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BMSC > Module 10 - 3 > Flashcards

Module 10 - 3 Flashcards

1
Q

What are the weak forces that stabilize the double helix?

A

Hydrophobic effects, stacking interactions, hydrogen bonds, charge-charge interactions.

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2
Q

What are major and minor grooves?

A

Unequal width grooves in a double helix where base pairs are exposed and accessible to interactions with other molecules.

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3
Q

What is the function of restriction endonucleases?

A

Recognize and cleave specific DNA sequences as a bacterial defense mechanism against viral invasion.

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4
Q

How do host cells protect their own DNA from restriction endonucleases?

A

By covalent modification of bases at the restriction site (e.g. methylation).

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5
Q

What is the origin of the names of restriction enzymes?

A

Reflects the origins of the bacteria they were first characterized from.

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6
Q

What type of sequences do restriction enzymes cut at?

A

Palindrome sequences that are self-complementary.

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7
Q

What is the use of restriction enzymes?

A

As molecular scissors for manipulation of DNA.

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8
Q

What is DNA fingerprinting?

A

Breaking DNA into pieces with restriction enzymes to identify differences in genome sequences.

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9
Q

What is the purpose of hydrophobic effects in stabilizing the double helix?

A

Burying purine and pyrimidine rings in the interior of the helix.

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10
Q

What is the purpose of stacking interactions in stabilizing the double helix?

A

Forming van der Waals contacts between stacked base pairs.

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11
Q

What is the purpose of hydrogen bonds in stabilizing the double helix?

A

Hydrogen bonding between base pairs.

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12
Q

What is the purpose of charge-charge interactions in stabilizing the double helix?

A

Decreasing electrostatic repulsion of negatively charged phosphate groups by cations (e.g. Mg 2+) and cationic proteins.

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13
Q

What is the function of DNA-binding proteins?

A

To read a specific sequence by using interactions with base pairs in the major and minor grooves.

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14
Q

What is the difference between major and minor grooves?

A

Major grooves are deeper and have more exposed base pairs.

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15
Q

What is the function of treating DNA with restriction enzymes in DNA fingerprinting?

A

To break DNA into pieces for identification of differences in genome sequences.

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16
Q

What is the difference in DNA fragments between different individuals in DNA fingerprinting?

A

Different number of fragments and fragments of different sizes due to differences in genome sequences.

17
Q

What is the purpose of methylation in protecting DNA from restriction endonucleases?

A

To covalently modify bases at the restriction site.

18
Q

What is the mirrored sequence of a palindrome?

A

A sequence that is not a palindrome but is mirrored.

19
Q

What is the example of a palindrome sequence?

A

TAGGAT and ATCCTA.

20
Q

What are RFLPs?

A

Restriction Fragment Length Polymorphisms that can be used to identify individuals.

21
Q

What is duplex DNA?

A

DNA containing two complimentary, anti-parallel strands.

22
Q

What determines the sequence of one strand in duplex DNA?

A

The sequence of the other strand.

23
Q

What is the direction of DNA sequences?

A

Always 5’ to 3’.

24
Q

Why is the complementary nature of DNA strands important?

A

For replication and repair

25
Q

What is denaturation of DNA?

A

Complete separation of double-stranded DNA by heat or chemical agents.

26
Q

Can denaturation be done multiple times?

A

Yes the process is very cooperative

27
Q

What is annealing?

A

Reforming the double-stranded helix from single strands.

28
Q

What is the melting point of DNA?

A

Temperature at which half the DNA has become single stranded. (Tm)

29
Q

What does the melting temperature of DNA reflect?

A

Sequence compositions; higher GC content leads to higher Tm.

30
Q

How can each strand of DNA be used?

A

As a template to produce the other.

31
Q

What will be the result of using each strand of DNA as a template?

A

Two identical DNA duplexes.

32
Q

What is the structure of DNA strands?

A

Complimentary and anti-parallel.

33
Q

What is the sequence of complimentary strands?

A

Opposite.

34
Q

How do DNA binding proteins use major and minor grooves

A

They use these interactions to read a specific sequence

BMSC (19 decks)

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