RNA Transcription & Remdesivir

repurposing

screened drugs already approved by FDA for other indications

EC50

effective concentration needde to give 50% response (lower is desired)

Remdesivir

repurposed Ebola drug to treat COVID-19

RdRp

RNA-dependent RNA polymerase

messenger RNA (mRNA)

carries info copied from DNA in the form of codons, code for proteins (amino acids)

transfer RNA (tRNA)

deciphers code by delivering specific amino acid to its associated codons

ribosomal RNA (rRNA)

associates with set of proteins to form ribosomes, acts as enzyme

gene

entire nucleic acid sequence on a chromosome

exons

1% of a gene, coding DNA within genes that is expressed

introns

24% of a gene, DNA that lies in between expressed segments in a gene, doesn’t code for a protein

extragenic

75% of a gene, DNA that lies between genes

promoter

where RNA polymerase binds upstreamin 5’ direction of the coding strand (opposite direction of transcription)

phylogeny

evolutionary history of an organism/group of organism

dendrogram

phylogenetic tree

mutation

change in nucleotide sequence

initiator protein binds to origin of replication

1st step of DNA replication

helicase separates/melts double-stranded DNA into single-stranded DNA

2nd step of DNA replication

single-straned binding proteins (SSBs) bind and prevent single-stranded DNA from re-annealing

3rd step of DNA replication

topoisomerases relieve DNA supercoiling

4th step of DNA replication

DNA polymerases add nucleotides against DNA template to 3’ end of growing strand (5’→ 3’ growth)

5th step of DNA replication

template strand

read by DNA polymerase 3’→5’

deoxyribonucleoside triphosphates (dNTPs)

source for nucleotide and energy source

primer, primase

short stretch of RNA added by DNA-dependent RNA polymerase called ___

RNA polymerase

can initiate new strand based on a template strand

DNA polymerase III

main polymerase in bacteria, 5’→3’ polymerase, synthesizes reverse complement of parent strand

3’→5’ exonuclease

proofreads, excises incorrect nucleotides as it polymerizes

exonuclease

cleaves polynucleotide ends

endonuclease

cleaves polynucleotides in the middle

upstream

in the 5’ direction on the coding strand

initiation

nucleoside triphosphates (NTPs) added one by one until 9 nucleotides have been added, then RNApol can move

elongation

undwinding of DNA, adding NTPs, DNA rewinds behind, RNA elongates from 5’→3’ end and RNApol moves along template from 3’→5’

terminator

secondary structure of the transcript, not primary sequence of the DNA

termination

forming a hairpin that is self-complementary, signal for ___

RNApol I

synthesizes pre-rRNA

RNApol II

synthesizes pre-mRNA

RNApol III

synthesizes pre-tRNA

core promoter (for RNApol II)

TATA box and initiator

transcription factor

binds to TATA box before RNApol II

basal transcription factor

always required to allow RNApol to bind to DNA

TFIID

basal transcription factor for RNApolII

pre-initiation complex

formed by TFs binding to TFIID through protein-protein interactions

5’ methylated cap

added during elongation, flag for nuclear export, protects against degradation, binding site for ribosome

capping enzyme

catalyzes 5’ cap, only associates with RNApol II

polyadenylation

transcripts are oto long so poly(A) polymerase (PAP) finds poly(A) signal (AAUAAA) that marks end of important stuff, cleaves transcript, and adds poly(A) tail

poly(A) tail

helps protect transcript from degradation, necessary for full initiation of translation

splicing

removes introns after transcription

alternative splicing

more than one exon in given domain means that different introns can be spliced out to make different versions of proteins

splice variants

different versions of proteins produced by alternative splicing

splice sites

specify beginning and end of introns

spliceosome

composed of various proteins and RNAs (snRNPs), catalyzes splicing

nucleotide analog

similar but not identical to ATP, results in RNA synthesis termination when incorporated

prodrug

has phosphate protecting groups that allow if to cross plasma membrane

primase

DNA-dependent RNA polymerase that adds primer

initiate a new strand based on a template strand

RNA polymerases are different from DNA polymerases as they can ___

processivity clamp

protein complex that holds DNA polymerase onto template strand during replication

leading strand

grows towards replication fork

lagging strand

grows in Okazaki fragments away from replication fork

DNA polymerase I (alpha in euks)

5’→3’ polymerase, 3’→5’ and 5’→3’ exonuclease that removes damaged bases/primers, slower than DNA pol III

1. initiator protein binds to/separates strands at replication origin

2. helicase separates strands at replication fork

3. gyrase relieves supercoiling

4. primase creates RNA primer

5. DNA polymerase III extends strand

6. DNA polymerase I replaces RNA primer with DNA

7. ligase repairs missing phosphodiester bonds between fragments

DNA replication steps

telomeres

ends of linear chromosomes

cell senescence

telomere erosion leads to this, when each round of DNA replication ends in losing telomeres/sequences, state of irreversible growht arrest in which a cell permanently stops dividing but remains metabolically active without undergoing cell death

telomerase

RNA-dependent DNA polymerase with a built-in RNA template

repair endonuclease

recognizes errors and removes damaged regions with helicase

homologous recombination

uses sister chromosome as template to anneal strands, slow and thorough

nonhomologous end joining

ligase joins ends quickly and messily through ligation