Cell Bio Exam 3 - Pt. 2 - DNA Replication and DNA repair

What are the three hypothetical models for DNA replication?

conservative, semiconservative, and dispersive

What is semiconservative replication?

when DNA replicates itself, it produces two copies that each contained one of the original strands and one entirely new strand

What are the 5 events in order for DNA replication?

1. determine start point 2. separate parent strands 3. prime the pump of DNA synthesis 4. make DNA 5. tidy up

Is DNA replication bidirectional?

yes

What is an origin of replication (ORI)?

a particular sequence in a genome at which replication is initiated

What bases in DNA make up the specific sequence for ORI?

AT-rich

What are replication forks?

a Y-shaped structure created by helicases

What do the helicases do to create replication forks?

they break the hydrogen bonds holding the two DNA strands together

Where does synthesis of new DNA occur?

at the ORI and on both parent strands in both directions away from the ORI

Where does replication of circular DNA begin?

at a single origin and proceeds bidirectionally around the circle

What are replicons?

replication units where replication occurs and replication bubbles form

How many replicons does the DNA of a typical large eukaryotic chromosome contain?

several thousand - 50-300 Kb in length

Is linear DNA replication initiated at multiple sites?

yes

What 3 things unwind the DNA at the replication fork?

DNA helicases, topoisomerases, and single-stranded DNA binding proteins

What does topoisomerase do?

forms a swivel ahead of the replication fork; relaxes the DNA from its super-coiled nature

What does DNA helicase do?

it unwinds and breaks the hydrogen bonds at the replication fork

What do single stranded DNA binding proteins do?

stabilize the unwound DNA in an extended position

What catalyzes the addition of the next nucleotide to the growing DNA strand?

DNA polymerase

What direction is a DNA strand synthesized in?

5' to 3'

Where does a new bond form between the terminal nucleotide and the incoming deoxynucleotide triphosphate?

the 3' hydroxyl group of the terminal nucleotide and the 5' phosphate of incoming dNTP

What kind of bond is it that forms between the terminal nucleotide and the incoming dNTP?

a phosphoester bond

Is DNA synthesis continuous or discontinuous?

both!

What direction can DNA polymerase only synthesize DNA chains in?

5'-3'

What kind of DNA synthesis occurs for the leading strand?

continuous

What kind of DNA synthesis occurs for the lagging strand?

discontinuous

What are okazaki fragments?

Short lengths of DNA made on the lagging strand

What joins the okazaki fragments together?

DNA ligase which forms a phosphoester bond

What is DNA synthesis initiated by in both bacteria and eukaryotes?

a short RNA primer

What is the length of RNA primers?

3-10 nucleotides in length

What enzyme synthesizes the RNA primers using DNA as a template?

primase

Does primase require a primer to initiate RNA synthesis?

no

What enzyme replaces the RNA primer with DNA?

DNA polymerase 1

What are telomeres?

stretches of repeated DNA located at the ends of eukaryotic chromosomes

What enzyme catalyzes the formation of additional copies of telomeric repeat sequences?

telomerase

What is the purpose of telomeres?

they compensate for the gradual shortening that occurs at both ends of the chromosome during DNA replication

How does DNA polymerase proofread DNA and fix mistakes?

it has 3' to 5' exonuclease activity

What is exonuclease activity?

DNA polymerase clips off nucleotides from the 3' end of a nucleotide chain

How do DNA alterations or mutations occur?

they arise spontaneously or through exposure to environmental agents

What 3 things can cause mutations to occur spontaneously?

1. spontaneous mispairing of bases due to transient formation of tautomers

2. slippage during replication

3. spontaneous damage to individual bases (depurination and deamination)

What is the most common form of spontaneous replication error?

mispairing of DNA nucleotides due to presence of tautomers

What are tautomers?

rare, alternate resonance structures of nitrogenous bases

What is a tautomeric shift?

When a nitrogenous base shifts from it's original form, keto to amino or vice versa, to allow bonding with a non-complementary base

What is the result of tautomers/tautomeric shifts?

a new daughter strand that carries an incorrect base at that position

What mutation can regions with repetitive DNA cause?

spontaneous replication errors

What is an example of repetitive DNA that is susceptible to strand slippage?

trinucleotide repeats

What is a strand slippage?

when DNA polymerase replicates a short stretch of DNA twice

What is an example of a trinucleotide repeat disorder caused by accumulation of various trinucleotide repeats?

huntington disease

What is depurination?

loss of a purine base (A or G)

What is deamination?

removal of a base's amino group (-NH2)

What is the result of deamination?

converts cytosine to uracil

What mutation can ultraviolet radiation cause?

covalent cross-links between adjacent pyrimidine bases (pyrimidine dimers) (thymine links to a thymine below it)

What are the consequences of pyrimidine dimers?

replication and transcription are blocked because the enzymes carrying them out cannot cope with resulting bulge in the DNA double helix

What is photoactive repair?

a DNA repair system that fixes pyrimidine dimers (light-dependent process)

What are the two types of excision repair?

base excision repair and nucleotide excision repair for nucleotides of abnormal chemical structures

What does mismatch repair fix?

improperly base-paired nucleotides with normal structures

What does homology-directed repair and nonhomologous end joining fix?

double-strand DNA breaks

What does base-excision repair fix?

single damaged bases in DNA (deaminated or depurinated bases)

What 4 enzymes are involved in base-excision repair?

DNA glycosylase, AP endonuclease, DNA polymerase, and DNA lligase

What does DNA glycosylase do in BER?

removes damaged base

What does AP endonuclease do in BER?

recognizes the sugar-phosphate unit of the missing base and cleaves it away

What does DNA polymerase do in BER?

synthesizes new DNA using the intact strand as a template

What does DNA ligase do in BER?

seals the single-stranded gap

Where do the lesions in DNA that BER fixes come from?

endogenous sources

What does nucleotide-excision repair fix?

it removes pyrimidine dimers and other bulky lesions in DNA

What enzymes does NER use?

NER endonuclease and DNA ligase

What does NER endonuclease do in NER?

makes two cuts in the DNA backbone

What does DNA ligase do in NER?

gap is filled in by DNA replication and sealed by DNA ligase

What creates the lesions that NER repairs?

exogenous agents

How does homology-directed repair work?

uses homologous DNA sequences in a sister chromatid to instruct repair

Is homology directed repair typically error free?

yes

How does Non-homologous end joining work?

it is not instructed by homologous DNA sequences and is error-prone