication
the hypothesis that if the parent helix was cut into short sections before being unwound, copied and put back together then new and old segments would alternate in each strand
What was the Meselson and Stahl Experiment
- wanted to mark parental/daughter strands of DNA to figure out if replication was disp, cons, or semi-cons
- used e.coli
- grew cells in different isotopes of nitrogen, N15 first then N14 (15 is heavier)
- if different N-isotopes were available when DNA was made then parental and daughter strands would have different densities
- used density gradient centrifugation
- N14 should form bands higher in tube and N15 should form bands lower
Generation 1: grew cells only in N15, purified some of the DNA then put the rest in an area only containing N14; allowed DNA to copy once then isolated it, let rest of sample divide again then isolated that DNA
- if cons: daughter cells should have N14 or N15 strands not both (one high band and one low band)
- if cons or semi-cons; after one generation DNA should contain an equal mix of both 15 and 14, and one intermediate band should form
Generation 2:
- if semi cons: half should only contain N14 (2 bands)
- if disp: still only one band forms
Results: after gen 1- one band so not not cons
after gen 2- 2 bands so semi conservative
What is the role of DNA polymerase
- polymerizes deoxynucleotides to DNA
- catalyzes DNA synthesis
- 3 types
- 1 and 3 are used during replication
- 2 repairs damaged DNA
What direction does synthesis proceed in
5’ to 3’ because DNA polymerases can only work in one direction and deoxyribonucleotides can only be added to the 3’ end of the growing DNA
-bi directional though, occurs in both strands at same time
Are the polymerization reactions in replication endo or exergonic
exergonic, because monomers are dNTPs which have high pot.E due to their 3 phosphates
How does replication get started
- bubble forms in chromosome when DNA is being synthesized
- first forms at a specific sequence of bases: the origin of replication (multiple form in eukaryotes bc we have multiple origin sites)
- more bubbles grow as replication proceeds
- once bubble opens enzymes initiate replication
What is the replication fork
- structure at the corners of each replication bubble where initiation of replication takes place
- Y shaped region where parent DNA is split into 2 single strands which are then copied
What is a helicase
an enzyme that breaks the hydrogen bonds between deoxyribonucleotides which causes the 2 DNA strands to separate
What are SSBPs and what do they do
single strand binding proteins, they attach to the separated strands of DNA and prevent them from snapping back into a double helix
How is the helix opened and stabilized
with the help of helicase and SSBPs which make both strands available for copying
What are topoisomerases
enzymes that cut DNA, allow it to unwind and rejoin it ahead of the advancing replication fork
- relieves twisting stress induced by helicase
- prevent kinks
What dictates which deoxyribonucleotide should be added next
single stranded template/3’ end
What is a primer and why does DNA polymerase need one
- a few nucleotides bonded to template strand
- needed because it provides a free 3’ hydroxyl that can combine with incoming dNTP to form a phosphodiester linkage
What is primase
enzyme that makes primer
- type of RNA polymerase
- does not require its own primer
What is RNA polymerase
enzyme that catalyzes the polymerization of ribonucleotides into RNA
How is the leading strand synthesized
- primase creates an RNA primer for DNA polymerase by complimentary base pairing to single strand of DNA
- DNA polymerase 3 adds deoxyribonucleotides to 3’ end of primer making a new complementary strand
- product is leading strand bc it leads into the replication fork and is continuously synthesized
What is the lagging strand
strand that is synthesized in the opposite direction of the replication fork/ lags behind the synthesis occurring in the fork
- can also be called discontinuous strand
How is the lagging strand synthesized
- RNA primer is put in place by primase, and DNA polymerase 3 adds bases to 3’ end
- however gaps appear because behind it helicase is continuing to unzip the DNA double helix
What is discontinuous replication
the hypothesis that once primase makes and RNA primer on the lagging strand, DNA polymerase 3 might synthesize short fragments of DNA along the lagging strand which would later be linked together to form a whole
What are Okazaki fragments
short sections of DNA created along the lagging strand of DNA during synthesis
How are Okazaki fragments joined together
DNA polymerase 1 removes RNA primer at start of each fragment and fills in appropriate nucleotides, DNA ligase catalyzes the formation of phosphodiester bonds between adjacent fragments
What is DNA ligase
catalyzes formation of phosphodiester bonds between okazaki fragments
What is the replisome
multi-enzyme machine (lagging strand loops out to make way for it)
How many replisomes are present in bacteria chromosome replication
2, each start at origin and travel around circular molecule; one clockwise and one counter
then they meet again at opposite side and break apart
What is a telomere
end of a linear chromosome
- do not contain genes that code for products needed in cell
- Act as buffers between ends of chromosome and DNA encoding for genes
What is the problem that arises during the replication of telomeres
DNA polymerase is unable to add DNA near the tip of the chromosome (lagging strand) because there is not enough room for primase to add a new RNA primer, so the single stranded DNA must remain single stranded
-eventually this strand is degraded which shortens the chromosome
What is telomerase
catalyzes the synthesis of DNA from an RNA template
- carries an RNA template which allows it to add DNA on to the end of a chromosome to prevent it from getting shorter
- only active in sperm and egg cells because if it was present in body cells it would allow too much replication/division leading to cancer
How can mistakes in DNA synthesis be corrected
- DNA polymerase 3 can proof read
- if it made a mistake, it pauses removes the mismatched base and then continues
What is mismatch repair
-occurs when a mismatched base is actually left in place and the bases are corrected after DNA synthesis is complete
What is nucleotide excision repair
- a mechanism used to repair damage from chemical attack, radiation, etc.
- once a damaged region is recognized, enzymes remove a segment of single stranded DNA containing the defective sequence
- complementary strand provides a template to synthesize the corrected strand
What are centromeres
Another source of non-coding DNA (like telomeres) are repeats usually associated with the centromeric region of the chromosome. These may be involved in binding kinetochore proteins.
-highly competitive DNA
What are transposable elements
DNA elements that can hop around the genome
What are retrotransposons (LTRs and non LTRs)
make copies of themselves by being transcribed and then using reverse transcriptase to make a DNA copy of the transcript that then re-inserts into the genome.
-move through RNA intermediate
LTRs look just like retroviruses and encode retroviral proteins but can never leave the cell because they can’t make functional coat proteins.
Non-LTRs (LINES) don’t look like a retrovirus but do encode reverse transcriptase and an endonuclease that helps them insert into the genome.
What are Alu elements
mutated versions of functional genes
don’t encode any proteins but rely on reverse transcriptase produced by other elements to allow them to jump
What are DNA transposons
splice themselves out of the genome and then jump back in by encoding a special enzyme called a transposase
-dna parasites, not useful
What are pseudogenes
- lack introns
- the result of when ordinary mRNAs get copied into DNA and inserted into the genome or when chromosomal duplication can produce multiple copies of a gene, some of which eventually are inactivated by mutation to make a pseudogene
Does non-coding DNA have a function
yes, centromeric regions have competitive DNA
