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mutation : variation in the nucleotide sequence of a genome | https://openstax.org/books/biology/pages/14-key-terms |
nucleotide excision repair : type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed | https://openstax.org/books/biology/pages/14-key-terms |
Okazaki fragment : DNA fragment that is synthesized in short stretches on the lagging strand | https://openstax.org/books/biology/pages/14-key-terms |
point mutation : mutation that affects a single base | https://openstax.org/books/biology/pages/14-key-terms |
primase : enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand | https://openstax.org/books/biology/pages/14-key-terms |
primer : short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides | https://openstax.org/books/biology/pages/14-key-terms |
proofreading : function of DNA pol in which it reads the newly added base before adding the next one | https://openstax.org/books/biology/pages/14-key-terms |
replication fork : Y-shaped structure formed during initiation of replication | https://openstax.org/books/biology/pages/14-key-terms |
silent mutation : mutation that is not expressed | https://openstax.org/books/biology/pages/14-key-terms |
single-strand binding protein : during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates | https://openstax.org/books/biology/pages/14-key-terms |
sliding clamp : ring-shaped protein that holds the DNA pol on the DNA strand | https://openstax.org/books/biology/pages/14-key-terms |
spontaneous mutation : mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent | https://openstax.org/books/biology/pages/14-key-terms |
telomerase : enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends | https://openstax.org/books/biology/pages/14-key-terms |
telomere : DNA at the end of linear chromosomes | https://openstax.org/books/biology/pages/14-key-terms |
topoisomerase : enzyme that causes underwinding or overwinding of DNA when DNA replication is taking place | https://openstax.org/books/biology/pages/14-key-terms |
transformation : process in which external DNA is taken up by a cell | https://openstax.org/books/biology/pages/14-key-terms |
transition substitution : when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine | https://openstax.org/books/biology/pages/14-key-terms |
transversion substitution : when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine | https://openstax.org/books/biology/pages/14-key-terms |
The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Almost every species on the planet uses the same genetic code. | https://openstax.org/books/biology/pages/15-chapter-summary |
In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and aÏprotein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin. | https://openstax.org/books/biology/pages/15-chapter-summary |
Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing. | https://openstax.org/books/biology/pages/15-chapter-summary |
Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized. | https://openstax.org/books/biology/pages/15-chapter-summary |
The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide âstepsâ of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation. | https://openstax.org/books/biology/pages/15-chapter-summary |
7-methylguanosine cap : modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation | https://openstax.org/books/biology/pages/15-key-terms |
aminoacyl tRNA synthetase : enzyme that âchargesâ tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid | https://openstax.org/books/biology/pages/15-key-terms |
anticodon : three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon | https://openstax.org/books/biology/pages/15-key-terms |
CAAT box : (GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors | https://openstax.org/books/biology/pages/15-key-terms |
Central Dogma : states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins | https://openstax.org/books/biology/pages/15-key-terms |
codon : three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation | https://openstax.org/books/biology/pages/15-key-terms |
colinear : in terms of RNA and protein, three âunitsâ of RNA (nucleotides) specify one âunitâ of protein (amino acid) in a consecutive fashion | https://openstax.org/books/biology/pages/15-key-terms |
consensus : DNA sequence that is used by many species to perform the same or similar functions | https://openstax.org/books/biology/pages/15-key-terms |
core enzyme : prokaryotic RNA polymerase consisting ofα,α,β, andβ' but missingÏ; this complex performs elongation | https://openstax.org/books/biology/pages/15-key-terms |
degeneracy : (of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous | https://openstax.org/books/biology/pages/15-key-terms |
downstream : nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA | https://openstax.org/books/biology/pages/15-key-terms |
exon : sequence present in protein-coding mRNA after completion of pre-mRNA splicing | https://openstax.org/books/biology/pages/15-key-terms |
FACT : complex that âfacilitates chromatin transcriptionâ by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by | https://openstax.org/books/biology/pages/15-key-terms |
GC-rich box : (GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter | https://openstax.org/books/biology/pages/15-key-terms |
hairpin : structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides | https://openstax.org/books/biology/pages/15-key-terms |
holoenzyme : prokaryotic RNA polymerase consisting ofα,α,β,β', andÏ; this complex is responsible for transcription initiation | https://openstax.org/books/biology/pages/15-key-terms |
initiation site : nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a â+1â | https://openstax.org/books/biology/pages/15-key-terms |
initiator tRNA : in prokaryotes, calledtRNAfMettRNAfMet; in eukaryotes, called tRNAi; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain | https://openstax.org/books/biology/pages/15-key-terms |
intron : nonâprotein-coding intervening sequences that are spliced from mRNA during processing | https://openstax.org/books/biology/pages/15-key-terms |
Kozakâs rules : determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5â-GCC(purine)CCunderlineAUGend underlineG-3â; the bolded bases are most important | https://openstax.org/books/biology/pages/15-key-terms |
nonsense codon : one of the three mRNA codons that specifies termination of translation | https://openstax.org/books/biology/pages/15-key-terms |
nontemplate strand : strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA | https://openstax.org/books/biology/pages/15-key-terms |
Octamer box : (ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter | https://openstax.org/books/biology/pages/15-key-terms |
peptidyl transferase : RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds | https://openstax.org/books/biology/pages/15-key-terms |
plasmid : extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes | https://openstax.org/books/biology/pages/15-key-terms |
poly-A tail : modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus | https://openstax.org/books/biology/pages/15-key-terms |
polysome : mRNA molecule simultaneously being translated by many ribosomes all going in the same direction | https://openstax.org/books/biology/pages/15-key-terms |
preinitiation complex : cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template | https://openstax.org/books/biology/pages/15-key-terms |
promoter : DNA sequence to which RNA polymerase and associated factors bind and initiate transcription | https://openstax.org/books/biology/pages/15-key-terms |
reading frame : sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein | https://openstax.org/books/biology/pages/15-key-terms |
Rho-dependent termination : in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template | https://openstax.org/books/biology/pages/15-key-terms |
Rho-independent : termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase | https://openstax.org/books/biology/pages/15-key-terms |
RNA editing : direct alteration of one or more nucleotides in an mRNA that has already been synthesized | https://openstax.org/books/biology/pages/15-key-terms |
Shine-Dalgarno sequence : (AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome | https://openstax.org/books/biology/pages/15-key-terms |
signal sequence : short tail of amino acids that directs a protein to a specific cellular compartment | https://openstax.org/books/biology/pages/15-key-terms |
small nuclear RNA : molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors | https://openstax.org/books/biology/pages/15-key-terms |
splicing : process of removing introns and reconnecting exons in a pre-mRNA | https://openstax.org/books/biology/pages/15-key-terms |
start codon : AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine | https://openstax.org/books/biology/pages/15-key-terms |
TATA box : conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription | https://openstax.org/books/biology/pages/15-key-terms |
template strand : strand of DNA that specifies the complementary mRNA molecule | https://openstax.org/books/biology/pages/15-key-terms |
transcription bubble : region of locally unwound DNA that allows for transcription of mRNA | https://openstax.org/books/biology/pages/15-key-terms |
upstream : nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA | https://openstax.org/books/biology/pages/15-key-terms |
While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is mostly regulated at the transcriptional level (some epigenetic and post-translational regulation is also present), whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels. | https://openstax.org/books/biology/pages/16-chapter-summary |
The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by thetrpoperon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last exampleâthelacoperonâtwo conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for thelacoperon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription. | https://openstax.org/books/biology/pages/16-chapter-summary |
In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription. | https://openstax.org/books/biology/pages/16-chapter-summary |
To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors tocis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription. | https://openstax.org/books/biology/pages/16-chapter-summary |
Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay. | https://openstax.org/books/biology/pages/16-chapter-summary |
Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein. | https://openstax.org/books/biology/pages/16-chapter-summary |
Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer. | https://openstax.org/books/biology/pages/16-chapter-summary |
3' UTR : 3' untranslated region; region just downstream of the protein-coding region in an RNA molecule that is not translated | https://openstax.org/books/biology/pages/16-key-terms |
5' cap : a methylated guanosine triphosphate (GTP) molecule that is attached to the 5' end of a messenger RNA to protect the end from degradation | https://openstax.org/books/biology/pages/16-key-terms |
5' UTR : 5' untranslated region; region just upstream of the protein-coding region in an RNA molecule that is not translated | https://openstax.org/books/biology/pages/16-key-terms |
activator : protein that binds to prokaryotic operators to increase transcription | https://openstax.org/books/biology/pages/16-key-terms |
catabolite activator protein (CAP) : protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available | https://openstax.org/books/biology/pages/16-key-terms |
cis-acting element : transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it | https://openstax.org/books/biology/pages/16-key-terms |
dicer : enzyme that chops the pre-miRNA into the mature form of the miRNA | https://openstax.org/books/biology/pages/16-key-terms |
DNA methylation : epigenetic modification that leads to gene silencing; commonly found in cancer cells | https://openstax.org/books/biology/pages/16-key-terms |
enhancer : segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene | https://openstax.org/books/biology/pages/16-key-terms |
epigenetic : heritable changes that do not involve changes in the DNA sequence | https://openstax.org/books/biology/pages/16-key-terms |
eukaryotic initiation factor-2 (eIF-2) : protein that binds first to an mRNA to initiate translation | https://openstax.org/books/biology/pages/16-key-terms |
gene expression : processes that control the turning on or turning off of a gene | https://openstax.org/books/biology/pages/16-key-terms |
guanine diphosphate (GDP) : molecule that is left after the energy is used to start translation | https://openstax.org/books/biology/pages/16-key-terms |
guanine triphosphate (GTP) : energy-providing molecule that binds to eIF-2 and is needed for translation | https://openstax.org/books/biology/pages/16-key-terms |
histone acetylation : epigenetic modification that leads to gene silencing; commonly found in cancer cells | https://openstax.org/books/biology/pages/16-key-terms |
inducible operon : operon that can be activated or repressed depending on cellular needs and the surrounding environment | https://openstax.org/books/biology/pages/16-key-terms |
initiation complex : protein complex containing eIF2-2 that starts translation | https://openstax.org/books/biology/pages/16-key-terms |
lac operon : operon in prokaryotic cells that encodes genes required for processing and intake of lactose | https://openstax.org/books/biology/pages/16-key-terms |
large 60S ribosomal subunit : second, larger ribosomal subunit that binds to the RNA to translate it into protein | https://openstax.org/books/biology/pages/16-key-terms |
microRNA (miRNA) : small RNA molecules (approximately 21 nucleotides in length) that bind to RNA molecules to degrade them | https://openstax.org/books/biology/pages/16-key-terms |
myc : oncogene that causes cancer in many cancer cells | https://openstax.org/books/biology/pages/16-key-terms |
negative regulator : protein that prevents transcription | https://openstax.org/books/biology/pages/16-key-terms |
operator : region of DNA outside of the promoter region that binds activators or repressors that control gene expression in prokaryotic cells | https://openstax.org/books/biology/pages/16-key-terms |
operon : collection of genes involved in a pathway that are transcribed together as a single mRNA in prokaryotic cells | https://openstax.org/books/biology/pages/16-key-terms |
poly-A tail : a series of adenine nucleotides that are attached to the 3' end of an mRNA to protect the end from degradation | https://openstax.org/books/biology/pages/16-key-terms |
positive regulator : protein that increases transcription | https://openstax.org/books/biology/pages/16-key-terms |
post-transcriptional : control of gene expression after the RNA molecule has been created but before it is translated into protein | https://openstax.org/books/biology/pages/16-key-terms |
post-translational : control of gene expression after a protein has been created | https://openstax.org/books/biology/pages/16-key-terms |
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