Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOCHEM EXAMs > L9 DNA denaturation, mutation, damage, and Repair system > Flashcards

L9 DNA denaturation, mutation, damage, and Repair system Flashcards

1
Q

Define DNA Denaturation

A

The process of breaking double-stranded DNA into single strands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What stabilizes the DNA duplex during denaturation?

A

Enthalpic component stabilizes duplex DNA.

H-bonding between complementary bases and van der Waals attraction between stacked bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Explain what happens during DNA denaturation

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

True or false?

DNA denaturation is not a reversible process.

A

False.

DNA denaturation is reversible: renaturation is promoted by slow cooling.

Rapid cooling creates a population of single-stranded random coils

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

During DNA denaturation at low temperatures, ΔG is _______.

A

ΔG is positive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

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 ______.

A

positive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Why is the entropy low for the transition from double-strand to random coil during DNA denaturation?

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

During denaturation at low temperatures the term TΔS is _____ than ΔH; therefore, ∆G is _____, and the helix is stable.

A

TΔS is smaller; ∆G > 0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

As the temperature is increased during DNA denaturation, what happens to TΔS and ΔG?

A

TΔS becomes greater than ΔH, and ΔG becomes negative

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

True or False?

At higher temperatures the double-stranded structure stays stable and together.

A

False.

At higher temperatures the double-stranded structure becomes unstable and falls apart.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What does the term Tm mean?

A

Melting temperature (Tm) at which half of the double-stranded DNA molecules are converted to single-stranded DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What determines the melting temperature of a DNA strand?

A

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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

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.

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

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?

A

At a pH less than 2.3 or greater than 11.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is another word for DNA renaturation?

A

Annealing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What happens during the annealing (renaturation) process?

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

True or False?

The rate of DNA renaturation is directly proportional to the concentration of complementary sequences.

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Define a DNA mutation.

A

Any change introduced into the base sequence of DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are the most common DNA mutations?

A

Substitution, addition, rearrangement, or a deletion of one or more bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Mutations introduced into somatic cells can cause

A

disease or cell death, but these are confined to the affected individual

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Mutations introduced into germline cells cause

A

Inheritable diseases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Define mutagens

A

Physical agents and chemical reagents that cause mutations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Radiation and chemicals cause what type of mutation?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

The process that produces a mutation is called ______.

A

Mutagenesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

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

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

True or False?

Damage to cellular DNA is involved in mutagenesis, but is not the cause of cancer development.

A

False

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Changes to the cellular genome can generate what?

A

Errors in the transcription of DNA and translation into proteins necessary for signaling and cellular function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What happens when enomic mutations if the mutation is not repaired prior to mitosis?

A

They can also be carried over into daughter generations of cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the response from from Cells with DNA Damage?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is a senescent cell?

A

A cell with DNA damage that is irreversibly dormant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

True or False?

A malignant cell develops immortal characteristics and begins uncontrolled division

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

True or False?

UV rays can produce a hydrogen bond between two adjacent pyrimidine bases in DNA to form pyrimidine dimers

A

False.

They produce a covalent linkage, usually between 2 of the same amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Ionizing radiation causes what type of cell damage?

A

The incoming photons collide with electrons dislodging the orbital electrons from the atom.

DNA is its critical target.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Define depurination

A

The hydrolysis of the N-glycosyl linkage to deoxyribose of A and G.
Happen about 5,000 times every day per cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is deamination?

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

True or False?

Deamination cannot happen at neutral pH.

A

False

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

True or False?

Deamination of cytosine to uracil happens at a higher rate in cells.

A

True.

At approximately 100/day to 100/cells a day

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Deaminated Cytosine can be recognized by the DNA repair system and corrected before DNA replication because of what?

A

Because DNA contains no Uracil so the error is usually immediately repaired.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Via deamination, adenine becomes _____.

A

Hypoxanthine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Deamination forms thymine from ______.

A

5-Methylcytosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Deamination forms Xanthine from _____.

A

Guanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

List the effects on DNA from polymerase errors.

A
  1. insertions and deletions (small or frameshift)
  2. Small repeats
  3. Point mutations
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Exogenous and Endogenous damage are source mutation that can also lead to what other type of source mutation?

A

Polymerase errors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Endogenous damage from physical damage or reactive oxygen species causes what effects to DNA?

A
  1. Oxidized DNA
  2. Crosslinked bases
  3. Double or single stranded breaks
45
Q

What is a missense mutation and what is its effect on DNA?

A

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.

46
Q

What type of mutation has no effect on a protein and why?

A

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

47
Q

What is the most devasting mutation and why?

A

A nonsense mutation because it replaces a codon for a particular amino acid with a STOP codon, causing a misshaped/incomoplete protein

48
Q

What are frame mutations?

A

An insertion or deletion that changes the reading frame of a nitrogenous base sequence.

49
Q

Frameshift makes a protein unviable, unless what?

A

Unless insertion occurs at the end of a base sequence or in multiples of 3 since base are read in 3s

50
Q

What is alkylation?

A

In alkylation, methyl groups (electrophiles) are transferred to reactive sites on the bases and to phosphates in DNA backbone.

51
Q

The alkylation of guanine and cytosine produces what products?

A

O5-ethylguanine and Thymine

52
Q

Methylation is a source of DNA damage that occurs where and produces what product?

A

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

53
Q

Why is DNA double-stranded?

A

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

54
Q

What is a transposon?

A

Repetitive DNA sequences that have the capability to move (transpose) from one location to another in genome.

55
Q

Transposons can cause what?

A

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

56
Q

What are the types of transposons?

A

Simple transposons

Complex transposons

Composite transposons

57
Q

Define a composite transposon

A

A composite transposon is a mobile genetic element consisting of two insertion sequences (ISs) flanking a segment of cargo DNA

58
Q

What is a complex transposon and how is it different form a simple transposon?

A

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.

59
Q

True or False?

Transposons only have an effect is inserted in the intergenic region of DNA.

A

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

60
Q

True or False?

DNA rearrangments, like transposons, generally don’t lead to repair mechanisims.

A

True

61
Q

Broken chromosomes from physical damage or X-rays are usually repair via what mechanisms?

A

Homologous-directed repair or non-homologous end joining

62
Q

What repair mechanisms fix mismatched, oxidized, crosslinked or dimered bases?

A

Mismatch repair or nucleotide excision repair

63
Q

A DNA molecule is inherently unstable because of what?

A

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

64
Q

What is the reason our genetic material does not disintegrate into complete chemical chaos?

A

a host of molecular systems continuously monitor and repair DNA

65
Q

What is a Metalating agent?

A

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

66
Q

What is base excision repair and how does it work?

A

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.

67
Q

What is nucleotide excision repair?

A

Discovered by Aziz Sancar, nucleotide excision repairs DNA injuries caused by UV radiation or carcinogenic chemicals

68
Q

How does nucleotide excision repair work?

A

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.

69
Q

True or False?

Base excision repair and nucleotide excision repair are the same thing.

A

True, but they used different enzymes.

Base excision uses glycosylase

Nucleotide excision uses endonucleases

70
Q

True or False?

Nucleotide and base excision repair can only happen before replication.

A

False.

While it is ideal for them to occur before replication, they can happen at any time.

71
Q

What is mismatch repair?

A

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
72
Q

True or False?

Mismatch repair happens during or shortly after replication.

A

True

73
Q

What mechanism allows mismatch repair to recognize the parent strand of a double-stranded helix that has a mismatched base pair?

A

The parent strand is methylated and the daughter strand is not.

74
Q

Congenital defects in mismatch repair are known cause

A

a hereditary variant of colon cancer

75
Q

How does mismatch repair work?

A

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.

76
Q

What is homolgy-directed repair?

A

The use of an identical sister chromatid as a template to fix a broken chromosome.

77
Q

When does homology-directed repair happen?

A

It must happen after replication because the sister chromatid has to be present.

78
Q

Non-homologous end-joining functions to _______

A

Ligate broken ends of a chromosome together.

This can also result in translocations.

79
Q

Why is Non-homologous end-joining a mutagenic repair mechanism?

A

Because you usually lose some base pairs in the process of ligating broken ends together.

80
Q

True or False?

Non-homologous end-joining can happen at any time.

A

True

81
Q

Why are Non-homologous end-joining and homology-directed repair not good repair mechanisms?

A

because there is a lot of room for error with both of them

82
Q

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?

A

Anticodon

83
Q

Which of the following statements is false regarding DNA damage?

  1. UV can produce a covalent linkage between two adjacent pyrimidine bases in DNA to form pyrimidine dimers.
  2. X-rays has sufficient energy to dislodge orbital electrons from atoms.
  3. Deamination of cytosine to uracil cannot be recognized by the DNA repair system.
  4. The methylation occurs at the 5-position of the cytosine ring of a cytidine base.
A
  1. 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

84
Q

Which of the following statements is false?

  1. The genetic stability of living organisms is mainly accomplished by an accurate DNA replication system and a DNA repair system.
  2. Any change introduced into the base sequence of DNA is called DNA denaturation.
  3. Damage to cellular DNA is involved in mutagenesis and the development of cancer.
  4. Once DNA is damaged, the cell may become malignant.
A
  1. Any change introduced into the base sequence of DNA is called DNA denaturation.

FALSE THIS WOULD BE MUTATION

85
Q

Which of the following statements is true regarding DNA denaturation?

  1. At low temperature, ΔG is negative.
  2. At low temperature the term TΔS is smaller than ΔH.
  3. As the temperature is increased TΔS becomes lesser than ΔH, and ΔG becomes positive.
  4. The greater the length of DNA is, the lower the Tm is.
A
  1. At low temperature the term TΔS is smaller than ΔH.
86
Q

True or False?

As the temperature is increased TΔS becomes lesser than ΔH, and ΔG becomes positive.

A

FALSE

TΔS BECOMES GREATER THAN ΔH AND ΔG BECOMES NEGATIVE AT LOW TEMPERATURES

87
Q

True or False?

Polynucleotides are at metastable state.

A

True

88
Q

True or False?

The DNA helicase separates the two strands by breaking phosphodiester bond.

A

False.

DNA helicase breaks the HYDROGEN bond to seperate the two strands of DNA strands.

89
Q

True or False?

To prevent the replication fork from reannealing, single-stranded DNA –binding proteins bind tightly separated strands.

A

True

90
Q

True or False?

In DNA denaturation at low temperature, ΔG is negative.

A

False.

ΔG is positive

91
Q

True or False?

The greater the length of DNA is, the lower the melting temperature (Tm) is.

A

False.

Tm is higher the longer a DNA strand is.

92
Q

True or False?

Hydrolysis of polynucleotides to nucleotides is the thermodynamically unfavored process.

A

Falsse.

Polynucleotide hydrolysis is thermodynamically FAVORED

93
Q

The structure where transcription occurs is the _______.

A

Nucleus

94
Q

On which molecules would you find a codon?

A

messenger RNA

95
Q

The structure that catalyzes protein synthesis, and which is sometimes called the protein factory is the _________.

A

Ribosome

96
Q

The structure that is responsible for modifying newly transcribed mRNA prior to translation is called the ________.

A

Spliceosome

97
Q

What role does small nuclear RNA play in the synthesis of proteins?

A

It modifies messenger RNA molecules prior to protein synthesis

98
Q

__________ translates the genetic code to a specific amino acid

A

Transfer RNA (tRNA)

99
Q

What catalyzes the process of protein synthesis?

A

Ribosomal RNA (rRNA)

100
Q

Which amino acid in the enzyme topoisomerase II is responsible for cleaving a phosphate-sugar link in a DNA strand?

A

Tyrosine

101
Q

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.

A

b. RNA contains uracil and not adenine

RNa contains uracil instead of THYMINE

102
Q

What term is used to describe the process by which proteins are synthesized from a genetic code?

A

Translation

103
Q

What term is used to describe the process by which DNA is copied to produce two daughter DNA molecules?

A

Replication

104
Q

What term is used to describe the process by which a segment of DNA is copied to produce a molecule of messenger RNA?

A

Transcription

105
Q

What non-covalent bonding interactions do the nucleic acid bases form in DNA secondary structure?

A

Hydrogen bonds and van der Waals interactions.

Hydrogen bonds b/t the bases themselves

Van der Waals b/t the stacked rings of bases

106
Q

What type of DNA structure is shown here?

What is the blue region called?

A

The primary structure of DNA.

The sugar-phosphate backbone

107
Q

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

A

c. UAU to UAA

108
Q

What type of enzyme is used in recombinant DNA technology to reform sugar phosphate bonds after annealing?

A

Ligase

109
Q

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

A

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.

BIOCHEM EXAMs (10 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions