Genetics - Ch. 10 Transcription & RNA Processing

This type of RNA assists in the destruction of foreign DNA molecules; this type of RNA interference-like system has recently been discovered only in prokaryotes

CRISPR RNAs (crRNAs)

In 1970, the actual form of the DNA template that transcribes RNA was found. A _____________________ structure was found within cells: central fibers to which were attached strings with granules. The addition of deoxyribonuclease (an enzyme that degrades DNA) caused the central fibers to disappear, indicating that the "tree trunks" were ___________ molecules. Ribonuclease (an enzyme that degrades RNA) removed the granular strings, indicating that the branches were ___________. Their conclusion was that each "Christmas tree" represented a gene undergoing transcription. The transcription of each gene begins at the (bottom/top) of the tree; there, little of the DNA has been transcribed, and the RNA branches are short. As the transcription proceeds down the tree, transcribing more of the template, the RNA molecules lengthen, producing long branches at the bottom.

Christmas-tree-like; DNA; RNA; top

RNA polymerase _____ transcribes rRNA

I

RNA polymerase _____ transcribes pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs

II

RNA polymerase _____ transcribes other small molecules, specifically tRNAs, small rRNAs, some miRNAs, and some snRNAs.

III

Fundamental difference between replication and translation relates to the length of the template used:

In replication, all the nucleotides in the DNA template are copied, but in transcription, only parts of the DNA molecule are transcribed into RNA.

Genes with rho-______________ terminators have a stretch of RNA upstream of the terminator that is devoid of any secondary structures. This unstructured RNA, called the ________ __________________ __________, serves as the binding site for the rho protein, which binds the RNA and moves toward its 3' end, following the RNA polymerase. When RNA polymerase encounters the terminator, it pauses, allowing rho to catch up. The rho protein has helicase activity, which it uses to unwind the DNA-RNA hybrid in the transcription bubble, bringing transcription to an end.

dependent; rho utilization (rut) site

The transcription apparatus is said to move _________________ as transcription occurs: it binds to the promoter (which is usually _______________ of the start site) and moves toward the terminator (which is ______________ of the start site).

downstream; upstream; downstream

The most commonly encountered consensus sequence, found in almost all bacterial promoters, is centered about 10 bp upstream of the start site. Called the ______ _____________ sequence, or sometimes the Pribnow box, this consensus sequence is often written simply as TATAAT. This sequence represents the most commonly encountered nucleotides at each of these positions. In most prokaryotic promoters, the actual sequence is not TATAAT.

-10 consensus

Another consensus sequence common to most bacterial promoters is TTGACA, which lies about 35 nucleotides upstream of the start site and is termed the _______ ________________ sequence. The nucleotides on either side of the -10 and -35 consensus sequences and those between them vary greatly from promoter to promoter, suggesting that they are not very important in promoter recognition.

-35 consensus

Like replication, transcription requires three major components:

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 differs from DNA in 4 major ways:

1. RNA nucleotides contain ribose sugars 2. RNA degrades rapidly under alkaline conditions with a free hydroxyl group on the 2'-carbon atom of the ribose sugar (makes it more reactive, less stable) 3. RNA contains uracil in place of thymine 4. Often has a single polynucleotide strand

Nucleotides are always added to the 3' end of the RNA molecule, and the direction of transcription is therefore ______ to ______, the same direction as DNA synthesis in replication. Thus, the newly synthesized RNA is complementary and antiparallel to the template strand. Unlike DNA synthesis, RNA synthesis does not require a _____________.

5'; 3'; primer

In the second step of RNA splicing, a cut is made at the ____ _________ _________, and simultaneously, the 3' end of the of exon 1 becomes covalently attached (spliced) to the 5' end of exon 2. The intron is released as a lariat. Eventually, a lariat debranching enzyme breaks the bond at the branch point, producing a linear intron that is rapidly degraded by nuclear enzymes. The mature mRNA, consisting of the exons spliced together, is exported to the cytoplasm, where it is translated. These splicing reactions occur within the spliceosome, which carries out the splicing reactions.

3' splice site

The last region of mRNA is the ______ _______________ _________________, a sequence of nucleotides that is at the 3' end of the mRNA and is not translated into protein. This region affects the stability of mRNA and the translation of the mRNA protein-coding sequence.

3' untranslated region (3' UTR, aka the trailer)

One type of modification of eukaryotic pre-mRNA is the addition of a structure called a _____ _______. This structure consists of an extra modified nucleotide at the 5' end of the mRNA as well as methyl groups (CH3) on the 2'-OH group of the sugar of one or more nucleotides at the 5' end. The addition of this structure occurs rapidly after the initiation of transcription. It functions in the initiation of translation. Cap-binding proteins recognize this structure and attach to it; a ribosome then binds to these proteins and moves downstream along the mRNA until the start codon is reached and translation begins. The presence of this structure also increases the stability of mRNA and influences the removal of introns.

5' cap

The ______ _________________ ________________, a sequence of nucleotides at the 5' end of the mRNA, does not encode any of the amino acids of a protein. In bacterial mRNA, this region contains a consensus sequence (UAAGGAGGU) called the __________-____________ sequence, which serves a the ribosome-binding site during translation; it is found approximately 7 nucleotides upstream of the first codon translated into an amino acid (called the start codon). This sequence is complementary to sequences found in one of the RNA molecules that make up the ribsome and pairs with those sequences during translation. In eukaryotic cells, ribosomes bind to a modified 5' end of mRNA.

5' untranslated region (5' UTR; aka the leader); Shine-Dalgarno

Both prokaryotic and eukaryotic mRNAs contain three primary regions:

5' untranslated region, the protein-coding region, 3' untranslated region

RNA interference was first demonstrated in the nematode _________________ when geneticists discovered that they could silence specific genes in this species by injecting the animals with double-stranded RNA that was complementary to the genes. The geneticists were studying C. elegans because this species had proved to be an excellent model genetic organism, particularly for studies of how genes influence development. For reasons that are not completely known, RNAi is particularly effective in this species. C. elegans has become widely used in genetic studies because of its simple body plan, ease of culture, and high reproductive capacity. C. elegans has made important contributions to the study of development, cell death, aging, and behavior.

C. elegans

The _________ sequence encodes how the transcription apparatus recognizes a transcription unit, as well as which DNA strand to read and where to start and stop.

DNA

Eukaryotic cells were found to contain far more ___________ than is required to encode proteins. Also, many large RNA molecules observed in the nucleus were absent from the ___________________, suggesting that nuclear RNAs undergo some type of change before they are exported to the cytoplasm.

DNA; cytoplasm

Stage of transcription in which DNA is threaded through RNA polymerase, and the polymerase unwinds the DNA and adds new nucleotides, one at a time, to the 3' end of the growing RNA strand

Elongation

Stage of transcription in which the transcription apparatus assembles on the promoter and begins the synthesis of RNA

Initiation

Transcription can be divided into three stages:

Initiation, Elongation, Termination

Although each tRNA molecule folds into a cloverleaf owning to the complementary pairing of bases, the cloverleaf is not the 3D dimensional (tertiary) structure of tRNAs found in the cell. The results of X-ray crystallographic studies have shown that the cloverleaf folds on itself to form an ______-_________ structure.

L-shaped

Type of RNA that consists of relatively long RNA molecules found in eukaryotes that do not code for proteins; instead, they provide a variety of functions, including regulation of gene expression.

Long noncoding RNAs (lncRNAs)

Type of RNA that carries the coding instructions for polypeptide chains from DNA to the ribosome

Messenger RNA (mRNA)

__________________ RNA functions as the template for protein synthesis; it carries genetic information from DNA to a ribosome and helps to assemble amino acids in their correct order. In bacteria, mRNA is transcribed directly from DNA, but in eukaryotes, a _________________ (the primary transcript) is first transcribed from DNA and then processes to yield the mature mRNA. _____________ are RNA molecules that have been completely processed and are ready to undergo translation.

Messenger; pre-mRNA; mRNA

___________________ have been found in all eukaryotic organisms examined to date as well as in viruses: they control the expression of genes taking part in many biological processes, including growth, development, and metabolism.

MicroRNAs

The nucleotide strand normally not used for transcription

Non-template strand

Type of RNA that has a role in suppressing the expression of transposable elements in reproductive cells; named after Piwi proteins, with which they interact

Piwi-interacting RNAs (piRNAs)

After attaching to a ribosome, an mRNA molecule specifies the sequence of the amino acids in a polypeptide chain and provides a template for the joining of those amino acids. Large precursor molecules, called __________________ RNAs, are the immediate products of transcription in eukaryotic cells.

Pre-messenger RNA (pre-mRNAs), aka primary transcripts

A DNA sequence that the transcription apparatus recognizes and binds; indicates which of the two DNA strands is to be read as the template and the direction of transcription; also determines the transcription start site, the first nucleotide that will be transcribed into RNA; in many transcription units, this is located next to the transcription start site but is not itself transcribed.

Promoter

The discovery of ribozymes complements other evidence suggesting that the original genetic material was (RNA/DNA).

RNA

Two types of very small and abundant RNA molecules found in the cytoplasm of eukaryotic cells, microRNAs (miRNAs) and small interfering RNAs (siRNAs), carry out __________ ________________ ,a process in which these small RNA molecules help trigger the degradation of mRNA or inhibit its translation into protein.

RNA interference (RNAi)

__________ _________________ is a powerful and precise mechanism used by eukaryotic cells to limit the invasion of foreign genes (from viruses and transpoons) and to censor the expression of their own genes. It is triggered by double-stranded RNA molecules, which may arise in several ways: by transcription of inverted repeats into an RNA molecule that then base pairs with itself to form double-stranded RNA; by the simultaneous transcription of two different RNA molecules that are complementary to one another and that pair, forming double-stranded RNA; or by infection by viruses that make double-stranded RNA. These double-stranded RNA molecules are chopped up by an enzyme called ______________, resulting in tiny RNA molecules that are unwound to produce siRNAs and miRNAs.

RNA interferences (RNAi); Dicer

Most eukaryotic cells possess three distinct types of RNA polymerase, each of which is responsible for transcribing a different class of RNA:

RNA polymerase I, RNA polymerase II, RNA polymerase III

Two additional RNA polymerases have been found in plants; these RNA polymerases transcribe RNAs that play a role in DNA methylation and chromatin structure.

RNA polymerase IV & RNA polymerase V

Transcription might initially appear quite different from DNA replication because a single enzyme, _________ ____________, carries out all the required steps of transcription, but actually the processes are quite similar. The action of this enzyme is enhanced by a number of ____________ proteins that join and leave the polymerase at different stages of the process. Each _______________ protein is responsible for providing or regulating a special function. Thus, transcription, like replication, requires an array of proteins.

RNA polymerase; accessory; accessory

A sequence of DNA nucleotides that is copied into an RNA molecule.

RNA-coding region

Both siRNA and miRNA molecules combine with proteins to form an ______-____________ ____________ _____________. Key to the functioning of this is a protein called Argonaute. This RNA multicomplex pairs with an mRNA molecule that possesses a sequence complementary to the RISC's siRNA or miRNA component, and then either cleaves the mRNA, leading to degradation of the mRNA, or represses translation of the mRNA. Some siRNAs also serve as guides for the methylation of complementary sequences in DNA, whereas other alter chromatin structure, both of which affect transcription.

RNA-induced silencing complex (RISC)

Bacterial cells possess two major types of terminators:

Rho-dependent & Rho-independent

This type of terminator is able to cause the termination of transcription only in the presence of an ancillary protein called the rho factor.

Rho-dependent terminator

This type of terminator is able to cause the termination of transcription in the absence of the rho factor.

Rho-independent terminator

Type of RNA that makes up the ribosome along with ribosomal protein subunits

Ribosomal RNA (rRNA)

Catalytic RNA molecules that can cut out parts of their own sequences, connect some RNA molecules together, replicate others, and catalyze the formation of peptide bonds between amino acids.

Ribozymes

____________ _______________ __________ are processed in a similar way to microRNAs. Double-stranded RNA from viruses or long hairpins is cleaved by DIcer to produce siRNAs, which combine with proteins to form RISC. The RISC then pairs with sequences on the target mRNA and cleaves the mRNA, after which the mRNA is degraded.

Small interfering RNAs

Type of RNA that combines with small protein subunits to form small nuclear ribonuclearproteins (snRNPs, "snurps")

Small nuclear RNAs (snRNAs)

Type of RNA that takes parts in the processing of rRNA

Small nucleolar RNAs (snoRNAs)

The nucleotide strand used for transcription

Template strand

Stage of transcription in which the end of the transcription unit is recognized and the RNA molecule is separated from the DNA template

Termination

A sequence of nucleotides that signals where transcription is to end; often part of the RNA-coding sequence; transcription stops only after this has been copied into RNA.

Terminator

The first step in the central dogma; the pathway of information transfer from DNA (genotype) to protein (phenotype); a complex process that requires precursors to RNA nucleotides, a DNA template, and a number of protein components.

Transcription

A stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription.

Transcription unit

_____________ __________ serves as a link between the genetic code in mRNA and the amino acids that make up a protein. Each tRNA attaches to a particular amino acid and carries it to the ribosome, where the tRNA adds its amino acid to the growing polypeptide chain at the position specified by the genetic instructions in the mRNA.

Transfer RNA

Type of RNA that serves as a link between the coding sequence of nucleotides in an mRNA molecule and the amino acid sequence of a polypeptide chain; Each of these attaches to one particular type of amino acid and helps to incorporate that amino acid into a polypeptide chain.

Transfer RNA (tRNA)

True or False? Because not all gene products are needed at the same time or in the same cell, the constant transcription of all of a cell's genes would be highly inefficient. Much of the DNA does not encode a functional product, and transcription of such sequences would be pointless.

True

Many eukaryotic mRNAs undergo ______________ _______________, in which a single pre-mRNA is processed in different ways to produce alternative types of mRNA, resulting in the production of different proteins from the same DNA sequence. One type of this is alternative splicing, in which the same pre-mRNA can be spliced in more than one way to yield multiple mRNAs that are translated into different amino acid sequences and thus different proteins. This processing is an important source of protein diversity in vertebrates; an estimated 60% of all human genes are alternatively spliced.

alternative processing

Each tRNA is capable of attaching to only one type of ____________ _________. The complex of tRNA plus its amino acid can be written in abbreviated form by adding a three-letter superscript representing the amino acid to the term "tRNA". For example, a tRNA that attaches to the amino acid alanine is written as tRNA^Ala.

amino acid

The concept of colinearity suggests that the number of nucleotides in a gene should be proportional to the number of ____________ ___________ in the protein encoded by that gene. In a general sense, this concept is true for genes found in bacterial cells and in many viruses, although those genes are slightly longer than would be expected if colinearity were strictly applied because the mRNAs encoded by the genes contain sequences at their ends that do not specify amino acids.

amino acids

All tRNAs are short RNA molecules that are similar in their secondary structure, a feature that is critical to tRNA function. Some of the nucleotides in a tRNA are complementary to each other and form intramolecular hydrogen bonds. As a result, each tRNA has a cloverleaf structure. All tRNAs have the same sequence (CCA) at the 3' end, where the amino acid attaches to the tRNA. On each tRNA is a set of three nucleotides that make up an __________________, which pairs with the corresponding codon on the mRNA during protein synthesis to ensure that the amino acids link in the correct order.

anticodon

In 1998, Fire, Mello and colleagues observed the inhibiting expression of genes in C. elegans by injecting single-stranded RNA molecules that were complementary to a gene's DNA sequence. Called ____________ RNA, such molecules are known to inhibit gene expression by binding to mRNA sequences and inhibiting translation. Subsequent research revealed an array of small RNA molecules with important cellular functions in eukaryotes, which now include at least three major classes: small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs). These small RNAs are found in many eukaryotes and are responsible for a variety of different functions. An analogous group of small RNAs with silencing functions - CRISPR RNAs (crRNAs) - have been detected in prokaryotes. For their discovery of RNA interference, Fire & Mello were awarded the Nobel Prize in 2006.

antisense

RNA interference is responsible for a number of key genetic and developmental processes, including changes in chromatin structure, translation, cell fate and proliferation, and cell death. Geneticists also use RNAi machinery as an effective tool for ______________ the expression of specific genes.

blocking

The third sequence important for splicing is at the ______________ ____________, which is an adenine nucleotide that lies from 18 to 40 nucleotides upstream of the 3' splice site. The sequence surrounding this is a weak consensus sequence. Deletion or mutation of the adenine nucleotide at this prevents splicing.

branch point

In mRNA, each amino acid in a protein is specified by a set of three nucleotides called a ______________.

codon

Research on mutations in bacteria and viruses led by Francis Crick in 1958 led him to propose that genes and proteins are ______________, that there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein.

colinear

During transcription, an RNA molecule that is __________________ and antiparallel to the DNA template strand is synthesized. The RNA transcript has the same polarity and base sequence as the non-template strand, except that it contains _____________ rather than thymine.

complementary; uracil

Although most promoters vary in sequence in bacteria, short stretches of nucleotides are common to many. Also, the spacing and location of these nucleotides relative to the transcription start site are similar in most promoters. These short stretches of common nucleotides are called ______________ _______________ because they possess considerable similarity, or consensus. The presence of consensus in a set of nucleotides usually implies that the sequence is associated with an important function.

consensus sequences

In 1970, it was discovered that not all genes are _____________________. Researchers found four coding sequences in a gene from a eukaryotic virus that were interrupted by nucleotides that did not specify amino acids. This discovery was made when viral DNA was hybridized (paired) with the mRNA transcribed from it and the hybridized structure was examined using an EM. The DNA was clearly much longer than the mRNA because regions of DNA looped out from the hybridized molecules. These regions of DNA contained nucleotide sequences that were absent from the coding nucleotides in the mRNA. It soon became apparent that most eukaryotic genes consist of stretches of coding and non-coding nucleotides.

continuous

At the heart of most bacterial RNA polymerases are five subunits (individual polypeptide chains) that make up the __________ ___________; this enzyme catalyzes the elongation of the RNA molecule by addition of RNA nucleotides.

core enzyme

Introns are common in ________________ genes but are rare in ________________ genes. All classes of eukaryotic genes - those that encode rRNA, tRNA, and proteins - may contain introns. The numbers and sizes of introns vary widely: some eukaryotic genes have no introns, whereas others may have more than 60; intron length varies from fewer than 200 nucleotides to more than 50,000. Introns tend to be longer than exons, and most eukaryotic genes contain more non-coding nucleotides than coding nucleotides. Most introns do not encode _______________: an intro of one gene is not often an exon for a different gene.

eukaryotic; bacterial; proteins

Many eukaryotic genes contain coding regions called __________ and non-coding regions called intervening sequences, or _____________.

exons; introns

Many geneticists define a ___________ as an entity that includes all sequences in DNA that are transcribed into a single RNA molecule. However, this definition is constantly changing. Currently, it is unclear what much of the genome is transcribed into RNA.

gene

After the sigma factor has associated with the core enzyme (forming a ________________), RNA polymerase binds stably only to the promoter region and initiates transcription at the proper start site. The sigma factor is only required for promoter binding and initiation; after a few RNA nucleotides have been joined together, sigma often detaches from the core enzyme. Many bacteria have multiple types of sigma factors; each type of sigma initiates the binding of RNA polymerase to a particular set of promoters.

holoenzyme; binding

After the sigma factor has associated with the core enzyme (forming a _________________), RNA polymerase binds stably only to the promoter region and initiates transcription at the proper start site. Sigma is required only for promoter _____________ and initiation; after a few RNA nucleotides have been joined together, sigma often detaches from the core enzyme. Many bacteria have multiple types of sigma factors; each type of sigma initiates the binding of RNA polymerase to a particular set of _________________.

holoenzyme; binding; promoters

In bacterial promoters, the sigma factor associates with the core RNA polymerase to form a _________________, which binds to the -35 and -10 consensus sequences in the DNA promoter. The holoenzyme initially binds weakly to the promoter, but then undergoes a change in structure that allows it to bind more tightly and _____________ the double-stranded DNA. The holoenzyme extends from -50 to +20 when bound to the promoter. Unwinding begins within the -10 consensus sequence and extends downstream for about 14 nucleotides, including the start site (from nucleotides -12 to +2).

holoenzyme; unwind

Transcription is a highly selective process: individual genes are transcribed only as their products are needed. However, this selectivity imposes a fundamental problem on the cell:

how to recognize individual genes and transcribe them at the proper time and place

Rho-__________________ terminators, which make up about 50% of all terminators in prokaryotes, have two common features. First, they contain inverted repeats (sequences of nucleotides on the same strand that are inverted and complementary). When these inverted repeats are transcribed into RNA and bind to each other, a secondary structure called a _______________ forms. Second, in these terminators, a string of 7 to 9 adenine nucleotides follows the inverted repeat in the template DNA. Their transcription produces a string of uracil nucleotides after the hairpin in the transcribed RNA. The string of uracil nucleotides in the RNA molecule causes the RNA polymerase to pause, allowing time for the hairpin structure to form. Evidence suggests that the formation of the _______________ destabilizes the DNA-RNA pairing, causing the RNA molecule to separate from its DNA template and transcription to terminate.

independent; hairpin; hairpin

All introns and exons are initially transcribed into RNA, but during or after transcription, the ___________ are removed and the ____________ are joined to yield a mature RNA.

introns; exons

All eukaryotic polymerases are (small/large), multimeric enzymes, typically consisting of more than a dozen subunits. Some subunits are common to all RNA polymerases, whereas others are limited to one type of polymerase. As in bacterial cells, a number of accessory proteins bind to the core enzyme and affect its function.

large

Within ribosomes, the genetic information contained in mRNA are translated into the amino acid sequences of polypeptides. RIbosomes are complex structures, each consisting of more than 50 different proteins and RNA molecules. A functional ribosome consists of two subunits, a ___________ ribosomal subunit and a ___________ ribosomal subunit, each of which consists of one or more RNA molecules and a number of proteins. The sizes of the ribosomes and their RNA components are given in Svedberg (S) units, a measure of how rapidly an object sediments in a centrifugal field.

large; small

Before splicing occurs, an intron lies between an upstream exon (exon 1) and a downstream exon (exon 2). Pre-mRNA is spliced in two distinct steps. In the first step of splicing, the pre-mRN is cut at the 5' splice site. This cut frees exon 1 from the intron, and the 5' end of the intron attaches to the branch point; that is, the intron folds back on itself, forming a structure called a __________. In this reaction, the guanine nucleotide in the consensus sequence at the 5' splice site bonds with the adenine nucleotide at the branch point through a transesterification reaction. As a result, the 5' phosphate group of the guanine nucleotide becomes attached to the 2'-OH group of the adenine nucleotide at the branch point.

lariat

Although the function of many _______________ is still unclear, there is increasing evidence that at least some play a role in controlling gene expression by affecting transcription. For example, lincRNA-p21 interacts with a protein p53, a transcription factor that activates numerous genes, including genes involved in cell cycle control and cancer. By repressing p53, lincRNA-21 affects the transcription of hundreds of genes. Other lncRNAs modify chromatin structure. One of the best-studied is Xist RNA, which plays a central role in dosage compensation in mammalian cells. Still other lncRNAs are complementary to mRNA sequences and function by base pairing with the mRNA and preventing translation or splicing. Evidence suggests that other lncRNAs bring about genomic imprinting.

lncRNAs

Transcription of eukaryotic genomes produces many long RNA molecules that do not encode proteins. Called _________ ______-___________ _________, these RNAs are typically over 100 nucleotides in length. Thousands of lncRNAs have been found in the last five years. The DNA that encodes them, along with other DNA of unknown function, has been called "the dark matter of the genome."

long non-coding RNAs (lncRNAs)

Some snRNAs participate in the processing of RNA, converting pre-mRNA into ___________.

mRNA

A unique feature of tRNA is the presence of rare _____________ __________. All classes of RNAs have nucleotides containing the four standard bases (adenine, cytosine, guanine, and uracil) specified by DNA, but tRNAs have nucleotides containing additional bases, including ribothymine, pseudoridine (which is also occasionally present in snRNAs and rRNA), and dozens of others.

modified bases

When DNA sequences are written out, often the sequence of the __________________ strand is listed because it will be the same as the sequence of the RNA transcribed from the template strand (except that U in RNA replaces T in DNA). By convention, the sequence of the non-template strand is written with the _____ end on the left and the ______ end on the right. The first nucleotide transcribed (the transcription start site) is numbered +1; nucleotides ________________ of the start site are assigned positive numbers, and nucleotides ______________ of the start site are assigned negative numbers. So, nucleotide +34 would be 34 nucleotides downstream of the start site, whereas nucleotide -75 would be 75 nucleotides upstream of the start site. There is no nucleotide numbered 0.

non-template; 5'; 3'; downstream; upstream

The template for RNA synthesis, as for DNA synthesis, is a single strand of the DNA double helix. Unlike replication, however, transcription of a gene occurs on ___________ of the two nucleotide strands of DNA.

one

A second type of modification to eukaryotic mRNA is the addition of 50-250 or more adenine nucleotides at the 3' end, forming a __________ _________. These nucleotides are not encoded in the DNA, but are added after transcription in a process termed polyadenylation. Many eukaryotic genes are transcribed well beyond the end of the coding sequence; most of the extra material at the 3' end is then cleaved, and this structure is added. For some pre-mRNA molecules, more than 1000 nucleotides may be removed from the 3' end before polyadenylation.

poly(A) tail

The __________ __________ confers stability on many mRNAs, increasing the time during which the mRNA remains intact and available for translation before it is degraded by cellular enzymes. The stability conferred by this depends on the proteins that attach to the tail and on its length. This also facilitates the attachment of the ribosome to the mRNA and plays a role in export of the mRNA into the cytoplasm.

poly(A) tail

Processing of the 3' end of pre-mRNA requires sequences, termed the polyadenylation signal, located upstream ad downstream of the site where cleavage occurs. The consensus sequence AAUAAA is often from 11 to 30 nucleotides upstream of the cleavage site and determines the point at which cleavage will occur. A sequence rich in uracil nucleotides (or guanine and uracil nucleotides) is often downstream of the cleavage site. A large number of proteins serve in locating the cleavage site and removing the 3' end. After cleavage has been completed, adenine nucleotides are added without a template to the new 3' end, creating the __________ ________.

poly(a) tail

In bacteria, a group of genes is often transcribed into a single RNA molecule, which is called ___________________ ____________. This is produced when a single terminator is present at the end of a group of several genes that are transcribed together, instead of each gene having its own terminator. The possession of this in eukaryotes is uncommon.

polycistronic RNA

Bacterial cells typically possess only one type of RNA ________________, which catalyzes the synthesis of all classes of bacterial RNA: mRNA, tRNA, and rRNA. Bacterial RNA polymerase is a large, ______________ enzyme (consists of several polypetide chains).

polymerase; multimeric

The genes that encode miRNA are transcribed into longer precursors, called _______________ _______________, that range from several hundred to several thousand nucleotides in length. This gene is then cleaved into one or more smaller RNA molecules with a hairpin, which is a secondary structure that forms when sequences on the same strand are complementary and pair with one another. Dicer binds to this hairpin structure and removes the terminal loop. One of the miRNA strands is incorporated into the RISC; the other strand is released and degraded. The RISC then attaches to a complementary sequence on the target mRNA, often in the 3' untranslated region of the mRNA.

primary microRNA (pri-miRNA)

To begin the synthesis of an RNA molecule, RNA polymerase pairs the base on a ribonucleoside triphosphate with its complementary base at the start site on the DNA template. No ______________ is required to initiate the synthesis of the 5' end of the RNA molecule. _______ of the 3 phosphate groups are cleaved from the ribonucleoside triphosphate as the nucleotide is added to the 3' end of the growing RNA molecule. However, because the 5' end of the first ribonucleoside triphosphate does not take place in the formation of a phosphodiester bond, all 3 of its phosphate groups _____________. An RNA molecule therefore possesses, at least initially, 3 phosphate groups at its 5' end.

primer; Two; remain

Initiation comprises all the steps (4) necessary to begin RNA synthesis, which include:

promoter recognition, formation of a transcription bubble, creation of the first bonds between rNTPs, and escape of the transcription apparatus from the promoter

Included within a transcription unit are 3 critical regions:

promoter, RNA-coding sequence, terminator

Essential information for the transcription apparatus - where it will start transcribing, which strand is to be read, and in what direction the RNA polymerase will move - is embedded in the nucleotide sequence of the ______________. In bacterial cells, promoters are usually adjacent to an ______________________ ___________________.

promoter; RNA-coding sequence

This section of mRNA comprises the codons that specify the amino acid sequence of the protein. This region beings with a start codon and ends with a stop codon.

protein-coding region

Numerous small RNA molecules (most of them 20-30 nucleotides long) have been found that greatly influence many basic biological processes, including the formation of chromatin structure, transcription, and translation. These small RNA molecules play important roles in gene expression, development, cancer, and defense against foreign DNA. They are also being harnessed by researchers to study gene function and treat genetic diseases. The discovery of small RNA molecules has greatly influenced our understanding of how genes are regulated and has shown the importance of DNA sequences that do not encode _____________.

proteins

Transcription initiation requires that the transcription apparatus ___________ and bind to the promoter. At this step, the selectivity of transcription is enforced: the binding of RNA polymerase to the promoter determines which parts of the DNA template are to be transcribed, and how often. Different genes are transcribed with different frequencies, and promoter binding is primarily responsible for determining the ______________ of transcription for a particular gene. Promoters also have different _____________ for RNA polymerase. Even within a single promoter, the affinity an vary with the passage of time, depending on the promoter's interaction with RNA polymerase and a number of other factors.

recognize; frequency; affinities;

RNA is synthesized from _________________ _________________. In synthesis, nucleotides are added one at a time to the 3'-OH group of the growing RNA molecule. Two phosphate groups are cleaved from the incoming ribonucleoside triphosphate; the remaining phosphate group participates in a phosphodiester bond that connects the nucleotide to the growing RNA molecule.

ribonucleoside triphosphates (rNTPs)

Other functional subunits join and leave the core enzyme at particular stages of the transcription process. The ____________ _____________ controls the binding of RNA polymerase to the promoter. Without this factor, RNA polymerase will initiate transcription at a random point along the DNA.

sigma factor

In bacterial cells, transcription and translation occur __________________: while the 3' end of an mRNA is undergoing transcription, ribosomes attach to the Shine-Dalgarno sequence near the 5' end and begin translation. Because transcription and translation are coupled, there is little opportunity for the bacterial mRNA to be _____________ before protein synthesis. In contrast, transcription and translation are separated in both time and space in ______________ cells. Transcription occurs in the _____________, whereas translation occurs in the _____________; this separation provides an opportunity for eukaryotic RNA to be modified before it is translated. Eukaryotic mRNA is extensively altered after transcription. Changes are made to the 5' end, the 3' end, and the protein-coding section of the RNA molecule.

simultaneously; modified; eukaryotic; nucleus; cytoplasm

After the holoenzyme has attached to the promoter, RNA polymerase is positioned over the start site for transcription (at position +1) and has unwound the DNA to produce a ____________-stranded template. The orientation and spacing of consensus sequences on a DNA strand determine which strand will be the template for transcription and thereby determine the direction of _________________.

single; transcription

Two abundant classes of RNA molecules that function in RNA interference in eukaryotes are __________ _____________ __________ and __________________. Although these two types of RNA differ in how they originate, they have a number of features in common, and their functions overlap considerably.

small interfering RNAs; microRNAs

Splicing occurs within a large structure called the ____________________, which is one of the largest and most complex of all molecular structures. This structure consists of five RNA molecules and almost three hundred proteins. The RNA components are small nuclear RNAs; these snRNAs associate with proteins to form small nuclear ribonucleoprotein particles (snRNPs). Each snRNP contains a single snRNA molecule and multiple proteins. The structure is composed of five snRNPs (U1, U2, U3, U4, U5, & U6) and some proteins not associated with an snRNA.

spliceosome

The other major type of modification of eukaryotic pre-mRNA is the removal of introns by RNA _______________. This modification occurs in the nucleus, before the RNA moves to the cytoplasm. _______________ requires the presence of three sequences in the intron. One end of the intron is referred to as the 5' splice site, and the other end is the 3' splice site these splice sites possess short consensus sequences. Most introns in pre-mRNAs begin with GU and end with AG, indicating that these sequences play a crucial role in splicing. Changing a single nucleotide at either of these sites prevents splicing.

splicing; Splicing

Within a gene, only one of the nucleotide strands is normally transcribed into RNA (there are some exceptions). Although only one strand within a single gene is normally transcribed, different genes may be transcribed from different ______________.

strands

RNA polymerase adds nucleotides to the 3' end of the growing RNA molecule until its transcribes a _______________. Most terminators are found upstream of the site at which termination actually occurs. Transcription therefore does not suddenly stop when polymerase reaches a terminator; Rather, transcription stops after the terminator has been ____________________. At the terminator, several overlapping events are needed to bring an end to transcription: RNA polymerase must stop synthesizing RNA, the RNA molecule must be released from RNA polymerase, the newly made RNA molecule must dissociate fully from the DNA, and RNA polymerase must detach from the DNA template.

terminator; transcribed

The overall purpose of transcription:

the selective synthesis of an RNA molecule

All cellular RNAs are synthesized from DNA templates through the process of __________________.

transcription

Many eukaryotic RNAs undergo extensive processing after __________________.

transcription

Transcription occurs within a short stretch of about 18 nucleotides of unwound DNA called the _________________ _____________. As it moves downstream along the template, RNA polymerase progressively unwinds the DNA at the leading ((up/down)stream) edge of the transcription bubble, joining nucleotides to the RNA molecule according to the sequence on the template, and rewinds the DNA at the trailing ((up/down)stream) edge of the bubble.

transcription bubble; downstream; upstream

Pre-mRNAs are modified extensively before becoming mRNA and exiting the nucleus for translation into protein. Bacterial cells do not possess pre-mRNA; in these cells, transcription occurs concurrently with __________________.

translation

Both bacterial and eukaryotic tRNAs are extensively modified after transcription. In E. coli, several tRNAs are often transcribed together as one large precursor tRNA, which is then cut up into pieces, each containing a single tRNA. Additional nucleotides may then be removed one at a time from the 5' and 3' ends of the tRNA in a process known as __________________. Base-modifying enzymes may then change some of the standard bases into modified bases. In some prokaryotes, the CCA sequence found at the 3' end of each tRNA is encoded in the tRNA gene and is transcribed into the tRNA; in other prokaryotes and in eukaryotes, this sequence is added by a special enzyme that adds the nucleotides without the use of any template. Eukaryotic tRNAs are processed in a manner similar to bacterial tRNAs: most are transcribed as part of larger precursors that are then cleaved, trimmed, and modified to produce mature tRNAs.

trimming