What is a gene?
A segment of DNA that is used to make a functional product.
What are structural genes?
Encode the amino acid sequence of a polypeptide.
What is the central dogma of genetics?
The usual flow of genetic information is from DNA to mRNA to polypeptide. This central dogma was first enunciated by Francis Crick in 1958.
What is translation?
During polypeptide synthesis, the sequence of nucleotides within the mRNA determines the sequence of amino acids in a polypeptide.
One key concept important in the process of transcription is that short base sequences define the beginning and ending of a gene and also play a role in what?
Regulating the level of RNA synthesis.
What is gene expression?
The overall process by which the information within a gene is used to produce a functional product, such as a polypeptide.
The _____ provides a site to being transcription, and the _____ specifies the end of transcription.
What are regulatory sequences?
Site for the binding of regulatory proteins; the role of regulatory proteins is to influence the rate of transcription. Regulatory sequences can be found in a variety of locations.
What is a promoter [DNA]?
Site for RNA polymerase binding; signals the beginning of transcription.
What is a terminator [DNA]?
Signals the end of transcription.
What is the ribosomal binding site [mRNA]?
Site for ribosome binding; translation begins near this site in the mRNA. In eukaryotes, the ribosome scans the mRNA for a start codon.
What is a start codon [mRNA]?
Specifies the first amino acid in a polypeptide sequence, usually a formylmethionine (in bacteria) or a methionine (in eukaryotes).
What is a codon [mRNA]?
3-nucleotide sequences within the mRNA that
specify particular amino acids. The sequence of codons within mRNA determines the sequence of amino acids within a polypeptide.
What is a stop codon [mRNA]?
Specifies the end of polypeptide synthesis.
T/F: Bacterial mRNA only encodes for one polypeptide.
False; Bacterial mRNA may be polycistronic, which means it encodes two or more polypeptides.
The base sequence in the RNA transcript
is complementary to the _____ strand of DNA, also called the _____ strand.
For genes that encode proteins, the non-template DNA strand is called the _____ strand or the _____ strand.
What are the three stages of transcription?
Initiation, elongation, and termination
Once they are made, RNA transcripts play different functional roles. Well over 90% of all genes are _____.
For structural genes, mRNAs are made first, but the final, functional products are polypeptides that operate within proteins.
For nonstructural genes, what is the functional product?
In some cases, the RNA transcript becomes part of a complex that contains both protein subunits and one or more RNA molecules. What are some examples?
Examples of protein-RNA complexes include ribosomes, signal recognition particles, RNaseP, spliceosomes and telomerase.
Our molecular understanding of gene transcription initially came from studies involving what?
Bacteria and bacteriophages
What is the function of mRNA?
Messenger RNA (mRNA) encodes the sequence of amino acids within a polypeptide. In bacteria, some mRNAs encode a single polypeptide. Other mRNAs are polycistronic—a single mRNA encodes two or more polypeptides. In most species of eukaryotes, each mRNA usually encodes a single polypeptide.
What is the function of tRNA?
Transfer RNA (tRNA) is necessary for the translation of mRNA.
What is the function of rRNA?
Ribosomal RNA (rRNA) is necessary for the translation of mRNA. Ribosomes are composed of both rRNAs and protein subunits.
What is the function of microRNA?
MicroRNAs (miRNAs) are short RNA molecules that are involved in gene regulation in eukaryotes
What is the function of scRNA?
Small cytoplasmic RNA (scRNA) is found in the cytoplasm of bacteria and eukaryotes. In bacteria, scRNA is needed for protein secretion. An example in eukaryotes is 7S RNA, which is necessary in the targeting of proteins to the endoplasmic reticulum. It is a component of a complex known as signal recognition particle (SRP), which is composed of 7S RNA and six different protein subunits.
What is the function of RNA of RNaseP?
RNaseP is an enzyme necessary in the processing of all bacterial tRNA molecules. The RNA is the catalytic component of this enzyme. RNaseP is composed of a 350- to 410- nucleotide RNA and one protein subunit.
What is the function of snRNA?
Small nuclear RNA (snRNA) is necessary in the splicing of eukaryotic pre-mRNA. snRNAs are components of a spliceosome, which is composed of both snRNAs and protein subunits.
What is the function of telomerase RNA?
The enzyme telomerase, which is involved in the replication of eukaryotic telomeres, is composed of an RNA molecule and protein subunits.
What is the function of snoRNA?
Small nucleolar RNA (snoRNA) is necessary in the processing of eukaryotic rRNA transcripts. snoRNAs are also associated with protein subunits. In eukaryotes, snoRNAs are found in the nucleolus, where rRNA processing and ribosome assembly occur.
What is the function of viral RNAs?
Some types of viruses use RNA as their genome, which is packaged within the viral capsid.
This sequences of bases directs the exact location for the initiation of RNA transcription.
Most of the promoter region is located just ahead of or upstream from the site where transcription of a gene actually begins.
This site is the first base used as a template for RNA transcription and is denoted +1.
Transcriptional start site. The bases preceding this site are numbered in a negative direction. No base is numbered zero. Therefore, most of the promoter region is labeled with negative numbers that describe the number of bases preceding the beginning of transcription.
T/F: The sequences at the -35 and -10 sites can vary among different genes.
Which nucleotide is denoted as number 0?
There is no zero nucleotide. The nucleotide that is immediately to the left of the +1 nucleotide is numbered -1, and the nucleotide to the right of the +1 nucleotide is numbered +2.
The enzyme that catalyzes the synthesis of RNA is _____.
Bacterial transcription is initiated when _____ binds at a promoter sequence.
RNA polymerase holoenzyme
After RNA polymerase holoenzyme is assembled into its _____ (how many?) subunits, it binds loosely to the DNA and then slides along the DNA.
When the holoenzyme encounters a promoter sequence, sigma factor recognizes the bases at both the -35 and -10 regions. Sigma factor protein contains a structure called a _____ that can bind tightly to these regions. [RNA transcription]
The process of transcription is initiated when sigma factor within the holoenzyme has bound to the promoter region to form the _____. [RNA transcription]
For transcription to begin, the double-stranded DNA must then be unwound into an open complex.
What marks the transition between the initiation and elongation phases of RNA transcription?
A short strand of RNA is made within the open complex, and then sigma factor is released from the core enzyme. The release of sigma factor marks the transition to the elongation phase of transcription. The core enzyme may now slide
down the DNA to synthesize a strand of RNA.
Where does the unwinding required to form the open complex occur? [RNA transcription]
This unwinding first occurs at the TATAAT sequence in the -10 region, which contains only AT base pairs.
The RNA transcript is made in what stage of transcription?
RNA polymerase moves along the template strand in a _____ direction, and RNA is synthesized in a _____ direction using nucleoside triphosphates as precursors.
3′ to 5′; 5′ to 3′
How is RNA transcription terminated?
By either an RNA-binding protein or intrinsic terminator.
What is rho-dependent termination? Rho-independent?
In _E. coli_, two different mechanisms for termination have been identified. For certain genes, an RNA-binding protein known as rho is responsible for terminating transcription, in a mechanism called rho-dependent termination.
For other genes, termination does not require the involvement of the rho protein. This is referred to as rho-independent termination.
What two components are required by rho-dependent termination?
First, a sequence near the 3' end of the newly made RNA, called the rut site for rho utilization site acts as a recognition site for the binding of the rho protein. The second component of rho-dependent termination is the site where termination actually takes place. At this terminator site, the DNA encodes an RNA sequence containing several GC base pairs that form a stem-loop structure to pause RNA polymerase until the rho protein can separate the RNA-DNA hybrid.
Describe rho-indepdent, or intrinsic, termination.
When RNA polymerase reaches the end of the gene, it transcribes a uracil-rich sequence. As this uracil-rich sequence is transcribed, a stem-loop forms just upstream from the open complex. The formation of this stem-loop
causes RNA polymerase to pause in its synthesis of the transcript. This pausing is stabilized by NusA, which binds near the region where RNA
exits the open complex. While it is pausing, the RNA in the RNA-DNA hybrid is a uracil-rich sequence. Because hydrogen bonds between
U and A are relatively weak interactions, the transcript and RNA polymerase dissociate from the DNA.
The genetic material within the nucleus of a eukaryotic cell is transcribed by _____ different RNA polymerase enzymes.
three; RNA polymerase I, II, and III.
What is the function of RNA polymerase I?
Transcribes all of the genes that encode ribosomal RNA (rRNA) except for the 5S rRNA.
What is the role of RNA polymerase II?
Plays a major role in cellular transcription because it transcribes all of the structural genes. It is responsible for the synthesis of all mRNA and also transcribes certain snRNA genes, which are needed for pre-mRNA splicing.
What is the role of RNA polymerase III?
RNA polymerase III transcribes all tRNA genes and the 5S rRNA gene.
For eukaryotic structural genes ,at least what three features are found in most promoters?
Regulatory elements, a TATA box, and a transcriptional start site
What is the core promoter?
Relatively 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.
What is basal transcription?
The low level of transcription produced by the core promoter by itself.
What are regulatory elements?
Affect the ability of RNA polymerase to recognize the core promoter and begin the process of transcription.
What are the two categories of regulatory elements? Where are they commonly located?
Enhancers (needed to stimulate transcription) and silencers (DNA sequences that inhibit transcription). A common location for regulatory elements is the -50 to -100 region.
What are cis-acting elements?
DNA sequences such as the TATA box, enhancers, and silencers exert their effects only over a particular gene. They are called cis-acting elements.
What are trans-acting factors?
The regulatory transcription factors that bind to cis-acting elements. The transcription factors that control the expression of a gene are themselves encoded by genes; regulatory genes that encode transcription factors may be far away from the genes they control.
Five different proteins called _____ are always needed for RNA polymerase II to initiate transcription of structural genes.
general transcription factors (GTFs)
What are mechanisms that disrupt the tight binding of DNA and histones within nucleosomes?
Histone acetylation and ATP-dependent chromatin remodeling.
Some large RNA transcripts are processed into smaller functional transcripts through what process?
Describe the processing of ribosomal RNA in eukaryotes.
The large ribosomal RNA gene is transcribed into a long 45S rRNA primary transcript. This transcript is cleaved to produce 18S, 5.8S, and 28S rRNA molecules, which become associated with protein subunits in the ribosome. This processing occurs within the nucleolus of the cell.
Splicing among what groups of introns occur via self-splicing?
Group I and group II;
Splicing doe not require the aid of other enzymes; instead, the RNA functions as its own ribozyme.
Experimentally, group I and II self-splicing can occur in vitro without the addition of any proteins. However, in a living cell, proteins known as _____ often enhance the rate of splicing of group I and II introns.
What is heterogeneous nuclear RNA (hnRNA)?
In eukaryotes, the transcription of structural genes produces a long transcript known as pre-mRNA, which is located within the nucleus. These large RNA transcripts are also known as heterogeneous nuclear RNA (hnRNA). Pre-mRNA splicing requires the aid of a multicomponent structure known as the spliceosome.
Unlike group I and II introns, which may undergo self-splicing, pre-mRNA splicing requires the aid of a multicomponent structure known as the _____.
Where are Group I introns found?
Found in rRNA genes within the nucleus of
Tetrahymena and other simple eukaryotes.
Found in a few structural, tRNA, and rRNA
genes within the mitochondrial DNA (fungi
and plants) and in chloroplast DNA. Found
very rarely in tRNA genes within bacteria.
Where are Group II introns found?
Found in a few structural, tRNA, and rRNA
genes within the mitochondrial DNA (fungi
and plants) and in chloroplast DNA. Also found
rarely in bacterial genes.
Where are pre-mRNA introns found?
Very commonly found in structural genes within
the nucleus of eukaryotes.
What is a snRNP?
One of several subunits that comprises the spliceosome. Each snRNP contains small nuclear RNA and a set of proteins.
What is the benefit of alternative splicing?
When a pre-mRNA has multiple introns, variation
may occur in the pattern of splicing, so the resulting mRNAs contain alternative combinations of exons. The variation in splicing
may happen in different cell types or during different stages of development. Such alternative splicing allows mature mRNAs to contain different patterns of exons.
What is capping?
In addition to splicing, pre-mRNAs in eukaryotes are also subjected to modifications at their 5' and 3' ends. At their 5' end, most mature mRNAs have a 7-methylguanosine covalently attached, an event known as capping.
Describe the attachment of a 7-methylguanosine cap to the 5' end of mRNA.
When the transcript is about 20 to 25 nucleotides in length, RNA 5'-triphosphatase removes one of the three phosphates, and then a second enzyme, guanylyltransferase, attaches GMP to the 5' end. Finally, a methyltransferase attaches a methyl group to the guanine base.
What are the functions of the 7-methylguanosine cap?
The cap structure is recognized by cap-binding proteins, which perform various roles. For example, cap-binding proteins are required for the proper exit of most mRNAs from the nucleus. Also, the cap structure is recognized by initiation factors that are needed during the early stages of translation. Finally, the cap structure may be important in the efficient splicing of introns, particularly the first intron located nearest the 5' end.
What is a poly-A tail?
Most mature mRNAs have a string of adenine nucleotides, referred to as a polyA tail, which is important for mRNA stability and in the synthesis of polypeptides.
T/F: The polyA tail is not encoded in the gene sequence.
True; Instead, it is added enzymatically after the pre-mRNA has been completely transcribed.
What is polyadenylation?
The process by which the polyA tail is added.
Describe the attachment of the polyA tail.
First, an endonuclease cuts the RNA at a location that is 11 to 30 nucleotides after the AAUAAA polyadenylation sequence, making the RNA shorter at its 3' end. Adenine-containing nucleotides are then attached, one at a time, to the 3' end by the enzyme polyA-polymerase.