Unit 8 - Gene Expression & Regulation

What is a gene? It used to be simply stated that one gene codes for one polypeptide. That definition has now been modified. Write in the following space the broader molecular definition in use today.

A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule

There seem to be two categories of genes involved in cancer: oncogenes, which code for proteins to regulate cell growth, and should not be stuck "on," much like the accelerator in a car; and tumor-suppressor genes, which work like the brakes on a car and must function! Let's begin with a look at the ras gene, which codes for a G protein and is an oncogene. Label the following two sketches, then explain how a ras mutation leads to cancer.

A normal pathway is triggered by a growth factor that binds to its receptor in the plasma membrane. The signal is relayed to a G protein called Ras. Like all G proteins, Ras is active when GTP is bound to it. Ras passes the signal to a series of protein kinases. The last kinase activates a transcription factor (activator) that turns on one or more genes for a protein that stimulates the cell cycle.

What is a nucleosome? Draw and label two nucleosomes including linker DNA.

A nucleosome is the bead of histones with DNA wrapped around it, the basic unit of DNA packing. Liner DNA is the "string" of DNA between beads.

The 2009 flu pandemic was caused by H1N1. The 2019-2020 COVID-19 pandemic was caused by a novel coronavirus, SARS-CoV. What is a pandemic? What does the name of the H1N1 signify?

A pandemic is a global epidemic (an epidemic is a widespread outbreak) .H1N1 signfies which forms of two viral surface proteins are present--hemagglutinin and neuraminidase (HA and NA).

What are SNPs? How are they used to help screen for certain diseases? What are some examples of diseases for which there are genetic markers?

An SNP (single nucleotide polymorphism) is a single base-pair site where variation is found in at least 1% of the population. Once a SNP is identified that is found in all people affected by the disease being studied, researchers focus on that region and sequence it. In nearly all cases, the SNP itself doesn't contribute directly to the disease by altering the encoded protein; in fact, most SNPs are in noncoding regions. Instead, having a particular SNP associated with a disease suggests that the gene whose mutation causes the disease is located very close to that SNP on the chromosome. Since the SNP and the gene are so close together, crossing over is rare so the SNP acts as a genetic marker for disease-causing alleles because they are almost always inherited together Ex: diseases: diabetes, heart disease, and several types of cancers

Why can only complementary DNA (cDNA) be used in engineering a plasmid that will be inserted into a bacterial cell?

Complementary DNA (cDNA) only includes the exons from eukaryotic genes. This is the only type of DNA in a plasmid that can be inserted into a bacterial cell because introns can make a eukaryotic gene very long and unwieldy, and they prevent correct expression of the gene by bacterial cells, which do not have RNA-splicing machinery.

Explain what is meant by epigenetic inheritance and give an example of epigenetic changes discussed in the text or in class.

Epigenetic inheritance is the inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself. Ex: DNA methylation patterns are largely erased during gamete formation. Furthermore, they are changeable, thus responding more rapidly to environmental conditions. This is seen with the "agouti" mice with were genetically the same, but one came out obese and yellow due to a lack of methyl groups fed to the mother during pregnancy, the other was normal and "agouti" colored due to methyl groups being fed to the mother during pregnancy.

State the hypothesis formulated by George Beadle while studying eye color mutations in Drosophila.

In the 1930s, the American biochemist and geneticist George Beadle and his French colleague Boris Ephrussi speculated that in Drosophila, each mutation affecting eye color blocks pigment synthesis at a specific step by preventing production of the enzyme that catalyzes the step.

What is a ribozyme?

RNA molecules that function as enzymes

Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand.

RNA polymerase

What is the source and original function of restriction enzymes?

Restriction enzymes protect the bacterial cell by cutting up foreign DNA from other organisms or phages.

The inactive mammalian X chromosome is heavily methylated. What is the result of this methylation?

The X chromosome is inactivated and is a barr body in the cell

What are sticky ends?

The portion of the fragment with a single-stranded end

What property of a virus determines its attachment to a host cell membrane?

Viruses usually identify host cells by a "handshake" fit between viral surface proteins and specific receptor molecules on the outside of cells..

small interfering RNA (siRNA)

can associate with the same proteins as miRNAs, producing similar results. Turns of expression of genes for related sequences like miRNAs

T2 bacteriophage

head, tail sheath, tail fiber, and DNA.

Single-strand binding proteins

holds DNA strands apart

DNA ligase

joins DNA fragments together

Translation: Template, Product Synthesized, Location in Eukaryotic Cell

mRNA, polypeptide, cytoplasm

What genes are active (producing mRNAs) in a particular tissue? RNA sequencing, or RNA-seq, is one method used to study gene expression across an entire genome. Study Figure 20.12 in your text to see how this is done. a.What occurs in step 1? . What occurs in step 4? c. What does the resulting data reveal? (RNA seq is DNA microarray)

mRNAs are isolated from the tissue being studied cDNAs are sequenced (from the previous mRNAs) The resulting data, including the number of times a sequence is present, indicate which genes are expressed in a given tissue and at what level

Primase

synthesizes RNA primer

DNA technology

technology-based techniques for manipulating DNA

Describe at least three types of post-translational modifications.

1. Certain amino acids may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additions 2. Enzymes may remove on or more amino acids from the leading (amino) end of the polypeptide chain 3. In some cases, a polypeptide chain may be enzymatically cleaved into two or more pieces. In other cases, two or more polypeptide that are synthesized may com together the protein has a quaternary structure like hemoglobin

What are Chargaff's rules? How did he arrive at them?

1. DNA base compisition varies between species 2. For each species, the percentages of A and T bases are roughly equal, as are those of G and C bases He arrived at the first rule by finding the percentage of base A in different species such as sea urchins and E.coli. For the second rule, he studied the percentages of each base in DNA of different species.

How many nucleotides are required to have a unique code for each of these 20 amino acids?

3

What is a restriction enzyme?

A type of enzyme that cuts DNA molecules at a limited number of specific locations and gene cloning and genetic engineering rely on the use of these enzymes.

Explain how this repressible trp operon can be turned off.

Accumulation of tryptophan, the end product of the pathway, represses transcription of the trp operon, thus blocking synthesis of all the enzymes in the pathway and shutting down tryptophan production. If the cell has a lot of tryptophan, it binds to repressor proteins and that binds to the operator, not allowing RNA polymerase to transcribe the genes.

How can proteins be activated, processed, and degraded? Give an example or describe each process.

Activated: cleavage of the initial insulin polypeptide (pro-insulin) forms that active hormone Processed: regulatory proteins are commonly activated or inactivated by the reversible addition of phosphate groups or sugars Degradation: the length of time each protein functions in the cell is regulated by selective degradation. Ex: cyclins are short-lived for their function.

RNA processing, sometimes also called mRNA editing, occurs only in eukaryotic cells. Prokaryotic cells lack the enzymes to edit mRNA. The primary transcript is altered at both ends, and sections in the middle are removed. What happens at the 3ʹ end?

An enzyme then adds 50-250 more adenine (A) nucleotides, forming a poly-A tail

Why is the promoter area important in beginning transcription?

Because this is the specific DNA sequence where RNA polymerase attaches and initiates transcription

Why did researchers originally think that protein was the genetic material?

Biochemists had identified proteins as a class of macromolecules with great heterogeneity and specificity of function, essential requirements for hereditary material. More so, little was known about nucleic acids, whose physical and chemical properties seemed far too uniform to account for the multitude of specific inherited traits exhibited by every organism. This changed as scientists studied bacteria and viruses and the role of DNA in these organisms

What situation did Archibald Garrod suggest caused "inborn errors of metabolism"?

He suggested the genes dictate phenotypes through enzymes, proteins that catalyze specific chemical reactions in the cell. He postulated that the symptoms of an inherited disease reflect an inability to make a particular enzyme. He later referred to these diseases as "inborn errors of metabolism"

As you can see, all viruses consist of a nucleic acid enclosed in a protein coat. Some viruses also have a membranous envelope. What are the components of a viral envelope? Which component is derived from the host cell, and which is of viral origin?

Membraneous envelope -membranes of the host cell and they contain host cell phospholipids and membraneous proteins. - Host Proteins and Glycoproteins - Virus

What are three ways bacteria may win the battle against the phages?

Natural selection favors bacterial mutants with surface proteins that are no longer recognized as receptors by a particular type of phage When phage DNA does enter a bacterial cell, the DNA often is identified as foreign and cut up by restriction enzymes, restricting the phage's ability to replicate within the bacterial cell CRISPR-Cas system in bacteria and archaea

Compare oncogenes and proto-oncogenes.

Oncogenes are cancer causing genes in a genome. The normal version of the cellular genes are called proto-oncogenes.

Use this figure to summarize the experiment in which Griffith became aware that hereditary information could be transmitted between two organisms in an unusual manner.

The S (smooth) strain can cause pneumonia in mice; it is pathogenice because the cells have an outer capsule that protects them from an animal's immune system. Cells of the R (rough) strain lack a capsule and are nonpathogenic. To test for the trait of pathogenicity, Griffith injected mice with the two strains. He found the living R bacteria had been transformed into pathogenic S bacteria by an unknown, heritable substance from the dead S cells that enabled the R cells to make capsules

What is the role of an envelope in animal viruses?

The envelope is an accessory structure that helps animal viruses infect their hosts.

Why are bacterial plasmids widely used as cloning vectors?

They can be readily obtained from commercial suppliers They can be manipulated to form recombinant plasmids by insertion of foreign DNA in a test tube (in vitro, "in glass") Then they can be easily introduced into bacterial cells

Viruses are obligate intracellular parasites. What does this mean?

They can replicate only within a host cell

What are three important functions of the 5ʹ cap and poly-A tail?

They seem to facilitate the export of the mature RNA from the nucleus They help protect the mRNA from degradation by hydrolytic enzymes They help ribosomes attach to the 5' end of the mRNA once it reaches the cytoplasm

An article in Scientific American about the giant protein complexes called proteasomes was titled "Little Chamber of Horrors." Explain how proteins are targeted for degradation, and give a specific example of when this might occur.

To mark a protein for destruction, the cell commonly attaches molecules of a small protein called ubiquitin to the protein. Giant protein complexes called proteasomes then recognize the ubiquitin tagged proteins and degrade them. Ex: to degrade cyclins

DNA polymerase III

adds DNA nucleotides to new strands

What is the start codon?

also codes for methionine (Met, or M) so polypeptide chains all begin with methionine, but an enzyme may later remove this amino acid

What is the function of aminoacyl-tRNA synthetases? How many different aminoacyl-tRNA synthetases are there?

aminoacyl-tRNA synthetases correctly match tRNA and its amino acid together. 20 different aminoacyl-tRNA synthetases

On February 4, 2020, the Centers for Disease Control and Prevention (CDC) released 2019-nCoV Real-Time RT-PCR Diagnostic Panel tests for emergency use to diagnose patients suspected to have the COVID-19. RT-PCR tests are able to detect RNA from SARS-CoV2 (the coronavirus that causes COVID-19 disease). What are the three tools of biotechnology that are employed in RT-PCR? (Refer to Figure 20.11 in your text.)

cDNA synthesis, PCR amplification, and Gel electrophoresis.

Briefly describe two ways genes may be edited or silenced.

in vitro mutagenesis - specific mutations are introduced into a cloned gene, and the mutated gene is returned is returned to a cell in such a way that it disables "knocks out" the normal cellular copies of the same gene. CRISPR-Cas9 system to knock out a gene or edit it. Gene drive is when the CRISPR-Cas9 system is used to make a genetically modified gene more prone to inheritance that the wild type allele in a population RNA interference (RNAi) - this experimental approach uses synthetic double-stranded RNA molecules matching the sequence of of a particular gene to trigger breakdown of the gene's messenger RNA or to block its translation

What are the monomers of DNA and RNA? __________ Of proteins? _______________

nucleotides, amino acids

Mutations that alter growth factors, their receptors, or intracellular signaling pathway molecules, or affect regulation of the cell cycle, can lead to cancer in somatic cells. Therefore, genetic mutation is the mechanism involved in the beginning of tumor growth. What are several mechanisms that can result in these cancer-causing mutations?

random spontaneous mutation, chemical carcinogens like tobacco, X-rays and other high-energy radiation, and some viruses

Stop codons

the stop of translation (termination codons) UAA, UAG, UGA

Now here is an important idea: DNA is DNA is DNA. By this we mean that the code is nearly universal. Because of this, fluorescent green jellyfish genes can be inserted into mosquito larvae, or firefly genes can make a tobacco plant glow.

-A shared genetic vocabulary is a reminder of the kinship of all life and also one species can be programmed with DNA to produce proteins characteristic of a second species because of this

How many nucleotide bases are there? __ How many amino acids? __

4, 20

Three key events occur in elongation. Explain the important features of each event.

An rRNA molecule of the large ribosomal subunit catalyzes the formation of a The ribosome translocates the tRNA in the A site to the P site. At the same time, the empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site.

a. What type of virus is this? b. What does its name mean? c. What is its host? d. Is the genome of this virus DNA or RNA?

Bacteriophage T4 Their capsids have elongated icosahedral heads enclosing their DNA and they have a tail apparatus. E. coli DNA

What are bacteriophages? Distinguish between virulent and temperate phages.

Bacteriophages are viruses that infect bacteria. Virulent phages replicate only by a lytic cycle, a replicative cycle that results in the death of the host cell. Temperate phages are viruses that can replicate using both the lytic cycle and lysogenic cycle, a replicative cycle that doesn't destroy the host cell.

Describe the two possible sources of viral genomes. You will see each of these important mobile genetic elements again.

Plasmids- small, circular DNA molecules found in bacteria and in unicellular fungi called yeasts. Plasmids exist apart from the genome, can replicate independently of the genome, and are occasionally transferred between cells Transposons-DNA segments that can move from one location to another within a cell's genome

What is the consequence of alternative splicing of identical mRNA transcripts?

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 polypeptide, depending on which segments are treated as exons during RNA processing (called alternative splicing).

What are four important applications of PCR?

PCR has been used t6o amplify DNA from a wide variety of sources: a 40,000-year-old frozen woolly mammoth fingerprints or tiny amounts of blood, tissue, or semen found at crime scenes single embryonic cells for rapid prenatal diagnosis of genetic disorders Cells infected with viruses that are difficult to detect, such as HIV

Distinguish between introns and exons. Perhaps it will help to remember this: Exons are expressed.

The noncoding segments of nucleic acids that lie between coding regions are called introns, and exons are the nucleotides sequences that are expressed into amino acid sequences.

What components of the host cell does a virus use to reproduce itself?

The nucleotides for nucleic acids, enzymes, ribosomes, tRNAs, amino acids, ATP, and other components needed for making the viral proteins.

operon

The operator, the promoter, and the genes they control--the entire stretch of DNA required for enzyme production for the tryptophan pathway for example-- is an operon

When a repressor is bound to the operator of the lac operon, is the operon off or on?

The operon is off. (negative regulation)

Explain the situation in which a lac operon is off

The operon shown is off because lactose is absent, so the repressor is active, and the operon is off because this is an inducer operon and the repressor protein naturally binds to the operator to keep the operon off (without the need for any small molecule to bind to the repressor protein to turn the operon off)

What is an anticodon?

The particular nucleotide triplet that base-pairs to a specific mRNA codon

The CRISPR-Cas9 offers a promising route to correct certain genetic defects without the associated problems of gene therapy. At present, what are the major concerns about this method?

The possible effects on genes that are not being targeted Ethical questions: is it moral to tamper with human genes? Issue of engineering human germ-line cells to try to correct a defect in future generations

What is the purpose of the primers? (Recall what you know about DNA synthesis.)

The primers are needed for DNA polymerase to replicate the DNA because it needs to move from a 5' → 3' direction and this only possible if RNA primers are put down

It is now known that much of the RNA that is transcribed is not translated into protein. These RNAs are called noncoding RNAs. Read carefully to discern a crucial role played by these ncRNAs. What is this role?

These ncRNAs can regulate translation and chromatin modification. They can also degrade mRNA or block mRNA transcription.

How can the rate of gene expression be modified by specific transcription factors (activators or repressors)?

These specific transcription factors (proteines) act with control elements (segments of regulating noncoding DNA) to either limit or increase transcription. These activator proteins have DNA-binding domains (a part of their structure that binds to DNA) and one or more activation domains (parts that bind to other regulatory proteins or components of the transcription machinery facilitating a series of protein-protein interactions that result in enhanced transcription of a gene). Repressors can bind and not allow transcription or remove acetyl groups from the chromatin.

What are maternal effect genes? Describe some effects they may control.

They are genes that when they are mutant in the mother, it results in a mutant phenotype in the offspring, regardless of the offspring's own genotype. They control the mRNA protien products in the eggs in a mother's ovary. They also determine pattern formation.

What is controlled by homeotic genes?

They control pattern formation. They are master regulator genes that control the development of body segments and structures

What process ensures that all the tissues and organs of an organism are in their characteristic places? Where do the molecular cues that control this process arise?

Pattern formation - Cytoplasmic determinants and inductive signals both contribute to spatially organizing the tissues and organs of an organism in their characteristic places. This developmental process is referred to as pattern formation.

What are plasmids? How are they different from the main bacterial chromosome?

Plasmids are small, circular DNA molecules that are replicated separately. They are different from the main bacterial chromosome because a plasmid only has 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.

What are stem cells?

a relatively unspecialized cell that can both reproduce itself indefinitely and and, under appropriate conditions, differentiate into specialized cells of one or more types. Stem cells have great potential for regenerating damaged tissues

corepressor

a small molecule that cooperates with a repressor protein to switch an operon off. Ex. tryptophan binds to repressor protein and regulates gene expression through allosteric regulation

What is a restriction site?

a specific, short, and particular DNA sequence that restriction enzymes recognize and cut the DNA at the site of restriction.

What are the four forms of viral genomes?

double-stranded DNA, single-stranded DNA, double-stranded RNA, and single-stranded RNA

Three key events occur in elongation. Explain the important features of each event. Peptide bond formation

peptide bond between the carboxyl end of the growing polypeptide in the P site and the amino group of the new amino acid in the A site. As shown in the next diagram, this step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site.

piwi-interacting RNA (piRNA)

small ncRNAs that induce the formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons. Establish proper methylation patens in the genome during gamete formation

rRNA Description and Function

structure made of proteins and RNAs Adds each amino acid brought to it by a tRNA to the growing end of a polypeptide chain

What are two viral elements that nearly all animal viruses have?

A viral envelope and a RNA genome

What is a totipotent cell?

A cell with a potential to "dedifferentiate" and then give rise to all the specialized cells cell types of an organism

genetic engineering

the direct manipulation of genes for practical purposes

Following Figure 17.28 in your text, label and explain the three major events in gene editing using the CRISPR-Cas9 system.

1. Cas9 protein and guide RNA are allowed to bind to each other forming a complex that is then introduced into a cell 2. In the nucleus, the complementary sequence of the guide RNA binds to part of the target gene. The active sites of the Cas9 protein cut the DNA on both strands 3. The broken strands of DNA are "repaired" by the cell in one of two ways: Scientists can disable ("knock out") the target gen to study its normal function. No template is provided, and repair enzymes insert and/or delete random nucleotides making the gene nonfunctional If the target gene has a mutation, it can be repaired by providing a normal copy of the gene. Repair enzymes use the normal gene as a template and synthesize the correct gene sequence.

Label the following figure then below the figure explain the six steps that show how proteins are targeted for the endoplasmic reticulum (ER).

1. Polypeptide synthesis begins on a free ribosome in the cytosol 2. An SRP binds to the signal peptide, (if present), halting synthesis momentarily 3. The SRP binds to a receptor protein in the ER membrane, part of a protein complex that forms a pore 4. The SRP leaves, and polypeptide synthesis resumes, with simultaneous translocation across the membrane 5. The signal peptide is cleaved by an enzyme in the receptor protein complex 6.The rest of the completed polypeptide leaves the ribosome and folds into its final conformation

Question 21 asked about cDNA. Using Figure 20.10 in your text, completely label the following figure and describe the five steps in the production of cDNA. Recall that cDNA is what is inserted into recombinant plasmids.

1. Reverse transcriptase is added to a test tube containing mRNAs, isolated from a sample of cells. 2. Reverse transcriptase makes the first DNA strand using the mRNA as a template and a short poly-dT as a DNA primer 3. mRNA is degraded by another enzyme 4. DNA polymerase synthesizes the second DNA strand, using a primer in the reaction mixture. (Several options exist for primers.) 5. The result is cDNA, which carries the complete coding sequence of the gene but no introns.

What is a cloning vector?

A DNA molecule that can carry foreign DNA into a host cell and be replicated there

What is a capsid? What different shapes may capsids have?

A capside is a protein shell enclosing the viral genome. Different shapes include: rod-shaped, polyhedral, or more complex in shape

What is meant by host range? Distinguish between a virus with a broad host range and one with an extremely limited host range and give an example of each.

A host range is the range of host species a particular virus can infect. Broad host range viruses can infect multiple species. Ex: West Nile virus and equine encephalitis virus can infect mosquitoes, birds, horses and humans. An extremely limited host range virus can only affect one species. Ex: measles virus can only infect humans

What is a polyribosome?

A polyribosome is a string of mRNA with multiple ribosomes translating the mRNA into polypeptide chains. This allows the cell to rapidly make many copies of a polypeptide

Compare and contrast a prophage and a provirus. Which one are you likely to carry?

A prophage exists in a bacterial cell and occurs when viral DNA is integrated into a bacterial chromosome during the lysogenic cycle of replication. However, the phage DNA leaves the host's genome at the start of the lytic cycle. A provirus occurs in an animal cell (eukaryote) and is the incorporation of the viral genome into the cell genome permanently. This viral DNA never leaves the host cell. You are most likely to carry a provirus

repressor

A protein (such as trp repressor for the tryptophan pathway) that binds to the operator, preventing RNA polymerase from transcribing the genes, often preventing RNA polymerase from binding

What is a nucleosome?

A region of DNA wound around histone proteins

What is a release factor? By what mechanism is termination accomplished?

A release factor is a protein shaped like an aminoacyl tRNA, binds directly to the stop codon in the A site. Termination is accomplished by reaching a special stop codon. The release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain. This reaction hydrolyzes (breaks) the bond between the completed polypeptide and the tRNA in the P site, releasing the polypeptide chain through the exit tunnel of the ribosome's large subunit. Breakdown of the translation assembly requires additional protein factors and the hydrolysis of two more GTP molecules.

regulatory genes

A repressor protein is encoded by a regulatory gene. In the tryptophan case, a gene called trpR is located some distance from the trp operon and has its own promoter.

operator

A segment of DNA that functions like the on-off switch for the multiple genes that are functionally related

Summarize the two key events in forming the translation initiation complex.

A small ribosomal subunit binds to an mRNA. In bacteria, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA, with the anticodon UAC, base pairs with the start codon, AUG. This tRNA carries amino acid methionine (Met). The arrival of a large ribosomal subunit completes the initiation complex. Proteins called initiation factors are required to bring all the translation components together. Hydrolysis of GTP provides the energy for the assembly. The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid

Use the following sketch to explain how enhancers and activators interact with transcription factors to affect gene expression. Label the following elements: TATA box, promoter, gene, enhancer, activators, mediator proteins, general transcription factors, transcription initiation complex, DNA-bending protein, RNA polymerase II, and DNA. Then place your explanation, including the three major points in the figure, to the left of the page.

Activator proteins bind to distal control elements grouped as an enhancer in DNA. This enhancer has 3 binding sites, each called a distal control element A DNA-bending protein brings the bound activators closer to the promoter. General transcription factors, mediator proteins and RNA polymerase II are nearby. The activators bind to certain mediator proteins and general transcription factors, helping them form an active transcription initiation complex on the promoter

Purine? Pyrimidine? DNA, RNA, or Both? Adenine Thymine Guanine Cytosine Uracil

Adenine Purine Both Thymine Pyrimidine Both Guanine. Purine Both Cytosine. Pyrimidine Both Uracil. RNA

The old view that the nuclear contents are like a bowl of chromosomal spaghetti has been replaced with a much more structured vision of chromosomal arrangement. Using Figure 18.13 in your text, explain the current understanding of chromosomal arrangement.

Although each chromosome has its own territory, loops of chromatin may extend into other sites in the nucleus. (Each loop may be a topologically associated domain, or TAD.) Some of these sites are transcription factories that are occupied by multiple chromatin loops from the same chromosome or other chromosomes

Transfer RNA has two attachment sites. What binds at each site? Sketch tRNA to indicate the two attachment sites and note where complementary base pairing and hydrogen bonding occur to give it shape. Figure 17.16 in your text will be helpful.

Anticodon site and amino acid attachment site

A new DNA strand can only be synthesized in one direction. Why? What is the direction of synthesis of the new strand?

As explained above, DNA polymerase III can only add nucleotides starting from the 3' end of the primer, so the enzyme elongates the new DNA in the mandatory 5' → 3' direction.

Explain how mutations in BRCA1 and BRAC2 are associated with an increased risk of breast cancer.

BCRA1 and BCRA2 are considered tumor-suppressor genes because their wind type alleles protect against breast cancer and their mutant alleles are recessive. If they are mutated, they increase the risk for cancer by not fixing damaged DNA, causing breast cancer

Post-transcriptional control includes regulation of mRNA degradation. Explain how this affects translation.

Bacterial mRNA typically are degraded by enzymes within a few minutes. This short life span of mRNA is one reason bacteria can change their patterns of protein synthesis so quickly in response to environmental changes. In contrast, some mRNAs in multicellular eukaryotes typically survive for hours, days, or even weeks. Ex: the mRNAs for hemoglobin peptides in developing red blood cells are unusually stable, and these long-lived mRNAs are translated repeatedly.

How can a nucleotide-pair substitution result in a silent mutation?

Because a change in a nucleotide pair may transform one codon into another that is translated into the same amino acid; this change is called a silent mutation, which has no observable effect on the phenotype.

Explain why CRP binding and stimulation of gene expression is positive regulation. What is the role of the activator?

By facilitating the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription of the operon, the attachment of CRP to the promoter directly stimulates gene expression. Therefore, this mechanism qualifies as positive regulation. CRP is the activator

A powerful new technique for gene editing is the CRISPR-Cas9 system. a.What is Cas9?

Cas9 is a bacterial protein that helps defend bacteria against the viruses that infect the (bacteriophages).

What are the two main ways of controlling metabolism in bacterial cells? Which is a short-term response, and which is a long-term response?

Cells can adjust the activity of enzymes already present. This is a short-term and quick response that relies on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic activity. In these pathways (like tryptophan) feedback inhibition is used Cells can adjust the production level of certain enzymes via a genetic mechanism; that is, they can regulate the expression of the genes encoding the enzymes. The control of enzyme production occurs at the level of transcription, the synthesis of messenger RNA from the genes that code for these enzymes. This is long-term

What are two potential uses for human iPS cells?

Cells from patients with diseases have been reprogrammed to become iPS cells, which act as model cells for studying the disease and potential treatments. Human iPS cell lines have already been developed from individuals with type 1 diabetes, Parkinson's disease, Huntington's disease, Down syndrome, and many other diseases. In the field of regenerative medicine, a patient's own cells could be reprogrammed into iPS cells and then used to replace nonfunctional tissues, such as cells of the retina of they eye that have been damaged by a condition called age-related muscular degeneration (AMD)

In prokaryotes, functionally related genes are usually clustered in a single operon. How are coordinately controlled genes in eukaryotes expressed at the same time even when the genes may be on different chromosomes?

Coordinate gene expression depends on every gene of a dispersed group having a specific combination of control elements. Transcription activators in the nucleus that recognize the control elements bind to them, promoting simultaneous transcription of the genes, no matter where they are in the genome. Coordinate control of dispersed genes in an eukaryotic cell often occurs in response to chemical signals from outside the cell. Ex: steroid molecule binds to protein and forms an intracellular receptor protein that acts as a transcription activator that binds to a specific control element.

Differential gene expression results from different activators in different cells. How do different sets of activators come to be present in two cells? Explain how each of these occurs: a. distribution of cytoplasmic determinants (Use Figure 18.17(a) in your text to frame your answer.) b. induction (Use Figure 18.17(b) to frame your answer.)

Cytoplasmic determinants are molecules encoded by the mother's genes that are placed in an unfertilized egg's cytoplasm. This influences development because of the uneven distribution of the maternal molecules. After fertilization and mitotic division, the cell nuclei of the embryo are exposed to different combinations of cytoplasmic determiannts and as a result, express different genes In induction, other embyronic cells sent signals to neighboring or target cells. The molecules that transmit these signals within the target cell are cell-surface receptors and other signaling pathway proteins. In general, the signal sends a cell down a specific developmental path by causing changes in its gene expression that lead to observable cellular changes

Compare the host range for the rabies virus to that of the human cold virus.

Human cold viruses infect only the cells lining the upper respiratory tract, while rabies virus can infect many mammals like humans, racoons, dogs, bats, etc.

What is DNA methylation? What role may it play in gene expression?

DNA methylation is when enzymes can methylate DNA itself on certain bases, usually cytosine. These methylated stretches of DNA are inactive and prevents transcription of them.

What is accomplished in DNA sequencing?

DNA sequencing allows researches to find the complete nucleotide sequence in a DNA molecule.

The polymerase chain reaction (PCR) is a Nobel Prize-winning idea that is used by scientists to amplify DNA, particularly when the quantity of DNA is very small or contaminated. Label this figure and explain the three initial steps that occur in cycle 1 of PCR.

Denaturation: Heat briefly to separate DNA strands. Annealing: Cool to allow primers to form hydrogen bonds with ends of target sequence Extension: DNA polymerase adds nucleotides to the 3' end of each primer

What is meant by determination? Explain what this means within an embryonic cell.

Determination refers to the point at which an embryonic cell is irreversibly committed to becoming a particular cell type. Differentiation s the process by which a cell attains its determined fate

ven though all cells of an organism have the same genes, there is differential gene expression. What does this mean?

Differential gene expression is the expression of different genes by cells with the same genome. This means that the differences between cell types are not due to different genes being present, but rather differential gene expression

What are induced pluripotent stem cells (iPS)?

Differentiated cells can be transformed into a type of ES cell by using a modified retrovirus to introduce extra, cloned copies of four "stem cell" master regulatory genes. The "deprogrammed" cells are known as induced pluripotent cells (iPS).

Name four diseases caused by prions and two possible neurodegenerative diseases that may involve prions.

Diseases: scrapie in sheep, mad cow disease, Creutzfeldt-Jakob disease, and Kurku Two possible neurodegenerative disease: Alzheimer's and Parkinson's disease

What are the respective roles of distal and proximal control elements?

Distal control elements are located far from the promoter and can be grouped together as enhancers. These are groups of segments of DNA that are noncoding and serve as binding sites for regulatory proteins. Proximal control elements are near the promoter and they are also segments of noncoding DNA that are binding sites for transcription factors that allow RNA polymerase to bind and transcribe.

Tumor-suppressor genes help prevent uncontrolled cell growth. One that is found mutated (and therefore nonfunctional) in more than 50% of human cancer is p53. So important is the p53 gene that it is sometimes called the "guardian angel of the genome." Describe the double whammy that results from mutation of p53.

Due to a mutation of p53, p21 cannot be activated to halt the cell cycle by binding to cyclin-dependent kinases. This is because p53 cannot activate the transcription of these inhibitory proteins. Therefore the cell with damaged DNA is replicated. Furthermore, p53 cannot initiate apoptosis when DNA is past repair, so this allows the cell to replicate with broken DNA

Explain what occurs in cell differentiation and morphogenesis.

During embryonic development, cells not only divide, but also undergo cell differentiation, the process by which cells become specialized in structure and function. Moreover, the different kinds of cells are not randomly distributed but are organized into tissues and organs in a particular three-dimensional arrangement. The physical processes that give an organism its shape constitute morphogenesis, the development of the form of an organism and its structures.

Given access to both glucose and lactose, E. coli will use the glucose. Describe the relationship between glucose supply, cAMP, and CRP.

E.coli will use the glucose because the enzymes for glucose breakdown in glycolysis are continually present, this is not the case for lactose breakdown. Only when glucose concentration is low and lactose concentration is high, does the cell go down the lactose pathway. The cell senses glucose concentration and relays this info to the lac operon by using cAMP which allosterically binds to the regulatory protein. cAMP only accumulates in the cell when glucose is scarce. The regulatory protein called cAMP receptor protein (CRP) is an activator that binds to DNA and stimulates transcription of a gene. Once cAMP binds to CRP, the complex can attach to a specific site on the lac promoter. This attachment increases the affinity for RNA polymerase to bind, which is pretty low even when a lac repressor protein is not bound to the operator. This is positive regulation

Why was the discovery of Taq polymerase a breakthrough for this process?

If a standard DNA polymerase were used, this enzyme would be denatured along with the DNA during the first heating step and would have to be replaced after each cycle. Taq polymerase was discovered to be an unusual heat-stable DNA polymerase enzyme which was the key to automating PCR. This was first isolated in the bacterial species Thermus aquaticus that lives in hot springs.

tRNA Description and Function

Each tRNA (transfer RNA) type has a specific anticodon (that base pairs with the mRNA strand) and 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 Translator or interpreter. The function of tRNA is to transfer an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome.

What are two techniques besides use of cloning vectors that can be used to introduce recombinant DNA into eukaryotic cells?

Electroporation - a brief electrical pulse applied to a solution containing cells creates temporary holes in their plasma membranes, through which DNA can enter Scientists can inject DNA directly into single eukaryotic cells cells using microscopically thin needles

How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical significance of this difference?

Eukaryotic ribosomes are slightly larger than bacterial ribosomes and differ somewhat in their molecular composition. The differences are medically significant because certain antibiotic drugs can inactivate bacterial ribosomes without affecting the ability of eukaryotic ribosomes to make proteins. These drugs are used to combat bacterial infections.

Describe the structure of a eukaryotic ribosome.

Eukaryotic ribosomes are slightly larger than bacterial ribosomes. A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs, or rRNAs. In eukaryotes, the subunits are made in the nucleus, then exported to the cytoplasm. One-third of the mass is proteins, the rest is three rRNA molecules in bacteria and four rRNA molecules in eukaryotes.

We tell our students "DNA is DNA is DNA." Cite an example from the EVOLUTION heading to explain what we mean.

Ex: the vertebrate Pax-6 gene results in the formation of the vertebrate eye, which has single lens. The fly Pax-6 gene leads to the formation of the compound fly eye. When the mouse Pax-6 gene was cloned and introduced into a fly embryo so it replaced the fly's own Pax-6 gene, te mouse version of the gene led to formation of a compound fly eye. The two versions of the Pax-6 gene can substitute for each other to trigger lens development.

Give two specific uses of gene cloning.

GMOs (genetically modified organisms) for creating pest resistant crops Harvesting human growth hormone from clone cultures

How might induced pluripotent stem (iPS) cells resolve the debate about using stem cells for medical treatments?

If the challenges are met, iPS cell created in this way could eventually provide tailor-made "replacement" cells for patients without using any human eggs or embryos, thus circumventing most ethical objections.

Explain the idea of gene therapy and discuss the problems with this technique as demonstrated in the treatment of SCID.

Gene therapy is the introduction of genes into an afflicted individual for therapeutic purposes. This treatment holds great potential for treating the relatively small number of disorders traceable to a single defective gene. The ain of this approach is to insert a normal allele of the defective gene into the somatic genes of the issue affected by the disorder One type of severe combined immunodeficiency (SCID) is caused by bone marrow cells that do not produce a vital enzyme because of a single defective gene. This treatment was successful but in the trials 3 people developed leukemia, a type of blood cell cancer. It was concluded that this happened because of the insertion of the retroviral vector that occurred near a gene that triggers the proliferation of blood cels.

What are general transcription factors, and how do they function?

General transcription factors are essential for transcription of all protein-coding genes. A few general transcription factors bind to a DNA sequence, such as the TATA box in most promoters, but many bind to proteins, including other transcription factors as well as RNA polymerase II. They are essential for initiation of transcription.

Cite four examples of genetically modified organisms (GMOs). Why are GMs controversial?

Genetically modified salmon (1) with the addition of a more active salmon growth hormone gene Genetically modified corn (2), soybean(3) and canola crops (4) in the U.S GMs are controversial because many Europeans are concerned about the safety of GM foods and the possible environmental consequences of growing GM plants. Others say transgenic plants might pass their new genes to close relatives in nearby wild areas, creating "super weeds"

What is genomic imprinting, and how is it maintained?

Genomic imprinting is the methylation pattern in which the methylation permanently regulates expression of either the paternal or paternal allele of particular genes at the start of development. This happens because once genes are methylated, they stay that way through successive cell divisions in an individual. At DNA sites where on strand is already methylated, enzymes methylate the correct daughter strand after each round of DNA replication. Methylation patterns are thus passed on to daughter cells, and cells forming specialized tissues keep a chemical record of what happened during embryonic development.

The infection of an animal cell by an RNA virus with an envelope is shown in this figure. In this viral infection the RNA genome serves as a template for mRNA synthesis. This is the pattern of infection for COVID-19, Ebola, influenza, measles, mumps, and rabies.Label this figure, and summarize the eight steps of infection as indicated by the label lines.

Glycoproteins on the viral envelope bind to receptors (not shown) on the host cell. For some viruses, the envelope fuses with the plasma membrane; others enter by endocytosis The capsid and viral genome enter the cell. Digestion of the capsid by cellular enzymes releases the viral genome The viral genome (red) functions as a template for synthesis of complementary RNA strands (pink) by a viral RNA polymerase New copies of viral genome RNA are made using complementary RNA strands as templates Complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER and Golgi apparatus) Vesicles transport envelope glycoproteins to the plasma membrane A capsid assembles around each viral genome molecule Each new virus buds from the cell, its envelope studded with viral glycoproteins embedded in the membrane derived from the host cell

Gene expression can be regulated by modifications of the chromatins that affect transcription. Distinguish between heterochromatin and euchromatin as to their structure and activity.

Heterochromatin is more densely arranged chromatin than euchromatin, making unreachable for transcription. Euchromatin is more loosely arranged and whether or not a gene is transcribed is affected by the location of nucleosomes along a gene's promoter and also the sites where the DNA attaches to the protein scaffolding of the chromosome.

Study text Figure 18.7b. What occurs in histone acetylation? How does it affect gene expression?

Histone acetylation is the addition of an acetyl group to an amino acid in a histone tail. This promotes transcription by opening up chromatin structure, while the addition of methyl groups to histones can lead to condensation of chromatin and reduced transcription.

. All genes are not "on" all the time. Using the metabolic needs of E. coli, explain how this conserves energy resources.

If the environment for E.coli (in the human colon) is lacking in the amino acid tryptophan, which the bacterium needs to survive, the cell responds by activating a metabolic pathway that makes tryptophan from another compound. If the human host later eats a tryptophan-rich meal, the bacterial cell stops producing tryptophan, thus avoiding wasting resources to produce a substance that is readily available from the surrounding solution.

What was some early evidence of the existence of viruses? Why were they difficult to study?

In 1883, Adolf Mayer was studying tobacco mosaic disease and discovered that he could transmit the disease from plant to plant by rubbing sap extracted from diseased leaves onto healthy plants. He could not find an infectious microorganism in the sap, so he suggested that the disease was caused by unusually small bacteria. Martinus Beijenrink then found that the mystery particle was much smaller than a bacterium and could replicate, terming the thing as a virus. Also, he passed the infected sap through a bacteria filter, and found that the sap was still infectious. They were difficult to study because at the time, they were not able to be seen under the microscope.

In early cloning experiments, John Gurdon and his colleagues transplanted nuclei from frogs into enucleated eggs (nuclear transplantation). What did they conclude from this work?

In Gurdon's experiments, the transplanted nucleus was often able to support normal development of the egg into a tadpole. However, he found that the potential of a transplanted nucleus to direct normal development was inversely related to the age of the donor: The older the donor nucleus, the lower the percentage of normal tadpoles. From these results, Gurdon concluded that something in the nucleus does change as animal cells differentiate. In frogs and other animals, nuclear potential tends to be restricted more and more as embryonic development and cell differentiation progress.

Chromosomal rearrangements are considered large-scale mutations. Point mutations are considered small-scale mutations and are of two general types. The first is a single nucleotide-pair substitution. What occurs here?

In a single nucleotide-pair substitution, there is replacement of one nucleotide and its partner with another pair of nucleotides.

How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?

In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns. Regulatory proteins specific to a cell type control intron/exon choices by binding to regulatory sequences within the primary transcript

What is the role of the guide RNA made from the CRISPR region of the bacterial genome?

In bacterial cells, Cas9 acts together with "guide RNA" made from the CRISPR region of the bacterial genome in order to alter the target gene. This happens by the Cas-9-guide RNA complex entering the nucleus and binding to the target gene. It then, cuts both strands of the DNA. Then scientists can cut out and experiment with a gene or enter a correct sequence to correct the genetic issue. Furthermore, the guide RNA is engineered to be complementary to the target gene for easy binding.

What is the major difference between embryonic stem (ES) cells and adult stem cells?

In contrast to embryonic stem cels, adult stem cells are not able to give rise to all cell types in the organism, though they can generate several defined types.

Cloned mammals were found to not always be identical to their parents or siblings. Often the cloned animals exhibit defects. What seems to be the reason for the high incidence of abnormalities?

In the nuclei of fully differentiated cells, a small subset of genes is turned on and expression of the rest of genes is repressed. This regulation often is the result of epigenetic changes in chromatic, such as acetylation of histones or methylation of DNA. During the nuclear transfer procedure, many of these changes must be reversed in the later-stage nucleus from a donor animal for genes to be expressed or repressed appropriately in earlier stages of development. DNA in cells from cloned embryos often have high numbers of methyl groups. This represses gene expression, so it has to be reprogrammed (epigenetically changed) for the embryo to even develop properly.

What are three applications of personal genome analysis?

Individuals can be tested by PCR and sequencing for a SNP that is correlated with an abnormal allele. The presence of a particular SNP is correlated with increased risk for an adverse health condition These genetic tests can help people understand genetic concerns, but cannot make predictions These companies compare a person's DNA segments with those from reference populations around the world which can give ancestry

The second category of point mutations includes nucleotide-pair insertions or deletions. These can result in frameshift mutations. What does this mean?

Insertion or deletion of nucleotides may alter the reading frame of the genetic message, the triplet grouping of nucleotides on the mRNA that is read during translation. Such a mutation, called a frameshift mutation, occurs whenever the number of nucleotides inserted or deleted is not a multiple of three.

What are the key ethical issues associated with using CRISPR-Cas9 in humans? How do you feel about the use of this system in humans?

Issues include possible effects on genes that are not being targeted and misuse of this technology by abusive authorities. I think that use of this system in humans will be useful, but only if its used cautiously and more research is done to correct any issues.

What is the role of DNA ligase in this process?

It catalyzes the formation of covalent bonds that close up the sugar-phosphate backbones of DNA strands

What is a prophage?

It is a bacterial cell's DNA in which viral DNA has been incorporated into the a specific site on the bacterial chromosome.

Why do RNA viruses have a high rate of mutation?

It is important to realize that many viruses have an RNA genome and therefore a high rate of mutation. Earlier you learned about the mechanisms of DNA repair that minimize mutation rates, but RNA replication lacks these repair enzymes.

What are the two advantages RNA-seq has over older methods?

It is not based on hybridization with a labeled probe, so it doesn't depend on knowing genomic sequences It can measure levels of expression over a a very wide rand A careful analysis provides a wealth of information about expression of a particular gene, such as relative levels of alternatively spliced mRNAs

You probably know someone who has been treated for breast cancer. Did you realize there were genetically distinct types? Study Figure 18.27 in your text to understand why the treatment varies from woman to woman. Why is it not surprising that signal receptors are over-expressed in most types of cancer?

It is not surprising that signal receptors are over-expressed because these over-expressed signals are what call the cell to divide rapidly, forming cancer

What important understandings about embryonic development resulted from the research into bicoid?

It led to the identification of a specific protein required for some of the earliest steps in pattern formation. Helped understand why different regions of the egg give rise to cells that go down different developmental pathways It increased our understanding of the mother's critical role in the initial phases of embryonic development The principle that a gradient of morphogens can determine polarity and position has proved to be a key developmental concept for a number of species

What is the promise of personalized medicine?

It provides a type of medical care in which each person's genetic profile can provide information about diseases or conditions for which the person is especially at risk and help make health-care decisions.

DNA sequencing techniques are changing rapidly, and your textbook describes three different "generations." Each technique is faster and less expensive than the previous one. The chapter opening photograph shows a single strand of DNA being moved through a nanopore in a membrane and the bases are identified one by one. Figure 20.3 in your text describes "next-generation sequencing." This procedure is an example of "high-throughput" DNA technology, and is currently the method of choice for studies where massive numbers of DNA samples are being sequenced. An interesting task is presented in the INTERPRET THE DATA question. Thoroughly study the figure for technique, then place the first 25 nucleotides seen in the flow-gram in the space below.

Just know this info

How does the lac operon have volume control?

Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. If glucose is scarce, the high level of cAMP activates CRP, which binds to the promoter and increases RNA polymerase binding there. The lac operon produces large amounts of mRNA coding for the enzymes that the cell needs for use of lactose Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP s scarce, and CRP is unable to stimulate transcription at a significant rate, even though no repressor is bound lac operon open has low transcription in volume the level of transcription increased when the level of cAMP increases

Besides lacking enzymes for RNA editing, describe how the lack of compartments in a prokaryotic cell results in a difference in gene expression from what was described in eukaryotic cells.

Like a one-room workshop, a bacterial cell ensures a streamlined operation by coupling the two processes of transcription and translation. With no nuclear envelope, it can simultaneously transcribe and translate the same gene, and the newly made proteinn can quickly diffuse to its site of function. In contrast, the eukaryotic cell's nuclear envelope segregates transcription fron translation and provides a compartment for extensive RNA processing. This processing state includes additional steps, discussed earlier, the regulation of which can help coordinate the eukaryotic cell's elaborate actvities.

What is always the first amino acid in the new polypeptide?

Methionine

What is the difference between a nonsense and missense mutation?

Missense mutations are substitutions that change one amino acid to another. Substitution mutations are usually missense mutations; that is, the altered codon still codes for an amino acid and thus makes sense, although not necessarily the right sense. But a point mutation can also change a codon for an amino acid into a stop codon. This is called a nonsense mutation and it causes translation to be terminated prematurely; the resulting polypeptide will be shorted than the polypeptide encoded by the normal gene. Most nonsense mutations lead to nonfunctional proteins.

Mutations provide the raw material of evolution. Define a mutation in terms of molecular genetics.

Mutations are changes to the genetic information (DNA) of a cell

Feedback inhibition is a recurring mechanism throughout biological systems. Is the regulation of tryptophan synthesis by E. coli achieved by positive or negative feedback? Explain your choice.

Negative feedback - the activity of the first enzyme in the pathway is inhibited by the pathway's end product, which is tryptophan

To demonstrate you understand how the lac and trp operon work, let's assume a human host has had a meal of turkey (rich in the amino acid tryptophan) and washed it down with milk. Explain your answer to each of the following: a. Will the trp operon of E. coli in the gut of the human be active?

No, it will be switched off by the repressor protein because tryptophan will bind to the protein, causing it to change shape and repress the operon. Furthermore, tryptophan is rich in the system, so the operon does not need to be on to produce even more tryptophan and waste resources.

How do viruses spread throughout plant bodies?

Once a virus enters a plant cell and begins replicating, viral genomes and associated proteins can spread throughout the plant through plasmodesmata, the cytoplasmic connections that permeate the walls between adjacent plant cells. The passage of viral macromolecules from cell to cell is facillitated by virally encoded proteins that cause enlargement of plasmodesmata. Viruses also must get past a plant's protective layer of cells (epidermis), so damaged plants are more susceptible to horizontal transmission.

Why don't restriction enzymes destroy the DNA of the bacterial cells that produce them?

The bacterium's own DNA is methylated in a way that prevents attack by its own restriction enzymes.

Mad cow disease and chronic wasting disease (seen in deer and elk) are both caused by prions. Twenty years ago, an outbreak of mad cow disease in Europe led to widespread testing and a shift of consumer meat preferences, at the time, away from beef or consumption of imported beef. What are prions? How are they transmitted? What do they do?

Prion are infectious proteins that appear to cause degenerative disease in various animal proteins. They are misfolded versions of normal proteins. Prions can be trasmitted in food. When a prion contacts a normally folded version of the same prtoein, it may induce the normal protein to assume the abnormal shape. Thus, may result in aggregation of prions and degeneration of the brain

What are two alarming characteristics of prions?

Prions act very slowly, with an incubation period of at least ten years before symptoms develop. The lengthy incubation period prevents sources of infection being indentified until long after the first cases are identified, allowing many more infections to occur Prions are not destroyed or deactivated by heating to normal cooking temperatures. No known cure against prion diseases yet

Label the figure and then describe the correspondence between exons and protein domains.

Proteins often have a modular architecture consisting of discrete structural and functional regions called domains. One domain of an enzyme, for example, might include the active site, while another might allow the enzyme to bind to a cellular membrane. In quite a few cases, different exons code for the different domains of a protein

nucleic acid hybridization

The base pairing of one strand of a nucleic acid to a complementary sequence from another nucleic acid strand, either DNA or RNA.

b. Plasmids may be altered by genetic engineering to create recombinant DNA molecules. What does this mean?

Recombinant DNA molecules are created when there is a molecule containing DNA from two different sources, very often different species.

DNA technology has been used in the development of certain drugs such as Gleevec that have been highly effective in cancer treatment. In many cases, persons appear to be in nearly complete remission only to have a relapse. Explain what occurs in these cases.

Relapse occurs because certain tumor cells have a random mutations that allows them to survive in the presence of a particular drug, and as a consequence of natural selection in the presence of the drug, these are the cells that survive and reproduce

Distinguish between inducible and repressible operons and describe one example of each type of operon.

Repressible operons are operons that have its transcription usually on but can be inhibited (repressed) when a specific molecule binds allosterically to a regulatory proteins. Ex: trp operon repressed by tryptophan binds to regulatory protein Inducible operons are usually off but can be stimulated (induced) to be on when a specific small molecule interacts with a different regulatory protein. Ex: lac (lactose) operon is stimulated by lactose to create enzyme B-galactosidase that breaks down lactose

What are restriction enzymes? How do they help prevent viral infections of bacteria?

Restriction enzymes are bacterial enzymes that identify phage DNA within the cell as foreign and cut it up. They help prevent viral infections of bacteria because these enzymes restrict a phage's ability to replicate within the bacterium

How is a plasmid engineered?

Restriction enzymes protect the bacterial cell by cutting up foreign DNA from other organisms or phages. A DNA fragment from another source is added. Base pairing of sticky ends produces various combinations. DNA ligase seals the strands

What is a retrovirus? How do retroviruses, such as HIV, replicate their genome?

Retroviruses are RNA animal viruses with the most complicated replicative cycle (class VI viruses). Their replication involves an enzyme called reverse transcriptase that takes an RNA template and transcribes into a DNA copy; RNA → DNA. After HIV enters a host cell, its reverse transcriptase molecules are released into the cytoplasm, where they catalzye the sythesis of viral DNA. The newly made viral DNA then enters the cell's nucleus and integrates into the DNA of a chromosome. The integrated viral DNA, called a provirus, never leaves the host's genome, remaining a permanent resident of the cell. The RNA polymerase of the host transcribes the proviral DNA into RNA molecules, which can function both as mRNA for the synthesis of viral proteins and as genomes for the new viruses that will be assembled and released from the cell

Describe how short tandem repeats (STRs) can produce a sensitive genetic profile. Don't miss the information about Earl Washington that goes with Figure 20.24 in your text.

Short tandem repeats (STRs) are variations in length of genetic markers. 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; even for a single individual, the two alleles of an STR may differ from each other.

Explain why shorter DNA molecules travel farther down the gel than larger molecules.

Shorter molecules are slowed down less than longer molecules, so shorter molecules move faster and farther down the gel than larger molecules.

Why are both the gene of interest and the plasmid cut with the same restriction enzyme?

Since, restriction enzymes always cut at the same exact DNA sequence, copies of any given DNA molecule exposed to the same restriction enzyme always yield the same set of restriction fragments.

Why do Tamoxifen and Herceptin not work against basal-like breast cancer?

Tamoxifen and Herceptin work to inhibit cell-signaling which results in overexpression, causing cancer. However, basal-like breast cancer involves a mutation in a tumor suppressor gene, so this type of cancer would be unaffected by tamoxifen and herceptin.

What portion of a phage enters the host cell? How does it do this?

The DNA of the phage enter the host cell. The phage does this by binding to the surface of the cell and injecting the DNA with its tail fibers.

explain the functions of the A, P, and E sites.

The P-site holds the tRNA carrying the growing polypeptide chain The A-site holds the tRNA carrying the next amino acid to be added to the chain The E-site is the site where discharged tRNAs leave the ribosome

Use the following figure to explain the process of a specific amino acid being joined to a tRNA. Label all parts of the figure. What are the three key points in matching the correct amino acid with the proper tRNA?

The amino acid and the appropriate tRNA enter the active site of the specific synthetase 2. Using ATP, the synthetase catalyzes the covalent bonding of the amino acid to its specific tRNA 3. The tRNA, charged with its amino acid, is released by the synthetase

Three key events occur in elongation. Explain the important features of each event. Codon recognition

The anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysis of GTP increases the accuracy and efficiently of this step. Although not shown, many different aminoacyl tRNAs are present, but only the one with the appropriate anticodon will bind and allow the cycle to progress

HIV infection steps:

The envelope glycoproteins enable the virus to bind to specific receptors (not shown) on certain white blood cells The virus fuses with the host cell's plasma membrane The capsid proteins are removed, releasing the viral proteins, RNA, and reverse transcriptase Reverse transcriptase catalyzes the synthesis of of a DNA strand, using the viral RNA as a template and then hydrolyzing it Reverse transcriptase catalyzes the synthesis of of second DNA strand complementary to the first The double-stranded DNA is incorporated as a provirus into the cell's DNA Proviral genes are transcribed into RNA molecules, which serve as genomes for progeny viruses and as mRNAs for translation into viral protein Viral envelope glycoproteins are made in the ER Viral capsid proteins and reverse transcriptase are made in the cytosol Vesicles transport the glycoproteins to the cell's plasma membrane Capsids are assembled around viral genomes and reverse transcriptase molecules New viruses, with viral envelope glycoproteins, bud from the host cell

Compare and contrast the lac operon and the trp operon.

The lac operon's inducer is allolactose and in the presence of the molecule, the repressor protein cannot bind to the operator because allolactose binds to it and changes the shape of the protein. For the trp operon, tryptophan is the molecule that binds to the repressor protein and shuts off the operon. The lac operon codes for inducer enzymes because their synthesis is induced by a chemical signal (catabolic pathways). Repressible enzymes generally function in anabolic pathways, which synthesize end products from precursor materials like the trp operon.

lytic cycle

The lytic cycle is a phage replicative cycle that culminates in death of the host cell. First, a phage attaches to a host cell and injects its DNA. Then, the phage DNA circularizes. Then, the new phage DNA and proteins are synthesized, and these self-assemble into phages. Then, the cell lyses and releases the phages.

One of the noncoding RNAs that regulate gene expression is microRNA (miRNA). Use the following sketch to label and explain the two modes of action of microRNAs.

The miRNA binds to a target mRNA with at least 7 complementary bases If miRNA and mRNA bases are complementary all along their length, the mRNA is degraded (left); if the match is less complete, translation is blocked (right)

When DNA is cut with restriction enzymes, DNA fragments result. Carefully study Figure 20.6 in your text to learn about gel electrophoresis. Why is the DNA sample to be separated by gel electrophoresis always loaded at the cathode or negative end of the power source?

The negative charges on the phosphate groups in the backbone cause the gel to travel from the negative end (cathode) to the positive end (anode) because negative charges want to combine with positive charges. Smaller molecules travel faster through the gel which allows researchers to separate the recombinant plasmid into foreign DNA and plasmid DNA to check if the recombinant chromosome is being transferred in cell divisions.

What is the fundamental difference between the repressor protein in a repressible operon versus the repressor protein in an inducible operon?

The repressor protein in an repressible operon requires a small molecule to bind to the protein in order for the protein to repress the operon, while in an inducible operon, there is no need for this small molecule to switch the operon off. The repressor protein naturally binds to the operon, while an inducer molecule binds to the repressor to turn it off.

What is the role of the inducer?

The role of the inducer is to inactivate the repressor. It is a small molecule that allosterically binds to the repressor protein

DNA Sequencing

a process where researches can exploit the principle of complementary base pairing to determine the complete nucleotide sequence of a DNA molecule

How does a DNA virus reproduce its genome?

They use the DNA polymerases of the host cell to synthesize new genomes along the templates provided by the viral DNA

How do most RNA viruses replicate their genomes?

They use virally encoded RNA polymerases that can use RNA as a template.

mRNA Description and Function

This strand of mRNA has specific codons that are decoded in order to form the polypeptide chain Acts as a script that is translated into amino acids.

Explain how transgenic "pharm" animals might be able to produce human proteins.

To do this, researchers use a transgene, a gene that has been transferred into one organism from another. They first remove eggs from a female of the recipient species and fertilize them in vitro. Meanwhile, they clone the desired gene from a donor organism. They then inject the cloned DNA directly into the nuclei of the fertilized eggs. Some of the cells integrate the foreign DNA, the transgene, into their genome and are able to express the foreign gene. The engineered embryos that arise from the zygotes are then surgically implanted in a surrogate female. If an organism develops, its a transgenic organism that expresses its new "foreign gene". Ex: this gene can produce proteins of in the milk of a goat

Isolating a single gene is like finding a needle in a haystack. To study a specific gene, scientists often use DNA cloning. What is this?

To study a specific gene, scientists have developed methods to isolate a segment of DNA carrying that gene and making multiple copies of it -- a process called DNA cloning.

What are the two categories of mutagens?

Two categories of mutagens: physical and chemical (Mutagens are chemical and physical agents that interact with DNA in ways that cause mutations)

DNA microarray assays can be used to determine a pattern of gene expression, such as what genes are expressed in an embryo on day 2 of development compared to day 5. The expression of thousands of genes can be measured at one time. Turn back to Figure 18.27 in your text and explain how microarrays are used to determine appropriate treatment for different types of breast cancer.

Using microarray analysis, researchers measured the relative levels of mRNA transcripts for every gene in hundreds of breast cancer tumor samples. They identified four major subtypes of breast cancer that differ in their expression of three signal receptors involved in regulating cell growth and division. They use fluorescent probes that bind to the cDNAs in each well to see which genes are expressed based on the color of the well.

What tools are in the medical arsenal against human viral diseases?

Vaccines, antiviral drugs (target nucleotide sequences that encode viral enzymes), and multidrug treatments

Explain what is meant by vertical transmission and horizontal transmission of plant viruses.

Vertical transmission of plant viruses involves a plant that has inherited a viral infection from a parent. In horizontal trasmission, an external source infects the plant

Briefly explain how viruses can play a variety of roles in cancer formation.

Viruses can interfere with gene regulation in several ways if they integrate their genetic material into the DNA of a cell. Viral integration may donate an oncogene to the cell, disrupt a tumor-suppressor gene, or convert a proto-oncogene to an oncogene. Some viruses produce proteins that inactivate p53 and other tumor-suppressor proteins, making the cell more prone to becoming cancerous

What are three ways that viruses make us ill? Why do we recover completely from a cold but not from polio?

Viruses may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes Some viruses cause infected cells to produce toxins that lead to disease symptoms Some viruses have molecular components that are toxic, such as envelope proteins People usually recover completely from colds because the epithelium of the respiratory tract, which the viruses infect, can efficiently repair itself. In contrast, damage inflicted by poliovirus to mature nerve cells is permanent because these cells do not divide and usually cannot be replaced

The CRISPR-Cas system was discovered when puzzling palindromic DNA repeats were found in the genomes of bacteria. These were found to be remnants from earlier phage infections, and it was learned that bacteria have nucleases (called Cas proteins) for cutting this phage DNA if it is encountered again. What happens when a phage infects a bacterial cell with the CRISPR-Cas system?

When a phage infects a bacterial cell that has the CRISPR-Cas system, the DNA of the invading phage is stored, integrated into the genome between two repeat sequences. If the cell survives the infection, any further attempt by the same type of phage to infect this cell (or its offspring) triggers transcription of the CRISPR region into RNA molecules. These RNAs are cut into pieces and then bound by Cas proteins, such as the Cas9 protein. The Cas protein uses a portion of the phage-related RNA as a homing device to identify the invading phage DNA and cut it, leading to its destruction

Because cells that have incorporated phage DNA into their genome may continue to divide and propagate the viral genome, this might be considered somewhat like the Trojan horse. What might trigger the switchover from lysogenic to lytic mode?

When the prophage DNA (viral DNA) exits the bacterial chromosome, it initiates the lytic cycle. This can be caused by an environmental signal, such as a certain chemical or high-energy radiation usually triggers the switchover from the lysogenic to the lytic mode.

How does the bacterial cell identify the phage DNA when it is encountered? What happens to the phage DNA?

When the same type of phage injects DNA, it triggers RNA transcription of the previous stored phage DNA. This complementary RNA binds to the Cas protein and the complementary RNA binds to the DNA from the invading phage. The Cas protein then cuts the phage DNA. After being cut, the entire phage DNA molecule is degraded and can no longer be replicated

Bicoid is a gene that produces a morphogen. What results when there is a high concentration of the bicoid protein in a developing embryo?

When there is a high concentration of bicoid mRNA in a developing embryo, the anterior end of the embryo is correctly set up and developed. Morphogens are substances that establish an embryo's axes and other features of its form.

How many molecules will be produced by four PCR cycles?

With each successive cycle, the number of target segment molecules of the correct length doubles, so the number of molecules equal 2^n, where n is the number of cycles: 2^4 = 16 molecules

Scientists expected to find one aminoacyl-tRNA synthetase per codon, but far fewer have been discovered. How does wobble explain this?

Wobble is the flexible base pairing at the third position of a codon. Meaning, the rules for base pairing between the third nucleotide base of a codon and the corresponding base of a tRNA anticodon are relaxed. For example, the nucleotide base U and the 5' end of a tRNA can pair with either A or G in the third position (at the 3' end) of an mRNA codon.

What advantages does use of yeast have over bacterial cells for an expression system?

Yeasts are single celled eukaryotic fungi, that are as easy to grow as bacteria, and they have plasmids which is a rarity among eukaryotes. They allow for RNA-splicing and yeast cells are advantageous because many eukaryotic proteins will not function unless they are modified after translation. (Ex: addition of carbohydrate groups or lipid groups in the ER and Golgi)

To demonstrate you understand how the lac and trp operon work, let's assume a human host has had a meal of turkey (rich in the amino acid tryptophan) and washed it down with milk. Explain your answer to each of the following: b. Will the lac operon of E. coli in the gut of the human be active?

Yes, the lac operon will be switched on because the allolactose will bind to the repressor protein to inactivate it. Once this happens, the pathway for creating lactose breaking-down enzymes will start up.

What is an expression vector?

a cloning vector that contains a highly active bacterial promoter just upstream of a restriction site where the eukaryotic gene can be inserted in the correct reading frame.

lysogenic cycle

a phage replication cycle that doesn't destroy the host cell. First, a phage attaches to a host cell and injects its DNA. Then, the phage DNA circularizes. Then, the phage DNA integrates into the bacterial chromosome, becoming a prophage. The bacterium reproduces normally, copying the prophage and transmitting it to the daughter cells.

In late December 2019, COVID-19 arose in China and spread worldwide to become a pandemic. This and other emerging viruses such as HIV, Ebola, SARS, Chikungunya, and Zika seem to burst upon the human scene. Explain the three processes that contribute to the sudden emergence of viral diseases.

a. Mutation of existing viruses into new viruses that can spread more easily. RNA viruses have a high rate of mutaiton because viral RNA polymerases do not proofreed and correct errors in replicating their RNA genomes. Some mutations change existing viruses into new viral strains than can cause disease, even in people immune to the original virus b. The spread of a viral disease from a small, isolated human population. As global factors make transmission more easier, viruses become more widespread c.The spread of existing viruses from other animals. Animals can act as vectors for viral diseases towards humans

Explain how each of the four mechanisms listed here are involved in converting a proto-oncogene to an oncogene. Figure 18.23 in your text helps clarify each of the four mechanisms. a. epigenetic modifications: b. translocations: c. gene amplification: d. point mutations:

alterations in epigenetic modifications that can lead to abnormal chromatin condensation in a cell are often found in tumor cells. If a mutation in a gene for a chromatin-modifying enzyme leads to loosening of chromatin in a region that is normally not being expressed, a proto-oncogene in that region could be expressed at abnormally high levels Cancer cells are frequently found contain chromosomes that have broken and rejoined incorrectly, translocating fragments from one chromosome to another. If a translocated proto-oncogene ends up near an especially active promoter (or other control element), its transcription may increase, making it an oncogene. increases the number of copies of the proto-oncogene in the cell through repeated duplication a point mutation in either the promoter of an enhancer that controls a proto-oncogene, could cause an increase in its expression. A point mutation in the coding sequence of the proto-oncogene could change the gene's product to a protein that is more active or resistant to degradation than the normal protein.

long noncoding RNAs (lncRNAs)

associated with specific diseases. Ex: X chromosome inactivation, prevents expression of genes located on one of the X chromosomes in most female mammals. lncRNAs are transcripts of the XIST gene located on the chromosome to be inactivated. They bind back to and coat the chromosome. This binding leads to condensation of the entire chromosome into heterochromatin

What three processes lead to the transformation of a zygote into the organism?

cell division, cell differentiation, and morphogenesis

Much as with transcription, we can divide translation into three stages. List them.

initiation, elongation, termination

Enzymatic pathways involve a series of different enzymes that catalyze reactions in sequence, as is shown in Figure 18.2 in your text. For this to occur in bacteria, the genes that code for these enzymes are coordinately controlled by being clustered in units known as operons. To better understand how an operon functions, begin by explaining the role of each of the following: promoter

the site on DNA where RNA polymerase can bind to DNA and begin transcription. A single promoter can serve for the multiple genes in the transcription unit due to multiple start and stop codons for each polypeptide

transcription

the synthesis (production) of RNA using information in the DNA. The informations is simply "rewritten" from DNA to RNA (complementary mRNA string to that of DNA)

What percentage of the genes of a typical human cell is expressed at any given time?

⅓ to ½ of its protein-coding genes at any given time

Leading strand replication

1. After RNA primer is made, DNA pol III starts to synthesize the leading strand 2. The leading strand is elongated continuously in the 5' → 3' direction as helicase opens up the fork further to the left

Explain what is meant by 5ʹ and 3ʹ ends of the nucleotide.

5' and 3' refer to the numbers assigned to the carbons in the sugar ring.

Of the 64 possible codons, how many code for amino acids?

61

The language of DNA is a triplet code. How many unique triplets exist?

64

How does a bacteriophage destroy a bacterial cell? Look ahead to Chapter 19, Figure 19.5 in your text, to explain this.

A bacteriophage (phage) attaches itself to a bacterial cell by attaching its tail fibers to the surface proteins of the bacterial cell. It then contracts the sheath of its tail and injects phage DNA into the cell and the cell DNA is hydrolyzed. The phade DNA directs production of phage proteins and copies of the phage genome by host and viral enzymes, using components in the cell. Then, three separate sets of protein self-assemble to form phage heads, tails, and tail fibers. The phage genome is packaged inside the capsid as the head forms. Lastly, the phage directs production of an enzyme that damages the cell wall, allowing fluid to enter. The cell swells and finally bursts, releasing 100 to 200 phage cells.

Define transformation.

A change in genotype and phenotype due to the assimilation of external DNA by a cell

Stages of Initiation of Transcription

A eukaryotic promoter commonly includes a TATA box (a nucleotide sequence containing TATA) about 25 nucleotides upstream from the transcriptional starting point Several transcription factors, one recognizing the TATA box, must bind to the DNA before RNA Polymerase II can bind in the correct position and orientation, as shown in step 3 Additional transcription factors (purple) bind to the DNA along with RNA polymerase II, forming the transcription initiation complex. RNA polymerase II then unwinds the DNA double helix, and RNA synthesis begins at the start point on the template strand

What is a thymine dimer? (See Figure 16.20 in your text.) How might it occur? How is it repaired?

A section of distorted DNA on a segment and is often caused by ultraviolet radiation. It is repaired by a nuclease enzyme cutting the damaged DNA strand at two points and removing the damaged DNA. Then, DNA polymerase fills in the missing nucleotides using the undamaged strand as a template. Lastly, DNA ligase seals the free end of the new DNA to the old DNA, making the strand complete.

Distinguish between the structure of pyrimidines and purines. Explain why adenine bonds only to thymine.

Adenine and guanine are purines which are nitrogenous bases with two organic rings, while cytosine and thymine are nitrogenous bases called pyrimidines which have a single ring. Adenine only bonds with thymine because adenine can form two hydrogen bonds with thymine and only thymine; guanine forms three hydrogen bonds with cytosine and only cytosine

Nuclease in Proofreading and Repair

An enzyme that cuts a segment of the strand containing the damage (excised) and the resulting gap is then filled with nucleotides, using the undamaged strand as a template

In elongation of the RNA strand how is the DNA unwound? What happens to the growing RNA strand?

As RNA polymerase moves along he DNA, it untwists the double helix, exposing about 10-20 nucleotides at a time for pairing with RNA nucleotides. The enzyme adds nucleotides to the 3' end of the growing RNA strand as it moves along the double helix. As transcription proceeds forward, the newly synthesized RNA molecule behind RNA polymerase peels away from its DNA template, and the DNA double helix re-forms

What are three properties of RNA that allow it to function as an enzyme?

Because RNA is single stranded, a region of an RNA molecule may base pair, in an antiparallel arrangement, with a complementary region elsewhere in the same molecule; this gives the molecule a particular three-dimensional structure. A specific structure is essential to the catalytic function of ribozymes, just as it is for enzymatic proteins b. Like certain amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that can participate in catalysis c. The ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity

How did Hershey and Chase "label" viral DNA and viral protein so that they could be distinguished? Explain why they chose each radioactive tag considering the chemical composition of DNA and protein.

Because protein, but not DNA, contains sulfur, radioactive sulfur atoms were incorporated only into the protein of the phage. In a similar way, the atoms of radioactive phosphorus labled only the DNA, not the protein, because nearly all the phage's phosphorus is in its DNA.

Why is the genetic code said to be redundant but not ambiguous?

Because there may be multiple codons coding for one amino acid (GAA and GAG for glutamic acid) hence redundancy, these codons do not reference any other amino acid (only codes for glutamic acid exclusively) hence no ambiguity.

Which organism did Beadle and Tatum use in their research? _________________. How did this organism's nutritional requirements facilitate this research?

Bread mold (Neurospora crassa) Wild-type Neurospora has modest food requirements. It can grow in the lab on minimal medium--a simple solution that contains minimal nutrients for growth--inorganic salts, glucose, and the vitamin biotin--incorporated into agar, a support medium. The wild-type mold cells use their metabolic pathways to produce all the nutrient molecules (like amino acids) they need for growth, division, and forming visible colonies of genetically identical cells. The scientists created different nutritional mutants of te cells, each of which had a mutation in one gene and was unable to synthesize a particular essential nutrient. These cells needed the complete medium (with 20 amino acids and nutrients) to grow. They were able to determine which nutrient each mutant strain was unable to synthesize.

Test tubes for Conservative, Semiconservative, and Dispersive models of DNA replication

Conservative model - The two parent strands reassociate after acting as templates for new strands, thus restoring the parental double helix Semiconservative model - The two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand Dispersive mode- each strand of both daughter molecules contains a mixture of old and newly synthesized DNA The Semiconservative model matches their data

What did Oswald Avery, McCarty, and MacLeod determine to be the transforming factor

DNA

Write the central dogma of molecular genetics, as proclaimed by Francis Crick in the boxes below. This is the essential direction of flow of genetic information. Memorize and understand the central dogma.

DNA -> RNA -> Protein

Transcription: Template, Product Synthesized, Location in Eukaryotic Cell

DNA Strand, mRNA strand, nucleus

What are the two chemical components of chromosomes?

DNA and protein

Distinguish between the leading and the lagging strands during DNA replication.

DNA polymerase II can only add nucleotides starting from the 3' end of the primer, so the enzyme elongates the new DNA in the mandatory 5' → 3' direction. DNA pol III remains in the replication form and continously adds nucleotides to the new complementary strand as the fork progresses. This DNA strand that is made this way is the leading strand. Only one primer is required for DNA pol III to synthesize the entire leading strand. To elongate the other new strand in the mandatory 5' → 3' direction, DNA pol II must work and along the other remplate strand in the direction away from the replication for. The DNA strand elongating in this way is the lagging strand. The lagging strand is synthesized discontinously as a series of segments.

. Distinguish between heterochromatin and euchromatin. How is this important to gene expression?

Euchromatic is loosely aranged 10-nm chromatic fiber and Heterochromatin is densely (folded and bent back on itself to a greater degree) arranged 10-nm fiber. The DNA in euchromatin is accessible to the proteins that carry out transcription, and its genes can be expressed. In heterochromatin, the 10-nm fiber is more densely arranged and less accessible to these proteins; genes in heterochromatin are generally not expressed.

Describe one example Garrod used to illustrate his hypothesis.

For ex, people with a disease called alkaptonuria have black urine because it contains a chemical called alkapton, which darkens upon exposure to air. Garrod reasoned that these people can't make an enzyme that breaks down alkapton, so alkapton is expelled in their urine.

What is gene expression?

Gene expression is the process by which DNA directs the synthesis of proteins (or, in some cases, just RNAs)

What types of cells produce telomerase? Why is this important?

Germ cells do. They produce telomerase, an enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shorting that occurs during DNA replication. This is important because this prevents essential genes to be missing from the gametes and keeps the genome virtually unchanged for many generations.

Distinguish between the virulent and nonvirulent strains of Streptococcus pneumoniae studied by Frederick Griffith.

Griffith found that when he killed the pathogenic bacteria with heat and then mixed the cell remains with living bacteria of the nonpathogenic strain, some of the living cells became pathogenic. Furthermore, this newly acquired trait of pathogenicity was inherited by all the descendants of the transformed bacteria. Apparently, some chemical component of the death pathogenic cells cause heritable change, although the identity of the substance was not know

Describe Marshall Nirenberg's experiment in which he identified the first codon. What codon/amino acid pair did he identify?

He synthesized an artificial mRNA made up of only uracil-bearing nucleotides, thus containing only one codon (UUU) over and over. When added to a test-tube mixture contained all 20 amino acids, ribosomes, and other components required for protein synthesis, the "poly-U" mRNA was translated into a polypeptide containing many units of phenylalanine (Phe, or F) amino acids, strung together as a poly-phenylalanine chain. He discovered that UUU codes for the amino acid phenylalanine.

What region signals the end of transcription?

In bacteria, the sequence that signals the end of transcription is called the terminator

How does the termination of transcription occur in bacteria?

In bacteria, transcription proceeds through a terminator sequence in the DNA. The transcribed terminator (an RNA sequence) functions as the termination signal, causing the polymerase to detach from the DNA and release the transcript, which requires no further modification before translation.

E. coli has a single circular chromosome, while eukaryotes have multiple linear chromosomes and much more DNA. How is the replication of eukaryotic DNA speeded up?

In contrast to the single origin of replication in E.coli, a eukaryotic chromosome may have hundreds or even a few thousand replication origins. Multiple replication bubbles form and eventually fuse, thus speeding up the copying of the very long DNA molecules.

What is the signal sequence in eukaryotes that ultimately ends transcription?

In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which specifies a polyadenylation signal (AAUAAA) in the pre-mRNA. This is called a "signal" cause once these six nucleotides appear, it is immediately bound by certain proteins in the nucleus. Then at a point about 10-35 nucleotides downstream from the sequence, these proteins cut the RNA transcript free from the polymerase, releasing the pre-mRNA

Describe the means by which Hershey and Chase established that only the DNA of a phage enters an E. coli cell. What conclusions did these scientists draw based on these observations?

In the experiment, separate samples of nonradioactive E.coli cells were infected separately with the protein-labeled and DNA-labeld batches of T2. The researches then tested the two samples shorty after the onset of infection to see which type of radioactively labeled molecule--protein or DNA-- had entered the bacterial cells and would therefore be capable of reprogramming the. They found that the phage T2 DNA entered the host cells, but the phage protein did not. Even more, when these bacteria were returned to a culture medium and the infection ran its course, the E.coli released phages that contained some radioactive phosphorus. They concluded that the DNA injucted by the phage must be the molecule carrying the genetic information that makes the cells produce new viral DNA and proteins.

RNA processing, sometimes also called mRNA editing, occurs only in eukaryotic cells. Prokaryotic cells lack the enzymes to edit mRNA. The primary transcript is altered at both ends, and sections in the middle are removed. a.What happens at the 5ʹ end?

It receives a 5' cap, a modified form of a guanine (G) nucleotide added onto the 5' end after transcription of the first 20-40 nucleotides have been transcribed.

Who are the two men who built the first molecular model of DNA and shared the 1962 Nobel Prize for the discovery of its structure?

James Watson and Francis Crick

Ligase in Proofreading and Repair

Ligase seals the new DNA to old DNA to make the strand complete

Repair enzymes in Proofreading and Repair

Mismatch repair - other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors and DNA polymerase has not caught these erors

How has our understanding of the arrangement of chromosomes in the nucleus changed from the time when interphase chromosomes were thought to be a tangled mass like a bowl of spaghetti?

Now, we know that interphase chromosomes lack an obvious scaffold, but there are proteins that further organize the 10 nm fiber into larger compartments and smaller looped domains. Some of the looped domains appear to be attached to the nuclear lamina, on the insdie of the nuclear envelope, and perhaps to the fibers of the nuclear matrix. These attachments may help organize regios of chromatin where genes are active. The chromatin of each chromosome occupies a specific restricted area within the interphase nucleus, and the chromatin fibers of different chromosomes do not appear to be entangled

What revision of detail (but not of basic principle) did this hypothesis undergo as more information was gained? Original hypothesis - one gene = one enzyme. Write this restatement and then box or highlight it. This is an important concept

One gene - one polypeptide

Define the origins of replication.

Origins of replication are short stretches of DNA that have a specific sequence of nucleotides and are specific sites where the replication of chromosomal DNA begins.

Explain the concept of reading frame in the context of red dogs eating bugs.

Our ability to extract the intended message from a written language depends on reading the symbols in correct groups, the correct reading frame. Ex: right frame: "The red dog ate the bug" vs. "her edd oga tet heb ug."

Lagging strand replication

Primase joins RNA nucleotides into the first primer for the lagging strand DNA polymerase III adds DNA nucleotides to the primer, forming Ozaki fragment 1 Afer reaching the next RNA primer to the right, DNA pol III detaches Fragment 2 is primed. Then DNA polymerase III adds DNA nucleotides, detaching when it reaches the fragment 1 primer DNA polymerase I replaces the RNA with DNA, adding nucleotides to the 3' end of fragment 1 (and, later, of fragment 2) DNA ligase forms a bond between the newest DNA and the DNA of fragment 1 The lagging strand in this region is now complete

DNA Polymerase in Proofreading and Repair

Proofread each nucleotide against its template as soon as it is covalently bonded to the growing strand. Upon finding an incorrectly paired nucleotide, the polymerase removes the nucleotide and then resumes synthesis. (action similar to fixing a texting error by deleting the wrong letter and then entering the correct one)

From the first paragraph in this section, find three ways in which RNA differs from DNA.

RNA is chemically similar to DNA except it contains ribose instead of deoxyribose as its sugar RNA has the nitrogenous base uracil rather than thymine (A,G,C,U) compared to DNA (A,G,C,T) An RNA molecule usually consists of a single strand

Recall from Chapter 16 that DNA polymerase III adds new nucleotides to the template DNA strand to assemble each new strand of DNA. Both enzymes can assemble a new polynucleotide only in the 5ʹ 🡪 3ʹ direction. Which enzyme, DNA polymerase III or RNA polymerase, does not require a primer to begin synthesis?

RNA polymerase

Study the figure and text carefully to explain how the splice sites are recognized.

Small RNAs within the spliceosome base-pair with nucleotides at specific sites along the intron; these are the splice sites.

What are telomeres and what two protective functions do they serve?

Telomeres are special nucleotide sequences at the ends of eukaryotic chromosomal DNA. They do not contain genes; instead, the DNA consists of multiple repetitions of one short nucleotide sequence. In each human telomere, the six-nucleotide sequence TTAGGG is repeated between 100 and 1,000 times. Their function is to prevent shortenic the genetic coding in the lagging strand because once the last primer is removed, DNA polymerase cannot attach anymore nucleotides because there is not 3' end, only 5'. (AKA prevent staggered ends of daughter moelcules of DNA) Second, telometric DNA acts as a kind of buffer zone that provides some protection against the organism's genes shortening

xplain telomere erosion and why it may be related to aging.

Telomeres become shorter during every round of replication. Thus, telomeric DNA tends to be shorter in dividing somatic cells of older individuals and in cultured cells that have divided many times. It has been proposed that shortening of telomeres is somehow connected tot he aging process of certain tissues and even to aging of the organism as a whole.

What is the TATA box? How do you think it got this name?

The TATA box is a nucleotide sequence containing TATA that is about 25 nucleotides upstream from the transcriptional start point. It is a crucial promoter DNA sequence for the formation of the transcription initiation complex. It got its name from containing the sequence of nucleotides TATA in it

What commonly held idea was rendered obsolete by the discovery of ribozymes?

The discovery of ribozymes invalidated the idea that all biological catalysts are proteins.

What are Okazaki fragments? How are they welded together?

The segments of the lagging strand when it is synthesized. First, each segment is primed separately; after, DNA pol III froms an Okazaki fragment, another DNA polymerase, DNA pol I, replaces the RNA nucleotides of the adjacent primer with DNA nucleotides one at a time. But DNA pol I can't join the final nucleotide of this replacement DNA segment to the first DNA nucleotide of the adjacent Okazaki fragment. DNA ligase does this by joining the sugar-phosphate backbones of all the Okazaki fragments into a continous DNA strand.

What is a transcription unit?

The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule

DNA is double-stranded; however, for each protein, only one of these two strands is used to produce an mRNA transcript. What is the strand called?

The template strand

What are the two components of spliceosomes? How do spliceosomes work?

The two components of spliceosomes are proteins and small RNAs. This complex binds to several short nucleotide sequences along an intron, including key sequences at each end. The intron is then released (and rapidly degraded), and the spliceosome joins together the two exons that flanked the intron. The small RNAs in the spliceosome not only participate in spliceosome assemby and splice site recognition, but also catalyze the splicing reaction; like proteins, RNAs can act as catalysts.

Study Figure 17.3 in your text carefully until the technique used to identify and isolate mutant fungi, the results of the experiment, and the conclusion that was drawn are clear to you. Using the Results Table for Class II mutants, explain why two test tubes show no growth and two test tubes show growth.

The two tubes that show growth are the original wild type cells growing on minimal medium and mutant type cells growing in minimal medium with arginine. Two test tubes without growth are minimal medium with valine and minimal medium with lysine. The reason the mutant type did not grow here is because they were lacking a nutrient for growth and arginine was that nutrient, so they grew in the test tube with arginine only. The wild-type cells naturally grow in minimal medium.

What significant findings from the research of Beadle and Tatum resulted in their receiving the Nobel Prize in 1958?

Their discovery that the function of a gene is to dictate the production of a specific enzyme. This is the one gene-one enzyme hypothesis

What strategy did Beadle and Tatum adopt to test this hypothesis?

They studied the haploid species of bread mold (Neurospora crassa). Because its genome contains only one copy of each gene, that single copy determines the individual's expressed phenotype. Therefore, when Beadle and Tatum wanted to discover the function of any gene, they only needed to mutate and disable that one allele. They chose to study the protein-coding genes required for a specific nutritional activity. They caused mutations in genes by bombarding Neurospora with X-rays and looked among the survivors for mutants that differed in their nutritional needs from the wild-type bread mold

How did Meselson and Stahl create "heavy" DNA for their experiments?

They took E.coli for several generations in a medium containing nucelotide precursors labeled with a heavy isotope of nitrogen, 15N. They then transferred the bacteria to a medium with only 14N, a lighter isotope. They took one sample after the first DNA replication and another after the second replication. They extracted DNA from the bacteria in the samples and then centrifuged to separate the DNA to different densities.

How were Neurospora spores treated to increase the mutation rate?

They were bombarded with X-rays to cause mutations of the genes

Why are cancer cells able to persist by continuing to divide while most body cells have a limited life span?

This is because telomerase activity is abnormally high in cancerous somatic cells, suggesting that its ability to stabilize telomere length may allow these cancer cells to persist. As for most normal cells, they have a limited lifespan because of normal telomerase activity and further-shortening of DNA through many cell divisions leads to self-destruction of the cells,

What do we mean when we say the two strands of DNA are antiparallel?

This means that the subunits of the DNA run in opposite directions similar to two lanes running in different directions.

What is the semiconservative model of replication?

Watson and Crick's model that predicts that when a double helix replicates, each of the two daughter molecules will have one onde strand, from the parental molecule, and one newly made strand.

How did Watson and Crick's model explain the basis for Chargaff's rules?

Wherever one strand of a DNA molecule has an A, the partner strand has a T. Similarly, a G in one strand is always paired with a C in the complementary strand. Therefore, in the DNA of any organism, the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine. Although the base-pairing rules dictate the combinations of nitrogenous bases that form the "rungs' of the double helix, they don't restrict the sequence of nucleotides along each DNA strand. The linear sequence of the four bases can be varied in countless ways, and each gene has a unique base sequence.

What was Rosalind Franklin's role in the discovery of the double helix?

While visiting Maurice Wilkins's laboratory, Watson saw an X-ray diffraction image of DNA produced by Wilkins's colleague Rosalind Franklin. Watson was familiar with the type of X-ray diffraction pattern of helical molecules, and seeing the photo that Wilkins showed him confirmed that DNA was helical in shape. The pattern in the photo implied that the helix was made up of two strands rather than Linus Pauling's three-stranded model. The two strands of DNA make the double helix.

List the three components of a nucleotide.

a nitrogenous (nitrogen-containing) base, a pentose sugar called deoxyribose, and a phosphate group

In eukaryotes, what is the pre-mRNA called?

a primary transcript (an intermediate RNA strand before it is modified into mRNA)

Topoisomerase

relieves strain caused by unwinding

DNA polymerase I

removes RNA primer and replaces it with DNA

Coding strand

the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine

translation

the synthesis of a polypeptide using the information in the mRNA

Helicase

untwists and separates strands