BIOL-1610: S.G. Unit Four
What is a point mutation?
chemical changes in just one base pair of a gene changes in a single nucleotide pair of a gene
Diagram mRNA termination
poly-A tail found in eukaryotes
What is an enhancer?
Groups of transcription factor binding sites called enhancers and silencers can turn a gene on/off in specific parts of the body.
What is differential gene expression?
The expression of different sets of genes by cells with the same genome. Each cell expresses the genome differently.
What are three methods used to determine what mRNA is being produced in a given biological tissue and briefly describe each method.
1.) In situ hybridization 2.) PT-PCR 3.) RNA-seq In situ hybridization and RT-PCR can detect the presence of a given mRNA in a tissue or an RNA sample, respectively Analysis of when and where a gene or group of genes is expressed can provide important clues about gene function The most straightforward way to discover which genes are expressed in certain cells is to identify the mRNAs being made
What direction do ribosomes read mRNA to make a protein?
5' to 3'
What direction does DNA polymerase synthesize a new strand of DNA?
5'-3' Since DNA polymerase requires a free 3' OH group for initiation of synthesis, it can synthesize in only one direction by extending the 3' end of the preexisting nucleotide chain. Hence, DNA polymerase moves along the template strand in a 3'-5' direction, and the daughter strand is formed in a 5'-3' direction.
What are the two categories of point mutations?
: (1) single nucleotide-pair substitutions and (2) nucleotide-pair insertions or deletions. Insertions and deletions can involve one or more nucleotide pairs.
define totipotent?
A cell that can become all of the different cells of an organism The successful cloning of whole plants from single differentiated cells was accomplished during the 1950s by F. C. Steward and his students at Cornell University, who worked with carrot plants (Figure 20.15). They found that differentiated cells taken from the root (the carrot) and incubated in culture medium could grow into normal adult plants, each genetically identical to the parent plant. These results showed that differentiation does not necessarily involve irreversible changes in the DNA. In plants, at least, mature cells can "dedifferentiate" and then give rise to all the specialized cell types of the organism. Any cell with this potential is said to be totipotent.
What is an oncogene?
A gene found in viral or cellular genomes that is involved in triggering molecular events that can lead to cancer Cancer research led to the discovery of cancer-causing genes called oncogenes (from the Greek onco, tumor) in certain types of viruses (see Chapter 19). Subsequently, close counterparts of viral oncogenes were found in the genomes of humans and other animals. The normal versions of the cellular genes, called proto-oncogenes, code for proteins that stimulate normal cell growth and division. How might a proto-oncogene—a gene that has an essential function in normal cells—become an oncogene, a cancer-causing gene? In general, an oncogene arises from a genetic change that leads to an increase either in the amount of the proto-oncogene's protein product or in the intrinsic activity of each protein molecule. The genetic changes that convert proto-oncogenes to oncogenes fall into three main categories: movement of DNA within the genome, amplification of a proto-oncogene, and point mutations in a control element or in the proto-oncogene itself
What is a proto-oncogene?
A normal gene which, when altered by mutation, becomes an oncogene that can contribute to cancer. Proto-oncogenes may have many different functions in the cell. Some proto-oncogenes provide signals that lead to cell division. Other proto-oncogenes regulate programmed cell death (apoptosis). Cancer research led to the discovery of cancer-causing genes called oncogenes (from the Greek onco, tumor) in certain types of viruses (see Chapter 19). Subsequently, close counterparts of viral oncogenes were found in the genomes of humans and other animals. The normal versions of the cellular genes, called proto-oncogenes, code for proteins that stimulate normal cell growth and division. How might a proto-oncogene—a gene that has an essential function in normal cells—become an oncogene, a cancer-causing gene? In general, an oncogene arises from a genetic change that leads to an increase either in the amount of the proto-oncogene's protein product or in the intrinsic activity of each protein molecule. The genetic changes that convert proto-oncogenes to oncogenes fall into three main categories: movement of DNA within the genome, amplification of a proto-oncogene, and point mutations in a control element or in the proto-oncogene itself
What is nuclear transplantation?
A nucleus is removed from an adult donor cell and is injected into a nucleus-free egg cell, and then induced to grow into an embryo that may give rise to a whole organism through cell division.
What is a polysome and what is its function?
A number of ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome). Polyribosomes enable a cell to make many copies of a polypeptide very quickly Once a ribosome is far enough past the start codon, a second ribosome can attach to the mRNA, eventually resulting in a number of ribosomes trailing along the mRNA. Such strings of ribosomes, called polyribosomes (or polysomes), can be seen with an electron microscope (see Figure 17.22). They enable a cell to make many copies of a polypeptide very quickly.
What is a prophage?
A phage genome that has been inserted into a specific site on a bacterial chromosome
What is a virulent phage?
A phage that reproduces only by the lytic cycle
What is a repressor?
A protein that inhibits gene transcription. In prokaryotes, repressors bind to the DNA in or near the promoter. In eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA.
What is a transcription unit?
A region of DNA that is transcribed into an RNA molecule The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule
What is the function of a 3' poly-A tail?
A sequence of 50-250 adenine nucleotides added onto the 3′ end of a pre-mRNA molecule. The tail makes the transcript more stable and helps it get exported from the nucleus to the cytosol. purpose of modifications: - facilitate export of mRNA - protects mRNA from hydrolytic enzymes (chew up RNA) - helps ribosomes attach to the 5' end
What is a TATA box?
A sequence on DNA that signals the beginning of a gene. DNA promoter region; "GOLD STAMP - this is the correct place to land" A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.
What are Short Tandem Repeats (STRs) and how do they help in forensic investigations?
A short tandem repeat (STR) in DNA occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. An STR is also known as a microsatellite. The pattern can range in length from 2 to 16 base pairs (bp) and is typically in the non-coding intron region. Today, forensic scientists use an even more sensitive method that takes advantage of variations in length of genetic markers called short tandem repeats (STRs). These are tandemly repeated units of two- to five-nucleotide sequences in specific regions of the genome. The number of repeats present in these regions is highly variable from person to person (polymorphic), and even for a single individual, the two alleles of an STR may differ from each other. For example, one individual may have the sequence ACAT repeated 30 times at one genome locus and 15 times at the same locus on the other homolog, whereas another individual may have 18 repeats at this locus on each homolog. (These two genotypes can be expressed by the two repeat numbers: 30,15 and 18,18.) PCR is used to amplify particular STRs, using sets of primers that are labeled with differentcolored fluorescent tags; the length of the region, and thus the number of repeats, can then be determined by electrophoresis. The PCR step allows use of this method even when the DNA is in poor condition or available only in minute quantities. A tissue sample containing as few as 20 cells can be sufficient for PCR amplification.
What are Single Nucleotide Polymorphisms (SNPs) and how do they help predict disease?
A single base-pair site where variation is found in at least 1% of the population is called a single nucleotide polymorphism (SNP, pronounced "snip"). Once a SNP is identified that is found in all affected people, researchers focus on that region and sequence it. In nearly all cases, the SNP itself does not contribute directly to the disease in question by altering the encoded protein; in fact, most SNPs are in noncoding regions. Instead, if the SNP and a disease-causing allele are close enough, scientists can take advantage of the fact that crossing over between the marker and the gene is very unlikely during gamete formation. Therefore, the marker and gene will almost always be inherited together, even though the marker is not part of the gene (Figure 20.14). SNPs have been found that correlate with diabetes, heart disease, and several types of cancer, and the search is on for genes that might be involved.
What is a co-repressor?
A small molecule that binds to a bacterial repressor protein and changes the protein's shape, allowing it to bind to the operator and switch an operon off.
What is a codon?
A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code
define the function of mRNA
A type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein. (In eukaryotes, the primary RNA transcript must undergo RNA processing to become mRNA.) codon message from DNA Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of a series of three-base code "words," each of which specifies a particular amino acid. it carries a genetic/codon message from the DNA to the protein-synthesizing machinery of the cell.
What is an operon?
A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway.
What is a provirus?
A viral genome that is permanently inserted into a host genome.
What is a bacteriophage?
A virus that infects bacteria Many of the most complex capsids are found among the viruses that infect bacteria, called bacteriophages, or simply phages. The first phages studied included seven that infect Escherichia coli. These seven phages were named type 1 (T1), type 2 (T2), and so forth, in the order of their discovery. The three T-even phages (T2, T4, and T6) turned out to be very similar in structure.
Diagram a repressible operon. Include brief descriptions.
ACTIVATES REPRESSOR; represses (turns off) operon A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription KAHN ACADEMY: Other operons are usually "on," but can be turned "off" by a small molecule. The molecule is called a corepressor, and the operon is said to be repressible. For example, the trp operon is a repressible operon that encodes enzymes for synthesis of the amino acid tryptophan. This operon is expressed by default, but can be repressed when high levels of the amino acid tryptophan are present. The corepressor in this case is tryptophan.
What are the two steps for accurate translation?
Accurate translation requires two steps - First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase - Second: a correct match between the tRNA anticodon and an mRNA codon Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon- redundancy in the code
What is an adult stem cell?
Adult stem cells can generate multiple (but not all) cell types and are used in the body to replace non-reproducing cells as needed -Multipotent stem cells The adult body also has stem cells, which serve to replace nonreproducing specialized cells as needed. In contrast to ES cells, adult stem cells are not able to give rise to all cell types in the organism, though they can generate multiple types. For example, one of the several types of stem cells in bone marrow can generate all the different kinds of blood cells (see Figure 20.20), and another can differentiate into bone, cartilage, fat, muscle, and the linings of blood vessels. To the surprise of many, the adult brain has been found to contain stem cells that continue to produce certain kinds of nerve cells there. Researchers have also reported finding stem cells in skin, hair, eyes, and dental pulp.
define multipotent?
Adult stem cells or cord blood stem cells that can develop into more than one cell type BUT are limited when compared to pluripotent cells.
define the function of tRNA
An RNA molecule that functions as a translator between nucleic acid and protein languages by carrying specific amino acids to the ribosome, where they recognize the appropriate codons in the mRNA. links single amino acid to anti-codon In the process of translation, a cell "reads" a genetic message and builds a polypeptide accordingly. The message is a series of codons along an mRNA molecule, and the translator is called transfer RNA (tRNA). The function of tRNA is to transfer amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome.
What is a retrovirus?
An RNA virus that replicates by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer causing viruses.
define the function of pre-mRNA
An initial RNA transcript from any gene; also called pre-mRNA when transcribed from a protein-coding gene. a type of primary transcript that becomes a messenger RNA (mRNA) after processing. When an RNA transcript is first made in a eukaryotic cell, it is considered a pre-mRNA and must be processed into a messenger RNA (mRNA). A 5' cap is added to the beginning of the RNA transcript, and a 3' poly-A tail is added to the end. In splicing, some sections of the RNA transcript (introns) are removed, and the remaining sections (exons) are stuck back together. Some genes can be alternatively spliced, leading to the production of different mature mRNA molecules from the same initial transcript. sequences, or introns. Expressed regions are called exons. RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence. Splicing can be carried out by enzymes made of protein called spliceosomes or enzymes made of RNA called ribozymes
Name a known proto-oncogene.
Another well-known proto-oncogene is HER2. This gene makes protein receptors that are involved in the growth and division of cells in the breast. Many people with breast cancer have a gene amplification mutation in their HER2 gene. This type of breast cancer is often referred to as HER2-positive breast cancer
RT-PCR describe (method to determine what mRNA is being produces)
Application RT-PCR uses the enzyme reverse transcriptase (RT) in combination with PCR and gel electrophoresis. RT-PCR can be used to compare gene expression between samples—for instance, in different embryonic stages, in different tissues, or in the same type of cell under different conditions. Technique In this example, samples containing mRNAs from six embryonic stages of Drosophila were analyzed for a specific mRNA as shown below. (In steps 1 and 2, the mRNA from only one stage is shown.) Results The mRNA for this gene first is expressed at stage 2 and continues to be expressed through stage 6. The size of the amplified fragment (shown by its position on the gel) depends on the distance between the primers that were used (not on the size of the mRNA).
Describe the viral Lytic Cycle.
Attachment. The T4 phage uses its tail fibers to bind to specific surface proteins on an E. coli cell that act as receptors. Entry of phage DNA and degradation of host DNA. The sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell's DNA is hydrolyzed Synthesis of viral genomes and proteins. The phage DNA directs production of phage proteins and copies of the phage genome by host and viral enzymes, using components within the cell. Self-assembly. Three separate sets of 3 proteins self-assemble to form phage heads, tails, and tail fibers. The phage genome is packaged inside the capsid as the head forms. 4 Release. The phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. The cell swells and finally bursts, releasing 100 to 200 phage particles.
What defense mechanism do bacteria utilize to remove viral DNA from the bacterial chromosome?
Bacterial Defense against viral infection • Natural Selection - fast-paced evolutionary war. • Restriction Enzymes - DNA cutters that restrict viral propagation by cutting unmarked cellular DNA. • CRISPR-Cas9 system (Clustered Regularly Interspersed Short Palindromic Repeats) Associated Proteins
What is a general transcription factor?
Basal, or general, transcription factors are necessary for RNA polymerase to function at a site of transcription in eukaryotes.
Which terminus of the polypeptide chain are new amino acids added to during translation?
C-terminus When a protein is translated from messenger RNA, it is created from N-terminus to C-terminus. The amino end of an amino acid (on a charged tRNA) during the elongation stage of translation, attaches to the carboxyl end of the growing chain. Schematic model with mRNA and tRNA. A tRNA fits into a binding site when its anticodon base-pairs with an mRNA codon. The P site holds the tRNA attached to the growing polypeptide. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. Discharged tRNAs leave from the E site. The polypeptide grows at its carboxyl end.
One method of determining a gene's function is the CRISPR-Cas9 system. Diagram how this works and describe the steps.
CRISPR Delivery into the cell 1. Electroporation 2. Transfection (Cationic lipid, Calcium phosphatase 3. Viral Infection (Adeno-associated virus, lentivirus, etc.) - Can Knock Out a given gene - Can replace a mutant allele with an introduced wild-type allele - Or modify an organisms ability to transmit infectious disease (gene-editing) An introduced allele can be engineered so that it removes, then replaces, the other existing allele on the homologous chromosome. If this is in a germ line cell, offspring will inherit the introduced allele, and offspring's "non-introduced" alleles will also be replaced by the engineered allele (gene drive)
define unipotent?
Capable of giving rise to only one kind of cell
What substances would be differentially expressed in a liver cells vs. a lens cell that would ensure that the cell produces proteins necessary for proper function. Be able to diagram this.
Cell type-specific transcription. Both liver cells and lens cells have the genes for making the proteins albumin and crystallin, but only liver cells make albumin (a blood protein) and only lens cells make crystallin (the main protein of the lens of the eye). The specific transcription factors made in a cell determine which genes are expressed. In this example, the genes for albumin and crystallin are shown at the top, each with an enhancer made up of three different control elements. Although the enhancers for the two genes both have a gray control element, each enhancer has a unique combination of elements. All the activator proteins required for high-level expression of the albumin gene are present only in liver cells (a), whereas the activators needed for expression of the crystallin gene are present only in lens cells (b). For simplicity, we consider only the role of specific transcription factors that are activators here, although repressors may also influence transcription in certain cell types.
What is cDNA?
Complementary strand of DNA synthesized from an RNA template by the enzyme reverse transcriptase - A complementary DNA (cDNA) library is made by cloning DNA made in vitro by reverse transcription of all the mRNA produced by a particular cell - A cDNA library represents only part of the genome only the subset of genes transcribed into mRNA in the original cells .One method that is widely used is called the reverse transcriptasepolymerase chain reaction, or RT-PCR. RT-PCR begins by turning sample sets of mRNAs into double-stranded DNAs with the corresponding sequences. First, the enzyme reverse transcriptase (from a retrovirus; see Figure 19.8) is used in vitro to make a single-stranded DNA reverse transcript of each mRNA molecule (Figure 20.11). Recall that the 3¿ end of the mRNA has a stretch of adenine (A) nucleotides called a poly-A tail. This allows use of a short complementary strand of thymine deoxyribonucleotides (poly-dT) as a primer for synthesis of this DNA strand. Following enzymatic degradation of the mRNA, a second DNA strand, complementary to the first, is synthesized by DNA polymerase. The resulting double-stranded DNA is called complementary DNA (cDNA). (Made from mRNA, cDNA lacks introns and can be used for protein expression in bacteria, as mentioned earlier.)
define pluripotent?
Embryonic stem cells that give rise to all cell types that make up the body except placenta
What is "wobble"?
Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon- redundancy in the code Such versatility is possible because the rules for base pairing between the third nucleotide base of a codon and the corresponding base of a tRNA anticodon are relaxed compared to those at other codon positions. For example, the nucleotide base U at the 5¿ end of a tRNA anticodon can pair with either A or G in the third position (at the 3¿ end) of an mRNA codon. The flexible base pairing at this codon position is called wobble. Wobble explains why the synonymous codons for a given amino acid most often differ in their third nucleotide base, but not in the other bases. A case in point is that a tRNA with the anticodon 3¿-UCU-5¿ can base-pair with either the mRNA codon 5¿-AGA-3¿ or 5¿-AGG-3¿, both of which code for arginine
Gel Electrophoresis allows scientists to separate genetic material. On what criteria is the material separated and how is this accomplished?
Gel electrophoresis. A gel made of a polymer acts as a molecular sieve to separate nucleic acids or proteins differing in size, electrical charge, or other physical properties as they move in an electric field. In the example shown here, DNA molecules are separated by length in a gel made of a polysaccharide called agarose Each sample, a mixture of different DNA molecules, is placed in a separate well near one end of a thin slab of agarose gel. The gel is set into a small plastic support and immersed in an aqueous, buffered solution in a tray with electrodes at each end. The current is then turned on, causing the negatively charged DNA molecules to move toward the positive electrode. Shorter molecules are slowed down less than longer ones, so they move faster through the gel. After the current is turned off, a DNA-binding dye is added that fluoresces pink in UV light. Each pink band corresponds to many thousands of DNA molecules of the same length. The horizontal ladder of bands at the bottom of the gel is a set of restriction fragments of known sizes for comparison with samples of unknown length
Describe histone acetylation.
Histone Modifications - In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails - This loosens chromatin structure, thereby promoting the initiation of transcription - The addition of methyl groups to chromatin (methylation) can condense chromatin, leading to suppression of transcription - The addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin. - DNA methylation will always lead to suppression of transcription The attachment of acetyl groups to certain amino acids of histone proteins. histone acetylation appears to promote transcription by opening up the chromatin structure (Figure 18.7b), while addition of methyl groups can lead to the condensation of chromatin and reduced transcription.
What is a spliceosome?
How is pre-mRNA splicing carried out? The removal of introns is accomplished by a large complex made of proteins and small RNAs called a spliceosome. This complex binds to several short nucleotide sequences along an intron, including key sequences at each end (Figure 17.12). The intron is then released (and rapidly degraded), and the spliceosome joins together the two exons that flanked the intron. It turns out that the small RNAs in the spliceosome not only participate in spliceosome assembly and splice site recognition, but also catalyze the splicing reaction.
What is a poly-A adenlyation signal?
How is the poly-A tail added? The 3' end of the RNA forms in kind of a bizarre way. When a sequence called a polyadenylation signal shows up in an RNA molecule during transcription, an enzyme chops the RNA in two at that site. Another enzyme adds about 100100100 - 200200200 adenine (A) nucleotides to the cut end, forming a poly-A tail. The tail makes the transcript more stable and helps it get exported from the nucleus to the cytosol.
Diagram an inducible operon. Include brief descriptions.
INACTIVE REPRESSOR; induces (turns on) operon An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription KAHN ACADEMY: Some operons are usually "off," but can be turned "on" by a small molecule. The molecule is called an inducer, and the operon is said to be inducible. For example, the lac operon is an inducible operon that encodes enzymes for metabolism of the sugar lactose. It turns on only when the sugar lactose is present (and other, preferred sugars are absent). The inducer in this case is allolactose, a modified form of lactose.
In situ hybridization describe (method to determine what mRNA is being produces)
Identified mRNAs can be detected by nucleic acid hybridization with complementary molecules - These complementary molecules, of either DNA or RNA, are nucleic acid probes - In situ hybridization uses fluorescent dyes attached to probes to identify the location of specific mRNAs in place in the intact organism Determining where genes are expressed by in situ hybridization analysis. A Drosophila embryo was incubated in a solution containing probes for five different mRNAs, each probe labeled with a different fluorescently colored tag. The embryo was then viewed from the belly (ventral) side using fluorescence microscopy; the resulting fluorescent micrograph is shown in the middle, above. Each color marks where a specific gene is expressed as mRNA. The arrows from the groups of yellow and blue cells above the micrograph show a magnified view of nucleic acid hybridization of the appropriately colored probe to the mRNA. Yellow cells (expressing the wg gene) interact with blue cells (expressing the en gene); their interaction helps establish the pattern in a body segment. The diagram at the bottom clarifies the eight segments visible in this view.
What is RNA splicing?
In RNA splicing, introns are removed and exons joined. RNA splicing is typically carried out by spliceosomes, but in some cases, RNA alone catalyzes its own splicing. The catalytic ability of some RNA molecules, called ribozymes, derives from the inherent properties of RNA. The presence of introns allows for alternative RNA splicing.
What is an operator?
In bacterial and phage DNA, a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon.
What is a frameshift mutation?
Insertions and deletions are additions or losses of nucleotide pairs in a gene • These mutations have a disastrous effect on the resulting protein more often than substitutions do • Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation
nucleotide-pair insertions and deletions
Insertions and deletions are additions or losses of nucleotide pairs in a gene. These mutations have a disastrous effect on the resulting protein more often than substitutions do.
Reverse Transcriptase describe and diagram
Making complementary DNA (cDNA) from eukaryotic genes. Complementary DNA is made in vitro using mRNA as a template for the first strand. The mRNA contains only exons, so the resulting double-stranded cDNA carries the continuous coding sequence of the gene. Only one mRNA is shown here, but the final collection of cDNAs would reflect all the mRNAs present in the cell sample. Figure 20.12 shows how the cDNA of interest is identified.
What is an embryonic stem cell?
Many early embryos contain stem cells capable of giving rise to differentiated embryonic cells of all type except placenta (pluripotent) - In culture, given specific chemical treatment and "feeder cells", these embryonic stem cells reproduce indefinitely - Depending on culture conditions, they can be made to differentiate into a variety of specialized cells The developmental potential of adult stem cells is limited to certain tissues. ES cells hold more promise than adult stem cells for most medical applications because ES cells are pluripotent, capable of differentiating into many different cell types. The only way to obtain ES cells thus far, however, has been to harvest them from human embryos, which raises ethical and political issues
What are three sources for a viral membrane envelope?
Many viruses that infect animals have a membranous envelope • 1. Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell 2. Some viral envelopes are formed from the host cell's plasma membrane as the viral capsids exit 3. Other viral membranes form from the host'snuclear envelope and are then replaced by an envelope made from Golgi apparatus membrane
List and describe four methods of post-transcriptional regulation.
Mechanisms of Post-Transcriptional Regulation • After transcription, additional mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes - RNA processing - mRNA degradation - Initiation of translation - Protein processing and degradation
How does a prion propagate itself?
Model for how prions propagate. Prions are misfolded versions of normal brain proteins. When a prion contacts a normally folded version of the same protein, it may induce the normal protein to assume the abnormal shape. The resulting chain reaction may continue until high levels of prion aggregation cause cellular malfunction and eventual degeneration of the brain
How do the results of nuclear transplantation of embryonic nuclei compare to transplantation of somatic nuclei?
Nuclear transplantation (NT) involves placing a nucleus from a donor cell into another (recipient) cell. transplantation of early embryo resulted in the most development of tadpoles, transplantation of differentiated intestinal cell less than 2% developed into a tadpole. Somatic nuclei are more specialized and no longer contain genes necessary to still be considered pluripotent
What is a reading frame?
On an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis.
What is an obligate parasite?
Parasite which cannot live without a host.
What are plasmids?
Plasmids are small circular DNA molecules that replicate separately from the bacterial chromosome - E.coli is commonly used In addition to their bacterial chromosome, E. coli and many other bacteria also have plasmids, small, circular DNA molecules that are replicated separately. A plasmid has only a small number of genes; these genes may be useful when the bacterium is in a particular environment but may not be required for survival or reproduction under most conditions To clone pieces of DNA using bacteria, researchers first obtain a plasmid (originally isolated from a bacterial cell and genetically engineered for efficient cloning) and insert DNA from another source ("foreign" DNA) into it (Figure 20.5). The resulting plasmid is now a recombinant DNA molecule, a molecule containing DNA from two different sources, very often different species. The plasmid is then returned to a bacterial cell, producing a recombinant bacterium
What is a signal peptide?
Polypeptide synthesis always begins in the cytosol • Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER • Polypeptides destined for the ER or for secretion are marked by a signal peptide • A signal-recognition particle (SRP) binds to the signal peptide • The SRP brings the signal peptide and its ribosome to the ER The polypeptides of proteins destined for the endomembrane system or for secretion are marked by a signal peptide, which targets the protein to the ER (Figure 17.21). The signal peptide, a sequence of about 20 amino acids at or near the leading end (Nterminus) of the polypeptide, is recognized as it emerges from the ribosome by a protein-RNA complex called a signal-recognition particle (SRP).
What two factors make them such a formidable and difficult pathogen?
Prions are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals. • Slow disease onset~10 years to become symptomatic • or high-pressure (several atmospheres) AND strong alkali (pH13+)
What is reproductive cloning?
Producing an individual who is genetically the same as another Since that time, researchers have cloned numerous other mammals, including mice, cats, cows, horses, pigs, dogs, and monkeys. In most cases, their goal has been the production of new individuals; this is known as reproductive cloning. We have already learned a lot from such experiments. For example, cloned animals of the same species do not always look or behave identically.
What is the difference between a prophage and a provirus?
Prophage is a bacteriophage DNA that is inserted into the bacterial cell by the virus and is integrated into the bacterial DNA. Provirus is a viral genome that is inserted into a eukaryotic host cell by the virus and is integrated into the host DNA. Prophage infects bacteria
define the function of rRNA
RNA molecules that, together with proteins, make up ribosomes; the most abundant type of RNA brings mRNA and tRNA together and polymerizes a chain of amino acids (polypeptide) Ribosomes facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis. A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs. (rRNAs make up ribosomal subunits) Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences: some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes
What direction does RNA polymerase synthesize pre-mRNA?
RNA polymerase synthesizes an RNA transcript complementary to the DNA template strand in the 5' to 3' direction. It moves forward along the template strand in the 3' to 5' direction, opening the DNA double helix as it goes.
Be able to diagram protein translation
Translation: the basic concept. As a molecule of mRNA is moved through a ribosome, codons are translated into amino acids, one by one. The interpreters are tRNA molecules, each type with a specific nucleotide triplet called an anticodon at one end and a corresponding amino acid at the other end. A tRNA adds its amino acid cargo to a growing polypeptide chain when the anticodon hydrogenbonds to the complementary codon on the mRNA. The figures that follow show some of the details of translation in a bacterial cell.
What are induced Pluripotent Stem Cells (iPSCs)?
Researchers can treat mature differentiated cells, and reprogram them to act like ES cells Researchers used retroviruses to induce extra copies of four stem cell master regulatory genes to produce induced pluripotent stem cells (iPSCs) iPSCs can perform most of the functions of ES cells iPSCs can be used as models for study of certain diseases and potentially as replacement cells for patients "turning back the clock on mature differentiated cells" The "deprogrammed" cells are known as induced pluripotent stem (iPS) cells because, in using this fairly simple laboratory technique to return them to their undifferentiated state, pluripotency has been restored.
What is alternative RNA splicing?
Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing. One important consequence of the presence of introns in genes is that a single gene can encode more than one kind of polypeptide. Many genes are known to give rise to two or more different polypeptides, depending on which segments are treated as exons during RNA processing; this is called alternative RNA splicing (see Figure 18.13). For example, sex differences in fruit flies are largely due to differences in how males and females splice the RNA transcribed from certain genes. Results from the Human Genome Project (discussed in Concept 21.1) suggest that alternative RNA splicing is one reason humans can get along with about the same number of genes as a nematode (roundworm). Because of alternative splicing, the number of different protein products an organism produces can be much greater than its number of genes
Diagram a positive regulating operon.
Some operons are also subject to positive control through a stimulatory protein or activator of transcription When glucose (a preferred food source of E. coli) is scarce,cyclic AMP (cAMP) receptor protein (CRP)is activated by binding with cAMP. Activated CRP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription (activator increases transcription) When glucose levels increase, CRP detaches from the lac operon, and transcription returns to a normal rate Positive control of the lac operon by catabolite activator protein (CAP). RNA polymerase has high affinity for the lac promoter only when CAP is bound to a DNA site at the upstream end of the promoter. CAP, in turn, attaches to its DNA site only when associated with cyclic AMP (cAMP), whose concentration in the cell rises when the glucose concentration falls. Thus, when glucose is present, even if lactose is also available, the cell preferentially catabolizes glucose and makes very little of the lactose-utilizing enzymes.
What is a viral membrane envelope?
Some viruses have accessory structures that help them infect their hosts. For instance, a membranous envelope surrounds the capsids of influenza viruses and many other viruses found in animals (Figure 19.3c). These viral envelopes, which are derived from the membranes of the host cell, contain host cell phospholipids and membrane proteins. They also contain proteins and glycoproteins of viral origin. (Glycoproteins are proteins with carbohydrates covalently attached.) Some viruses carry a few viral enzyme molecules within their capsids.
What is a mutagen?
Spontaneous mutations can occur during DNA replication, recombination, or repair • Mutagens are physical or chemical agents that can cause mutations A number of physical and chemical agents, called mutagens, interact with DNA in ways that cause mutations.
What is the function of a 5' cap?
The 5' cap is added to the first nucleotide in the transcript during transcription. The cap is a modified guanine (G) nucleotide, and it protects the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it to make a protein. purpose of modifications: - facilitate export of mRNA - protects mRNA from hydrolytic enzymes (chew up RNA) - helps ribosomes attach to the 5' end
What is epigentic inheritance?
The Inheritance of traits transmitted by mechanisms that do not involve the nucleotide sequence. One example of an epigenetic change is DNA methylation — the addition of a methyl group, or a "chemical cap," to part of the DNA molecule, which prevents certain genes from being expressed. Another example is histone modification. Histones are proteins that DNA wraps around
What are the E, P, and A sites within the ribosomal translation complex?
The P site (peptidyl-tRNA binding site) holds the tRNA carrying the growing polypeptide chain, while the A site (aminoacyl-tRNA binding site) holds the tRNA carrying the next amino acid to be added to the chain. Discharged tRNAs leave the ribosome from the E site (exit site).
What is a transcription initiation complex?
The completed assembly of transcription factors and RNA polymerase II bound to a promoter The whole complex of transcription factors and RNA polymerase II bound to the promoter
Describe the role of tRNA in ribosomal translation and be able to define anticodon
The function of tRNA is to transfer amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome The loop extending from one end of the L includes the anticodon, the particular nucleotide triplet that base-pairs to a specific mRNA codon Translation: the basic concept. As a molecule of mRNA is moved through a ribosome, codons are translated into amino acids, one by one. The interpreters are tRNA molecules, each type with a specific nucleotide triplet called an anticodon at one end and a corresponding amino acid at the other end. A tRNA adds its amino acid cargo to a growing polypeptide chain when the anticodon hydrogen bonds to the complementary codon on the mRNA. The figures that follow show some of the details of translation in a bacterial cell.
What are the four schemes of viral genome composition?
The genome of a virus may consist of DNA or RNA, which may be single stranded (ss) or double stranded (ds), linear or circular.
Describe the viral Lysogenic Cycle.
The lysogenic cycle replicates the phage genome without destroying the host The viral DNA molecule is incorporated into the host cell's chromosome This integrated viral DNA is known as a prophage Every time the host divides, it copies the phage DNA and passes the copies to daughter cells The lytic and lysogenic cycles of phage L, a temperate phage. After entering the bacterial cell and circularizing, the l DNA can immediately initiate the production of a large number of progeny phages (lytic cycle) or integrate into the bacterial chromosome (lysogenic cycle). In most cases, phage l follows the lytic pathway, which is similar to that detailed in Figure 19.5. However, once a lysogenic cycle begins, the prophage may be carried in the host cell's chromosome for many generations. Phage l has one main tail fiber, which is short.
Be able to diagram mRNA transciption
The stages of transcription: initiation, elongation, and termination. This general depiction of transcription applies to both bacteria and eukaryotes, but the details of termination differ, as described in the text. Also, in a bacterium, the RNA transcript is immediately usable as mRNA; in a eukaryote, the RNA transcript must first undergo processing.
What is the one gene-one polypeptide hypothesis?
The theory that each gene is responsible for the synthesis of a single polypeptide As researchers learned more about proteins, they made revisions to the one gene-one enzyme hypothesis. Beadle and Tatum's idea was therefore restated as the one gene-one polypeptide hypothesis. Even this description is not entirely accurate, though. First, in many cases, a eukaryotic gene can code for a set of closely related polypeptides via a process called alternative splicing, which you will learn about later in this chapter. Second, quite a few genes code for RNA molecules that have important functions in cells even though they are never translated into protein. For now, we will focus on genes that do code for polypeptides. (Note that it is common to refer to these gene products as proteins—a practice you will encounter in this book—rather than more precisely as polypeptides.)
What is therapeutic cloning?
The ultimate aim of research with stem cells is to supply cells for the repair of damaged or diseased organs. ES cells present ethical and political issues ES cells are currently obtained from embryos donated by patients undergoing infertility treatments or from long-term cell cultures originally established with cells isolated from donated embryos. If scientists were able to clone human embryos to the blastocyst stage, they might be able to use such clones as the source of ES cells in the future. Furthermore, with a donor nucleus from a person with a particular disease, they might be able to produce ES cells that match the patient and are thus not rejected by his or her immune system when used for treatment. When the main aim of cloning is to produce ES cells to treat disease, the process is called therapeutic cloning. Although most people believe that reproductive cloning of humans is unethical, opinions vary about the morality of therapeutic cloning.
What is the difference between a transcription factor and a general transcription factor?
Transcription factors are proteins that regulate the transcription of genes—that is, their copying into RNA, on the way to making a protein. In humans and other eukaryotes, there is an extra step. RNA polymerase can attach to the promoter only with the help of proteins called basal (general) transcription factors. They are part of the cell's core transcription toolkit, needed for the transcription of any gene.
What is an activator?
Transcription factors that are activators boost a gene's transcription. Repressors decrease transcription.
Briefly describe polymerase chain reaction (PCR). Make sure that you describe the three basic steps. What is the benefit of PCR to a scientist?
With PCR, any specific segment (the so-called target sequence) within a DNA sample can be copied many times (amplified), completely in vitro. In the PCR procedure, a three-step cycle brings about a chain reaction that produces an exponentially growing population of identical DNA molecules. During each cycle, the reaction mixture is heated to denature (separate) the strands of the double-stranded DNA and then cooled to allow annealing (hydrogen bonding) of short, single-stranded DNA primers complementary to sequences on opposite strands at each end of the target sequence; finally, a heat-stable DNA polymerase extends the primers in the 5' - 3' direction
What is a transcription factor?
a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. transcription factors ensure that RNA poly should sit down on promoter and promote a certain gene. These factors ends up forming a transcription initiation complex. In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. Only after transcription factors are attached to the promoter does RNA polymerase II bind to it.
What is a Stem Cell?
a relatively unspecialized cell that can reproduce itself indefinitely, or under certain conditions can differentiate into one or more types of specialized cells
What is an exon?
a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence.
What is an intron?
a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.
What nucleotides comprise any RNA sequence? Which of the nucleotides engage in complimentary pairing?
adenine, uracil, guanine, cytosine Adenine w/ uracil guanine w/ cytosine
What are "sticky ends"?
an end of a DNA double helix at which a few unpaired nucleotides of one strand extend beyond the other. The most useful restriction enzymes cleave the sugarphosphate backbones in the two DNA strands in a staggered manner, as indicated in Figure 20.6. The resulting double-stranded restriction fragments have at least one single-stranded end, called a sticky end. These short extensions can form hydrogen-bonded base pairs with complementary sticky ends on any other DNA molecules cut with the same enzyme.
What are restriction enzymes?
bacterial enzymes that cut DNA at specific palindrome sequences Gene cloning and genetic engineering generally rely on the use of enzymes that cut DNA molecules at a limited number of specific locations. These enzymes, called restriction endonucleases, or restriction enzymes, were discovered in the late 1960s by biologists doing basic research on bacteria. Restriction enzymes protect the bacterial cell by cutting up foreign DNA from other organisms or phages (see Concept 19.2).
What is a temperate phage?
bacteriophages which can choose between a lytic and lysogenic pathway of development In contrast to the lytic cycle, which kills the host cell, the lysogenic cycle allows replication of the phage genome without destroying the host. Phages capable of using both modes of replicating within a bacterium are called temperate phages. A temperate phage called lambda, written with the Greek letter l, has been widely used in biological research. Phage l resembles T4, but its tail has only one short tail fiber.
What is a signal recognition particle?
binds to signal peptide and attaches it to receptor protein in ER membrane This particle functions as an escort that brings the ribosome to a receptor protein built into the ER membrane. The receptor is part of a multiprotein translocation complex.
What is a nonsense mutation?
change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein stop codon created
What is a silent mutation?
have no effect on the amino acid produced by a codon because of redundancy in the genetic code wobble protects from these kinds of mutations
What does in vitro mean?
in a test tube rather than an organism in vitro mutagenesis A technique used to discover the function of a gene by cloning it, introducing specific changes into the cloned gene's sequence, reinserting the mutated gene PCR!
What is Crick's Central Dogma?
in general, genetic information flows from DNA to RNA to protein. Overview: the roles of transcription and translation in the flow of genetic information. In a cell, inherited information flows from DNA to RNA to protein. The two main stages of information flow are transcription and translation. A miniature version of part (a) or (b) accompanies several figures later in the chapter as an orientation diagram to help you see where a particular figure fits into the overall scheme.
What does in situ mean?
in its original place/ inside the organism in situ hybridization A technique using nucleic acid hybridization with a labeled probe to detect the location of a specific mRNA in an intact organism
What is a prion?
infectious protein Prions Infectious proteins - Scrapie (sheep disease) - Mad cow - Chronic Wasting Disease (deer, elk, moose) - Cruetzfeldt-Jacob disease (UK) - Kuru (New Guinea) • Slow disease onset~10 years to become symptomatic. - Nearly indestructible. Destroyed only by incinerating temperatures (>1000°C) - Temp reference: 500°F oven = 260°C campfire = 600°C or 1100°F incinerator = 1000°C or 1800°F • or high-pressure (several atmospheres) AND strong alkali (pH13+)
What are the three stages of transcription?
initiation, elongation, termination
Of all the types of mutations, which are the most disastrous for the cell and why?
insertions and deletions!!! All nucleotides downstream of the deletion or insertion will be improperly grouped into codons; the result will be extensive missense, usually ending sooner or later in nonsense and premature termination. Unless the frameshift is very near the end of the gene, the protein is almost certain to be nonfunctional.
What is a promoter?
landing pad for RNA polymerase A specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place. the DNA sequence where RNA polymerase attaches and initiates transcription
What is a capsid?
protein coat surrounding a virus - The protein shell enclosing the viral genome is called a capsid. Depending on the type of virus, the capsid may be rod-shaped, polyhedral, or more complex in shape. Capsids are built from a large number of protein subunits called capsomeres, but the number of different kinds of proteins in a capsid is usually small.
What is a capsomere?
protein subunits that build capsids Viruses are made up of nucleic acid (DNA or RNA) enclosed in a protein coat (the capsid) and sometimes further wrapped in a membranous envelope. The individual protein subunits making up the capsid are called capsomeres. Although diverse in size and shape, viruses have many common structural features. (All micrographs are colorized TEMs.)
Of prophage and provirus, of these two, which one bceomes a permanent part of the host genome?
provirus
What is a template stand?
refers to the strand used by DNA polymerase or RNA polymerase to attach complementary bases during DNA replication or RNA transcription, respectively; either molecule moves down the strand in the 3' to 5' direction, and at each subsequent base, it adds the complement of the current DNA base to the growing nucleic acid strand (which is thus created in the 5' to 3' direction). Because this new strand is created by complementarity, it matches the opposing strand of DNA, which is called the coding strand.
nucleotide-pair substitutions
replaces one nucleotide and its partner with another pair of nucleotides
What was the Human Genome Project?
sequencing and mapping of the entire human genome. (all of the nucleotide base pairs) Officially begun as the Human Genome Project in 1990, the sequencing was largely completed by 2003. Provides a generic basis of the DNA sequence that defines human beings.
What is missense mutation?
still code for an amino acid, but not the correct amino acid
What is a terminator?
tells RNA polymerase to break off In bacteria, a sequence of nucleotides in DNA that marks the end of a gene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA. in bacteria, the sequence that signals the end of transcription
