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EOM Test 2 > DNA Structure > Flashcards

DNA Structure Flashcards

1
Q

What is Rett Syndrome?

A

A genetic disorder that causes defects in the methyl-CpG-binding protein 2 involved in chromatin conformation.

Neurodevelopment disorder that only affects females, lethal in males.

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2
Q

What is the central dogma?

A

Flow of information from DNA to RNA and eventually to proteins

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3
Q

What type of covalent bond joins deoxyribonucleotides?

A

3’,5’-phosphodiester bonds

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4
Q

What is the primary structure of DNA?

A

Covalent makeup and base pair sequence

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5
Q

What is the secondary structure of DNA?

A

Stable structure taken up by some or all of the nucleotides.

I.e. double helix

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6
Q

What is the tertiary structure of DNA?

A

Complex folding of eukaryotic chromatin and bacterial nucleoids to form large chromosomes.

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7
Q

What are some features of the DNA molecules?

A
  • Joined by 3’,5’-phosphodiester bonds
  • Each strand has a 5’ and 3’ end, and thus polarity
  • the two strands are antiparallel
  • the two strands are complementary
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8
Q

What are Chargaff’s Rules?

A

Adenosine=thymine and guanosine=cytidine

Purines=Pyrimidines

Species have different base compositions

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9
Q

What are four characteristics of the DNA double helix?

A
  • Two strands coiled around the axis of symmetry.
  • antiparallel
  • Hydrophilic backbone on outside, hydrophobic bases on the inside.
  • Major and minor grooves
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10
Q

What is Actinomycin D?

A

Anti cancer drug that intercalates between the planar bases

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11
Q

What is B-DNA?

A

Right-handed double helix.

Hydrophilic backbone on outside, bases on the inside.

10 bp/turn

Most common form of DNA in nature

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12
Q

What is Z-DNA?

A

Rare left-handed double helical form of DNA

Occurs in G-C rich sequences

May be related to gene regulation

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13
Q

What is A-DNA?

A

Right-handed helix produced by dehydrating the B form.

11 bp/turn and planes are tilted away from the perpendicular to the axis

Conformation found in DNA-RNA hybrids or RNA-RNA double-stranded regions

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14
Q

What is the importance of denaturing DNA molecules?

A

Allows access to encoded information.

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15
Q

What causes DNA denaturation?

A

Heat

-pH extremes

Urea

Other denaturing agents

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16
Q

What is the hyperchromic effect?

A

Absorbance to UV light goes up as DNA becomes denatured (more single-stranded)

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17
Q

What causes the Tm of a region of DNA to be higher or lower and why?

A

The amount of GC base pairs in the region, due to GC having 3 H-bonds instead of 2.

More GC = higher Tm

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18
Q

How is DNA packaged in viruses?

A

Genome surrounded by a protein coat

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19
Q

How is DNA packaged in bacteria?

A

A single circular chromosome housed in their nucleoid and smaller circular plasmids that often have no function, but can give antibiotic resistance.

20
Q

How is DNA packaged in eukaryotes?

A

Packaged into chromatin

21
Q

What is chromatin?

A

The complex of nucleic acids (DNA and RNA) and proteins (histones and nonhistones) comprising eukaryotic chromosomes

22
Q

What is the difference between Euchromatin and heterochromatin?

A

Euchromatin - loosely packaged and transcriptionally active, beads on a string DNA

Heterochromatin - tightly packaged and transcriptionally inactive

23
Q

What are histones?

A

DNA-binding proteins that contain large amounts of basic amino acids (positively charged) such as lysine and arginine which attract negatively charged DNA.

24
Q

What are nucleosomes?

A

The structural unit for packaging chromatin consisting of a DNA strand around a histone core.

25
Q

What is the histone core of a nucleosome comprised of?

A

Two copies of histones H2A, H2B, H3, and H4.

26
Q

What is the role of histone H1?

A

Associated with linker DNA found between nucleosomes to help package chromatin into higher order structures that eventually form chromosomes.

27
Q

What is positive supercoiling?

A

Winding the DNA duplex in the same direction as that of the turns of the double helix.

28
Q

What is negative supercoiling?

A

Twisting the duplex DNA molecule in a direction opposite to the turns of the strands of the double helix.

29
Q

What is the biological significance of supercoiling?

A

Maintaining a negatively supercoiled state allows easier separation of the strands for processes such as replication and transcription.

30
Q

What is the function of topoisomerases?

A

Relax supercoiling stress and maintain negative supercoiling by breaking DNA and resealing the breaks

31
Q

What is the target of ciprofloxacin (a quinolone) and doxorubicin (anti cancer)?

A

Topoisomerases

32
Q

What are the three structures in chromosomes necessary for propagation?

A

Centromere

Telomere

Origin of replication

33
Q

What is a Centromere?

A

Region of a chromosome to which spindle tration fibers attach during mitosis and meiosis

34
Q

What is a telomere?

A

A specialized repeated DNA sequence, along with specialized proteins, found at the ends of chromosomes.

Shortening of telomeres provides a mitotic clock

35
Q

What is an origin of replication in a chromosome?

A

Nucleotide sequence at which DNA synthesis begins.

Spaced about every 50,000 bp in humans.

36
Q

What is a karyotype and what is it in humans?

A

Chromosomal complement of a cell

23 pairs of chromosomes in humans.

37
Q

What are epigenetic modifications?

A

Non-sequence based changes to DNA that are propagatable through mitosis or meiosis.

38
Q

What are the two mechanisms for DNA methylation?

A
  • sterically inhibiting the binding of trans-acting factors, repressing transcription, but sometimes can activate if factors are repressive.
  • serving as a recognition motif for binding of specific factors.
39
Q

What catalyzes DNA methylation?

A

DNA methyltransferases, using S-adenosyl methionine (SAMe) as the donor.

40
Q

What is removal of DNA methylation catalyzed by?

A

Ten-eleven translocation enzymes (TET)

Thymine-DNA glycosylase (TDG)
-removes thymine moieties from G/T mismatches

41
Q

How does histone acetylation occur?

A

Transfer of an acetyl group from acetyl CoA to the e-amino group of a lysine residue

Causes partial neutralization of the positive charge of histones.

42
Q

What are 6 forms of histone modifications?

A

Acetylation

Methylation

Phosphorylation

ADP-ribosylation

Ubiquitination

Biotinylation

43
Q

What controls the acetylation of histones?

A

Histone aceytltransferases (HATs)

Histone deacetylases (HDACs)

44
Q

What are used in treating myelodysplastic and myelodysplastic/myeloproliferative overlap syndromes?

A

Hypomethylating agents

45
Q

How is Sezary syndrome treated?

A

HDAC inhibitors

EOM Test 2 (20 decks)

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