Cell Biology Chapter 17 Flashcards
Cells must be able to accurately do what? Without it what would result? Cells must also repair damage to what?
accurately reproduce, or replicate, their genetic material at each cell division; unaccurate replication, the genetic material of resulting cells would be damaged with errors; their genetic material
New DNA molecules are derived from what and what is it called?
derived from when the parent molecule and the other strand is newly synthesized; semiconservative replication
Replication is very similar in what? What are replication forks?
in Prokaryotes and eukaryotes; formed where replication begins and then proceeds in bidirectional fashion away from the origin
At each origin of replication what happens? What is the origin of replication?
two replication forks synthesize DNA in opposite directions forming a “replication bubble”; the site where DNA replication initiates by several groups of initiator proteins. Consist of AT-rich regions
The sequence varies among what? Replication origins of multicellular eukaryotes are generally what and more what?
bacterial species but contains recognizable similar sequences, called consensus sequences; generally larger and more variable in sequence but also contain regions that are AT-rich
In E. Coli how many enzymes bind and to what and what does it initiate? Binding to part of the what sequence results in what?
3 enzymes bind to oriC (origen of replication) and initiate replication; part of the oriC sequence results in unwinding of DNA
To stabilize the single strands of DNA what binds? DNA helicase unwinds what?
SSB (single stranded binding protein) binds to the unwound regions; unwinds the DNA strands as replication proceeds
DNA polymerase is a what? Incoming nucleotides are added to what?
an enzyme that can copy DNA molecules; added to 3’ hydroxyl end of the growing DNA chain, so elongation occurs in the 5’ to 3’ direction
DNA is synthesized in which direction, but the 2 strands of the double helix are oriented where? The lagging strand is synthesized in what?
5’ to 3’ direction, oriented in opposite directions; in discontinuous fragments called Okazaki fragments
The leading strand is synthesized as what? DNA synthesis from the lagging strand is synthesized in what? These are then joined by what to form what?
as a continuous chain; synthesized in Okazaki fragments; joined by DNA ligase to form a continuous new 3’ to 5’ DNA strand
About how many nucleotides incorporated during DNA replication is incorrect? How are the mistakes usually fixed? Almost all DNA polymerases have a what?
1 of every 100,000 nucleotides; fixed by proofreading mechanism; have a 3’ -> 5’ exonuclease activity
Exonucleases degrade what? The exonuclease activity of DNA polymerase allows it to remove what?
degrade nucleic acids from the ends of the molecules; remove incorrectly base-paired nucleotides and incorporate the correct base
DNA polymerase can add nucleotides only to what? Cells contain an enzyme called what that synthesizes what?
only to the 3’ end of an existing nucleotide chain; contain an enzyme called primase that synthesizes short chains of RNA using DNA as a template
After the RNA primer is made, DNA polymerase adds what? For the leading strand what is needed? For the lagging strand a series of what are needed?
deoxynucleotides to the 3’ ends of the primer; just one primer is needed; a series of primers are needed to initiate each Okazaki fragment
When DNA chain reaches the next Okazaki fragment the RNA is what? Then, adjacent fragments are joined together by what?
degraded and replaced with DNA; DNA ligase
During DNA replication, the two strands of the double helix must unwind at each what? 3 classes of proteins facilitate the what?
each replication fork; the unwinding;
DNA helicases: The DNA double helix is what? Helicases breaks the what between what of the what?
unwound ahead of the replication fork by helicase; the hydrogen bonds between nitrogeneous bases of the nucleotides of the DNA duplex as they go
Single-stranded DNA binding proteins: Once strand separation has begun, molecules of SSB move how and attach to what? They keep the DNA how?
move in quickly and attach to the exposed single strand; unwound and accessible to the replication machinery
Topisomerases: The unwinding of the helix would create too much what?
supercoiling if not for topisomerases
What proteins are involved in replication? What is a replisome?
DNA helicase, DNA topoisomerase, SSBs, primase, DNA polymerase, and DNA ligase; proteins that are closely associated in a large complex
As the replisome moves along the DNA, it must accomadate what? A key element of the replisome is what?
for the fact that DNA is being produced on both leading and lagging strands; the folding of the lagging strand template into a loop
What is the trombone model? What is a sliding clamp protein?
model for how the replisome works; attaches to a DNA polymerase catalytic subunit allows the polymerase to “process” along the DNA without falling off
The leading and lagging strand differ regarding how?
how long the sliding clamp and associated polymerase remain attached
It can remain associated with the what? On the lagging strand as each Okazaki fragment is completed, the polymerase what?
with the leading strand throughout replication; detaches and the sliding clamp must be reloaded
Linear DNA molecules have a problem in completing what? Each round of replication would end with what?
in completing DNA replication on the lagging strand because primers are required; with the loss of some nucleotides from the ends of each linear molecules
Eukaryotes solve this problems with what? A polymerase called what can do what?
telomeres, highly repeated sequences at the ends of chromosomes; telomeres can catalyze the addition of repeats to chromosome ends
Telomerase is composed of what? This enzyme-bound RNA acts as a template for what?
of protein and RNA; for adding the DNA repeat sequence to the telomere ends
Telomere capping proteins bind to what to protect what? In multicellular organisms, telomerase function is restricted to what?
the exposed 3’ end to protect from degradation; to germ cells and a few other types of actively proliferating cells
Telomere length is a what? If a cell divides too many times what could be lost? Cells at risk of loss of what undergo what?
counting device for how many times a cell has divided; telomeres; loss of telomeres undergo apoptosis programmed cell death
Telomerase has been detected in almost what?
all types of human cancers
Several mechanisms are in place to ensure what? What are the 3 types of mechanisms?
minimal mistakes on DNA; Accuracy, Immediate proofreading, Post replication repair
What is accuracy?
incorporation of correct nucleotide (complementary base pairing)
What is immediate proofreading?
DNA polymerase proofreading mechanism
What is post-replication repair?
Mismatch double strand breaks
Trinucleotide repeats are susceptible to what? In this process DNA polymerase replicates what?
strand slippage; a short stretch of DNA twice due to repeats matching with each other
Errors remaining after DNA replication are repaired by what?
excision repair in which abnormal nucleotides are removed and replaced
How does excision repair happen?
a protein detects the mismatch, a repair endonuclease introduces a nick in the unmethylated strand, an exonuclease removes the incorrect nucleotides form the nicked strand and these are replaced with the correct sequence, DNA ligase seals the DNA backbone
Double-strand breaks cleave DNA into what? It is difficult for the repair system to what?
2 fragments; identify and rejoin the correct broken ends without loss of nucleotides
What two pathways are used for double-strand break repair?
non homologous end-joining, homologous recombination
Non homologous end-joining uses a set of what?
proteins that bind to ends of broken DNA fragments and join them together
Non homologous end-joining is error-prone because of what?
nucleotides can be lost from the broken ends, and there is no way to ensure the correct DNA fragments are joined
Homologous recombination involves the process of what?
crossing over, genetic exchange between DNA molecules with extensive sequence similarity
IF the DNA molecule from one chromosome is broken, the homologue is what?
available as a template to guide accurate repair
