Gene
A segment of DNA that is used to make a functional product, either RNA or a polypeptide
Transcription
The act or process of making a copy, or the process of synthesizing RNA from a DNA template
Protein encoding genes, or structural genes
Carry the info for the amino acid sequence of a polypeptide
Flow of genetic material
DNA—>mRNA—>to polypeptide
Gene expression
He overall process by which the information within a gene is used to produce a functional product, such as a polypeptide
Promoter vs. Terminator
Promoter provides a site for RNA polymerase binding at the beginning of transcription, and the terminator specifies the end of transcription
Template strands
The base sequence in the RNA transcript is complementary to the template strand of DNA
The opposite strand of DNA is the nontemplate strand
Coding strand
the DNA strand whose base sequence corresponds to the base sequence of the RNA transcript produced. It is this strand which contains codons
Template strand AKA
The non-coding strand or antisense strand
Ribosome binding site
mRNA site for ribosome binding, translation begins near this site
In Eukaryotes, the ribosome scans the mRNA for a start codon
Start codon
The first amino acid on a polypeptide sequence, usually
Bacteria: formylmethionine
Eukaryote: methionine
Codons
a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule
The sequence of codons within mRNA determines the sequence of amino acids within a polypeptide
Stop codon
The end of polypeptide synthesis
Transcription factors
Controls the rate of transcription
Some bind directly to the promoter and facilitate transcription
Others transcribe regulatory sequences or elements, regulating or inhibiting transcription
Transcription stages
Initiation: The specific binding of transcription factors to the promoter identifies the starting site for transcription
Elongation: RNA polymerase slides along the DNA in an open complex to synthesize RNA
Termination: causes RNA polymerase and the RNA
Transcriptional start site
The first base used as a template for transcription and is denoted +1
Bases before this site are numbered in a negative direction
Consensus sequence
The most commonly occurring bases within a specific type of sequence
Efficiently recognized by proteins that initiate transcription
E. coli, core enzyme subunits
α, α, β´, β, and ω
With a sixth subunit called the sigma factor, which creates RNA polymerase holoenzyme and recognizes the promoter
The two α units are important in the proper assembly of the holoenzyme and in the process of binding to DNA
The β´and β subunits are needed for binding to the DNA and catalyzes RNA
ω important for proper core enzyme assembly
Holoenzyme
Required to initiate transcription
Released sigma factor
Marks the transition to the elongation phase of transcription, which allows the core enzyme to slide down the DNA to synthesize a strand of RNA
ρ-dependent termination
This termination process first requires the rho utilization site to encode a sequence in the RNA that acts as a recognition site for the binding of ρ protein
Next, ρ protein binds to the RNA and moves in the direction of RNA polymerase
Secondly, at the termination site, the DNA encodes an RNA sequence containing several GC base pairs that form a stem loop structure, RNA synthesis terminates several nucleotides
RNA synthesis is paused by hairpin that binds to rna polymerase, p protein then catches up and breaks hydrogen bonds between DNA & RNA within open complex, finally the RNA is separated from DNA
ρ protein function
Acts as a helicase, an enzyme that can separate RNA-DNA hybrid regions
p independent termination or intrinsic termination
Does not require p protein, instead involves adjacent nucleotide sequences. One of the sequences forms a stem loop, another is a uracil rich sequence located at 3’ end of RNA that pauses RNA synthesis
The uracil rich sequence to the DNA template strand Is weak, causing the RNA transcript to spontaneously dissociate from DNA stopping transcription
RNA Polymerase 1 function
Transcribes all of the genes for ribosomal RNA except for 5S rRNA
RNA Polymerase 2 function
Transcribes all protein encoding genes, meaning it’s responsible for all mRNA synthesis
Also transcribes most snRNAs for RNA splicing
Lastly, it transcribes several non-coding RNAs like most microRNAs and snoRNAs
RNA Polymerase 3
Transcribes all tRNA genes and the 5S rRNA gene lesser than RNA pol 2
Also transcribes few non-coding RNAs, such as snRNAs, long non-coding RNAs, microRNAs, and snoRNAs
Core Promoter
Short DNA sequence that is necessary for transcription to take place
Consists of a TATAAA sequence called the TATA box and the transcriptional start site, where transcription begins
Produces a low level of transcription by itself
TATA box
About 25 bp upstream from a transcriptional start site,
Regulatory elements
Short DNA sequences that affect the ability of RNA pol to recognize the core promoter and begin the process of transcription
They are recognized by transcription factors
Two categories: Enhancers and Silencers
Usually located: at -50 to -100 region
Enhancers
Activating sequences that are needed to stimulate transcription
Silencers
DNA sequences that are recognized by transcription factor that inhibit transcription
Cis-acting elements
Regulate particular genes
Located far from core promoter, and are always found within the same chromosome as the gene they regulate
TATA BOX
Enhancers
Silencers
Trans-acting factors
Protein factors that bind to die acting sequences to control gene expression
Proteins needed for basal transcription at the core promoter
RNA Polymerase 2
General transcription factors
Mediator
General transcription factors (GTFs)
Five different proteins that are needed for RNA polymerase 2 to imitate transcription of protein-encoring genes
Assembly of GTFs and RNA polymerase 2 at TATA box
Transcription factor IID first binds to the TATA box and thereby plays a critical role in recognizing the core promoter
TATA binding protein directly bonds to TATA box and TBP associated factors
Next it associates with TFIIB, promoting the binding of RNA pol 2 and TFIIF
Lastly, TFIIE and TFIIH bind to the complex
Completing the assembly of proteins to form a closed complex
Nasal transcription apparatus
TFIID TFIIB TFIIF TFIIE TFIH RNA Pol 2 TATA Box Transcriptional start site
DNA is then transcribed to RNA
Mediator
Mediates the interactions between RNA Pol 2 and regulatory transcription factors that bind to enhancers or silencers
Interface between RNA pol 2 and many diverse regulatory signals
Elliptically shapes and wraps around RNA pol 2
Phosphorylates CTD of RNA pol 2
Allosteric model
RNA Pol 2 becomes destabilized after it has transcribed the polyA signal sequence, and it eventually dissociates from the DNA
Torpedo model
RNA Pol 2 is physically removed from the DNA
RNA is cleaved by an exonuclease that degrades the transcript in the 5’ to 3’ direction
Lastly when the exonuclease catches up to the RNA Pol 2, this causes it to dissociate from the DNA
colinearity
Correspondence between the sequence of codons in the DNA coding strand and the amino acid sequence of the polypeptide
Exons
Where coding genes are found, which are regions that are contained within functional mRNA
Intervening sequences or introns
Found between exons
RNA splicing
To produce a functional mRNA, the sequences in the pre-mRNA that correspond to the introns are removed and the exons are connected or spliced together
Common genetic phenomenon in eukaryotes, occasionally in bacteria
Exonuclease
Cleaves a bond between two nucleotides at the end of a strand
Starting at one end, an exonuclease digests a strand, one nucleotide at a time
Endonuclease
Cleaves the bond between two adjacent nucleotides within a strand
Ribozyme
RNaseP for example, is a RNA molecule with catalytic activity
Self splicing
Group 1 and Group 2 splices without requiring the aid of other catalysts
Instead RNA functions as its own ribozyme
Group 1 introns
First, binding of a single guanosine to a guanosine binding site within the intron
Guanosine breaks the bond between the first Exon and the intron and attaches to 5’end of the intron
3’—-OH group of exon 1 then breaks the bond next to a diff nucleotide
Exon 1 forms a covalent bond with 5’ end of Exon 2, degrading the intron RNA
Group 2 introns
2’—OH group on ribose in an adenine (A) nucleotide already within the intron strand behind the catalytic process
Maturases
Enhances the rate of splicing of group 1 and 2 introns
Pre-mRNA
Produced by the transcription of protein encoding genes, which is made in the nucleus
Altered by splicing, required the aid of a spliceosome
Spliceosome, needed to recognize the boundaries of the intron and to properly remove it
Spliceosome
Large complex that splices pre-mRNA
Composed of (U1, U2, U4, U5, U6): known as snRNPs
Each snRNPs contains small nuclear RNA and a set of proteins
Functions: recognizes the intron-exon boundary, catalysts the chemical reactions that removes introns and covalently linked exons
Alternative splicing
Produces 2 or more polypeptides from the same gene that have differences in their amino acid sequences
Allows an organism to carry fewer genes in its genome
Constitutive exons
Encode polypeptide segments of the alpha-tropomyosin protein that are necessary for its general structure and function
Alternative exons
The polypeptide sequences encoded by these exons May subtly change the function of alpha-tropomyosin to meet the needs of the cell type in which it is found
Varies
Regulated by splicing factors
Splicing factors
Key role in the choice of particular splice sites and modulate the ability of a spliceosome to choose 5’ and 3’ sites
Some inhibit (exon skipping) or enhance ^^
SR Proteins: A splicing factor
Cap protein
Required for the proper exit of most mRNAs from the nucleus
Recognized by Initiation factors
Important in the efficiency of first intron splicing (5’ end)
polyA tail
Important for mRNA stability, the exit of mRNA from the nucleus, and synthesizes polypeptide
transcribed by polydenylation
RNA Editing
The process of making a change in the nucleotide sequence of an RNA molecule that involves additions or deletions of particular nucleotide or a conversion of one type of base to another, such as cytosine to a Uracil
Effects, start and stop codon generation and Changing the code in sequence for a polypeptide