LECTURE 5: In-depth Central Dogma Process Flashcards

1
Q

4 CHARACTERISTICS of DNA REPLICATION

A
  1. Semiconservative (uses old DNA strand as template for synthesis of new strand)
  2. Semi-discontinuous (involves both continuous (leading strand) and discontinuous (lagging strand) synthesis)
  3. Unidirectional synthesis (5’ to 3’ synthesis w/ respect to NEW STRAND)
  4. Bidirectional progress (lagging and leading strand is simultaneously synthesized)
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2
Q

DIRECTION OF SYNTHESIS OF THE FF:

  1. DNA replication
  2. Transcription
  3. Translation
A
  1. 5’ to 3’ w/ respect to new strand
  2. 5’ to 3’ w/ respect to the RNA
  3. 5’ to 3’ w/ respect to mRNA template
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3
Q

DNA REPLICATION

  • direction of synthesis?
  • direction of addition of nucleotides?
A
  • 5’ to 3’ w/ respect to new strand
  • new nucleotides are added at the 3’ OH end
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4
Q

DNA REPLICATION - INITIATION

ENZYMES/PROTEINS (5) + steps

+ location of binding (first 3 proteins)
+ function (1 ; 2 ; 3 ; 1 ; 1)

A
  1. INITIATOR PROTEINS
    - binds near oriC (specifically at the A=T “bonding site”)
    - melts the double bond to partially open up the oriC
  2. Helicase
    - binds to ONE STRAND of DNA
    - further unwinds and opens the dsDNA
  3. Single-strand DNA-binding Proteins
    - binds to ONE STRAND of DNA
    - prevents reannealing
    - prevents formation of internal pairings between bases which may cause changes in overall DNA shape
    - prevents DNA degradation from nucleases
  4. Topoisomerase/Gyrase
    - relieve the torsional strain caused by helicase
  5. Primase
    - makes RNA primers to help the DNA Polymerase III to start synthesizing
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5
Q

DNA REPLICATION - INITIATION

why do initiator proteins bind at A=T instead of G≡C?

A

double bonds are weaker and easier to break

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6
Q

DNA REPLICATION - INITIATION

what type of strain do HELICASES cause to DNA due to unwinding and opening up?

A

torsional strain

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7
Q

DNA REPLICATION - INITIATION

HELICASE consumes ____ to unwind the parent DNA

A

ATP

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8
Q

DNA REPLICATION - INITIATION

what will happen if TOPOISOMERASE or GYRASE does not do its job?

A

the DNA will break

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9
Q

DNA REPLICATION - INITIATION

what are IN primers that make it possible for DNA Polymerase III to add bases?

A

short RNA base sequences that contain 3’ OH

remember that DNA Polymerase III can only add bases to an existing 3’ OH

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10
Q

TROMBONE MODEL

  • what specific process does it show?
  • a _____mechanism that shows the ______ progress of DNA Replication
A
  • physically orients the lagging strand towards the replication fork during synthesis
  • looping
  • bidirectional
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11
Q

DNA REPLICATION - ELONGATION

ENZYME/PROTEINS (3) + steps

+ function (1 ; 3 ; 1)

A
  1. DNA Polymerase III
    - adds complementary bases for both lagging and leading strands
  2. DNA Polymerase I
    - proofreading and repair
    - removal of primers and replaces with DNA
    - removal of mismatched bases and replaces with DNA
  3. Ligase
    - seals the breaks produced during lagging strand synthesis
  4. Telomerase (additional)
    - extends parent DNA ends para madikitan yung mga old primers ng nitrogenous bases (since nga 3’ OH is needed for synthesis
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12
Q

How many DNA polymerases does E. coli have?

A

At least 3

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13
Q

What types of enzyme is DNA Polymerase III?

A

holoenzyme

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14
Q

DNA REPLICATION - ELONGATION

what is the MAIN POLYMERASE in this step?

A

DNA polymerase III

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15
Q

DNA REPLICATION - ELONGATION

LIMITATION for function of ligases?

A

only seals breaks between nitrogenous bases in lagging strand if its 1 PHOSPHATE AWAY

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16
Q

DNA REPLICATION - TERMINATION

  • when does it end?
  • replication products?
A
  • ends once all the nucleotide bases of the PARENT DNA STRANDS are complemented
  • 2 identical daughter DNA
17
Q

TRANSCRIPTION

  • 3 important GENE STRUCTURES
A
  1. Promoter
    - binding site of RNA polymerase
  2. Coding Region
    - gene region transcribed by RNA polymerase
  3. Terminator
    - signals the RNA polymerase to stop transcribing
18
Q

TRANSCRIPTION - INITIATION

ENZYMES/PROTEINS (2) + steps

+ functions (1 ; 1)

A
  1. Sigma Subunit
    - guides the RNA polymerase to promoter
  2. RNA Polymerase
    - unwinds the promoter by itself
19
Q

TRANSCRIPTION - ELONGATION

ENZYME/PROTEIN (1)

+ function (2)

A

RNA Polymerase
- unwinds DNA and
continues elongation until “termination signal”
- proofreads

20
Q

TRANSCRIPTION - TERMINATION

ENZYME/PROTEIN (1)

+ function (2)

A

Rho-protein

  • binds to and pulls RNA DURING ELONGATION
  • pulls away RNA and terminate transcription
21
Q

TRANSCRIPTION - TERMINATION

  • 3 products
A
  1. mRNA
  2. tRNA
  3. rRNA
22
Q

TRANSLATION

  • ____ is the site for translation
  • ____ is read in triplets of adjacent nucleotides called ____
  • one codon = ___ amino acid/s
  • mRNA codons are read from ___ to ____ in a ____ but ____-_____ manner
A
  • ribosomes
  • mRNA
  • codons
  • one
  • 5’ to 3’
  • continuous but non-overlapping manner
23
Q

GENETIC CODE CHART

  • start codon (1)
  • stop codons (3)
A
  • AUG
  • UAG, UAA, UGA
24
Q

TRANSLATION - INITIATION

ENZYMES/PROTEINS (4) + steps

A
  1. Aminoacyl-tRNA synthetase
    - loads correct amino acids onto tRNAs
  2. Initiation Factor 1
    - dissociates 50S and 30S ribosomal subunit
  3. Initiation Factor 3
    - attaches to 30S subunit to prevent re-association
  4. Initiation Factor 2
    - brings and attaches the FIRST amino acyl-tRNA (carrying fmet) to 30S subunit, P-site

*IF1 attaches to 30S subunit
*50S subunit attaches to 30S subunit
*All initiation factors dissociates

25
Q

TRANSLATION - ELONGATION

ENZYMES/PROTEINS (3) + steps

A
  1. Elongation Factor Tu
    - escorts the correct amino acyl-tRNA to A site
  2. Peptidyl transferase
    - catalyzes formation of peptide bond between amino acids
  3. Elongation Factor G
    - moves ribosome along the mRNA to elongate the peptide chain until A-site encounters stop codon
26
Q

TRANSLATION - TERMINATION

ENZYMES/PROTEINS (3) + steps

A
  1. Release Factor 1
    - recognizes UAG, UAA
    - breaks bond between polypeptide chain and tRNA to release the chain from ribosome
  2. Release Factor 2
    - recognizes UGA, UAA
    - breaks bond between polypeptide chain and tRNA to release the chain from ribosome
  3. Release Factor 3
    - assists release factors 1 and 2
27
Q

TRANSLATION - TERMINATION

product?

A

polypeptide chain (NOT protein)

28
Q

TRANSCRIPTION

initiation site vs promoter

A

PROMOTER: where RNA Polymerase binds to

IS: specific location on the DNA where RNA polymerase begins synthesizing RNA.