Pharm 411: DNA structure, synthesis, and repair Flashcards
What does DNA stand for and what does it do?
Deoxyribonucleic acid
and it encodes the genetic makeup of a cell
How are the strands of DNA composed?
two antiparallel strands wound around each other in a right-handed helix
-The bases on one strand are complementary to, and hydrogen bond to, the bases on the opposite strand
What are the ingredients of nucleic acids?
- purine or pyrimidine bases
- pentose sugar (either ribose or deoxyribose)
- phosphate groups
What is DNA composed of?
deoxyribonucleotides, which are composed of purine and pyrimidine bases, deoxyribose, and phosphate
What is a nucleoside?
A base + pentose sugar
- Ribonucleoside
- deoxyribonucleoside
What is a nucleotide?
Base+ pentose+ phosphate
- Ribonucleotide
- Deoxyribonucleotide
What does it mean if the nucleic acid ends with -ine?
Means its a nucleoside
What does it mean if the nucleic acid ends with -ylate
Means its a nucleotide
What is a phosphodiester bond?
The linkage with the phosphate linking 5’ hydroxyl of one nucleotide to the 3’ hydroxyl of another
What does it mean when they say DNA has directionality?
As the DNA molecule grows, the strand always has an unreacted 5’ phosphate group while the other has an unreacted 3’
hydroxyl group
**DNA is always synthesized 5’ to 3’
What is the secondary structure of DNA?
Formed by the hydrogen bonding between complementary bases
- the acidic hydrophilic phosphate backbone is on the outside
- the hydrophobic bases stack inside
- they are coiled around axis of symmetry
- This nature causes it to form major and minor grooves
What must two strands of DNA be in order to pair?
They must be complementary
What does it mean if DNA is complementary?
- the sequences must be appropriately paired
- Sequences must be paired AGCT must match TCGA
- the strands must be in opposite directions
- 3’ end of one strand will pair with the 5’ end of the other (antiparallel)
What does it mean if DNA can reanneal?
Complementary strands combine upon meeting, and refrom double-stranded DNA
Can DNA be denaturated?
Yes. It separated into single strands by breaking apart hydrogen bonds -Change pH -Inc heat - proteins involved in replication
What is the melting temp (Tm) of DNA?
The temp needed to separate the strands of the DNA
- higher Tm means DNA strands are more stable
What does the melting temp (Tm) depend on?
The relative amount of purine-pyrimidine pairs
- G-C pairs have 3 hydrogen bonds
- A-T pairs have 2 hydrogen bonds
- the more G-C pairs in the DNA the higher the Tm
What areas of DNA that open for replication or synthesis of RNA usually have?
more A-T content, meaning a lower melting point and easier to separate
How many chromosomes does a human have?
23 pairs or 46 total chromosomes
- has 3.2 x10^9 base pairs
What are histones?
They are proteins that bind to the DNA and coil it into compact structures called nucleosomes
What happens if DNA in not condensed into chromosomes?
Cell division cannot occur
What is replication?
DNA synthesis
What are the steps in DNA replication?
- identification of the origin of replication at a specific base pair sequence
- Unwinding (denaturation) of the double strand to provide two single strand templates forming the replication fork
- initiation of DNA synthesis on each side of the fork
- elongation, and ligation of newly synthesized DNA segments
What does it mean by DNA is semi-conservative?
Each new DNA molecule contains one strand from the parent, and one newly synthesized strand
What direction does DNA replication proceed?
In a 5’ to 3’ direction on both strands
Where can DNA polymerase add nucleotides?
To the 3’ hydroxyl on an existing chain of nucleotides (CAN NOT initiate a new chain)
What are RNA primers?
They are synthesized by an enzyme called primase (RNA polymerase) which provide a starting point for DNA synthesis
What is DNA helicase?
An enzyme that binds single-stranded DNA at the origin of DNA replication and “unzips” the DNA
What is single-stranded DNA binding protein?
Enzyme that stabilizes the single-stranded DNA so that it stays unwound
What is Toposiomerase?
Enzyme that cuts one or both strands of DNA to remove coils and knots in the DNA
What is Primase?
Enzyme that synthesizes the RNA primers to prime the DNA synthesis
What is DNA polymerases (I, II, III)
replicates the DNA
What is DNA polyerase III?
enzyme that is the main synthesizing enzyme (both leading and lagging strands)
What is DNA polymerase I?
Enzyme that removes the RNA primers and replaces them with DNA on the lagging strand
What are Ligases?
Enzymes that link the DNA by catalyzing phosphodiester bonds
Does DNA replication have high processive?
YES
-Processivity is how long the DNA polymerase stays on a single stranded DNA making new DNA before falling off
What is the processivity of DNA polymerase III compared to I?
DNA polymerase III is highly processivity
DNA polymerase I, DNA, and other repair enzymes have low processivity
Does DNA have high fidelity?
Yes
- Fidelity is the measure of accuracy of the synthase
- The error rate of DNA polymerase III is around 1 error per billion nucleotides
- DNA has around 3 billion base pairs, so each time a cell divides it adds about 3 random errors
What enhances fidelity in DNA replication?
The ability of the polymerase enzymes to “proofread”
- when an incorrect base is recognized, DNA polymerase reverses its direction by one pair and cuts it out using exonuclease function
How does polymerase work?
it activily selects the correct nucleotide, determined by hydrogen bonding, and forms the phosphodiester bond moving in the 5’ to 3’ direction
What is exonuclease?
It hydrolyzes phosphodiester bonds and removes one nucleotide
- base removal from the 3’ terminus (3’ to 5’) removes errors (proofreading)
- base removal from the 5’ terminus (5’ to 3’) removes DNA primers (only DNA polynerase I)
What is a description of DNA damage
- Physical abnormalities in the DNA or chemical modifications
- Can not be inherited
- Can be recognized and repaired by enzymes
- repair requires the correct info on the undamaged strand
- May lead to mutations if not repaired prior to replication
What is a description of DNA mutation?
- a change in the base sequence of the DNA
- Can be inherited
- Can be repaired prior to DNA replication
- After DNA replication, the base pair will not be mismatched, and cannot be repaired
What is direct reversal of DNA repair mechanisms?
Enzymatic reaction, no template needed
- Pyrimidine dimers
- Methylation of guanine bases
- methylation of cytosine and adenine
What is Single-strand break of DNA repair mechanisms?
- Base excsion repair (uses glycosylases)
- Nucleotide excision repair (uses endonucleases)
- Mismatch repair
What is double-strand breaks in DNA repair mechanisms?
- Non-homologous end joining
- microhomology- mediated end joining
- homologous recombination
How does reversal repair of pyrimidine dimers work?
Pyrimidine dimers form between two adjacent thymine or cytosine bases catalyzed by light
- Photolyase is an enzyme that can convert the dimer back to the two individual bases
- requires light to function
What does a base excision repair?
Fixes a loss of base or incorrect SINGLE NUCLEOTIDE
What is involved with Base excision repair?
- removal of the abnormal base by glycosylase
- recognition of the site without a base
- repair of the site
What does Mismatch repair do?
It repairs errors made during replication which were not corrected by DNA polymerase
What does Mismatch repair involve?
- ID of the mismatch
- ID of the parent strand by RECIGNIZING THE METHYLATED DNA (old strand) as different from the new strand (non-methylated)
- A segment of the daughter strand is cut out
- DNA polymerase I resynthesizes the DNA
- DNA ligase joins the fragment to the strand
What does nucleotide excsion repair do?
Can fix a greater variety of errors (MOST GENERAL repair mechanism)
What does nucleotide excision repair involve?
- recognition of dmg tho detecting a distortion in the DNA strand
- Cutting the DNA with specific endonucleases and removing a 12 base section
- DNA polymerase I then fills in the gap
- DNA ligase joins the strands
What are the stages of the Central Dogma?
Replication to transcription then translation
DNA to RNA to Protein
What is reverse transcriptase?
A RNA-dependent, DNA polymerase
- synthesizes DNA from RNA
- this goes against the central dogma
Can humans do reverse transcriptase?
NO, we can not make DNA from RNA
Whats the key method of treating AIDS?
Inhibition of reverse transcriptase in the virus
- unfortunately, reverse transcriptase is extremely error-prone, and mutations occur frequently leading to drug resistance
What are Nucleoside reverse transcriptase inhibitors (NRTIs)?
Its phophorylated to the 5’ triphosphates
- this means its incorporated into the growing DNA strand, but DNA synthesis cannot progress (no 3’ OH)
- *remember its incorporated INTO the DNA
What is Non-Nuceloside reverse transcriptase Inhibitors (NNRTIs)
1 bind to reverse transcriptase in a pocket, change the shape of the enzyme, and prevent it from binding the viral RNA strand
-NOT INCORPORATED INTO DNA!
-
What is the glycosidic bond?
connects the 5c sugar with its base
What are the purines
Adenine and Guanine
What are the pyrimidine?
Cytosine and thymine (uracil in RNA)
What are the complemntary base pairs?
Guanine (g) to Cytosine (c) and Adenine (a) to Thymine (t)
What contributes to the secondary structure of DNA?
Complementary base pairing G to C and A to T with hydrogen bonding between them
Would DNA with a large number of G-C bonds be more stable than one with a large number of A-T bonds?
Yes, this is because the G-C bonds have 3 hydrogen bonds while the A-T only have 2 which makes it easier to separate
