L9 DNA denaturation, mutation, damage, and Repair system Flashcards
Define DNA Denaturation
The process of breaking double-stranded DNA into single strands
What stabilizes the DNA duplex during denaturation?
Enthalpic component stabilizes duplex DNA.
H-bonding between complementary bases and van der Waals attraction between stacked bases
Explain what happens during DNA denaturation
When a DNA solution is heated enough, the double-stranded DNA unwinds and the hydrogen bonds that hold the two strands together weaken and finally break into two higher energy strands.
True or false?
DNA denaturation is not a reversible process.
False.
DNA denaturation is reversible: renaturation is promoted by slow cooling.
Rapid cooling creates a population of single-stranded random coils
During DNA denaturation at low temperatures, ΔG is _______.
ΔG is positive
During denaturation, the DNA double-stranded structure is stabilized both by base pairing and by base stacking interactions. This contribution is largely enthalpic, meaning that ΔH appears to be ______.
positive
Why is the entropy low for the transition from double-strand to random coil during DNA denaturation?
Because the double-stranded structure is much more highly organized than the two separate DNA strands, and therefore can adopt a limitless number of conformations.
During denaturation at low temperatures the term TΔS is _____ than ΔH; therefore, ∆G is _____, and the helix is stable.
TΔS is smaller; ∆G > 0
As the temperature is increased during DNA denaturation, what happens to TΔS and ΔG?
TΔS becomes greater than ΔH, and ΔG becomes negative
True or False?
At higher temperatures the double-stranded structure stays stable and together.
False.
At higher temperatures the double-stranded structure becomes unstable and falls apart.
What does the term Tm mean?
Melting temperature (Tm) at which half of the double-stranded DNA molecules are converted to single-stranded DNA
What determines the melting temperature of a DNA strand?
The length and the specific sequence of a DNA.
- The greater the length of DNA, the higher the Tm
- The higher the GC content of a DNA molecule, the higher its Tm
True or False?
The two antiparallel strands of a DNA double helix can be separated when hydrogen bonding between bases on opposite strands is disrupted by denaturing agents such as pH, ionic strength, and heat.
True
The negatively charged hydroxide ion can pull hydrogen ions from base pairs, forming H bond between two strands, causing the strands to separate at what pH levels?
At a pH less than 2.3 or greater than 11.5
What is another word for DNA renaturation?
Annealing
What happens during the annealing (renaturation) process?
Denatured DNA strands reassemble into a double-stranded DNA helix when denaturing agents are removed. This is effected by cooling.
H bonds form between complementary base pairs. Upon renaturation, viscosity increases.
True or False?
The rate of DNA renaturation is directly proportional to the concentration of complementary sequences.
True
Define a DNA mutation.
Any change introduced into the base sequence of DNA
What are the most common DNA mutations?
Substitution, addition, rearrangement, or a deletion of one or more bases
Mutations introduced into somatic cells can cause
disease or cell death, but these are confined to the affected individual
Mutations introduced into germline cells cause
Inheritable diseases
Define mutagens
Physical agents and chemical reagents that cause mutations
Radiation and chemicals cause what type of mutation?
Exogenous damage.
UV radation causes pyrimidine dimers.
X-Rays can cause double-stranded breaks and translocations
Chemicals cause physical damage or intercalation which cause polyermerase errors
The process that produces a mutation is called ______.
Mutagenesis
True or False?
The DNA in a human cell undergoes several thousand to a million damaging events per day, generated by both external (exogenous) and internal metabolic (endogenous) processes
True
True or False?
Damage to cellular DNA is involved in mutagenesis, but is not the cause of cancer development.
False
Changes to the cellular genome can generate what?
Errors in the transcription of DNA and translation into proteins necessary for signaling and cellular function
What happens when enomic mutations if the mutation is not repaired prior to mitosis?
They can also be carried over into daughter generations of cells
What is the response from from Cells with DNA Damage?
If a healthy cell attains exogenous/endogenous damage before replication, that damaged DNA is transferred to the new cell. If this damage is left unrepaired, it is passed on to other cells made from that cell and the damage accumulates.
If the cell with the accumlated DNA damage is replicated it will be come one of either three options:
Senescent cell
Apotoic cell
Cancer cell
What is a senescent cell?
A cell with DNA damage that is irreversibly dormant
True or False?
A malignant cell develops immortal characteristics and begins uncontrolled division
True
True or False?
UV rays can produce a hydrogen bond between two adjacent pyrimidine bases in DNA to form pyrimidine dimers
False.
They produce a covalent linkage, usually between 2 of the same amino acids
Ionizing radiation causes what type of cell damage?
The incoming photons collide with electrons dislodging the orbital electrons from the atom.
DNA is its critical target.
Define depurination
The hydrolysis of the N-glycosyl linkage to deoxyribose of A and G.
Happen about 5,000 times every day per cell
What is deamination?
Deamination occurs when an excess in protein is consumed, resulting in the removal of an amine group, which is then converted into ammonia and expelled via urination.
True or False?
Deamination cannot happen at neutral pH.
False
True or False?
Deamination of cytosine to uracil happens at a higher rate in cells.
True.
At approximately 100/day to 100/cells a day
Deaminated Cytosine can be recognized by the DNA repair system and corrected before DNA replication because of what?
Because DNA contains no Uracil so the error is usually immediately repaired.
Via deamination, adenine becomes _____.
Hypoxanthine
Deamination forms thymine from ______.
5-Methylcytosine
Deamination forms Xanthine from _____.
Guanine
List the effects on DNA from polymerase errors.
- insertions and deletions (small or frameshift)
- Small repeats
- Point mutations
Exogenous and Endogenous damage are source mutation that can also lead to what other type of source mutation?
Polymerase errors
Endogenous damage from physical damage or reactive oxygen species causes what effects to DNA?
- Oxidized DNA
- Crosslinked bases
- Double or single stranded breaks
What is a missense mutation and what is its effect on DNA?
A missense mutation is when a codon for a particular amino acid is becomes a new codon for a different amino acid. This changes the amino acid of a protein.
What type of mutation has no effect on a protein and why?
Silent mutation.
Because it is just when a codon for a particular amino acid is replaced with a new codon for the same amino acid
What is the most devasting mutation and why?
A nonsense mutation because it replaces a codon for a particular amino acid with a STOP codon, causing a misshaped/incomoplete protein
What are frame mutations?
An insertion or deletion that changes the reading frame of a nitrogenous base sequence.
Frameshift makes a protein unviable, unless what?
Unless insertion occurs at the end of a base sequence or in multiples of 3 since base are read in 3s
What is alkylation?
In alkylation, methyl groups (electrophiles) are transferred to reactive sites on the bases and to phosphates in DNA backbone.
The alkylation of guanine and cytosine produces what products?
O5-ethylguanine and Thymine
Methylation is a source of DNA damage that occurs where and produces what product?
At the 5-position of the cytosine ring of a cytidine base (C) resulting in the spontaneous deamination of the 5-methylcytosine product of methylation.
Loss of the amine group results in a thymine base, which is not detected by DNA repair enzymes as an unnatural base, which is retained in DNA replication, creating a C→T point mutation
Why is DNA double-stranded?
For safe storage of genetic information.
When one strand is damaged, the complementary strand retains an intact copy of the same information, and the copy is generally used to restore the correct nucleotide sequences to the damaged strand
What is a transposon?
Repetitive DNA sequences that have the capability to move (transpose) from one location to another in genome.
Transposons can cause what?
Transposon movement can result in mutations, alter gene expression, induce chromosome rearrangements and, due to increase in copy numbers, enlarge genome sizes.
Mutations it can cause are large insertions/deletions, inversions or duplications
What are the types of transposons?
Simple transposons
Complex transposons
Composite transposons
Define a composite transposon
A composite transposon is a mobile genetic element consisting of two insertion sequences (ISs) flanking a segment of cargo DNA
What is a complex transposon and how is it different form a simple transposon?
The complex transposons are those consisting of other genes apart from those needed for insertion.
Complex transposons code for additional genetic elements while Simple transposons only code for the transposase gene essential for the tranposon itself.
Complex transposons are found in multiple locations in the target DNA; simple transposons are found only in one location.
True or False?
Transposons only have an effect is inserted in the intergenic region of DNA.
False.
The intergenic region is a region of junk DNA so this would have no effect on the DNA.
A transposon would only have an effect if inserted in the coding region, which would cause disrupted genes and therfore mutogensis
True or False?
DNA rearrangments, like transposons, generally don’t lead to repair mechanisims.
True
Broken chromosomes from physical damage or X-rays are usually repair via what mechanisms?
Homologous-directed repair or non-homologous end joining
What repair mechanisms fix mismatched, oxidized, crosslinked or dimered bases?
Mismatch repair or nucleotide excision repair
A DNA molecule is inherently unstable because of what?
The daily external and internal attacks it receives.
Thousands of spontaneous changes happen to a cell’s genome on a daily basis.
Defects can also arise when DNA is copied during cell division, a process that occurs several million times every day in the human body
What is the reason our genetic material does not disintegrate into complete chemical chaos?
a host of molecular systems continuously monitor and repair DNA
What is a Metalating agent?
Metalation is a chemical reaction that forms a bond to a metal.
This reaction usually refers to the replacement of a halogen atom in an organic molecule with a metal atom, resulting in an organometallic compound
What is base excision repair and how does it work?
Base excision repair was discovered by Tomas Lindahl and happens when a nucleotide is damaged by either a bad base or if a base is replaced with an incorrect one.
The enzyme glycosylase detects the defect and excisizes the bad base. Other enzymes remove the rest of the nucleotide from the DNA strand. Then DNA polymerase fills in that gap and the strand is sealed with DNA ligase.
What is nucleotide excision repair?
Discovered by Aziz Sancar, nucleotide excision repairs DNA injuries caused by UV radiation or carcinogenic chemicals
How does nucleotide excision repair work?
Uv radiation can cause 2 thymines to bind together. Excinuclease (UV-specific endonuclease) finds this error and cuts 12 nucleotides from the strand. DNa polymerase fills the gap and then it is sealed with DNA ligase.
True or False?
Base excision repair and nucleotide excision repair are the same thing.
True, but they used different enzymes.
Base excision uses glycosylase
Nucleotide excision uses endonucleases
True or False?
Nucleotide and base excision repair can only happen before replication.
False.
While it is ideal for them to occur before replication, they can happen at any time.
What is mismatch repair?
Paul Modrich discovered how the cell corrects errors that occur when DNA is replicated during cell division. Out of thousands of mismatched nucleotides, this repair mechanism can fix all but one.
- This mechanism reduces the error frequency during DNA replication by about a thousandfold
True or False?
Mismatch repair happens during or shortly after replication.
True
What mechanism allows mismatch repair to recognize the parent strand of a double-stranded helix that has a mismatched base pair?
The parent strand is methylated and the daughter strand is not.
Congenital defects in mismatch repair are known cause
a hereditary variant of colon cancer
How does mismatch repair work?
Enzymes mutS and mutL detect the mismatch. MutH recognizes the methylated portions of the parent strand. The faulty section on the daughter strand is cut out. DNA polymerase fills the gap and DNA ligase seals the strand.
What is homolgy-directed repair?
The use of an identical sister chromatid as a template to fix a broken chromosome.
When does homology-directed repair happen?
It must happen after replication because the sister chromatid has to be present.
Non-homologous end-joining functions to _______
Ligate broken ends of a chromosome together.
This can also result in translocations.
Why is Non-homologous end-joining a mutagenic repair mechanism?
Because you usually lose some base pairs in the process of ligating broken ends together.
True or False?
Non-homologous end-joining can happen at any time.
True
Why are Non-homologous end-joining and homology-directed repair not good repair mechanisms?
because there is a lot of room for error with both of them
What expression is given for the three nucleic acid bases present on transfer RNA that base pair with a triplet of bases on messenger RNA?
Anticodon
Which of the following statements is false regarding DNA damage?
- UV can produce a covalent linkage between two adjacent pyrimidine bases in DNA to form pyrimidine dimers.
- X-rays has sufficient energy to dislodge orbital electrons from atoms.
- Deamination of cytosine to uracil cannot be recognized by the DNA repair system.
- The methylation occurs at the 5-position of the cytosine ring of a cytidine base.
- Deamination of cytosine to uracil cannot be recognized by the DNA repair system.
False because it this mistake can be recognized and it usually is by mismatch repair before replication is even complete
Which of the following statements is false?
- The genetic stability of living organisms is mainly accomplished by an accurate DNA replication system and a DNA repair system.
- Any change introduced into the base sequence of DNA is called DNA denaturation.
- Damage to cellular DNA is involved in mutagenesis and the development of cancer.
- Once DNA is damaged, the cell may become malignant.
- Any change introduced into the base sequence of DNA is called DNA denaturation.
FALSE THIS WOULD BE MUTATION
Which of the following statements is true regarding DNA denaturation?
- At low temperature, ΔG is negative.
- At low temperature the term TΔS is smaller than ΔH.
- As the temperature is increased TΔS becomes lesser than ΔH, and ΔG becomes positive.
- The greater the length of DNA is, the lower the Tm is.
- At low temperature the term TΔS is smaller than ΔH.
True or False?
As the temperature is increased TΔS becomes lesser than ΔH, and ΔG becomes positive.
FALSE
TΔS BECOMES GREATER THAN ΔH AND ΔG BECOMES NEGATIVE AT LOW TEMPERATURES
True or False?
Polynucleotides are at metastable state.
True
True or False?
The DNA helicase separates the two strands by breaking phosphodiester bond.
False.
DNA helicase breaks the HYDROGEN bond to seperate the two strands of DNA strands.
True or False?
To prevent the replication fork from reannealing, single-stranded DNA –binding proteins bind tightly separated strands.
True
True or False?
In DNA denaturation at low temperature, ΔG is negative.
False.
ΔG is positive
True or False?
The greater the length of DNA is, the lower the melting temperature (Tm) is.
False.
Tm is higher the longer a DNA strand is.
True or False?
Hydrolysis of polynucleotides to nucleotides is the thermodynamically unfavored process.
Falsse.
Polynucleotide hydrolysis is thermodynamically FAVORED
The structure where transcription occurs is the _______.
Nucleus
On which molecules would you find a codon?
messenger RNA
The structure that catalyzes protein synthesis, and which is sometimes called the protein factory is the _________.
Ribosome
The structure that is responsible for modifying newly transcribed mRNA prior to translation is called the ________.
Spliceosome
What role does small nuclear RNA play in the synthesis of proteins?
It modifies messenger RNA molecules prior to protein synthesis
__________ translates the genetic code to a specific amino acid
Transfer RNA (tRNA)
What catalyzes the process of protein synthesis?
Ribosomal RNA (rRNA)
Which amino acid in the enzyme topoisomerase II is responsible for cleaving a phosphate-sugar link in a DNA strand?
Tyrosine
Which of the following is not true when RNA is compared with DNA?
a. RNA contains ribose and not deoxyribose.
b. RNA contains uracil and not adenine.
c. RNA does not form a double helix.
d. RNA is smaller than DNA.
b. RNA contains uracil and not adenine
RNa contains uracil instead of THYMINE
What term is used to describe the process by which proteins are synthesized from a genetic code?
Translation
What term is used to describe the process by which DNA is copied to produce two daughter DNA molecules?
Replication
What term is used to describe the process by which a segment of DNA is copied to produce a molecule of messenger RNA?
Transcription
What non-covalent bonding interactions do the nucleic acid bases form in DNA secondary structure?
Hydrogen bonds and van der Waals interactions.
Hydrogen bonds b/t the bases themselves
Van der Waals b/t the stacked rings of bases
What type of DNA structure is shown here?
What is the blue region called?
The primary structure of DNA.
The sugar-phosphate backbone
Which of the following mutations is most likely to be disruptive to protein synthesis or function?
a. UAU to UAC
b. UAU to UUU
c. UAU to UAA
d. UAU to CAU
c. UAU to UAA
What type of enzyme is used in recombinant DNA technology to reform sugar phosphate bonds after annealing?
Ligase
Epigenetics is the heritable increases or decreases in gene expression due to environmental (among other) causes. One of the mechanisms involved this differential expression is DNA methylation. What is the most likely mechanism for this process?
A. Addition of a methyl group to ribose, decreasing the interaction with histones
B. Addition of a methyl group to cytosine, resulting in methyl-cytosine base-pairing with guanine
C. Addition of a methyl group to diphosphate, increasing the interaction with histones
D. Addition of a methyl group to cytosine, resulting in methyl-cytosine mismatch base-pairing with thymine
B. Addition of a methyl group to cytosine, resulting in methyl-cytosine base-pairing with guanine
Given that epigenetics involves change in gene expression, and is not the expression of mutant products, it is unlikely that cytosine will mismatch with thymine after methylation.
