Chapter 13: Transcription

Ribozyme

RNA molecule that can act as a biological catalyst. These catalytic RNA molecules can cut out parts of their own sequences, connect some RNA molecules together, replicate others, and even catalyze the formation of peptide bonds between amino acids

Transfer RNA (tRNA)

RNA molecule that carries an amino acid to the ribosome and transfers it to a growing polypeptide chain in translation. - bacterial and eukaryotic - cytoplasm

Messenger RNA (mRNA)

RNA molecule that carries genetic information for the amino acid sequence of a protein. - bacterial and eukaryotic - nucleus and cytoplasm

Ribosomal RNA (rRNA)

RNA molecule that is a structural component of the ribosome (a site of protein assembly); Make up the ribosome - bacterial and eukaryotic - cytoplasm

Transcriptional Pausing

breaking the elongation stage of transcription - pauses are caused by backtracking - when the RNA polymerase slides backward along the DNA template strand - important in the coordination of transcription and translation in bacteria and RNA processing in eukaryotes

Christmas Tree Structure

- Christmas trees represent a gene undergoing transcription - The addition of deoxyribonuclease (an enzyme that degrades DNA) = loss of trunk only - The addition of ribonuclease (an enzyme that degrades RNA) = loss of branches only

Eukaryotic RNA Polymerases

- RNA Polymerase I - RNA Polymerase II - RNA Polymerase III - RNA Polymerase IV - RNA Polymerase V

Classes of RNA

- Ribosomal RNA (rRNA) - Messenger RNA(mRNA) - Transfer RNA (tRNA) - Small Nuclear RNA (snRNA) - Small Nucleolar RNA (snoRNA) - MicroRNA (miRNA) - Small Interfering RNA (siRNA) - Piwi-Interacting RNA (piRNA) - CRISPR RNA (crRNA)

Initiation

-Bacterial promoters: sequences recognized by the transcription apparatus (holoenzyme) and required for transcription. Tells where to start, what strand to use, and what direction to transcribe -Consensus sequences: Sequences that possess similarity. -10 consensus :10 bp upstream of the start site. Pribnow box: 5 TATAAT 3 3 ATATTA 5 -35 consensus sequence: Lies approximately 35 nucleotides upstream of the start site TTGACA Fig. 13.11 - Usually adjacent to to an RNA-coding sequence in bacteria cells

CRISPR RNA (crRNA)

-Small RNA molecules found in prokaryotes that assist in the destruction of foreign DNA.

Transcription

-highly selective (only transcribes what is needed) -only small parts of the DNA molecule are transcribed into RNA (a gene or a few genes at most) -requires 1. a DNA template 2. the raw materials (ribonucleotide triphosphates) needed to build a new RNA molecule 3. the transcription apparatus, consisting of the proteins necessary for catalyzing the synthesis of RNA

RNA Synthesis

1.) RNA polymerase pairs the base on a ribonucleoside triphosphate with its complementary base at the start site on the DNA template. 2.) does not require a primer to start synthesis at the 5' end. 3.) Two of the three phosphate groups are cleaved from the ribonucleoside triphosphate as the nucleotide is added to the 3' end of the growing

Pre-Messenger RNA (pre-mRNA)

Are the immediate product of transcription - Are modified extensively before becoming mRNA and exiting the nucleus for translation into a protein - BACTERIAL CELLS DO NOT POSSESS PRE-mRNA

Holoenzyme

Complex of an enzyme and other protein factors necessary for complete function.

Basal Transcription Apparatus

Complex of transcription factors, RNA polymerase, and other proteins that assemble on the promoter and are capable of initiating minimal levels of transcription.

Consensus Sequence

Comprises the most commonly encountered nucleotides found at a specific location in DNA or RNA. - implies that the sequence is associated with an important function

TATA Box

Consensus sequence (TATAAAA) commonly found in eukaryotic RNA polymerase II promoters; usually located from -25 to -30 bp upstream of the transcription start site. The TATA box determines the start point for transcription.

-10 Consensus Sequence (Pribnow box)

Consensus sequence (TATAAT) found in most bacterial promoters approximately 10 bp upstream of the transcription start site.

-35 Consensus Sequence

Consensus sequence (TTGACA) found in many bacterial promoters approximately 35 bp upstream of the transcription start site.

Upstream Element

Consensus sequence found in some bacterial promoters that contains a number of A-T pairs and is found about 40 to 60 bp upstream of the transcription start site.

Regulatory Promoter

DNA sequence located immediately upstream of the core promoter that affects transcription; contains consensus sequences to which transcriptional regulator proteins bind. - Transcriptional activator proteins bind to these sequences and either directly or indirectly bind, make contact with the basal transcription apparatus, and affect the rate at which transcription is initiated

Promoter

DNA sequence to which the transcription apparatus binds so as to initiate transcription; indicates the direction of transcription, which of the two DNA strands is to be read as the template, and the starting point of transcription. In many transcription units, the promoter is located next to the transcription start site but is not, itself, transcribed.

RNA polymerase

Enzyme that synthesizes RNA from a DNA template during transcription.

RNA Polymerase I

Eukaryotic RNA polymerase that transcribes large ribosomal RNA molecules (18 S rRNA and 28 S rRNA). - all eukaryotes

RNA Polymerase II

Eukaryotic RNA polymerase that transcribes pre-messenger RNA (pre-mRNA), some small nuclear RNAs (snRNA), and some microRNAs (miRNA). - all eukaryotes

RNA Polymerase III

Eukaryotic RNA polymerase that transcribes transfer RNA (tRNA), small ribosomal RNAs (5 S rRNA), some small nuclear RNAs (snRNA), and some microRNAs (miRNA) - all eukaryotes

bacterial transcription

Initiation: when the transcription apparatus assembles on the promoter and begins the synthesis of RNA Elongation: DNA is threaded through RNA polymerase, the polymerase unwinds the DNA and adds new nucleotides, one at a time, to the 3′ end of the growing RNA strand Termination: recognition of the end of the transcription unit and the separation of the RNA molecule from the DNA template

Core Promoter

Located immediately upstream of the eukaryotic promoter, is the site to which the basal transcription apparatus binds.

Sigma (σ) Factor

Other functional subunits join and leave core enzyme at particular stages of the transcription process. Subunit of bacterial RNA polymerase that allows the RNA polymerase to recognize a promoter and initiate transcription. Without sigma, RNA polymerase will initiate transcription at a random point along the DNA - only required by promoter for binding and initiation - when a few RNA nucleotides have been joined together, sigma detaches from core enzyme.

Core Enzyme

Part of bacterial RNA polymerase that, during transcription, catalyzes the elongation of the RNA molecule by the addition of RNA nucleotides; consists of four subunits: two copies of alpha (α), a single copy of beta (β), and a single copy of beta prime (β′). - The (ω) is not essential for transcription, but helps in stabilizing the enzyme.

TATA-Binding Proteins (TBP)

Polypeptide chain found in several different transcription factors that recognizes and binds to sequences in eukaryotic promoters. -binds to the minor groove and straddles the DNA as a molecular saddle, bending the DNA and partly unwinding it.

Abortive Initiation

Process during initiation of transcription in which RNA polymerase repeatedly generates and releases short transcripts, from 2 to 6 nucleotides in length, while still bound to the promoter. Occurs in both prokaryotes and eukaryotes.

Internal Promoter

Promoter located (downstream of the start site) within the sequences of DNA that are transcribed into RNA.

General Transcription Factor

Protein that binds to eukaryotic promoters near the start site and is a part of the basal transcription apparatus that initiates transcription.

Transcription Apparatus

Said to move downstream during replication; it binds to the promoter (which is usually upstream of the start site) and moves toward the terminator (which is downstream of the start site) - First nucleotide transcribed is a +1 - Nucleotides downstream from start site are numbered positive (+) numbers - Nucleotides upstream from start site are numbered negative (-)

Rho-Independent Terminator

Sequence in bacterial DNA that does not require the presence of the rho subunit of RNA polymerase to terminate transcription. 1.) Contain inverted repeats which are sequences of nucleotides on one strand that are inverted and complementary 2.) A string of 7-9 adenine nucleotides follow the second inverted repeat in the template DNA - Uses a string of uracils that will slow down the RNA polymerase allowing a hairpin to form which will destabilize the RNA-DNA hybrid allowing it to separate and stop.

Rho-Dependent Terminator

Sequence in bacterial DNA that requires the presence of the rho subunit of RNA polymerase to terminate transcription. 1.) Consists of DNA sequences that cause the RNA polymerase to pause 2.) DNA sequence that encodes a stretch of RNA upstream of the terminator that is usually rich in cytosine nucleotides and devoid of any secondary structures - when RNA polymerase encounters the terminator, it pauses, allowing rho to catch up and unwinds the RNA-DNA hybrid to stop translation

Terminator

Sequence of DNA nucleotides that causes the termination of transcription (signals where translation is to end) - usually part of the RNA-coding sequence; transcription stops only after the terminator has been copied into RNA

RNA-Coding Region

Sequence of DNA nucleotides that is copied into an RNA molecule.

Transcription Unit

Sequence of nucleotides in DNA that encodes a single RNA molecule, along with the sequences necessary for its transcription; normally contains a promoter, an RNA-coding sequence, and a terminator. - in this unit, there is: - promoter - RNA-coding sequence - terminator

Enhancer

Sequence that stimulates maximal transcription of distant genes; affects only genes on the same DNA molecule (is cis acting), contains short consensus sequences, is not fixed in relation to the transcription start site, can stimulate almost any promoter in its vicinity, and may be upstream or downstream of the gene. The function of an enhancer is independent of sequence orientation.

Polycistronic mRNA

Single bacterial RNA molecule that encodes more than one polypeptide chain; uncommon in eukaryotes. - uses one terminator for several genes, rather than each gene having its own terminator

Small Interfering RNA (siRNA)

Single-stranded RNA molecule (usually from 21 to 25 nucleotides in length) produced by the cleavage and processing of double-stranded RNA; binds to complementary sequences in mRNA and brings about the cleavage and degradation of the mRNA. Some siRNAs bind to complementary sequences in DNA and bring about their methylation. - carry out RNA interference (RNAi), a process in which these small RNA molecules help trigger degradation of mRNA or inhibit its translation into protein. - eukaryotic - nucleus and cytoplasm

Piwi-Interacting DNA (piRNA)

Small RNA molecule belonging to a class named after Piwi proteins with which these molecules interact; similar to microRNA and small interfering RNA and thought to have a role in the regulation of sperm development. - eukaryotic - nucleus and cytoplasm

Small Nuclear RNA (snRNA)

Small RNA molecule found in the nuclei of eukaryotic cells; functions in the processing of pre-mRNA. (pre-mRNA into mRNA) - combine with small protein subunits to form small nuclear ribonucleoproteins (snRNPs) - eukaryotic - nucleus

Small Nucleolar RNA (snoRNA)

Small RNA molecule found in the nuclei of eukaryotic cells; functions in the processing of rRNA and in the assembly of ribosomes. - eukaryotic - nucleus

microRNA (miRNA)

Small RNA molecule, typically 21 or 22 bp in length, produced by cleavage of double-stranded RNA arising from small hairpins within RNA that is mostly single stranded. The miRNAs combine with proteins to form a complex that binds (imperfectly) to mRNA molecules and inhibits their translation. - Eukaryotic - Nucleus and cytoplasm - Carry out RNA interference (RNAi), a process in which these small RNA molecules help trigger degradation of mRNA or inhibit its translation into protein.

Small Nuclear Ribonucleoprotein (snRNP) or "Snurps"

Structure found in the nuclei of eukaryotic cells that consists of small nuclear RNA (snRNA) and protein; functions in the processing of pre-mRNA.

Ribonucleoside Triphosphate (rNTP)

Substrate of RNA synthesis; consists of ribose, a nitrogenous base, and three phosphates linked to the 5′-carbon atom of the ribose. In transcription, two of the phosphates are cleaved, producing an RNA nucleotide. - Nucleotides are added at 3' end of the molecule, but move in a 5' -> 3' manner

Rho Factor

Subunit of bacterial RNA polymerase that facilitates the termination of transcription of some genes in rho-dependent terminators

Nontemplate Strand

The DNA strand that is complementary to the template strand; not ordinarily used as a template during transcription.

Template Strand

The nucleotide strand of DNA that is used as a template during transcription. The RNA synthesized during transcription is complementary and antiparallel to the template strand.

RNA Polymerase V

Transcribes RNA that has a role in heterochromatin formation in plants.

RNA polymerase IV

Transcribes small interfering RNAs in plants.

Eukaryotic Transcription (differences between bacterial transcription)

Transcription and nucleosome structure Chromatin modification before transcription to make DNA accessible. -promoter recognition is carried out by accessory proteins that bind to the promoter and then recruit a specific RNA polymerase - The Existence of 3 different eukaryotic RNA polymerases which recognize different types of promotors. Promoters: -Basal Transcription apparatus = RNA polymerase -General Transcription factors initiate transcription. -Transcriptional activator proteins: Bring basal transcription apparatus to the promoter RNA polymerase II - mRNA synthesis Core promoter TATA box TATAAAA, -25 to -30 bp, binded by general transcription factors.