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Life Science 3 > L6: RNA Structure > Flashcards

L6: RNA Structure Flashcards

1
Q

Flow of biological infomation

A

DNA –(transcription)–> RNA –(translation)–> Protein

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2
Q

Polymer of AA nucleotide sequence of genes determine _____ _____

A

protein sequence

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3
Q

Protein sequence determines _____ _____ and _____

A

protein structure, function

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4
Q

Building blocks of RNA and DNA

A
  • Nucleoside: pentose + base
    • Pyrimidine type (one ring)
      C (cytidine)
      T (thymidine)
      U (uridine)
    • Purine (two-ring)
      A (adenosine)
      G (guanosine)
  • Nucleotide: nucleoside + phosphate
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5
Q

Pentose in RNA

A

Ribose

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6
Q

Pentose in DNA

A

2-Deoxyribose

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7
Q

Bases in RNA

A
  • Purine
    • A (adenine)
    • G (guanine)
  • Pyrimidines
    • U (uracil)
    • C (cytosine)
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8
Q

Bases in DNA

A
  • Purine
    • A (adenine)
    • G (guanine)
  • Pyrimidines
    • T (thymine)
    • C (cytosine)
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9
Q

Condensation reaction

A
  • H20 removed to form the phosphodiester bond
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10
Q

RNA

A
  • single strand polynucleotide
  • composed of 4 ribonucleotides
    • A, C, G, U
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11
Q

ssDNA is stable in _____ solution, but RNA is not

A

Alkaline

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12
Q

Why is ssDNA stable in alkaline solution but not RNA?

A

The 2’-OH group makes RNA unstable in alkaline conditions, because it can attack the phosphodiester bonds of the RNA chain and break RNA into small pieces of nucleotide monomers

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13
Q

DNA vs. RNA: sugar

A

DNA: Deoxyribose (2’-H)
RNA: Ribose (2’-CH)

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14
Q

DNA vs. RNA: base

A

DNA: A, C, G, T
RNA: A, C, G, U

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15
Q

DNA vs. RNA: structure

A

DNA: double strand
RNA: single strand

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16
Q

DNA vs. RNA: size

A

DNA: large (kb-Mb)
RNA: small (bp-kb)

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17
Q

DNA vs. RNA: stability in alkaline

A

DNA: stable
- dsDNA denatured at high pH but is not hydrolyzed
RNA: unstable
- hydrolyzed to nucleotides

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18
Q

A single strand RNA molecules can form short stretches of double strands when there are enough intra-molecule _____ _____

A

base pairing

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19
Q

Base pairing:

 - G=C --> forms \_\_\_\_\_ H bonds
 - U=A --> forms \_\_\_\_\_ H bonds
A

3, 2

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20
Q

RNA secondary structure

A
  • Are stem-loops and hairpins

- Formed through intra-molecule complementary base pairing

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21
Q

RNA tertiary structure

A
  • 3D sructures (i.e. pseudoknotes found in t/rRNA)

- formed by folding stem-loops and hairpins

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22
Q

Major types of RNA in the cell

A
  1. mRNA
  2. tRNA
  3. rRNA
  4. others:
    • hnRNA
    • snRNA
    • miRNA
    • siRNA
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23
Q

mRNA

A
  • message RNA
  • used as template for protein translation
  • linear structure
  • (eukaryotic) contains sequences encoding a specific polypeptide
  • contains noncoding regions at 3’ and 5’ ends, which help translation
  • mainly in cytosol, where translation occurs
  • (eukaryotic) has special modifications that are 5’ cap and 3’ polyA, neither modifications are found in prokaryotic or other eukaryotic RNAs
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24
Q

message RNA

A

mRNA

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25
Q

RNA used as template for protein translation

A

mRNA

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26
Q

RNA with linear structure

A

mRNA

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27
Q

RNA in (eukaryotic) that contains sequences encoding a specific polypeptide

A

mRNA

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28
Q

RNA that contains noncoding regions at 3’ and 5’ ends, which help translation

A

mRNA

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29
Q

RNA found mainly in cytosol, where translation occurs

30
Q

RNA in (eukaryotic) that has special modifications that are 5’ cap and 3’ polyA, neither modifications are found in prokaryotic or other eukaryotic RNAs

31
Q

tRNA

A
  • transfer RNA
  • used to bring AA for translation reaction
  • has a unique clover-leaf like structure
  • each has a primary, secondary, and tertiary structure
32
Q

transfer RNA

33
Q

RNA used to bring AA for translation reaction

34
Q

RNA that has a unique clover-leaf like structure

35
Q

Each of its RNA has a primary, secondary, and tertiary structure

36
Q

rRNA

A
  • ribosomal RNA
  • always associate with proteins from ribosomes
    • Ribosomes: protein synthesis apparatus
37
Q

ribosomal RNA

38
Q

RNA that always associate with proteins from ribosomes

39
Q

Protein synthesis apparatus

40
Q

hnRNa

A
  • heterogenous nuclear RNA

- stability, processing

41
Q

snRNA

A
  • small nuclear RNA

- processing

42
Q

miRNA

A
  • micro RNA
  • regulation
  • regulators of endogenous genes
43
Q

siRNA

A
  • small inferring RNA
  • regulation
  • defenders of genome integrity in response to foreign or invasive nucleic acids (viruses, tranposons, and transgenes)
44
Q

hnRNP

A
  • heterogenous ribonucleoprotein particle
  • (hnRNA + proteins)
  • function:
    • stabilization of ssRNA
    • RNA processing
    • RNA transportation
45
Q

RNA interface (RNAi)

A
  • protects against RNA virus infections
  • secures genome stability by keeping mobile elements silent
  • triggered by dsRNA helices that have been introduced exogenously into cells as small interfering siRNAs or that have been produced endogenously from small non-coding RNAs (miRNA)
    • miRNA: regulators of endogenous genes
    • siRNA: defenders of genome integrity in response to foreign or invasive nucleic acids (viruses, tranposons, and transgenes)
  • functions:
    • regulation of gene expression
    • defense of viral infection
    • standard experimental tool
    • can be used as a therapeutic strategy
46
Q

All cellular RNAs are made by _____

A

Transcription

47
Q

Transcription

A
  • DNA dependent RNA synthesis process
    • catalyzed by the RNA polymerase
  • only one of the two strands of DNA are copied into RNA for a given gene
  • sequence of nucleotides in the NDA determines the sequence of nucleotides in the RNA, which determines the sequence of AA in the protein
48
Q

DNA dependent RNA synthesis process

- catalyzed by the RNA polymerase

A

Transcription

49
Q

_____ of the two strands of DNA are copied into RNA for a given gene

50
Q

_____ _____ _____ in the NDA determines the sequence of nucleotides in the RNA, which determines the sequence of AA in the protein

A

Sequence of nucleotides

51
Q

Sequence of nucleotides in the NDA determines the sequence of nucleotides in the RNA, which determines the sequence of _____ _____ in the protein

A

Amino Acids

52
Q

Isotopes

A

Atoms that contain the same number of protons but different number of neutrons

53
Q

Atoms that contain the same number of protons but different number of neutrons

54
Q

Isotopes that can decay and emit electromagnetic radiation

A

Radioisotopes

55
Q

Radioisotopes

A
  • Isotopes that can decay and emit electromagnetic radiation
  • widely used in molecular bio studies because:
    • they are physically distinguishable but chemically identical from each other
  • presence of various particles emitted during decay of a radioisotope can be detected by:
    • Geiger counter (monitor)
    • exposure to X-ray fim (autoradiography)
56
Q

Radioisotopes are physically _____ but chemically _____ from each other

A

distinguishable, identical

57
Q

Presence of various particles emitted during decay of a radioisotope can be detected by:

A
  • Geigner counter (monitor)

- exposure to X-ray film (autoradiography)

58
Q

Pulse-Chase Experiments

A
  • Pulse: short exposure to labeled precursors (RNA, DNA, protein)
  • synthesis of DNA, RNA, or protein involves the polymerization of precursor molecules (nucleotides or AA)
  • if precursors are radioactively labeled and supplied to cells in a cultured media, then he cells will transport them into the cell and use them to synthesize the macromolecule
  • if cells are examined immediately for he location of the radioactivity, the site of synthesis can be determined
59
Q

Position of macromolecules in cell are _____ and _____ while AA are _____ _____

A

fixed, free, washed away

60
Q

_____ detects location of a labeled protein

A

Autodiogram

61
Q

X-ray film is _____ when radioactive emissions are detected

62
Q

The Chase experiment

A
  • wash or dilute out label and allow the cell to continue growing for a period
  • during this period, no new incorporation of radioactive precursor in macromolecule occurs, however, macromolecules may move around in the cell (determines the final location of macromolecule)
63
Q

Pulse-Chase: protein

A

35S-methionine

64
Q

Pulse-Chase: RNA

65
Q

Pulse-Chase: DNA

A

3H-thymine

66
Q

Pulse-Chase conclusion

A
  • Protein: synthesized in cytoplasm and later may move to the nucleus
  • RNA: synthesized in nucleus and migrates to cytoplasm
  • DNA: synthesized in nucleus and remains there
67
Q

Protein is synthesized in the _____ and later may move to the _____

A

cytoplasm

nucleus

68
Q

RNA is synthesized in the _____ and migrates to the _____

A

nucleus

cytoplasm

69
Q

DNA is synthesized in the _____ and remains in the _____

A

nucleus

nucleus

70
Q

Central Dogma

A
  • DNA –(transcription)–> RNA –(translation)–> protein
  • RNA –(reverse transcription)–> DNA
  • RNA –(RNA-directed RNA synthesis)–> RNA

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