RNA and Transcription

DNA vs RNA

• double vs single stranded

• Deoxyribose vs ribose sugar backbone

• Thymine vs Uracil nucleotide

• H vs OH

DNA

deoxyribonucleic 

Deoxyribose sugar backbone

Double helix

Thymine base(nucleotides)

RNA

Ribonucleic Acid

Ribose sugar backbone

single stranded

Uracil base(ribonucleotides)

3 steps of transcription

Initiation, elongation, termination

Transcription Initiation

RNA polymerase recognizes the promoter and starts transciption

What’s required for transcription

DNA template, transcription factors, RNA polymerase, free nucleotides

DNA template

Anti-sense, non-coding strand

Strand of DNA that mRNA is transcribed from

3 to 5 strand

MRNA FORMS 5 TO 3 ALWAYS

DNA non-template

Sense, coding strand

strand of DNA that has the same code as mRNA EXCEPT FOR Ts ARE Us

5 to 3 strand

mRNA forms ___

5 to 3

Promoter

1. Promoter, -10 and -35 region, where RNA polymerase binds

2. TSS, +1 region, transcription start site

3. Transcription Unit, stretch of dna that is transcribed

promoter -10 region is made up of mostly __

ATATAT, easy to break

prokaryotic transcription factors

• sigma factors: DIRECT PROKARYOTIC RNA POLYMERASE WHERE TO START

  • Different sigma factors can recognize different promoters 

• Various proteins influence sigma to prevent or facilitate binding

what regulate the rate transcription of specific gens

• activator: increase gene expression, recruit and stabilize RNA polymerase

• Repressor: decrease gene expression block RNA polymerase from binding to DNA

which way does the RNA polymerase move

towards 3 end of coding or mRNA strand

RNA polymerase

• Enzyme that performs transcription

• has its own helicase activity

• Reads template strand 3’ to 5’

Transcription Elongation

the RNA strand grows

Transcription Termination

RNA polymerase strops synthesis and newly made RNA is separated from the DNA template

Termination of transcription ways

Intrinsic(Rho-independent), extrinsic(Rho-dependent)

intrinsic termination

RNA forms secondary structure(stem-loop) that destabilizes the RNA polymerase’s hold on RNA

extrinsic termination

protein(rho) binds to terminator signal on RNA and stops RNA polymerase

prokaryotic transcription

Paired with translation

Eukaryote vs prokaryote transcription

• genes are usually switched off by default vs on by default

• Large amounts of post-transcriptional processing vs none

• Done in nucleus vs cytoplasm

• Not coupled with translation

Sigma factor

Directs prokaryotic RNA polymerase where to start

Protein

DNA polymerase vs RNA polymerase

• DNA requires a primer and is highly accurate

• DNA uses T deoxyribnucleotides

• DNA requires helicase enzyme

3 types of RNA

mRNA - messenger RNA, copied from genes that direct synthesis of proteins

rRNA - ribosome RNA, form basic structure of ribosome 

tRNA - transfer RNA, adaptors between mRNA and amino acids

direct transcriptional repression

• transcriptional repressor binds to operator region

• Results from steric hindrance

• Can be activated following as stimulus 

Steric Hindrance

Steric hindrance is the physical blockade of another molecule

• blocking RNA polymerase

Indirect transcriptional repression

• Repressor protein binds to activator protein(sigma factor)

• results from inactivation of sigma factors

2 types of repression

Direct and indirect

Alleviation of repression, transcription activation

• reverse of direct repression

• Result of protein mediated or metabolite mediated removal of a repressor

Recruitment of transcriptional machinery, transcriptional activation

• certain factors search for sigma factors/RNA polymerase

2 types of transcriptional activation

alleviation of repression

Recruitment of transcriptional machinery

Operator

• binding site for repressor and activators

• Between promoter and structural gene