Lec 13 - Eukaryotic Transcription

pre-mRNA

- The first (primary) transcript from a protein coding gene is often called a pre-mRNA and contains both introns and exons. - Pre-mRNA requires splicing (removal) of introns to produce the final mRNA molecule containing only exons.

Spliceosome

- The ribonucleoprotein processing complex that removes introns from eukaryotic mRNAs. -A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

Capping

-Modified guanosine attached to 5' end -Needed for mRNA to exit nucleus and bind ribosome Cap- cap A special structure, consisting of a 7-methylguanosine residue linked to the transcript by three phosphate groups, that is added in the nucleus to the 5′ end of eukaryotic mRNA. The cap protects an mRNA from degradation and is required for translation of the mRNA in the cytoplasm.

TATA box

A DNA sequence found in many eukaryotic genes that is located about 30 bp upstream of the transcription start site

rRNA

A class of RNA molecules, encoded in the nucleolar organizer, that have an integral (but poorly understood) role in ribosome structure and function. integral = necessary to make a whole complete; essential or fundamental.

Codon

A section of RNA (three nucleotides in length) that encodes a single amino acid. -A set of three adjacent nucleotides, also called triplet, in mRNA that base-pair with the corresponding aniticodon of tRNA molecule that carries a particular amino acid, hence, specifying the type and sequence of amino acids for protein synthesis.

5' cap

A specially altered nucleotide end to the 5' end of precursor messenger RNA and some other primary RNA transcripts as found in eukaryotes and caliciviruses, vital to creating mature messenger RNA which is then able to undergo translation.

poly(A) tail

A string of adenine nucleotides added to mRNA after transcription.

Preinitiation -preinitiation complex (PIC)

A very large eukaryotic protein complex comprising RNA polymerase II and the six general transcription factors (GTFs), each of which is a multiprotein complex.

intervening sequence

An intron; a segment of largely unknown function within a gene. This segment is initially transcribed, but the transcript is not found in the functional mRNA.

3' splice junction ('AG' donor site)

At the 5' end the DNA nucleotides are GT [GU in the premessenger RNA (pre-mRNA)]; at the 3' end they are AG

5' splice junction ('GU' donor site)

DONOR-SPLICE: splicing site at the beginning of an intron, intron 5' left end.

Polycistronic "polygenic mRNA"

Describing a type of messenger RNA that can encode more than one polypeptide separately within the same RNA molecule. Bacterial messenger RNA is generally polycistronic. -Pertaining to mRNA carrying information for the synthesis of more than one protein. -A cistron is an alternative term to a gene. - polypeptide: a linear organic polymer consisting of a large number of amino-acid residues bonded together in a chain, forming part of (or the whole of) a protein molecule. - polymer: a substance that has a molecular structure consisting chiefly or entirely of a large number of similar units bonded together, e.g., many synthetic organic materials used as plastics and resins. ---polumeros 'having many parts', from polu- 'many' + meros 'a share'.

Eukaryotic Transcription

Eukaryotic transcription is carried out in the nucleus of the cell and proceeds in three sequential stages: initiation, elongation, and termination. Eukaryotes require transcription factors to first bind to the promoter region and then help recruit the appropriate polymerase.

branch site

In RNA splicing, the site to which the 5'-guanylate at the end of an intron is joined to an adenylate residue within the intron through a 2',5'-phosphodiester bond to form a 'lariat' intermediate.

compartmentalization

Membrane-bound organelles allow different parts of the cell to perform different functions at the same time

Co-transcriptional

Modifications of amino acid side groups after a protein has been translated. Post-transcriptional modification or Co-transcriptional modification is the process in eukaryotic cells where primary transcript RNA is converted into mature RNA. A notable example is the conversion of precursor messenger RNA into mature messenger RNA (mRNA) that occurs prior to protein translation.

RNA splicing

Process by which the introns are removed from RNA transcripts and the remaining exons are joined together.

SnRNP

Small nuclear ribonucleoprotein (RNA plus protein) particle. Component of the spliceosome, the intron-removing apparatus in eukaryotic nuclei .

RNA polymerase holoenzyme

The bacterial multisubunit complex composed of the four subunits of the core enzyme plus the σ factor.

Monocistronic

The coding pattern of eukaryotes in which one mRNA molecule codes for only one protein.

alpha-tropomyosin

The α-tropomyosin gene (TPM1) is organized into 15 exons on chromosome 15 (68) and encodes a 284-amino-acid protein expressed in both fast skeletal and cardiac muscle (69). α-tropomyosin forms a complex with troponin T that regulates actin-myosin interaction in response to intracellular Ca2+ concentration.

degradation

a decline to a lower condition, quality, or level

assembly

a group of people gathered together in one place for a common purpose.

exon

a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence. -from expressed (see express1) + -on.

intron

a segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes. -from intra- 'within' + -on.

Central Dogma

a theory in genetics and molecular biology subject to several exceptions that genetic information is coded in self-replicating DNA and undergoes unidirectional transfer to messenger RNAs in transcription which act as templates for protein synthesis in translation.

trans-acting

able to control the expression of genes on other DNA molecules -A diffusible regulatory molecule (almost always a protein) that binds to a specific cis-acting element. -is usually a DNA sequence that contains a gene. This gene codes for a protein (or microRNA or other diffusible molecule) that will be used in the regulation of another target gene.

cis-acting

able to control the expression of genes only when on the same piece of DNA -A site on a DNA (or RNA) molecule that functions as a binding site for a sequence-specific DNA- (or RNA-) binding protein. -The term cis-acting indicates that protein binding to this site affects only nearby DNA (or RNA) sequences on the same molecule.

mosaics

an individual (especially an animal) composed of cells of two genetically different types. - is a creature whose body is built of a mixture of cells of two or more different genotypes. In mammals they arise by several different mechanisms: The fusion of two different zygotes, or early embryos, into one.

adenoviruses

any of a group of DNA viruses first discovered in adenoid tissue, most of which cause respiratory diseases -adenoid: a mass of enlarged lymphatic tissue between the back of the nose and the throat, often hindering speaking and breathing in young children.

isoforms

any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed.

General Transcription Factors (GTFs)

are proteins that help to position Pol II correctly on the promoter, the region of a gene where transcription is initiated, pull aside the two strands of DNA and then move Pol II into the elongation mode.

constituent

being a part of a whole. = component

intervening - meaning "between," and venire, meaning "come."

coming between so as to hinder or modify

7-Methylguanosine (m7G)

is a modified purine nucleoside. It is a methylated version of guanosine and when found in human urine, it may be a biomarker of some types of cancer. in the RNAs, 7-Methylguanosine have been used to study and examine the reaction evolving methylguanosine.

An enhancer

is a short piece or sequence of DNA that works to enhance or speed up the rate of genetic transcription. An enhancer is also often called a cis-regulatory element and is between 20 to 400 base pairs of DNA in size.

mRNA

is a subtype of RNA. An mRNA molecule carries a portion of the DNA code to other parts of the cell for processing. mRNA is created during transcription. During the transcription process, a single strand of DNA is decoded by RNA polymerase, and mRNA is synthesized.

tRNA

is a type of RNA molecule that helps decode a messenger RNA (mRNA) sequence into a protein. tRNAs function at specific sites in the ribosome during translation, which is a process that synthesizes a protein from an mRNA molecule.

RNA Pol II

is the central enzyme that catalyses DNA-directed mRNA synthesis during the transcription of protein-coding genes. -is the enzyme that transcribes mRNA along with many types of noncoding functional RNA. Each different RNA polymerase is a holoenzyme made up of different components.

C-terminal Domain (CTD)

is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH).

retained

kept or continued to have

Extensive

large amount

recruitment

locating, identifying, and attracting capable applicants

machinery

n. The parts of a machine or engine, taken collectively.

noncontiguous sites

not adjoining along a boundary or consisting of parts that adjoin (next to or joined with.)

Colinear

points that lie on the same line - a set of loci in two different species which are located on the same chromosome in each, and are conserved in the same order. - From Latin: co- "together" , -linearis "belonging to a line,"

Splicing

the process of removing introns and reconnecting exons in a pre-mRNA -join or connect (a rope or ropes) by interweaving the strands.

Gene regulation

the process of turning genes on and off

RNA Pol III

transcribes small untranslated RNAs, such as tRNAs. - transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions.