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EoM Exam 2 - Sollars > DNA Structure > Flashcards

DNA Structure Flashcards

1
Q

What is the primary, secondary, and tertiary structure of DNA?

A 
Primary = Covalent makeup and base pair sequence
Secondary = Interactions of two strands to form stable double helix
Tertiary = Complex folding of eukaryotic chromatin (and bacterial nucleoids) to form chromosomes
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2
Q

What is the central dogma of molecular biology?

A

The flow of genetic information from DNA —> RNA

—> proteins

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3
Q

Where do the steps of central dogma take place?

A

In nucleus, Replication (DNA replicates to make a copy of itself.), Transcription (RNA is transcribed from a DNA template strand.), Processing (RNA is processed and spliced then transported to the cytoplasm.)

In cytoplasm, Translation (RNA is translated into polypeptide chains on ribosomes.) Protein Assembly (The polypeptide chain is folded into a complete protein.)

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4
Q

What are Chargaff’s 2 rules? Why are they important?

A
  1. Amount of A = Amount of T &
    Amount of G = Amount of C
  2. Composition of DNA varies from ones species to another but not within the organism.

They were the basic precepts used by Watson, Crick, and Wilkins to discover the double helix structure of DNA.

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5
Q

What is the composition of DNA?

A

DNA is a polymer of nucleotides joined by 3’,5’-phosphodiester bonds. It is usually double stranded and contains thymine (T) and deoxyribose.

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6
Q

What is the composition of RNA?

A

RNA is a polymer of nucleotides joined by 3’,5’-phosphodiester bonds. It is usually single stranded and contains uracil (U) and ribose.

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7
Q

Each strand of DNA is a polymer of what?

A

Deoxynucleotides

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8
Q

The pentose-phosphate backbone of each DNA strand is linked by what?

A

3’,5’-phosphodiester bonds in which the phosphate group links the 3’C of a pentose to the 5’C of the next pentose in the chain.

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9
Q

What is found at the ends of each DNA strand?

A

Each strand has a distinct 5’ end and 3’ end (and thus, has polarity). A phosphate group is often found at the 5’ end and a hydroxyl group is found at the 3’ end.

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10
Q

In what direction do the two DNA strands run?

A

They are antiparallel (opposite in direction).

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11
Q

How are the two DNA strands complimentary?

A

A always pairs with T (2 H bonds) and G always pairs with C (3 H bonds) so that the base sequence on one strand defines the base sequences on the other strand.

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12
Q

How does specific base pairing reflect Chargaff’s rules?

A

Because of specific base pairing, amount of A always equals that of T and amount of G always equals that of C, so total purines will equal total pyrimidines.

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13
Q

What is carried in the base sequence of a DNA molecule?

A

Genetic information

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14
Q

What is the primary structure of DNA?

A

Primary structure is the base sequence and covalent makeup written in the 5’ —> 3’ direction (left to right).

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15
Q

In what secondary structure form does DNA occur in nature?

A

Right-handed double helical molecule (Watson-Crick DNA form) also referred to as B-DNA.

The hydrophilic backbone is on the outside and the hydrophobic base pairs are on the inside. There are about 10 base pairs per complete turn of the helix.

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16
Q

What is Z-DNA?

A

Z-DNA is a rare, left-handed double-helical form of DNA that occurs in G-C rich sequences and is longer and more narrow. The biological function of Z-DNA is unknown but may be related to gene regulation.

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17
Q

What A-DNA?

A

A form is produced by moderately dehydrating B-DNA. It is also a right-handed double helix but there are 11 base pairs per turn and the planes of the base pairs are tilted 20 degrees away from the perpendicular to the helical axis (shorter, wider). The biological significance is that the conformation found in DNA-RNA hybrids or RNA-RNA double stranded regions is probably close to A form.

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18
Q

What is denaturation and how is it caused?

A

Denaturation is the disruption of the non-covalent interactions which hold the DNA duplex together. This can be caused by heat, extremes of pH, urea, and other agents.

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19
Q

What happens to DNA upon denaturation?

A

DNA solutions become less viscous and they absorb more ultraviolet light. This is the hyperchromic effect.

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20
Q

What determines the different melting temperatures of different regions of DNA?

A

Relative amounts of GC base pairs determine melting temperature because A has 2 hydrogen bonds to T (easier to break) and G has 3 hydrogen bonds to C (harder to break).

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21
Q

Why does DNA have to denature slightly?

A

It denatures to access information but will reform to the stabilized double helix as long as it does not completely separate.

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22
Q

What is true about the size of chromosomal DNA of every class of organism or viral parasite?

A

Chromosomal DNA is often magnitudes longer than the cells or viruses in which they are located.

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23
Q

What is the genome of viruses?

A

Viruses consist of a genome surrounded by a protein coat. The genome of HIV is about 9,000 nucleotides.

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24
Q

What is the genome of bacteria?

A

Bacteria usually have a single chromosome housed in their nucleoid and smaller circular DNAs called plasmids that have no function but can give antibiotic resistance. The genome of E. coli is 4.5 million basepairs.

25
Q

What is the genome of humans?

A

The human genome is approximately 3 billion base pairs with most cells having 2 copies. Eukaryotic DNA is packaged into chromatin.

26
Q

What is chromatin?

A

Chromatin is the complex of nucleic acids (DNA, RNA) and proteins (histones and non-histones) comprising chromosomes.

27
Q

What is the basic structure of chromatin? How is it formed?

A

The basic structure of chromatin is the nucleosome.
DNA wraps around histone complexes to form the basic structure that can form more complex and condensed structures (chromosomes).

28
Q

What are histones?

A

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

29
Q

What is a nucleosome? What is it made of?

A

Nucleosomes are the structural unit for packaging chromatin. They are made of a DNA strand wrapped around a histone core.

30
Q

What makes up the histone core?

A

The histone core consists of 2 copies of each of the 4 histones: H2A, H2B, H3, H4.

31
Q

What is the function of histone H1?

A

H1 is associated with linker DNA found between the nucleosomes to help package chromatin into higher order structures that eventually form chromosomes.

32
Q

What are the two types of chromatin? How do they vary?

A

Euchromatin: loosely packed & transcription-active
Heterochromatin: tightly packed & transcription-inactive
They vary based on cell type of the body.

33
Q

What is supercoiling?

A

Twisting of a helical (coiled) molecule on itself, a coiled coil

34
Q

What is positive supercoiling?

A

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

35
Q

What is negative supercoiling?

A

Twisting of the DNA duplex in the opposite direction of the turns of the double helix

36
Q

What is the biological significance of supercoiling?

A
  1. Cells actively maintained negative supercoiled state necessary to facilitate access to DNA (Underwinding).
  2. Winding of DNA around histones induces positive supercoiling in linker regions.
37
Q

What is the importance of underwinding?

A

Underwinding of the DNA double helix allows for easier separation of strands for processes such as replication and transcription.

38
Q

What are the functions of topoisomerases?

A

Topoisomerases are enzymes critical to maintaining the underwinding of DNA and to relaxing effects of supercoiling.

39
Q

How doe topoisomerases work?

A

Topoisomerases create breaks in either one (Topoisomerase 1) or both (Topoisomerase 2) strands, allow the strand to twist, then reseal the break.

40
Q

What drugs target topoisomerases?

A

Antibiotics such as the quinolones (Ciprofloxacin) and anti-cancer drugs such as doxorubicin target topoisomerases.

41
Q

How is DNA organized into the chromosomes of humans, mitochondria, and bacteria?

A

DNA is organized into chromosomes in vivo, which are linear structures of chromatin in humans and circular structures loosely termed “chromosomes” in mitochondria and bacteria.

42
Q

What 3 structures make up linear chromosome architecture and how were they discovered?

A

The three structures are the centromere, telomere, and origins of replication. (Prokaryotic chromosomes only have one origin of replication.)

This was discovered by constructing a mitotic/meiotic-stable artificial chromosome, an important tool for cloning large sections of the human genome.

43
Q

What is a centromere?

A

A region of chromosome to which spindle traction fibers attach during mitosis and meiosis.

44
Q

Where do 2 sister chromatids join in a replicated chromosome?

A

Two sister chromatids joined at the centromere region.

45
Q

What is primary chromosomal constriction?

A

The centromere of metaphase chromosomes is narrower than regions distal to it.

46
Q

What is a telomere?

A

A specialized repeated DNA sequence found (along with specialized proteins) at the ends of eukaryotic chromosomes.

47
Q

What is a mitotic clock?

A

Chromosomes lose about 100 nucleotides from their ends with each cell division. This shortening of the telomere suggests that a cell may have a limited number of divisions, or a mitotic clock.

48
Q

What are origins of replication?

A

A nucleotide sequence at which DNA synthesis begins, termed an ori site.

49
Q

Where are origins of replication located?

A

Humans have one ori site spaced every 50,000 base pairs. Bacteria only have one because their genomes are circular.

50
Q

What are the p arm and q arm of sister chromatids?

A

The p arm is the short arm attached at the centromere. The q arm is the long arm attached at the centromere.

51
Q

What is the karyotype? How many pair of chromosomes are in the human karyotype?

A

The karyotype is the chromosomal complement of a cell, individual, or species. The human karyotype includes 23 pair of chromosomes.

52
Q

What are epigenetic modifications?

A

Non-sequence based changes to DNA that are propagatable through mitosis or meiosis and can affect the ability of the cell to access information.

53
Q

Epigenetic modifications control gene expression during what critical times?

A

Development, disease states (cancer), cellular differentiation

54
Q

What is an example of an environmental influence (such as diet) causing changes in gene expression through epigenetic modifications?

A

All bees have the same genome, but larvae that larvae that ingest royal jelly undergo epigenetic changes to alter the morphology and lifespan and become queen bees.

55
Q

How is DNA methylation an example of epigenetic modification?

A

DNA methylation inhibits binding of transacting factors, typically repressing factors if at the promoter sequence but sometimes inhibiting binding of repressive factors and thus activating transcription.
DNA methylation also serves as a recognition motif for binding of specific factors.

56
Q

What are epigenetic histone modifications?

A

Histone modifications are primarily acetylation but also include phosphorylation, methylation, ADP-ribosylation, glycosylation, and ubiquitination.

57
Q

What are the effects of epigenetic histone modifications?

A

Epigenetic histone modifications can affect the ability of nucleosomes to interact and form repressive complexes (prevent higher levels of tertiary structure) because the histones are positive and the DNA strands are negative.

58
Q

Where do epigenetic modifications take the form of post-translational modifications?

A

On the amino-terminal tail and internal sites of histones

EoM Exam 2 - Sollars (5 decks)

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