LECTURE 5a PART 1: Chapter 6 - How Cells Read the Genome: From

DNA to Protein (the Central Dogma)

TRANSCRIPTION

- Overview of the steps that are involved in protein synthesis

- Central Dogma of Biology
- Genes are expressed with different efficiencies
- Less transcription = less translation
- More transcription = more translation

- Transcription of DNA yields a single stranded RNA that is complementary

to one strand of DNA
Transcription General Features
- Transfer of genetic information from DNA to RNA
- Synthesis of RNA is similar to DNA synthesis except:
- ribonucleoside triphosphates are monomers
- Only one strand of DNA is template for RNA
- No primer required, de novo synthesis
- RNA is unstable, short-lived compared to DNA
- Is the relative instability of RNA a good thing???
- Occurs in nucleus
- DNA → RNA → Protein

Transcription General Features Continued

- RNA produced is
- Single-stranded
- complementary to DNA template strand
- Can be:
- Messenger RNA (mRNA)
- Transfer RNA (tRNA)
- Small nuclear RNA (snRNA)
- Ribosomal RNA (rRNA)
- Micro RNA (miRNA)
- Identical to DNA nontemplate strand
- Thymidines replaced with uracil
 - RNA synthesis uses only one DNA strand of a gene as template

Transcription General Features

- RNA polymerases catalyzes the synthesis of an RNA complement to DNA
- Occurs in the 5’ to 3’ direction
- Nucleophilic attack by 3’OH on the nucleotidyl phosphorus atom with
the elimination of pyrophosphate
- Unwinds and rewinds DNA
- No primer required to initiate polymerization
- Transcription is carried out by RNA polymerase in a 5’ to 3’ direction

- RNA synthesis occurs within a locally unwound segment of DNA.

- RNA synthesis occurs within a locally unwound segment of DNA. This
transcription bubble allows a few nucleotides in the template strand to
base-pair with the growing end of the RNA chain. The unwinding and
rewinding of the DNA molecule are catalyzed by RNA polymerase.

- The RNA chain elongation reaction catalyzed by RNA polymerase.

Important General Features of Transcription and Definitions
- Transcriptional Unit
- segment of DNA transcribed to produce one RNA molecule
- One or several genes
- Gene
- Unit of genetic information that controls the synthesis of one protein
or structural RNA molecule
- Downstream or Upstream
- Refer to 3’ and 5’ regions, respectively, of a gene
- Sense or Antisense RNA strands
- “sense” strands encode nucleotides that specify amino acids of gene
products
- “anti-sense” strands are complementary to “sense” strands

Eukaryotic Transcription Overview

- More complex than prokaryotic:
- 1) mRNA synthesized in nucleus
- 2) Proteins synthesized in cytoplasm
- 3) Prokaryotic often multigenic mRNAs
- 4) Eukaryotic usually monogenic mRNAs
- 5) Three RNA polymerases
- 6) Three modifications of mRNA
- 7-Methyl guanosine cap on 5’ end
- Poly-A tail on 3’ end
- Splicing out introns
Protein synthesis involves two steps: transcription and translation, in both
prokaryotes (a) and eukaryotes (b). In addition, in eukaryotes, the primary
transcripts or pre-mRNAs often must be processed by the excision of introns and
the addition of 5’7-methyl guanosine caps (MG) and 3’poly(a) tails [(A)​n​].
In eukaryotes, most gene transcripts undergo three different types of posttranscriptional
processing:

Three different types of peri- and post-transcriptional processing:

1) 5’ end 7 methyl-guanosine cap

2) 3’ end polyadenylation

3) Introns: non-coding, “intervening” sequences

An overview of protein synthesis, emphasizing the transcriptional origin of
snRNA, tRNA, rRNA, and mRNA, the splicing function of snRNA, and the
translational roles of tRNA, rRNA, mRNA and ribosomes.

- An overview of protein synthesis, emphasizing the transcriptional origin of

snRNA, tRNA, rRNA, and mRNA, the splicing function of snRNA, and the
translational roles of tRNA, rRNA, mRNA and ribosomes.
- Eukaryotic Transcription
- primary transcripts in nucleus – heterogeneous nuclear RNA
(hnRNA)
- transported to cytoplasm
 - Transcripts coated with RNA binding protein for protection from
RNases
- Eukaryotic RNA t1/2 ~5hrs vs 5min prokaryotic

Eukaryotic RNA Polymerases

- Protein cofactors required for initiation- Transcription factors

- Roles/jobs/functions of the polymerases

Bacterial RNA polymerase and the RNA polymerase II of eukaryotes

are structurally similar…
- but, there are differences between eukaryotic & prokaryotic transcription
 -
- Bacteria RNA pol requires a single additional protein for transcription
initiation( factor), whereas eukaryotic RNA pol requires many
additional proteins (called general transcription factors).
- Eukaryotic transcription initiation must deal with packing of DNA into
nucleosomes & higher order forms of chromatin structure; these
features are absent in bacterial chromosomes

Transcriptional Initiation
- Initiation of transcription requires??
- Help from proteins called Transcription factors
- Binding of Polymerase complex to specific site
- Unwinding of DNA
- Characteristics of sequences??

Initiation at Promoters

-
- Structure of a promoter recognized by RNA polymerase II: TATA box

General Transcription Factors

-
- Required for Initiation of transcription by RNA Pol II
- Proteins--- denoted “TFII-X” (TFII = TF for Pol II)
- Bind promoter in a specific order
- Phosphorylation of Pol II “tail” required for escape from preinitiation
complex (begins elongation)

-
- TATA box: part of eukaryotic promoter sequences
 - Other transcription factors and roles

Consensus sequences found near eukaryotic RNA pol II start sites

The direction of transcription is determined by the promoter at the beginning of

each gene & transcription can occur off of either strand of DNA

-
- Green ones are promoters

DNA bending by TF may serve as a “recruitment site” for other proteins that take
part in transcription
 -

Transcription initiation by RNA pol II in eukaryotic cell

 -

Elongation by RNA Polymerase II

- Same process as prokaryotes
- Extension of RNA chain occurs within transcription bubble
- RNA polymerase unwinds and rewinds DNA
- No primer required
- Short RNA/DNA heteroduplex