DNA Introduction, Structure, Replication, and Repair Flashcards
Macromolecule that stores and expresses genetic information
-DNA and RNA
Nucleic Acids
In cellular organisms, genes are composed of DNA. Some viral genomes are composed of
RNA (HIV)
What are four functions associated with DNA?
- ) Replication
- ) Transcription
- ) Repair
- ) Recombination
Joins two parental DNA segments to form a hybrid molecule
Recombination
Nucleic acids are polymers of
Deoxyribonuleotides or ribonucleotides
What are the three components of a nucleotide?
- ) A base (Purine or pyrimidine)
- ) A pentose sugar
- ) A phosphate group
Allows DNA recognition by proteins that control gene expression
Base methylation
Salmonella typhimurium bacteria cause food poisoning and virulence is absolutely dependent upon
DNA Methylation
Blocks expression of virulence genes and prevents disease development in mice
Inactivation of DNA Adenine Methylase (dam)
Consist of a base linked to a pentose sugar via an N-linked glycosidic bond, but no phosphate group
Nucleosides
Nucleosides are converted to nucleotides by the addition of 1, 2 or 3 phosphate groups to
Position C-5 on the sugar
What do we call the RNA nucleosides?
Adenosine, Guanosine, Cytidine, Uridine
Can be potent drugs in anti-viral and anti-cancer therapy
Nucleoside analogs
The pyrimidine analogs 3ʼ-azido-2ʼ-deoxythymidine (AZT; zidovudine) and dideoxycytidine (ddC;zalcitabine) are used to treat
HIV
Nucleoside analogs are incorporated into growing DNA strands during viral or cellular DNA replication to
Block further DNA synthesis
Formed between the 3ʼ-hydroxyl group on the sugar of one nucleotide and the 5ʼ-phosphate group of the next nucleotide, releasing a pyrophosphate group
-Connects nucleotides to make nucleic acids
Phosphodiester bond
Enzymes that cleave polynucleotide chains by hydrolyzing phosphodiester bonds
Nucleases
Remove nucleotides from either the 5’ or 3’ ends of polynucleotide chains, depending on the specificity
Exonucleases
Only cleave internal phosphodiester bonds
Endonucleases
One type of endonucleases that cleave DNA in a sequence specific manner and that are particularly useful in molecular biology.
Restriction enzymes
The double helix has how many base pairs per helical turn?
10
Proteins that regulate gene expression bind to the
Major groove
Histone proteins found in chromatin bind to the
Minor groove
Certain anti-cancer drugs, such as dactinomycin (actinomycin D) exert their cytotoxic effect by
Intercalating into the minor groove, thereby disrupting DNA and RNA synthesis
How many H bonds are between
- ) A and T
- ) G and C
- ) 2
2. ) 3
Energetically favored and they facilitate DNA strand separation during replication, repair, recombination and transcription.
-when a molecule has fewer helical turns than relaxed DNA
Negative Supercoils
Can force DNA into a negative supercoil
Histones
Transiently break one or both DNA strands, pass the strand(s) through the break, and rejoin them.
Topoisomerases
Cuts a single strand of the double helix and does not require ATP
Topoisomerase I
Cuts both strands of the double helix and requires ATP
Topoisomerase II
Bacterial topoisomerase II that can introduce negative supercoils into relaxed DNA in addition to removing negative and positive supercoils
DNA gyrase
Drugs that inhibit topoisomerases are used in
-Lead to cell death
Chemotherapy and as antibiotics
In prokaryotes, DNA is associated with non-histone proteins that can condense DNA to form a
Nucleoid
The complex of DNA in the nucleus with associated proteins is called
Chromatin
Small basic proteins rich in Arg and Lys
-5 types
Histones
In chromatin, DNA is wound around a histone octamer comprised of two molecules each of H2A, H2B, H3, and H4. This complex is called a
Nucleosome
During interphase, when the cell is not dividing, chromatin can be distinguished as
-extended, active form of DNA
Euchromatin
Affect the regional compaction of chromatin and the regulation of gene expression
Histone modifications
As soon as eukaryotic DNA replication is completed, one unit of histone H1 binds the spacer DNA to promote the tight packing of nucleosomes. As a result, the chromatin winds into a helical tubular coil called the
Solenoid
DNA replication is semiconservative, meaning replicated DNA molecules contain
1 new strand and 1 parental strand
Molecular machine in prokaryotes that carries out DNA replication
Replisome
Binds near the replication fork and uses ATP to force the DNA strands apart.
DNA Helicase
Synthesizes a short primer (~10 nucleotides) in the 5ʼ to 3ʼ direction by copying the DNA template strand.
-Allows for DNA polymerase to begin replication
Primase (RNA polymerase)
Continuously synthesized at the replication fork on the lagging strand
-Provide a free 3’-hydroxyl that serves as an acceptro for the first deoxyribonucleotide
Primers
Synthesized continuously in the 5ʼ to 3ʼ direction toward the replication fork
Leading strand
Synthesized discontinuously in short 5ʼ to 3ʼ Okazaki fragments directed away from the fork.
Lagging strand
- ) Which polymerase(s) does most of the DNA synthesis?
2. ) Which proofread?
- ) DNA Polymerase III
2. ) DNA Polymerases I and III
Functions in replication (primer removal and gap synthesis) and repair. Has 3’ to 5’ and 5’ to 3’ exonuclease activity
-Only polymerase with 5’ to 3’ exonuclease activity
DNA polymerase I
Covalently joins Okazaki fragments by catalyzing the ATP-dependent formation of a phosphodiester bond between the leading and lagging strands
DNA Ligase
Has many origins of replication and is linear
Eaukaryotic DNA replication
What are the three eukaryotic DNA polymerases?
Polymerase alpha, delta, and epsilon
Contains a primase activity and synthesizes hybrid RNA/DNA primers
alpha polymerase
Synthesizes the bulk of lagging strand DNA, and displaces the 5ʼ ends of primers from Okazaki fragments, which are degraded by “flap exonuclease” FEN1 and other nucleases.
Polδ
Synthesizes the bulk of leading strand DNA.
Polε
What performs DNA replication in mitochondria?
Polγ
Consist of short non-coding G-rich repetitive DNA sequences (TTAGGG) and associated proteins at the ends of linear chromosomes.
Telomeres
A ribonucleoprotein complex with reverse transcriptase activity (hTERT): it synthesizes DNA using its RNA subunit as the template. It adds short DNA repeats to the 3ʼ-ends of linear chromosomes to prevent the loss of coding sequences
Telomerase
Telomerase inhibitors can limit
Cancer cell proliferation
Cancer cells typically display
Indefinite cell division and uncontrollable telomerase
Stable changes in DNA sequence (substitutions, deletions, insertions) that can lead to a phenotypic change in the cell
Mutations
Agents that damage DNA
Mutagens
In prokaryotes, strand-specificity for mismatch repair (MMR) is provided by DNA
Methylation
An endonuclease cleaves the newly synthesized strand on either side of the mismatch. A helicase and an exonuclease remove DNA from the newly synthesized strand between the site of incision and the mismatch. DNA Pol III fills the gap, followed by DNA ligase
Mismatch repair
One of the biggest causes of cancer in humans
-accounts for 90% of patients with Lynch syndrome
Defects in the MMR
Repairs spontaneously occuring DNA base modifications (e.g. base damage caused by deamination of cytosine into uracil, depurination, alkylation, oxidation etc).
Base Excision Repair
The damaged base is recognized by a base-specific DNA glycosylase that cuts the N-glycosidic bond between the damaged base and the sugar deoxyribose and the base is released upon action of a helicase
Base excision repair
Can remove an infinite number of lesions including photoproducts, chemical adducts and intrastrand DNA adducts. However, it is the only mechanism that can remove bulky DNA adducts.
Nucleotide excision repair (NER)
What type of NER is used if the damage is in a transcriptionally inactive region of DNA?
Global Genomic NER
What type of NER is utilized if the damage is in a transcriptionally active region of DNA?
Transcription-Coupled NER
A gene-specific repair process that is triggered when a helix distortion caused by DNA damage blocks progression of RNA polymerase II along the transcribed (template) strand of the DNA double helix.
Transcription-coupled NER
Used to remove pyrimidine dimers caused by UV light
NER
Commonly caused by oxidative damage and are usually associated with loss of a single nucleotide, and by damaged 5ʼ- and/or 3ʼ-termini at the site of the break.
Single-strand breaks (SSBs)
Can be induced by ionizing radiation (gamma- and X rays), oxidizing agents (e.g. bleomycin) or topoisomerase inhibitors used for chemotherapy (e.g. camptothecin), some plant and microbial products (e.g. aflatoxins in moldy peanuts) or mechanical stress
Double-strand breaks (DSBs)
Can severely compromise genome stability and can lead to loss of chromosome fragments during mitosis, or chromosomal translocations that can induce cancer due to joining of the wrong DNA ends.
Failure to repair DSBs
What are the two different repair pathways of DSBs?
- ) Non-homologous end-joining (NHEJ) repair
2. ) Homologous recombination
The major pathway to repair DSBs, because it does not require any sequence homology. It can thus occur throughout the cell cycle without needing alingment with a homologous chromosome
NHEJ repair
NHEJ is very
-Leads to the accumulation of random genetic mutations
Error Prone
NHEJ can also lead to
Chromosomal translocations
Non-mutagenic because it involves alignment of highly homologous DNA molecules, so that the information on the homologous sequence can be used to repair the broken DNA.
Homologous recombination
Restricted to the S and G2 phases of the cell cycle, when a sister chromatid is present
Homologous recombination
