LECTURE 5: In-depth Central Dogma Process Flashcards
4 CHARACTERISTICS of DNA REPLICATION
- Semiconservative (uses old DNA strand as template for synthesis of new strand)
- Semi-discontinuous (involves both continuous (leading strand) and discontinuous (lagging strand) synthesis)
- Unidirectional synthesis (5’ to 3’ synthesis w/ respect to NEW STRAND)
- Bidirectional progress (lagging and leading strand is simultaneously synthesized)
DIRECTION OF SYNTHESIS OF THE FF:
- DNA replication
- Transcription
- Translation
- 5’ to 3’ w/ respect to new strand
- 5’ to 3’ w/ respect to the RNA
- 5’ to 3’ w/ respect to mRNA template
DNA REPLICATION - INITIATION
ENZYMES/PROTEINS (5) + steps
+ location of binding (first 3 proteins)
+ function (1 ; 2 ; 3 ; 1 ; 1)
- INITIATOR PROTEINS
- binds near oriC (specifically at the A=T “bonding site”)
- melts the double bond to partially open up the oriC - Helicase
- binds to ONE STRAND of DNA
- further unwinds and opens the dsDNA - 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 - Topoisomerase/Gyrase
- relieve the torsional strain caused by helicase - Primase
- makes RNA primers to help the DNA Polymerase III to start synthesizing
DNA REPLICATION - INITIATION
why do initiator proteins bind at A=T instead of G≡C?
double bonds are weaker and easier to break
DNA REPLICATION - INITIATION
what type of strain do HELICASES cause to DNA due to unwinding and opening up?
torsional strain
DNA REPLICATION - INITIATION
HELICASE consumes ____ to unwind the parent DNA
ATP
DNA REPLICATION - INITIATION
what will happen if TOPOISOMERASE or GYRASE does not do its job?
the DNA will break
DNA REPLICATION - INITIATION
what are IN primers that make it possible for DNA Polymerase III to add bases?
short RNA base sequences that contain 3’ OH
remember that DNA Polymerase III can only add bases to an existing 3’ OH
TROMBONE MODEL
- what specific process does it show?
- a _____mechanism that shows the ______ progress of DNA Replication
- newest model that shows dna replication
- physically orients the lagging strand towards the replication fork during synthesis
- looping
- bidirectional
DNA REPLICATION - ELONGATION
ENZYME/PROTEINS (3) + steps
+ function (1 ; 3 ; 1)
- DNA Polymerase III
- adds complementary bases for both lagging and leading strands - DNA Polymerase I
- proofreading and repair
- removal of primers and replaces with DNA
- removal of mismatched bases and replaces with DNA - Ligase
- seals the breaks produced during lagging strand synthesis - Telomerase (additional)
- extends parent DNA ends para madikitan yung mga old primers ng nitrogenous bases (since nga 3’ OH is needed for synthesis
How many DNA polymerases does E. coli have?
At least 3
What types of enzyme is DNA Polymerase III?
holoenzyme
DNA REPLICATION - ELONGATION
what is the MAIN POLYMERASE in this step?
DNA polymerase III
DNA REPLICATION - ELONGATION
LIMITATION for function of ligases?
only seals breaks between nitrogenous bases in lagging strand if its 1 PHOSPHATE AWAY
DNA REPLICATION - TERMINATION
- when does it end?
- replication products?
- ends once all the nucleotide bases of the PARENT DNA STRANDS are complemented
- 2 identical daughter DNA
TRANSCRIPTION
- 3 important GENE STRUCTURES
- Promoter
- binding site of RNA polymerase - Coding Region
- gene region transcribed by RNA polymerase - Terminator
- signals the RNA polymerase to stop transcribing
TRANSCRIPTION - INITIATION
ENZYMES/PROTEINS (2) + steps
+ functions (1 ; 1)
- Sigma Subunit
- guides the RNA polymerase to promoter - RNA Polymerase
- unwinds the promoter (Pribnow Box) by itself
TRANSCRIPTION - ELONGATION
ENZYME/PROTEIN (1)
+ function (2)
RNA Polymerase
- unwinds DNA and
continues elongation until “termination signal”
- proofreads
TRANSCRIPTION - TERMINATION
ENZYME/PROTEIN (1)
+ function (2)
Rho-protein
- binds to and pulls RNA DURING ELONGATION
- pulls away RNA and terminate transcription
+ may also include RNA polymerase
TRANSCRIPTION - TERMINATION
- 3 products
- mRNA
- tRNA
- rRNA
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
- ribosomes
- mRNA
- codons
- one
- 5’ to 3’
- continuous but non-overlapping manner
GENETIC CODE CHART
- start codon (1)
- stop codons (3)
- AUG
- UAG, UAA, UGA
TRANSLATION - INITIATION
ENZYMES/PROTEINS (4) + steps
- Aminoacyl-tRNA synthetase
- loads correct amino acids onto tRNAs - Initiation Factor 1
- dissociates 50S and 30S ribosomal subunit - Initiation Factor 3
- attaches to 30S subunit to prevent re-association - 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
TRANSLATION - ELONGATION
ENZYMES/PROTEINS (3) + steps
- Elongation Factor Tu
- escorts the correct amino acyl-tRNA to A site - Peptidyl transferase
- catalyzes formation of peptide bond between amino acids - Elongation Factor G
- moves ribosome along the mRNA to elongate the peptide chain until A-site encounters stop codon
TRANSLATION - TERMINATION
ENZYMES/PROTEINS (3) + steps
- Release Factor 1
- recognizes UAG, UAA
- breaks bond between polypeptide chain and tRNA to release the chain from ribosome - Release Factor 2
- recognizes UGA, UAA
- breaks bond between polypeptide chain and tRNA to release the chain from ribosome - Release Factor 3
- assists release factors 1 and 2
TRANSLATION - TERMINATION
product?
polypeptide chain (NOT protein)
TRANSCRIPTION
initiation site vs promoter
PROMOTER: where RNA Polymerase binds to
IS: specific location on the DNA where RNA polymerase begins synthesizing RNA.
DNA REPLICATION - INITATION
ori-site vs origin of replication
ori-site (prokaryotes)
origin of replication (eukaryotes)
TRANSCRIPTION - INITIAITON
- 2 promoter sites for eukaryotes & prokaryotes?
- found upstream
PROKARYOTES
- -35 element (TTGACA) - helps with RNA polymerase binding to PRIBNOW BOX + where sigma subunit binds to
- -10 element (pribnow box: TATAAT) - main binding site
EUKARYOTES
1. Goldberg-Hogness Box (TATA)
2. CAAT box
3 TYPES OF RNA POLYMERASE
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
WHAT is the set of 64 codons and the amino acids they stand for?
GENETIC CODE
8 CHARACTERISTICS of CODONS
- triplet genetic code
- degenerate (one amino acid may be coded by one or more codons)
- non-overlapping yung pagbasa (need successive)
- universal
- continuous, comma free
- the genetic code has start and stop signals
- wobble occurs in anticodon
- unambiguous (it is RARE that one codon will code for multiple amino acids)
