LECTURE 5: In-depth Central Dogma Process

Question 1

4 CHARACTERISTICS of DNA REPLICATION

Answer 1

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)

Question 2

DIRECTION OF SYNTHESIS OF THE FF:

1. DNA replication
2. Transcription
3. Translation

Answer 2

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

Question 3

DNA REPLICATION - INITIATION

ENZYMES/PROTEINS (5) + steps

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

Answer 3

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

Question 4

DNA REPLICATION - INITIATION

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

Answer 4

double bonds are weaker and easier to break

Question 5

DNA REPLICATION - INITIATION

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

Answer 5

torsional strain

Question 6

DNA REPLICATION - INITIATION

HELICASE consumes ____ to unwind the parent DNA

Answer 6

ATP

Question 7

DNA REPLICATION - INITIATION

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

Answer 7

the DNA will break

Question 8

DNA REPLICATION - INITIATION

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

Answer 8

short RNA base sequences that contain 3’ OH

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

Question 9

TROMBONE MODEL

• what specific process does it show?
• a _____mechanism that shows the ______ progress of DNA Replication
• newest model that shows dna replication

Answer 9

• physically orients the lagging strand towards the replication fork during synthesis
• looping
• bidirectional

Question 10

DNA REPLICATION - ELONGATION

ENZYME/PROTEINS (3) + steps

+ function (1 ; 3 ; 1)

Answer 10

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

Question 11

How many DNA polymerases does E. coli have?

Answer 11

At least 3

Question 12

What types of enzyme is DNA Polymerase III?

Answer 12

holoenzyme

Question 13

DNA REPLICATION - ELONGATION

what is the MAIN POLYMERASE in this step?

Answer 13

DNA polymerase III

Question 14

DNA REPLICATION - ELONGATION

LIMITATION for function of ligases?

Answer 14

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

Question 15

DNA REPLICATION - TERMINATION

• when does it end?
• replication products?

Answer 15

• ends once all the nucleotide bases of the PARENT DNA STRANDS are complemented
• 2 identical daughter DNA

Question 16

TRANSCRIPTION

• 3 important GENE STRUCTURES

Answer 16

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

Question 17

TRANSCRIPTION - INITIATION

ENZYMES/PROTEINS (2) + steps

+ functions (1 ; 1)

Answer 17

1. Sigma Subunit
   - guides the RNA polymerase to promoter
2. RNA Polymerase
   - unwinds the promoter (Pribnow Box) by itself

Question 18

TRANSCRIPTION - ELONGATION

ENZYME/PROTEIN (1)

+ function (2)

Answer 18

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

Question 19

TRANSCRIPTION - TERMINATION

ENZYME/PROTEIN (1)

+ function (2)

Answer 19

Rho-protein

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

+ may also include RNA polymerase

Question 20

TRANSCRIPTION - TERMINATION

• 3 products

Answer 20

1. mRNA
2. tRNA
3. rRNA

Question 21

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

Answer 21

• ribosomes
• mRNA
• codons
• one
• 5’ to 3’
• continuous but non-overlapping manner

Question 22

GENETIC CODE CHART

• start codon (1)
• stop codons (3)

Answer 22

• AUG
• UAG, UAA, UGA

Question 23

TRANSLATION - INITIATION

ENZYMES/PROTEINS (4) + steps

Answer 23

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

Question 24

TRANSLATION - ELONGATION

ENZYMES/PROTEINS (3) + steps

Answer 24

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

Question 25

TRANSLATION - TERMINATION ENZYMES/PROTEINS (3) + steps

Answer 25

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

Question 26

TRANSLATION - TERMINATION product?

Answer 26

polypeptide chain (NOT protein)

Question 27

TRANSCRIPTION initiation site vs promoter

Answer 27

PROMOTER: where RNA Polymerase binds to IS: specific location on the DNA where RNA polymerase begins synthesizing RNA.

Question 28

DNA REPLICATION - INITATION ori-site vs origin of replication

Answer 28

ori-site (prokaryotes) origin of replication (eukaryotes)

Question 29

TRANSCRIPTION - INITIAITON - 2 promoter sites for eukaryotes & prokaryotes? * found upstream

Answer 29

PROKARYOTES 1. -35 element (TTGACA) - helps with RNA polymerase binding to PRIBNOW BOX + where sigma subunit binds to 2. -10 element (pribnow box: TATAAT) - main binding site EUKARYOTES 1. Goldberg-Hogness Box (TATA) 2. CAAT box

Question 30

3 TYPES OF RNA POLYMERASE

Answer 30

RNA POL 1 (eu + pro) : large rRNA RNA POL 2 (eu): mRNA RNA POL 3 (eu): tRNA + small rRNA * but prokaryotes only have 1 RNA polymerase

Question 31

WHAT is the set of 64 codons and the amino acids they stand for?

Answer 31

GENETIC CODE

Question 32

8 CHARACTERISTICS of CODONS

Answer 32

1. triplet genetic code 2. degenerate (one amino acid may be coded by one or more codons) 3. non-overlapping yung pagbasa (need successive) 4. universal 5. continuous, comma free 6. the genetic code has start and stop signals 7. wobble occurs in anticodon 8. unambiguous (it is RARE that one codon will code for multiple amino acids)