MCB exam 3

DNA->RNA-> protein

central dogma

RNA->RNA->protein

central dogma in RNA base viruses

-single stranded
-uracil
- secondary (stem loops)
-tertiary (RNA folds on itself)

RNA structure

ribozyme

RNA enzyme catalyzing a chemical reaction

ribonuclease P (RNase P)

ribonucleoprotein endonuclease processing 5' end of pre-tRNA

hammerhead ribozyme

cleave RNA at NUH (N= any nucleotide, U= uracil, H = any nucleotide but guanidine) triplets 3' to the H

spliceosome

splice introns to join exons

ribosomes

peptide bond formation

1. RNA forms from inorganic sources
2. RNA self-replicates via ribozymes
3. RNA catalyzes protein synthesis
4. Membrane formation → New functionality
5. RNA codes for both DNA and protein
6. DNA becomes master template, Proteins catalyze cellular activities

RNA world hypothesis

mRNA

- translation (protein synthesis) - regulatory

rRNA

- translation (protein synthesis) - catalytic

tRNA

-translation (protein synthesis)

hnRNA (heterogeneous nuclear)

precursors and intermediates of mature mRNAs and other RNAs

scRNA (small cytoplasmic)

-signal recognition particle (SRP)
- catalytic
- tRNA processing

snRNA(small nuclear) snoRNA (small nucleolar)

-mRNA processing
- polyA addition
-catalytic
- rRNA processing/maturation/methylation

regulatory RNAs (siRNA, miRNA, etc.)

regulation of transcription and translation

80%

relative amount of rRNA

15%

relative amount of tRNA

5%

relative amount of mRNA

RNA polymerase

involved in elongation stage of transcription process (turning DNA into messenger RNA)

promotors

specific DNA sequences that direct RNA polymerase to initiation sites

consensus sequence

average sequence of the gene sequences given

termination

RNA polymerase stops the elongation process

UAA, UAG, UGA

what are the stop codons

rho-independent

hair pin with G:C base pairs and unpaired uracil residues

rho-dependent

ATP-dependent protein climbing up mRNA and yanking it out of polymerase

exons

coding regions

introns

noncoding regions

introns

there are no (introns/exons) in prokaryotes

-5' cap
-3' poly A tail

pre-mRNA -> mature mRNA

translation: cytosol
transcription: nucleus

where does transcription and translation occur in eukaryotes

simultaneously in the cytosol

where does transcription and translation occur in prokaryotes

top right- amino acid attachment site
top left- phorphoylated 5c terminus
bottom anticodon

label the tRNA structure

large subunit = 23S rRNA
small subunit = 16S rRNA

rRNA structure

A = incoming tRNA
P= bind tRNA with growing peptide chain
E = tRNA exits

what is the function of the A, P, and E site

AUG

start codon

silent, nonsense, missense

point mutations

silent mutation

same amino acid

nonsense mutation

results in stop codon

missense mutation

-conservative = different amino acid, same charge/ property
- nonconservative = different amino acid, different charge/property

insertion, deletion

frameshift mutation (both alter open reading frame)

- catalyzes the nucleophilic attack of the 3' hydroxyl group of the last nucleotide in the chain on the alpha (first) phosphoryl group of the incoming nucleoside triphosphate (causes pyro phosphate to be relased which drives the energy to form a new phosphodiester bond) - composed of multiple subunits (active site has metal ion in center)

RNA polymerase (an enzyme)

sigma subunit, core enzsyme, holoenzyme

how many subunits does prokaryotic RNA polymerase have?

-same thing as core enzyme but does contain sigma
- required for initiation but not for elongation

holoenzyme

-catalytic moiety
- contains alpha, beta, beta 1, and omega
- does not contain sigma
- required for elongation

core enzyme

- associates and dissociates as it pleases
- binds to the promotor and initiates transcription
- allows RNA polymerase to be directed to the promotor
- helps find the site where transcription begins
- participates in initiation of RNA synthesis
- dissociates from the rest of the enzyme after 9-10 BPs

sigma subunit

- can start without a primer (de novo)
- RNA polymerase searches and binds to the promotor sequences
- unwinds the DNA helix (short stretch)

RNA synthesis: initiation

-selects the ribonucleoside triphosphate that matches and catalyzes the formation of the phosphodiester linkage

RNA synthesis: elongation

keep going until termination signals are reached and that halts transcription

RNA synthesis: termination

bacterial promotor

core promotor upstream of the start sequence (same in prokaryotes and eukaryotes)

TTGACA

-35 core promotor

-10 core promotor

TATAAT

sigma factor

- part of the holoenzyme that binds to both core promotor units by decreasing the affinity RNA polymerase for general regions of DNA which allows for better recognition of the promotor site

will be further away from the consensus sequence

weak promotor

the closer the promotor is to the consensus sequence the stronger it is, almost identical to the consensus sequence

strong promotor

recA

example of a strong promotor

araBAD

example of a weak promotor

- going form a closed DNA complex to an open one (open complex is RNA polymerase with unwound helix inside of about 17 BPs)
- houses DNA-RNA hybrid

transcription bubble

- first nucleotide is added while being catalyzed at the +1 site
- 5' end of the primary transcript is tagged with 3 phosphates and a purine
- nucleophilic attack removes phosphate and creates a phosphodiester bond

nucleotide addition

- clearing the active site
- enzyme shifts the DNA over so new nucleotide can come in

translocation

- translocation in a backward direction
- hydrolyzes the nucleotide and brings a new one in

backtracking

- it doesnt need to be as fast
- it doesnt need to worry about mistakes as much (can just try again and dont become inherited traits)

why is RNA synthesis slower and more error prone?

-uses rho and ATPase
-binds to rut (where rho can bind) and sends termination signal
- climbs up mRNA
- unwinds DNA-RNA hybrid using helicase activity
- competitive inhibitor of ribosomes so when it binds it kicks off ribosomes (uses ATP)

rho-dependent

-hairpin/stem loop
-no use of rho
-hairpin yanks the RNA polymerase off RNA and it becomes detached
G-C followed by a lot of U

rho-independent

actinomycin

-intercalates into DNA
-binds in between DNA bases
- blocks DNA from being a template for RNA synthesis
-prokaryotic and eukaryotic

rifampicin

- prokaryotic only
- binds in the site where DNA-RNA hybrid is made and prevents translocation of DNA
- blocks newly formed RNA