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MABS Biochemistry > Nucleic Acid Structure > Flashcards

Nucleic Acid Structure Flashcards

1
Q

The middle of what century was when DNA was identified as the genetic material and its structure determined?

A

middle of the 20th century

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2
Q

How is the genetic information encoded?

A

DNA (deoxyribonucleic acid)

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3
Q

the molecular mechanisms of inheritance involves this process?

A

replication

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4
Q

the expression of genes within cells requires these 2 processes

A

transcription of DNA to RNA and translation of RNA to protein structure

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5
Q

transcription of DNA to RNA and translation of RNA to protein structure is known as?

A

central dogma of molecular biology

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6
Q

what is the central dogma of biology?

A

transcription of DNA to RNA and translation of RNA to protein structure (Central Dogma)

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7
Q

the regulation of gene expression determines which proteins are synthesized at any given time and this allows for?

A

cell development and differentiation

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8
Q

what are the purines?

A

adenine and guanine

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9
Q

what are the pyrimidines?

A

cytosine and thymine, in RNA thymine is replaced with uracil

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10
Q

how many ring structures do the purines have?

A

two

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11
Q

how many ring structures do the pyrimidines have?

A

one

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12
Q

this scientist first isolated DNA?

A

Frederick Miescher

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13
Q

this scientist identified the building blocks of DNA?

A

Pheobus Levene

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14
Q

how is DNA called a nucleotide?

A

DNA contained adenine, guanine, thymine, cytosine, deoxyribose, and a phosphate.

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15
Q

how is a nucleoside comprised?

A

comprised of a heterocyclic nitrogenous base linked to a sugar

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16
Q

how is a nucleotide comprised?

A

comprised of a heterocyclic nitrogenous base linked to a sugar and a phosphate. If two phosphates then the nucleotide can also be called a nucleoside diphosphate and even a nucleoside triphosphate

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17
Q

How were nucleotides joined together according to Leon Heppel?

A

inorganic phosphate joins the nucleotide monomers, forming a phosphodiester bond between the 3’-carbon of one sugar and the 5’-carbon of the next along the polynucleotide chain.

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18
Q

whats formed when nucleotides join together?

A

a polynucleotide

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19
Q

how are nucleotide monomers linked together?

A

by joining the α phosphate group, attached to the 5’ carbon of one nucleotide, to the 3’ carbon of the next nucleotide.

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20
Q

what is the linkage between nucleotides called?

A

phosphodiester bond

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21
Q

what is the direction of polynucleotides?

A

All DNA synthesis occurs in the 5’  3’ direction

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22
Q

what creates the polarity in the nucleotide chain?

A

5’-P terminus and 3’-OH terminus

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23
Q

how did James Watson and Francis Crick describe the structure of DNA?

A

a double helix consisting of 2 polynucleotide strands joined by hydrogen bonding between the bases

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24
Q

which purines and pyrimidines join together?

A

A and T (2 bonds), G and C (3 bonds)

Although the hydrogen bonds hold the bases and thus the two polynucleotide strands together, they are weaker than covalent bonds and allow the DNA strands to separate during replication and transcription

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25
Q

what is the direction the 2 complimentary strands of DNA run?

A

opposite directions - antiparallel

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26
Q

what do the two DNA strands twist to form?

A

a double helix

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27
Q

how are the base pairs oriented in the helix?

A

like a spiral staircase along the central axis

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28
Q

how are the base pairs stabilized in the helix?

A

Stabilized by van der Waals interactions, hydrophobic effect and hydrogen bonding

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29
Q

where is the sugar phosphate backbone located on the helix?

A

on the outside of the helix

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30
Q

which -OH group on the phosphate is free and the effect of dissociation of hydrogen at physiologic pH?

A

the third -OH group on the phosphate is free; dissociation of hydrogen at physiologic pH creates a net negative charge on the surface

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31
Q

what is created as a result of the twisitng of the DNA helix?

A

major and minor groove

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32
Q

what is the handedness of the helix spirals?

A

right and left handedness; These grooves are exposed and therefore can interact with proteins or other molecules.

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33
Q

what is the distance between the 2 phosphodiester backbones?

A

11 angstroms

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34
Q

what do the H-bond base pairs create?

A

stacking forces with adjacent base pairs

35
Q

what is important to note about the phosphate group on the nucleotide?

A

contains one negatively charged oxygen atom that provides the phosphodiester backbone with a negative charge.

36
Q

If you look up through the bottom of a helix along the central axis and the helix spirals away from you in a clockwise direction (toward the arrowhead in the drawing), it is a _____ helix? . If it spirals away from you in a counterclockwise direction, it is a _____ helix?

A

right handed helix; left handed helix

37
Q

what are the three different forms of DNA?

A

B-DNA, A-DNA, Z-DNA

38
Q

describe B-DNA?

A

Described by Watson and Crick. Right-handed. Most predominate form in vivo

39
Q

describe A-DNA?

A

Predominates in DNA-RNA hybrids. Similar to B-DNA but more compact.

40
Q

describe Z-DNA?

A

Left-handed helix. Formed transiently in cells and linked to transcriptional initiation

41
Q

what is the clinical use of Doxorubicin?

A

used to treat cancers (e.g., lymphomas)

a natural product with a complex multiring structure that intercalates between the stacked base pairs of DNA and inhibits replication and transcription. It is part of a group of chemotherapy drugs known as anthracycline antibiotics. Its slows or stops the growth of cancer cells.

42
Q

In terms of cell size, prokaryotes have small or large cells?

A

small cells

43
Q

prokaryotes are unicellular or multicellular

A

always unicellular

44
Q

prokaryotes are single chromosome (circular) or multiple chromosomes (1 continuous linear DNA helix)

A

single chromosomes

45
Q

T/F, prokaryotes have a nucleus?

A

F, no nucleus

46
Q

T/F, prokaryotes have membrane bound organelles?

A

F, they have no membrane bound organelles

47
Q

eukaryotes have large or small cells?

A

large

48
Q

T/F, eukaryotes are multicellular?

A

T, multicellular

49
Q

T/F, eukaryotes have multiple chomosomes (ea. with 1 continuous linear DNA helix)?

A

T, multiple chromosomes

50
Q

T/F, eukaryotes are membrane bound organelles?

A

T, membrane bound organelles

51
Q

how are prokaryotic chromosomes packaged?

A

Circular DNA is supercoiled and attached to an RNA-protein core

52
Q

how are eukaryotic chromosomes packaged?

A

more complex, DNA binds to histones forming DNA/protein complex called chromatin

53
Q

what are the four histone classes that make up the center of the core in eukaryotes when it comes to packaging?

A

(H2A, H2B, H3, H4) – 2 molecules from each class

54
Q

how many base pairs wrap around the core and connect continuously to the next core?

A

140 bp

55
Q

DNA joining the core is complexed with?

A

H1

56
Q

Further compaction occurs when the strings of nucleosomes wind into helical and tubular coils called?

A

solenoid structures

57
Q

eukaryotic DNA binds to small basic proteins called?

A

histones

58
Q

the complex of DNA and proteins is called?

A

chromatin

59
Q

the genome, or total genetic content, of a human haploid cell ( sperm or egg) is distributed in how many chromosomes?

A

23 chromosomes

60
Q

RNA is similar to DNA, T/F?

A

T

61
Q

how are the nucleotides joined in RNA?

A

3’-to- 5’ phosphodiester bonds

62
Q

what are the purine bases in RNA?

A

Adenine and Guanine (A and G)

63
Q

what are the pyrimidine bases in RNA?

A

Cytosine and Uracil [Adenine H-bond with Uracil; A = U]

64
Q

whats the sugar in RNA?

A

Sugar: Ribose [Hydroxyl group on the 2’-carbon]

65
Q

chains are single or double stranded?

A

Chains are usually single stranded [lack continuous helical structure of dsDNA

RNA still has secondary and tertiary structure where strand loops back on itself

66
Q

describe the pairing between bases of RNA?

A

complementary and antiparallel

67
Q

what are the three major types of RNA?

A

Messenger RNA – mRNA
Ribosomal RNA – rRNA
Transfer RNA – tRNA

68
Q

what is the clinical use for 5-fluorouracil (5-FU)?

A

5-FU – a pyrimidine base similar to uracil and thymine that inhibits the synthesis of thymine nucleotides required for DNA replication by binding tightly to the thymidylate synthase complex that converts dUMP to dTMP. The rate of tumor cell proliferation is greatly reduced.

69
Q

briefly describe how the mRNA is generated into a protein?

A

Messenger RNA (mRNA) is transcribed from protein coding genes (DNA) in the process called transcription. Each mRNA molecule contains a nucleotide sequence that is converted into the amino acid sequence of a protein.

70
Q

Describe the RNA in eukaryotes?

A

mRNA is extensively processed in the nucleus before the mature mRNA is formed and leaves and migrates into the cytosol. [pre-mRNA, 5’-cap, pol(A) tail, introns]

71
Q

Describe the RNA in prokaryotes?

A

mRNA is usually generated from an operon as a polycistronic transcript. The polycistronic transcript is translated as it is transcribed.

72
Q

what does eukaryotic mRNA consist of?

A

a leader sequence at the 5′-end, a coding region, and a trailer sequence at the 3′-end.

73
Q

in eukaryotic mRNA, what does the leader sequence begin with?

A

Eukaryotic mRNA consists of a leader sequence at the 5′-end, a coding region, and a trailer sequence at the 3′-end. The leader sequence begins with a guanosine cap structure at its 5′-end. The coding region begins with a trinucleotide start codon that signals the beginning of translation, followed by the trinucleotide codons for amino acids, and ends at a termination signal. The trailer sequence terminates at its 3′-end with a poly(A) tail that may be up to 200 nucleotides long. Most of the leader sequence, all of the coding region, and most of the trailer are formed by transcription of the complementary nucleotide sequence in DNA. However, the terminal guanosine in the cap structure and the poly(A) tail do not have complementary sequences; they are added after transcription has been completed (posttranscriptionally).

74
Q

in prokaryotes, describe rRNA?

A

3 types of rRNA molecules with sedimentation coefficients 16S, 23S, and 5S.

30S subunit = 16S rRNA + proteins
50S subunit = 23S + 5S rRNAs + proteins
30S + 50S = 70S ribosome (location of protein synthesis)

75
Q

in eukaryotes, describe the rRNA?

A

4 types of rRNA molecules of 18S, 28S, 5S, and 5.8S.

40S subunit = 18S rRNA + proteins
60S subunit = 28S + 5S+ 5.8S rRNAs + proteins
40S + 60S = 80S ribosome (location of protein synthesis)
Mitochondrial ribosomes = 55S (similar to 70S in bacteria)

76
Q

Although larger macromolecules generally have higher sedimentation coefficients than do smaller macromolecules, sedimentation coefficients are not additive, T/F?

A

T, Because frictional forces acting on the surface of a macromolecule slow its migration through the solvent, the rate of sedimentation depends not only on the density of the macromolecule but also on its shape.

77
Q

what is the clinical use for Azithromycin?

A

antibiotic that inhibits protein synthesis on prokaryotic ribosomes by binding to the 50S ribosomal subunit

78
Q

what is tRNA?

A

tRNA molecules carry amino acids to ribosomes during protein synthesis

79
Q

what are the general features of tRNA?

A

Cloverleaf structure - ~4 loops

3’ – Amino acid attachment site

10-20% of nucleotides in tRNA are modified posttranscriptionally (in eukaryotes)

80
Q

how are the tRNA’s modified posttranscriptionally?

A

Ribothymidine (rT)
Dihydrouridine (D)
Pseudouridine (ψ)

81
Q

what is Ribothymidine (rT)?

A

a methyl group is added to uridine to form ribothymidine.

82
Q

what is Dihydrouridine (D)?

A

in which one of the double bonds of the base is reduced

83
Q

what is Pseudouridine (ψ)?

A

in which uracil is attached to ribose by a carbon–carbon bond rather than a nitrogen–carbon bond

84
Q

what is the an exception to the central dogma of biology?

A

According to the “central dogma” information flows from DNA to RNA to proteins. However, retroviruses provide one violation to this rule:

When retroviruses invade cells, their RNA genome is transcribed to produce a copy of DNA by reverse transcriptase.

This DNA copy integrates into the genome of the infected cell, and enzymes of the host cell are used to produce many copies of the viral RNA.

MABS Biochemistry (54 decks)

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