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GCD 3022 : Exam 3
| Question | Answer |
|---|---|
| gene regulation | the phenomenon in which the level of gene expression can vary under different conditions, coded proteins are produced only when they are required, avoid wasting energy |
| constitutive genes (unregulated genes) | have constant levels of gene expression all the time, code proteins that are continuously needed for the survival of the bacterium |
| regulatory transcription factors (RTFs) | transcriptional regulation involves the actions of proteins called ___, which can bind to regulatory elements in DNA and affect the rate of transcription of nearby genes |
| repressor (RTF) | an RTF that binds to a regulatory element in the DNA and inhibits transcription rate |
| activator (RTF) | an RTF that binds to a regulatory element in DNA and increases transcription rate |
| negative control | transcriptional regulation by repressor is termed ___ |
| positive control | transcriptional regulation by activators is termed ___ |
| inducer | a small effector molecule that increases the rate of transcription. can bind to a repressor protein and prevent it from binding to the DNA, or it can bind to an activator protein and cause it to bind to the DNA |
| inducible genes | increased gene transcription by inducer proteins |
| corepressor | a small effector molecule that binds to a repressor protein, causing the repressor to bind to the DNA |
| inhibitor | a small effector molecule that binds to an activator protein and prevents it from binding to DNA |
| repressible genes | the genes that corepressor and inhibitors regulate to reduce transcription rate by inhibiting the initiation of transcription |
| enzyme adaptation | the observation that a particular enzyme appears within a living cell only after the cell has been exposed to the substrate for that enzyme |
| operon | a group of two or more genes under the transcriptional control of a single promoter, allows a bacterium to coordinately regulate a group of two or more genes that are involved with the expression of the genes occurs as a single unit |
| polycistronic | coded by operon, an RNA that contains the sequence of two or more genes |
| promoter | signals the start of transcription |
| terminator | signals the end of transcription |
| lac operon | contains several DNA sequences: a CAP site; a lac promoter (lacP); an operator site (lacO); three protein-coding genes, lacZ, lacY, and lacA; and a terminator. |
| lacZ gene | codes β-galactosidase, an enzyme that cleaves lactose into galactose and glucose |
| regulatory elements | short DNA segments that are recognized by regulatory transcription factors (RTFs). The binding of RTFs affect transcription |
| CAP site | a DNA sequence recognized by an activator protein called catabolite activator protein (CAP) |
| operator site (operator) | a sequence of bases that provides a binding site for a repressor protein called lac repressor. |
| Iac repressor | a protein that regulates the Iac operon by binding to the operon site and inhibiting transcription |
| induced | When four molecules of allolactose bind to lac repressor, a conformational change occurs in the repressor that prevents it from binding to the operator site. Under these conditions, RNA polymerase is free to transcribe the operon |
| allosteric regulation | The action of a small effector molecule, such as allolactose, is called ___. The binding of allolactose alters the function of lac repressor by preventing it from binding to the DNA. |
| allosteric sites | The functioning of allosteric proteins, such as lac repressor, is controlled by effector molecules that bind to the proteins’ ___ |
| merozygote | partial diploid |
| trans-effect | a form of genetic regulation that can occur even though two DNA segments are not physically adjacent. The action of lac repressor on the lac operon is a transeffect. |
| trans-acting factor | An RTF, such as lac repressor, is called ___. |
| cis-acting element | a DNA segment that must be adjacent to the gene(s) that it regulates, and it is said to have a cis-effect on gene expression. |
| catabolic repression | the form of transcriptional regulation influenced by glucose presence, which is a catabolite—a substance that is broken down inside the cell. The presence of glucose ultimately leads to repression of the lac operon. |
| diauxic growth | The sequential use of two sugars by a population of dividing bacterial cells, common in bacteria |
| cyclic-AMP(cAMP) | Diauxic growth is a form of regulation that involves a small effector molecule___, which is produced from ATP via an enzyme known as adenylyl cyclase |
| attenuation (trpL) | transcription begins but stopped prematurely, or attenuated, before most of the trp operon is transcribed |
| trp operon | regulated by repressor protein |
| trp repressor (trpR) | a protein coded by trpR gene |
| attenuator sequence | a DNA segment that facilitates termination, When attenuation occurs, the mRNA from the trp operon is made as a short piece that terminates at the attenuator sequence, which is just downstream from the trpL gene |
| posttranslational regulation | the functional control of proteins that are already present in the cell rather than the regulation of transcription or translation. Posttranslational regulation can either activate or inhibit the function of a protein |
| translational regulatory protein | recognizes sequences within the mRNA, similar to the way that transcription factors recognize DNA sequences, |
| translational repressor | translational regulatory proteins that act to inhibit translation |
| antisense RNA | another way bacteria can regulate translation is synthesizing ___, an RNA strand that is complementary to a strand of mRNA |
| feedback inhibition | Common mechanism regulating activity of metabolic enzymes is ___. Synthesis of amino acids, vitamins, & nucleotides convert precursor molecules to particular products. The final product in a metabolic pathway inhibits an enzyme--acts early in the pathway. |
| allosteric enzyme | contains two different binding sites. The catalytic site is responsible for the binding of the substrate and its conversion to intermediate 1. The second site is a regulatory, or allosteric, site. This site binds the final product of the metabolic pathway |
| posttranslational covalent modification | A second strategy to control the function of proteins is the covalent modification of their structure, a process called ___ |
| Gene expression | the process by which the information within a gene is accessed, 1st to synthesize RNA and polypeptides, then to affect the properties of cells and phenotypes of multicellular organisms |
| gene regulation | level of gene expression can vary under different conditions—the level can be increased or decreased. |
| Importance of gene regulation | Respond to environmental changes such as nutrient availability, stress, etc. 2. Produce different cell types in multicellular species 3. Facilitate changes during development |
| importance of Transcription | Regulatory transcription factors- activate or inhibit transcription • Arrangement and composition of nucleosomes • DNA methylation inhibits transcription |
| importance of RNA modification | Alternative splicing alters exon choices. 2. RNA editing alters the base sequence of RNAs |
| importance of translation | 1. Proteins that bind to the 5′ of mRNA regulate translation and those that bind to the 3′ end may influence mRNA degradation. 2. Small RNAs, called miRNAs and siRNAs, silence the translation of mRNA, a process called RNA interference. |
| importance of posttranslation | Feedback inhibition and covalent modifications regulate protein function. The ability to regulate gene expression provides many benefits to eukaryotic organisms—a category that includes protists, fungi, plants, and animals. |
| combinatory control | the combination of many factors determines the expression of any given gene since eukaryotic species are transcriptionally regulated by many factors, |
| transcription factor | a category of proteins that influence the ability of RNA polymerase to transcribe DNA to RNA |
| general transcription factors (GTFs) | required for the binding of RNA polymerase to the core promoter and for progression to the elongation stage, necessary for any transcription to occur |
| regulatory transcription factors (RTFs) | serve to regulate the rate of transcription of target genes |
| domains | regions of protein with specific function |
| motif | When a domain or a portion of a domain has a very similar structure in many different proteins, the structurally similar region is called ___ |
| regulatory elements (regulatory sequences or response elements) | DNA sequences are analogous to the operator sites found near bacterial promoters |
| enhancer | a DNA region that contains one or more regulatory elements |
| activator | If the binding of an RTF to an enhancer increases the rate of transcription, such a regulatory transcription factor is termed an ___ |
| repressor | regulatory transcription factors may act as ___ by binding to enhancers and preventing transcription from occurring. |
| up regulation | When an activator binds to an enhancer, such binding can stimulate transcription 10- to 1000-fold, a phenomenon known as ___ |
| down regulation | the binding of repressors that inhibit transcription |
| orientation-independent (bidirectional) | regulatory element can function in either the forward or the reverse direction. |
| closed conformation (heterochromatin) | If chromatin is in a ___, then transcription may be difficult or impossible |
| open conformation (euchromatin) | chromatin that is in a ____ is more easily accessed by transcription factors and RNA polymerase, allowing transcription to occur |
| ATP-dependent chromatin remodeling (chromatin remodeling) | dynamic changes in the structure of chromatin that occur during the life of a cell. Carried out by diverse multiprotein machines that reposition and restructure nucleosomes • Makes the DNA more or less amenable to transcription |
| DNA translocase | All chromatin-remodeling complexes have a catalytic ATPase subunit called ___, similar to what is found in motor proteins, moves along the DNA. Energy of ATP hydrolysis is used to drive change in location and/or composition of nucleosomes |
| histone variants | mutations that change the amino acid sequences of histone proteins |
| histone acetyltransferases (HATs) | The attachment of the acetyl group (—COCH3) eliminates the positive charge on the lysine side chain, thereby disrupting the electrostatic attraction between the histone protein and the negatively charged DNA backbone and favoring the open conformation |
| Histone deacetylases (HDACs) | remove acetyl groups from acetylated histones and thereby favor a tighter contact between histones and the DNA |
| histone code hypothesis | the pattern of histone modification acts much like a language or code in specifying alterations in chromatin structure, usually inhibits eukaryotic gene transcription |
| DNA methylation | A methyl group (CH3) can be attached to the cytosine base in DNA, a process called ___. |
| DNA methyltransferase | eukaryotic DNA methylation occurs via an enzyme called ___, which attaches a methyl group to the carbon at the number 5 position of the cytosine base, forming 5-methylcytosine. |
| CpG islands | In vertebrates and plants, CpG islands occur near many promoters of genes. (Note: CpG refers to a dinucleotide of C and G in DNA that is connected by a phosphodiester linkage.) |
| housekeeping genes | genes that code proteins required by most cells of a multicellular organism, the cytosine bases in the CpG islands are unmethylated. Therefore, housekeeping genes tend to be expressed in most cell types. |
| tissue-specific genes | genes that are highly regulated and may be expressed only in a particular cell type |
| methyl-CpG-binding proteins | bind to methylated CpG islands. These proteins contain a domain called the methyl-binding domain that specifically recognizes a methylated CpG island. Once bound to DNA, the ___ recruits to that region other proteins that inhibit transcription. |
| de novo methylation | the methylation of DNA that was previously unmethylated |
| maintenance methylation | The hemimethylated DNA is efficiently recognized by DNA methyltransferase, which makes it fully methylated. |
| gene activation | a series of events that enable a gene to be transcribed to produce an RNA molecule |
| nucleosome-free region (NFR) | a region of DNA where nucleosomes are not found, located at the transcriptional start site at the core promoter and transcriptional termination site, act as barriers to heterochromatin formation |
| coactivators | proteins that increase transcription rate but do not bind to DNA directly, ___ enhance transcription many ways by chromatin remodeling, histone modification, recruitment/stimulation of preinitiation complex, and stimulation of transcriptional elongation. |
| preinitiation complex | The actions of chromatin-remodeling complexes and histone-modifying enzymes facilitate the binding of general transcription factors, mediator, and RNA polymerase II to the core promoter, thereby allowing the formation of a ___ |
| insulator, topologically associating domains (TADs) | The segments within a TAD are more likely to interact with each other than they are with segments in other TADs. In this regard, each TAD boundary acts as an ___, which is a structure that limits genetic interactions to a specific region. |
| closed complex (preinitiation complex) | the DNA strands are still bound to each other. TFIIH, which a component of the preinitiation complex, separates the DNA strands to convert the preinitiation complex to an open complex. |
| open complex | For transcription to occur, the strands must be separated into an ___ so that one of them can act as a template for RNA synthesis. |
| promoter escape | For elongation to occur, RNA polymerase II must be released from this binding, an event called ___ |
| proximal promoter pausing | RNA polymerase II pauses in RNA synthesis while it is still fairly close to the transcriptional start site |
| steroid receptor | steroid bind directly to protein |
| cAMP response element-binding protein (CREB protein) | a regulatory transcription factor that becomes activated in response to cell-signaling molecules that cause an increase in the cytoplasmic concentration of the molecule cyclic adenosine monophosphate (cAMP) |
| gene repression | any mechanism that inhibits the transcription of a gene and thereby results in a lower level of RNA synthesis from that gene |
| corepressors | repressors may exert their effects by interacting with other proteins or protein complexes without directly bind to DNA |
| gene silencing | a gene is subjected to changes in chromatin structure that are more permanent in nature |
| chromatin immunoprecipitation sequencing (ChIP-Seq) | a method that enable them to identify the DNA site(s) in a genome where a particular protein binds. |
| immunoprecipitation | The antibodies bind to DNA-protein complexes and cause the complexes to form a pellet following centrifugation. Because an antibody is made by the immune system of an animal, this step is called __ |
| MicroRNAs (miRNAs), Non-coding RNAs (ncRNAs) | ncRNAs that are transcribed from endogenous eukaryotic genes—genes that are normally found in the genome. They play key roles in regulating gene expression, particularly during embryonic development in animals and plants. |
| small interfering RNAs (siRNAs) | ncRNAs that usually originate from sources that are exogenous, which means they are not normally made by cells, The source of siRNAs can be viruses that infect a cell, or researchers can make siRNAs to study gene function experimentally |
| RNA-induced silencing complex (RISC) | a multi-protein complex that facilitates RNA interference (RNAi), a process where non-coding RNAs target and silence protein-encoding genes by guiding the degradation of their mRNA targets |
| processing body (P-body) | The RISC-mRNA complex may remain in a cellular structure called a processing body (P-body), where it can be stored until it is reused or degraded |
| Recombinant DNA technology | the use of in vitro molecular techniques to isolate and manipulate fragments of DNA to produce new arrangements |
| recombinant DNA molecules | Both groups were able to isolate and purify pieces of DNA in a test tube and then covalently link DNA fragments from two different sources. |
| gene cloning | Once inside a host cell, the recombinant molecules are replicated to produce many identical copies of a gene—a process called _____ |
| vector | a small DNA molecule that replicates independently of the chromosomal DNA and produces many identical copies of an inserted gene. The purpose of vector DNA is to act as a carrier of the DNA segment to be cloned. |
| host cell | a cell that harbors a vector |
| plasmids | most vectors are ____ which are small pieces of DNA that are usually circular. |
| origin of replication | plasmids contain a DNA sequence known as __, which is recognized by the replication enzymes of the host cell and allows the plasmid to be replicated, determines whether or not the vector can replicate in a particular type of host cell. |
| selectable marker | expression of the gene selects for the growth of the host cells, resistant to antibiotic or other toxic substances |
| restriction enzymes or restriction endonucleases | used in cloning experiments bind to a specific base sequence and then cleave the DNA backbone at two defined locations, one in each strand |
| DNA ligase | catalyzes covalent bond formation in the sugar-phosphate backbones of both DNA strands after the sticky ends have hydrogen-bonded with each other. |
| palindromic | the sequence in one strand is the same as that in the complementary strand when read in the opposite direction. |
| recombinant vector | The vector containing a piece of chromosomal DNA |
| competent cells | Cells that can take up DNA from the extracellular medium |
| trasformation | Cells that can take up DNA from the extracellular medium are called competent cells. This step in the procedure is called transformation. |
| reverse transcriptase | uses RNA as a template to make a single-stranded or double-stranded DNA molecule |
| complementary DNA (cDNA) | When DNA is made using an RNA template, the DNA is called ___. |
| DNA library | a collection of recombinant vectors |
| genomic library | When the starting material is chromosomal DNA, the library is called a ___ |
| cDNA library | contains recombinant vectors with cDNA inserts |
| Gibson assembly | to insert two different DNA fragments into a vector in a particular order for cloning DNA |
| polymerase chain reaction (PCR) | Another way to copy DNA, without the aid of vectors and host cells, is to use a technique called ___ |
| primers | The primers are oligonucleotides, which are short segments of DNA |
| template DNA | a sample of chromosomal DNA that contains a gene of interest |
| Taq polymerase | a thermostable form of DNA polymerase isolated from the bacterium Thermus aquaticus. A thermostable form of DNA polymerase is necessary because PCR includes heating steps that inactivate most other natural forms of DNA polymerase |
| primer annealing | As the temperature is lowered, oligonucleotide primers hydrogen bond to complementary sequences in the DNA, which is a process called |
| primer extension | Once the primers have annealed, the temperature is raised slightly, and Taq polymerase catalyzes the synthesis of complementary DNA strands in the 5′ to 3′ direction, starting at the primers, which doubles the amount of template DNA |
| thermocycler | automates the timing of the temperature changes in each cycle. The experimenter mixes the DNA sample, dNTPs, Taq polymerase, and an excess amount of primers together in a single tube |
| reverse transcriptase PCR (RT-PCR) | amplify RNA and detect the expression of small amounts of RNA from a single cell |
| quantitative PCR (qPCR) | allows a researcher to follow the amount of a specific PCR product in real time as PCR is taking place in a thermocycler. |
| cycle threshold method (Ct method) | is reached when the accumulation of fluorescence is significantly greater than the background level, for measuring the initial template concentration |
| CRISPR-Cas technology | can be used to edit genes in living cells, provides bacteria with a defense against invasion by bacteriophages |
| enhancements | changing traits that are not involved with causing a disease |
| Northern blotting | used to identify a specific RNA within a mixture of many RNA molecules |
| Western blotting | determine if a specific protein is made in a particular cell type or at a particular stage of development. |
| antibody | An important difference between Western blotting and Northern blotting is that Western blotting uses an antibody as a probe, rather than a labeled DNA strand. Antibodies bind to sites known as epitopes |
| epitope | has a structure that is recognized by an antibody, sequence of an amino acid in the case of protein |
| antigen | any molecule that is recognized by an antibody, contains one or more epitope |
| genetically modified organisms (GMOs) | Recombinant methods also enable the introduction of genetic material into animals and plants |
| transgenic organism | An organism that has received genetic material from a different species |
| transgene | A gene from one species that is introduced into another species |
| biological control | the control of a pest by the introduction of a natural enemy, predator, or a biological product |
| bioremediation | the use of living organisms or their products to decrease pollutants in the environment |
| biotransformation | During bioremediation via microorganisms, enzymes produced by a microorganism modify a toxic pollutant by altering or transforming its structure |
| biodegradation | the toxic pollutant is degraded, yielding less complex, nontoxic metabolites, a form of biotransformation |
| vaccine | a biological preparation that provides active acquired immunity to a particular infectious disease or to a disease such as cancer. |
| vaccination | The practice of administering a vaccine. The term vaccination is from the Latin word vaccina meaning “derived from a cow” because development of the first vaccine involved a cowpox virus |
| cross immunity | antibodies that are made against the cowpox virus can also recognize certain proteins from the smallpox virus and thereby prevent a smallpox infection, immunity of one leads to another immunity against another disease |
| Whole-Pathogen Vaccines | consist of entire pathogens that have been completely inactivated or weakened so they cannot cause serious disease symptoms, include inactivated and attenuated vaccines: |
| inactivated vaccines | contain a pathogen that has been treated in such a way that it cannot cause an infection. Such vaccines typically provide significant short-term immunity, but may not be as strong as attenuated vaccines |
| attenuated vaccines | created by reducing virulence of pathogen, but keep it viable. e.g infectious agent used in vaccine might contain mutations that render it less virulent while retain ability to induce protective immunity, long-lasting, strong, effective immune response |
| viral vector vaccine | use a modified version of a virus that is different from the virus that the vaccine is directed against |
| subunit vaccines | contain only certain components, or antigens, that best stimulate the immune system. The term subunit means that the vaccine contains only a portion of a disease-causing agent. |
| protein (vaccine) | In some therapeutic cancer vaccines, the vaccine contains proteins that are produced by cancer cells. Exposure to these proteins can bolster the immune system to kill the cancer cells |
| polysaccharides (vaccine) | complex carbohydrates composed of sugar units that are linked to each other. e.g., pneumococcal polysaccharide (PPS) vaccine contains a capsular polysaccharide that results in the production of antibodies against 23 species of pathogenic bacteria. |
| PPS vaccine | The antibodies that are produced following PPS vaccination allow immune system cells to phagocytize (engulf) bacteria and thereby destroy them |
| nucleic acid vaccine | production involves introducing genetic material coding the protein antigen or antigens against which an immune response is sought. The body’s own cells then use this genetic material to produce the antigen(s). Include DNA Plasmid Vaccines & mRNA vaccines |
| DNA plasmid vaccine | contain a small circular piece of DNA called a plasmid that carries genes coding proteins from a specific pathogen |
| mRNA vaccine | Vaccines based on messenger RNA (mRNA) usually work by introducing an mRNA that codes a viral spike glycoprotein, which is normally found on the virus’s outer membrane. activates the immune system,which produces antibodies against the spike glycoprotein |
| pandemic | —a disease that occurs over a wide geographic area and usually affects a high proportion of the population |
| Gene editing | alters the DNA sequence of a gene experimentally. Different approaches can be followed to modify genes |
| gene knockout | For diploid species, when both copies of a gene are rendered inactive, the organism is said to carry a ___ |
| Gene addition | involves the insertion of a cloned gene into a genome, such as the genome of a mouse |
| gene knockin | a gene of interest has been inserted into a particular site in the mouse genome |
| GloFish | a strain of transgenic zebrafish (Danio rerio) that glow with bright green, red, or yellow fluorescent color |
| gene redundancy | when one type of gene is inactivated, another gene with a similar function may be able to compensate for the inactive gene, phenotypic change in a knockout mouse |
| mouse model | A strain of mice engineered to carry a mutation that is analogous to a disease-causing mutation of a human gene is termed a __ |
| xenotransplatation | the transplantation of cells, tissues, organ from one animal species to another. |
| molecular pharming | production of medically important proteins in the mammary gland of livestocks |
| Reproductive cloning | biotechnology methods that produce two or more genetically identical individuals. Such individuals occasionally occur in nature; identical twins are genetic clones that began from the same fertilized egg |
| stem cells | supply the various kinds of cells required to construct a multicellular organism, such as an animal or plant, starting from a fertilized egg |
| totipotent | can give rise to all cell types in the adult organism. |
| embryonic stem cells (ES cells), | found in the inner cell mass of the blastocyst |
| pluripotent | they can differentiate into any or almost any cell type of the body. |
| embryonic germ cells (EG cells) | During the early fetal stage of development, the germ-line cells found in the gonads also are pluripotent |
| multipotent | stem cell can differentiate into several cell types but far fewer than an ES cell. |
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