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Biochemistry 304 > CH4 DNA, RNA, Flow of Genetic Info P2 > Flashcards

CH4 DNA, RNA, Flow of Genetic Info P2 Flashcards

1
Q

During which phases must the 2 strands of DNA double helix be sep’d?

A

replication

transcription

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2
Q

Denaturation (Melting)

A

when the double helix is reversibly melted.

DNA strand separation via heating soln.

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3
Q

Hypocrhomism

A

how DNA melting is observed.

bases stacked in double helix absorb less UV light than those in single-stranded molecule.

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4
Q

Reannealing

A

process when cooling two strands bind to e/o, reform double helix.

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5
Q

Polymerase

A

replicate DNA.
catalyze phosphodiester-bridge formation.
instructions from templates.

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6
Q

(DNA)n + dNTP (DNA)n+1 + PPi

A

DNA replication.

rxn catalyzed by DNA polymerase.

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7
Q

What are the key characteristics of DNA synthesis?

A
  1. 4 Deoxynucleoside triphosphates and Mg2+
  2. template strand
  3. primer
  4. DNA polymerase w/ nuclease activity
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8
Q

Deoxynucleoside Triphosphates

A

activate precursors

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9
Q

Template Strand

A

directs DNA synthesis

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10
Q

Primer

A

what the new strand grows from

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11
Q

Nuclease Activity (of DNA polymerase)

A

allows for removal of mismatched bases

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12
Q

The polymerization reaction is catalyzed by?

A

DNA polymerases

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13
Q

dNTPs

A

incorporates a phosphate
activated precursors
subsequent breakdown of released pyrophosphate helps drive phosphodiester bond formation

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14
Q

Pyrophosphate Hydrolysis

A

drive strand elongation

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15
Q

Tobacco Mosaic Virus

A

RNA genomes replicated by RNA-directed RNA polymerases

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16
Q

Retroviruses (ex HIV-1)

A

single-stranded RNA genomes converted to DNA double helices via reverse transcriptase

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17
Q

Flow of Info

RNA to DNA in Retroviruses

A

Each step uses Reverse Transcriptase

  1. Viral DNA
    - Synthesis of DNA complementary to RNA
  2. DNA-RNA Hybrid
    - RNA digestion
  3. DNA Transcript of Viral RNA
    - Synthesis of 2nd Strand of DNA
  4. Double-Helical Viral DNA
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18
Q

Reverse Transcriptase

A

enzyme that converts RNA genome of retrovirus into DNA.

catalyzes synthesis of complementary DNA strand, digests RNA, subsequent synthesis of DNA strand.

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19
Q

Gene Expression

A

transformation of DNA Info into functional molecules

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20
Q

What are the most abundant types of RNA?

A

tRNA
mRNA
rRNA

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21
Q

RNA polymerase

A

catalyzes transcription (synthesis of RNA from DNA template)
initiates and elongates RNA product w/ chain growing 3’ to 5’
no primer needed
3’ OH of growing chain attacks innermost phosphoryl alpha group of incoming nucleoside triphosphate

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22
Q

What are the 3 requirements of RNA polymerase?

A
  1. DNA template
  2. activated precursors in form of 4 ribonucleoside triphosphates
  3. Divalent metal ions (ex Mg2+, Mn2+)
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23
Q

DNA Template

A

complementary seq of newly synthesized RNA

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24
Q

Coding Strand

A

DNA strand w/ same seq as RNA product (w/ T instead of U)

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25
Q

RNA polymerase catalyzes this rxn:

A

(RNA)n residues + ribonucleoside triphosphate (RNA)n+residues + PPi

26
Q

Transcription Mech of Chain-Elongation Rxn Catalyzed by RNA Polymerase

A

driven thermodynamically by hydrolysis of pyrophosphate

27
Q

Transcription begins near?

A

promoter sites

28
Q

Transcription Ends at?

A

terminator sites

29
Q

Promoters

A

specific DNA seq’s that direct polymerase to proper initiation site.

30
Q

Consensus Seq

A

average variation in seq of promoter for diff genes

31
Q

Promoter Sites for Transcription in Prokaryotes

A

-35 Region
-10 Pribbenow box
+1 Start of RNA

32
Q

Promoter Sites for Transcription in Eukaryotes

A

-75 CAAT box
-25 TATA box
+1 Start of RNA

33
Q

Elongation continues until?

A

detects termination signal

34
Q

Transcription Termination 1: Palindromic DNA

A

simplest stop signal is a transcribed product of a segment of this

35
Q

Transcription Termination 2: Hairpin Loop

A

RNA complement of DNA stop signal forms this followed by several uracil residues

36
Q

Transcription Termination 3:

Hairpin Synthesis

A

polymerase stalls
RNA product released
DNA double helix reforms

37
Q

Transcription Termination 4:

Protein

A

rho

sometimes req’d

38
Q 
Post Transcription (Eukaryotes):
mRNA Modification
A

5’ nucleotide “cap” added

3’ poly(A) tail added

39
Q

What are the adaptor molecules in protein synthesis?

A

tRNA

40
Q

tRNA

A

react w/ specific AAs in rxn catalyzed by aminoacyl-tRNA synthetases

41
Q

Anticodon

A

template recognition site in tRNA molecules
consists of 3 bases
recognizes a complementary codon

42
Q

Codon

A

complementary 3 base seq in mRNA

43
Q

Aminoacyl-tRNA

A

attached at 3’ end of RNA
anticodon is template-recognition site
cloverleaf structure w/ many H-bonds btw bases

44
Q

Protein Synthesis is a process of?

A

translation

NA seq info translated into AA seq info

45
Q

The genetic code links?

A

NA info and AA info

46
Q

Genetic Code Characteristics

A
  1. 3 nucleotides (codon) encode AA
  2. nonoverlapping
  3. no punctuation
  4. has directionality, read 5’ mRNA to 3’
  5. degenerate - some AA’s encoded by >1 codon, minimizes deleterious effects of mutations
47
Q

mRNA

A

translated on ribosomes

1st codon almost always AUG - codes for methionine

48
Q

AUG in prokaryotes

A

preceded by purine-rich seq Shine-Dalgarno seq.

49
Q

AUG in eukaryotes

A

5’ end is initiator codon

50
Q

The location of the initiator codon establishes the?

A

reading frame

51
Q

Start Codons

A

req’d for initiation of protein synthesis in prokaryotes and eukaryotes

52
Q

The genetic code is nearly?

A

universal

53
Q

Exons

A

coding regions in eukaryotic genes that are discontinuous.

54
Q

Introns

A

noncoding regions
initially detected by e- microscopy
size range 50-10,000 nucleotides
~ human has 8, some > 100

55
Q

RNA processing generates?

A

mature mRNA

56
Q

Eukaryotic Pre-Messenger RNA

A

contains exons and introns
1st modified by 5’ cap and 3’ poly(A) tail
mature mRNA generated by splicesosomes

57
Q

Splicesosomes

A

large complexes that splice introns to generate mature mRNA

recognize specific seq’s w/i intron that specify splice sites

58
Q

Introns almost always begin w/?

A

GU

59
Q

Introns almost always end w/?

A

AG

60
Q

Once mRNA precursors are spliced mature mRNA if formed because these come together.

A

Exon 1 and Exon 2

61
Q

TPA Tissue Plasminogen Activator

A

was generated by Exon shuffling

encodes enzyme that functions in hemostasis

62
Q

Alternative Splicing

A

forms set of proteins that are variants of basic motif w/o requiring separate gene for each protein

Biochemistry 304 (14 decks)

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