3/27/24

The Central Dogma

~Genes- the units of heredity- are composed of DNA Sequences required for Gene Expression ~

Genotype: Genes→ RNA→ Phenotype: Proteins

Pyrimidines: simple structure, single ring (Thymine, Cytosine, and Uracil)

Purines: complex structure, double rings (Adenine, and Guanine)

RNA Structure:

• Primary Structure

• Secondary Stricture: hairpin loop

• Tertiary Structure:

What Do All Those RNAs Do?

• mRNA-

• rRNA-

• tRNA

• miRNA-

• snRNA-

The Molecular Definition of A Gene- all the Dna sequences necessary to synthesize a functional RNA and/or a protein

Genetic Information is NEEDED to:

• Recognize a DNA region to be made into an RNA. ARecognice a region withing an mRNA to be translated into a protein

• Control the rate og flow of information from DNA→RNA→ Protein (regulatory sequences often termed noncoding, contain “regulatory code” )

• Determine the amino acid sequence that codes for a protein (protein code)

The Parts of a Gene:

• Prokaryotic genes: Information for multiple proteins is expressed in a single polycistronic mRNA

  • polycistrinic- an mRNA corresponding to multiple genes whose expression is also controlled by a single promoter and a single terminator

• Eukaryotic Genes: A monocistronic mRNA is transcribed from a genes. The code is broken into chunks called exons.

  • monocistronic- contains only one structural gene, coding for a single polypeptide chain

  • There is a coding strand running 5’ top 3’

  • Polymerase reads a 3’ to 5’ template strand to make a 5’ to 3’ RNA

  • Upstream= 5’ end of stream

  • Downstream= after the 3’ end of the stream

Rules of Transcription in Prokaryotes

• When and Where?: In an undivided compartment, simultaneous with translation

• Transcription is a selective process: Only certain parts of DNA are transcribed (downstream of the transcription start )

• Promoters: contain short sequences or motifs critical in the binding of RNA polymerase to the DNA strand

• Transcription starts at +1 (first nucleotide transcribed)

No nucleotide 0

• There is no nucleotide 0

• +1 is the first nucleotide transcribed

• +30 is the thirtieth nucleotide transcribed

• -35 is 35 bases before the +1 site

• Positions are approximate, there is some variation

• Transcription depends on the RNA synthesis by RNA polymerase

• RNA polymerase is a multisubunit complex that binds to a promoter and catalyzes the synthesis of RNA from a ssDNA template, no primer needed!

• RNA is transcribed form ssDNA

• RNA is antiparallel and complimentary to the ssDNA

• Transcription is in the 5’ to 3’ direction with respect to the growing molecule adding RNA nucleotide to the 3’ end

• First and last bases coded are par of the 5’ UTR and the last bases coded are part of the 3’ UTR

• One strand is transcribed per gene, the strand that is the template strand can be different

Which DNA coding strand below would be
associated with the mRNA 5’-CGUACGG-3’?
a) 5’-CGTACGG-3’
b) 5’-GCATGCC-3’
c) 5’-GGCATGC-3’
d) 5’-CCGTACG-3’

Stages of Transcription

Transcription starts with recognition

• The promoter is required for transcription to occur.

• The RNA Pol Subunits:

  • core enzyme- polymerase activity

  • Sigma Subunit- recognizes specific sets of gene

  • these combine to for the Holoenenzyme- in particular the holoenzyme is attracted to the consensus sequences ( the -35 and the -10)

Initiation is required before Synthesis

Initiation: unwind the DNA to create the transcription bubble; starts with tighter binding forming the closed promoter complex; TATA box is where the DNA will be opened up (the open promoter complex)

Recognition: involves recruitment and binding of the holoenzyme to the promoter and loose binding

Transcription initiation required a template strand (ooen DNA) to make a single stranded RNA

Elongation: Transcription by bacterial RNA polymerase- after the

• DNA is unwound ahead of the RNA polymerase by the core enzyme. This maintains the transcription bubble

• Termination sequence that come at the end if the 3’ UTR destabilizes the Polymerase

Intrinsic Termination- sequence only

• an inverted repeat is a DNA sequence that has two copies each in an opposite direction; inverted repeats cause a 3D structure to form by creating antiparallel and complimentary strands that can hydrogen bond together to form double stranded stem structure, spacer forms a loop - hairpin

• Done through the termination sequences

• Termination is caused when the hairpin breaks off the rest of the RNA through weak U-T bonds that are weak and allow it to break off.

Rho-Dependent Termination- involves a different termination sequence and a specialized protein that binds to the RNA

Important- Transcription is not a one time event, it will proceed in multiple cycles making more than one copy of the MRNA of a gene. regulation determine how much, when, and where

Imagine you want to prevent transcription of a single bacterial gene by creating a new
mutation in the gene. Which part of the gene would you target for a mutation?
a) Terminator
b) Start codon
c) Promoter
d) Sigma Subunit