bio exam 3 review

Compare/contrast each pair of terms: (a) action of DNA polymerase vs RNA polymerase action, (b) primer vs promoter.

(a) RNA polymerase makes RNA from DNA. It doesn't need helicase or a primer. It adds complementary nucleotides to the 3' end of the growing RNA chain. DNA polymerase makes copies of DNA by adding complementary nucleotides to the 3' end of the chain. It needs helicase and a primer. (b) Primer- starts replication of DNA, Promoter- starts transcription of RNA

What were early arguments supporting each of the following hypotheses? (a) protein is the genetic material, (b) DNA is the genetic material.

20 different amino acids, great variety in shapes, known to control cell reactions (goes everywhere in the cell) Only 4 different nucleotides, all long & stringy, stays in the nucleus

The trp operon genes code for enzymes in a pathway that makes the amino acid tryptophan from a precursor molecule. What are two different ways a bacterial cell can turn off making tryptophan? Why is the trp operon a good example of end-product feedback inhibition for both enzyme & gene activity?

A bacterial cell can turn off making tryptophan through enzyme feedback inhibition or gene inhibition. Tryptophan acts as a corepressor: when there's a build up of it, it'll bind to the repressor to activate it. The active repressor stops RNA polymerase.

A bacterial operon consists of what? Are human genes organized in operons?

A bacterial operon has several protein-coding genes, one promoter, and an operator. No, there are no operons in eukaryotes.

Tell how a point mutation like a base substitution or insertion/deletion can affect the resulting protein. What's an example of a frameshift mutation?

A base substitution can cause a change in the amino acid produced by the codon (missense mutation), can result in the same amino acid sequence with different codon (silent mutation), or can create an early stop codon (nonsense mutation). An insertion/deletion shifts the way the sequence is read and leads to a completely different amino acid sequence (frameshift mutation).

What is the process of gel electrophoresis?

A mix of DNA fragments (perhaps those cut by restriction enzymes) can be separated according to their lengths by running them across a gel in an electric field.

Explain what is meant by a "triplet code". Why is a "doublet code" (2 bases) insufficient?

A triplet code = every three nucleotides in the RNA sequence is read as a separate codon to encode an amino acid. A doublet code = every 2 nucleotides in the RNA sequence is read as a separate codon. It is insufficient because it can only specify 16 amino acids, whereas a triplet code can specify 64 amino acids.

A short single-stranded DNA probe can potentially bind to a DNA strand by complementary base pairing. Which of these four probes, if any, would bind (somewhere) to this DNA sequence?

A. 3' A C T G A C T T A 5'

Which one of these is true of Activator proteins?

A. Binds near promoter and increases transcription rate

Bacteria must make ATP by metabolizing a particular sugar (that newly appeared in their cell)

A. Genes are usually off and only turned on when the food is present (genes in inducible operon)

Which of the following statements best describes the significance of the TATA box in the promoters of eukaryotes?

A. It is the recognition site for the binding of a specific transcription factor

1. In which ways do Bacteria differ from Eukarya? Which of these holds true for Bacteria, but not Eukarya?

A. They have circular, loop chromosomes C. Translation of a mRNA molecule can occur before it is completely transcribed

A eukaryotic gene will only be transcribed at high rates if there is an activator bound to an enhancer interacting with the promoter transcription complex.

A. True

RNA polymerase will only transcribe a eukaryotic gene having a normal promoter & DNA when transcription factors are present.

A. True

One completed mRNA molecule can contain multiple start and stop codons. This is:

A. True for Prokaryotes (Bacteria)

Okay, so we know which bacteria have the recombinant plasmid with our human gene. We grow the bacteria, but they do not produce the gene product. Why not?

A. We used a human gene promoter

Which of the following mutations, in the middle of a coding region, will lead to the greatest change in the resulting protein?

A. a single base insertion

4. How does a tRNA get connected with the correct amino acid?

A. an enzyme recognizes both of them and attaches them

Undifferentiated human cells mature and become specialized for different functions by:

A. differential gene expression

Which gene will this patient, now cured, pass to offspring?'

A. disease gene

Semiconservative replication of DNA involves

A. each of the original strands acting as a template for a new strand

Where is tRNA synthesized

A. in the nucleus

Which of these is a difference between DNA molecules and RNA molecules?

A. presence of T C. type of 5-carbon sugar

Initiation of transcription of eukaryotic gene requires which of these?

A. promoter

Lac operon genes are:

A. usually turned off, turned ON in the presence of lactose sugar

In what three ways do eukaryotic cells modify the messenger RNA (pre-mRNA) after transcription?

Adding 5' cap Adding Poly A Tail RNA processing (cutting out introns)

A certain bacterial operon contains genes that code for enzymes controlling a pathway for synthesis of amino acid X from precursor molecule B. Choose the optimal - most efficient - pattern for regulation of that operon.

B operon genes should be generally on and only inactivated when X is abundant

A bacterial operon with 1 regulatory region and 3 protein-coding genes will have how many promoters?

B. 1

Operon DNA with 1 regulatory region and 4 protein‐coding genes will contain (how many?) ____promoters and _____ triplets for start codons.

B. 1, 4

Rank the following one-base point mutations 1-4 with respect to their likelihood of affecting the structure of the corresponding polypeptide (from most likely to least likely). 1.Base insertion mutation in the middle of an intron2. Base substitution mutation at the third position of a codon in an exon3. Base substitution mutation at the second position of a codon in an exon4. Base deletion mutation within the first exon of the gene

B. 4, 3, 2, 1

In the DNA double helix molecule, hydrogen bonds form between which pair of bases? (abbreviations)

B. A and T

Which of these could be one side of the DNA for a restriction enzyme cutting site?

B. ATAT

Okay, so we have bacteria with the recombinant plasmid and a bacterial promoter (like lac) so they produce a protein - HOORAY! But the protein is abnormal - much longer than normal and has odd segments in the middle of it. Why?

B. Bacteria don't have spliceosomes

For DNA profiling, all DNA samples are processed in the same way. Why is it necessary to treat all samples with the same restriction enzyme? (or the same combination of specific restriction enzymes?)

B. Because they indicate the presence of the same base sequence at their cutting site

Which one of these is true of Repressor proteins?

B. Binds near promoter and blocks transcription

A student isolates, purifies, and combines in a test tube a variety of molecules needs for DNA replication. After adding some DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has the student probably left out of the mixture?

B. DNA ligase

Bacteria must make needed amino acids from reactant molecules

B. Genes are usually on and only turned off when the product accumulates and is very abundant (genes in a repressible operon)

To get bacteria to make a human protein, we make a recombinant plasmid with:

B. Human gene with prokaryotic promoter

DNA in which of the following chromatin states is LEAST likely to be expressed?

B. Methylated DNA, packed close to histone

Eukaryotic DNA in which of the following chromatin states is LEAST likely to be expressed?

B. Methylated DNA, packed close to histone

Is somatic cell gene therapy the same as making a transgenic organism?

B. No

Is this child now a transgenic organism?

B. No

Which of the following processes occurs during transcription?

B. RNA is synthesized

Why do we cut the two sources of DNA with the same restriction enzyme?

B. So their ends will have complementary unpaired bases

Why do we prepare plasmids with marker genes like the one for antibiotic resistance?

B. So we can tell which bacteria have taken up the plasmids and which not

Which of these could be one side of the DNA for a restriction enzyme cutting site?

B. TCGA

What is meant by the description "antiparallel" regarding the two strands that make up the DNA double helix?

B. The 5' to 3' direction of one strand runs counter to the 5' to 3' direction of the other strand.

How are lac operon genes regulated?

B. When lactose sugar de-activates a repressor

The original ancestors of mitochondria were aerobic bacteria that became engulfed and endo-symbiotic. Therefore, mitochondria have their own prokaryotic-type DNA, which is in:

B. a circular loop chromosome in the mitochondrial matrix

When a sample is run in gel electrophoresis the DNA segments are separated from one another by which of these?

B. by fragment length

2. To get bacteria to make a human protein, we will insert

B. cDNA version of the human gene

In eukaryotic cells, transcription occurs in _____ and translation occurs in ________

B. nucleus, cytosol

Site on the DNA where transcription of RNA begins is the

B. promoter

In gel electrophoresis, which moves faster through the gel?

B. shorter fragments

11. What is the advantage of alternate mRNA splicing in different specialized cells?

B. slightly different protein forms can be made from the same gene

What is the advantage of alternate mRNA splicing in different cells?

B. slightly different protein forms can be made from the same gene

6. Which one of the following statements about mRNA processing is correct?

B. snRNA's bind to mRNA at the splice sites

If the DNA helix is viewed as a structure similar to a ladder, the uprights of the ladder (not the steps/rungs) would consist of

B. sugars and phosphates linked in a chain

Investigators want to measure the amount of expression of a certain gene (to what extent is the gene turned on) in particular cells. They can use a color-tagged nucleic acid probe with a sequence that is complementary to which of these?

B. the mRNA sequence

Thymine makes up 22% of the nucleotides in a sample of DNA from an organism. Approximately what percentage of the nucleotides in this sample will be guanine?

C. 28%

If a 5' to 3' nucleotide sequence on the transcribed DNA strand is GAT, what is the corresponding codon (5' to 3') on mRNA made from that DNA?

C. AUC

If the 5' to 3' nucleotide sequence of a mRNA codon is CAU, what is the corresponding anticodon (5' to 3') on the tRNA?

C. AUG

Which of these is the best description of "cDNA"?

C. DNA that is made to be complementary to a messenger RNA molecule

Liver cells express different genes from eye cells because:

C. Different genes are turned on in Iiver cells and eye cells

Liver cells express different genes from eye cells because:

C. Different genes are turned on in Iiver cells and eye cells.

The part of the genome used for DNA profiling is which of these?

C. Non-coding regions that vary greatly from individual to individual

5. In eukaryotic cells, transcription factors are

C. Protein that binds to promoter

Gel electrophoresis is a lab technique that

C. Separates DNA restriction fragments according to length

Alternate splicing refers to which of these?

C. Splicing out all introns and different exons from the messenger RNA

Imagine that you've isolated a yeast (eukaryotic organism) mutant that contains histones that are resistant to acetylation. What would you predict to be true for this mutant?

C. The mutant will show decreased levels of gene expression.

How is cDNA prepared in the lab?

C. Use enzyme reverse transcriptase working from mRNA

Purines are double-ring nitrogenous bases, while pyrimidines are single-ring nitrogenous bases. Chargaff's ratios of bases found in the DNA of different species suggested that

C. a base pair consisted of one purine and one pyrimidine

Which one of the following describes the action true for both DNA polymerase and RNA polymerase?

C. adds the phosphate end of a new nucleotide to a free 3' OH group of a sugar in the growing chain

From question 6 in the worksheet: Which of these is the effect of a base substitution of the C at #6 to become a T?

C. early stop codon

From question 5 in the worksheet - Which of these is the effect of adding another G nucleotide in between the two G's at #5?

C. frameshift mutation

Which of these is the function of tRNA?

C. has anticodon that is complementary to mRNA codon

Which of the following molecules are required in the process of translation?

C. mRNA, tRNA, and rRNA

9. Which of these is a post-translational modification of proteins? (occurs after translation)

C. phosphorylation

The reason for differences in the sets of proteins expressed in a skin cell and a muscle cell of the same person is that skin and muscle cells contain different

C. sets of regulatory proteins

Which of the following would NOT be required for a substance to serve as a molecule of heredity?

C. stores energy for cell reactions

If a particular operon encodes enzymes for making an essential amino acid and is regulated like the trp operon, then which would happen?

C. the amino acid acts as a co-repressor, activates the repressor

Which one of the following is different between DNA replication in cells and the Polymerase Chain Reaction?

C. the source of the primers

If (almost) all cells in a person's body have exactly the same genes, then how do various cells differentiate (i.e., become specialized) into different cell types in different body tissues?

Cells can differentiate based on the kind of signals they receive from the environment. For example, high levels of testosterone (a puberty hormone in men) can signal the growth of facial hair. Cells differentiate into different cell types in body tissues by having certain activators present that bind to the enhancers associated with the specific tissue.

A bacterial operon with 1 regulatory region and 3 protein-coding genes will have how many DNA sequences for the start codon (AUG)?

D. 3

3. A particular mRNA codon is 5' GGC 3' The tRNA that binds to it will have what anticodon?

D. 5' GCC 3'

When DNA profiling patterns are used to determine the parents of a child, which parts of the genome are used?

D. DNA segments with short tandem repeats

E. coli bacteria cells are grown on 15N medium (with only heavy nitrogen) then transferred to 14N medium (only low density light nitrogen only) and allowed to grow for two more generations (two rounds of DNA replication) producing four cells from each original. DNA extracted from these four cells is centrifuged. What density distribution of DNA molecules would you expect in this experiment?

D. Half with low-density and half with intermediate-density

In eukaryotic cells, activators are

D. Protein that binds to enhancer

In an experimental situation, a researcher inserts an mRNA molecule into the cytoplasm of a eukaryotic cell after she has removed its 5′ cap and poly-A tail. Which of the following processes would you expect her to find to have occurred?

D. The molecule is digested by enzymes because it is not protected at the ends.

What would occur if the repressor of an inducible operon were mutated so it could not bind the operator?

D. continuous transcription of the operon's genes

Which of these would be a consequence of a mutation in the termination sequence?

D. mRNA would be made, but it would be abnormal

Which of the following is NOT true about the type of RNA and its function in eukaryotes?

D. ribosomal RNA is made in the nucleus and functions in the nucleus

Which one of these types of RNA is NOT found in Bacteria?

D. snRNA

As human erythrocytes (red blood cells) differentiate they become specialized to produce mainly hemoglobin. In a final maturation step, their DNA and nuclei break down & disintegrate, yet individual erythrocyte cells can live for weeks, continuing to make hemoglobin protein and binding O2. Which of these could be the explanation?

D. their mRNA molecules endure and can be translated many times

(d) DNA that is associated with acetylated histone or DNA with non-acetylated histone.

DNA associated with acetylated histone: the acetyl group neutralizes the positive histone protein so that DNA is loosened

Why is there a difference between replication processes at the leading & lagging strands? What are Okazaki fragments? Why is DNA ligase needed in on the lagging strand?

DNA is antiparallel. Okazaki fragments are single-stranded pieces made on the lagging strand; DNA ligase sutures the okazaki fragments together without adding new nucleotides.

(c) DNA that is wrapped closely to histone or DNA that is not;

DNA not wrapped closely: easier for the RNA polymerase and other necessary molecules to bind to the DNA

Describe the structure of DNA nucleotide components (phosphate, sugar, A T C G bases), their arrangement in DNA, and the types of bonds (hydrogen or covalent) between various components.

DNA nucleotides are composed of a phosphate group, a 5-carbon sugar, and a nitrogenous base (A ,T, G, or C). The 1' Carbon of the sugar is covalently bound to the nitrogenous base. The 3' Carbon of the sugar is where one nucleotide is joined to another (by a condensation reaction). The 5' carbon is where the phosphate group is attached. There are hydrogen bonds between A&T (2 hydrogen bonds) and C&G (3 hydrogen bonds).

How does the technique of gel electrophoresis separate DNA fragments?

DNA samples are cut with restriction enzymes and the resulting fragments are separated by their length by gel electrophoresis

Why is Methylated DNA packed close to the histone least likely to be expressed?

DNA with methylated bases has an altered shape, more packed, that is unlikely to be expressed.

A nucleic acid probe is a short length of single-stranded nucleic acid labeled with a fluorescent tag. How can probes be used to locate where, within a cell or in an embryo, a certain messenger RNA is located? [this is the basic idea of in situ hybridization]

Design a single stranded nucleic acid probe with a sequence that is perfectly complementary to the target looking for If it finds a match, the probe will light up in-situ hybridization: leave embryo alone, introduce probes all over and see where they light up to see where the mRNA are

If there's a mutation in the lac operon promoter (see figure) proteins from which genes will be made?

E. none of these

What is the structure of a eukaryotic chromosome - how is DNA arranged with histone proteins?

Eukaryotic chromosomes consist of DNA tightly wound around clusters of 8 histone proteins.

Explain the Polymerase Chain Reaction. Compare/contrast this lab technique with DNA replication in cells in terms of what separates the strands and where the primers come from.

First, the two strands of DNA are separated by heat. After it is cooled down, primers, DNA polymerase, and other raw materials are added. The primers are manufactured in a lab to be complementary to a specific sequence we want. The DNA polymerases extend the primers. We do this multiple times.

How did experiments on transformed pneumonia-causing bacteria (Griffith) and radioactively-labeled bacterial viruses (Hershey & Chase) inform scientists that the genetic material was indeed DNA and not protein?

Griffith's experiment helped conclude that DNA was the genetic material because a mixture of a heat killed pathogenic (the one that killed) and living nonpathogen caused the mouse injected with it to die. Cells with the pathogen were found living, despite the fact that there were originally no living pathogenic cells. In the Hershey & Chase experiment they knew that DNA contained phosphorus but not sulfur, and proteins contained sulfur but not phosphorus. So they grew 2 batches of viruses, one with radioactive phosphorus, the other with radioactive sulfur. The batches were injected into bacteria and found that all of phosphorus was found inside the cell, while all of the sulfur was found outside. Therefore it is DNA that goes into the cell to transform it.

What is the general concept of the lab process of gene editing by CRISPR? Include the role of the 'guide RNA'.

Guide RNA directs the Cas9 enzyme to the target DNA. Cas9 unzips the target DNA and the guide RNA matches up. The cut target DNA can be disabled or have some engineered DNA inserted in its place.

Describe the process of DNA replication, including the role of these major enzymes (helicase, primase, DNA polymerase, ligase), the role of primers for starting, use of triphosphate nucleotides as building blocks (& energy), and addition of new nucleotides to the 3' end of the growing strand.

Helicase- unzips the helix Primase (RNA polymerase)- makes RNA primer DNA polymerase- adds 5' phosphate of new nucleotide to 3' sugar of the growing chain Ligase- joins 3' sugar of one okazaki to 5' phosphate of another okazaki fragment (sutures ends together) When the bond between phosphates is broken, the energy released is used to form a bond between the incoming nucleotide and the growing chain.

What is meant by the term "recombinant DNA"? What enzymes do scientists use to produce recombinant DNA?

Human gene in bacterial plasmid = recombinant DNA Restriction enzymes (endonucleases), DNA ligase used to seal the strands

What are introns and exons? What complex of proteins & snRNA's splices introns out of the mRNA? Does this splicing occur in the nucleus or in the cytosol?

Introns are cut out from the original mRNA and broken down during RNA splicing. Exons are kept as part of the completed mRNA and expressed in translation. The spliceosome (snRNA- part of SnRNP and proteins) splices introns out of the mRNA; splicing occurs in the nucleus.

An operon with 1 regulatory region and 3 protein‐coding genes will have how many promoters? Explain how bacteria can make one mRNA molecule that contains the code for several proteins.

It will have one promoter. Bacteria can transcribe and translate at the same time with no mRNA processing (splicing or any of that stuff) so it is possible for it to make 1 mRNA molecule that contains the code for several proteins.

Approximately how much of the human nuclear genome consists of protein-coding genes?

Less than 2% (exons), 21,000 protein coding genes

Why is a substitution mutation on the 2nd position of a codon on an exon more likely to affect the polypeptide than a mutation on the 3rd

Look at the codon chart. In many cases where multiple codons code for the same amino acid they are identical for the 1st and 2nd base but differ only at the 3rd base.

From a mRNA sequence, how do you use the codon chart to translate the mRNA into a protein?

Look for the start codon AUG and continue adding amino acids using the triplet codons from the 5' to 3' end until you reach a stop codon. (Another AUG in a sequence does not mean that a new amino acid is beginning)

In each pair of items, which DNA is more likely to be transcribed and why? (a) DNA in tightly-packed regions of chromatin or DNA in loose, unwound chromatin.

Loose, unwound chromatin: easier for the RNA polymerase and other necessary molecules to bind to the DNA

How did Meselson & Stahl use bacteria with different N isotopes to determine DNA replication is semi-conservative?

Meselson & Stahl were able to use a heavy N-15 isotope and a light N-14 isotope. They could raise the bacteria to be only in the N-15 isotope and see the results. The bacteria cultured in the N-15 and N-14 isotopes were mixed and they found that after the first replication of DNA, it wasn't all heavy or all light, but instead was a mix of the

Tell how new genes can arise over evolutionary time by gene duplication and mutation.

Mutations are changes to genes that may occur during gene duplication. These changes may be favorable to the environment, giving organisms a higher chance of survival. These changes will then be passed on to future generations.

If molecule of heredity is DNA, will it still transform bacteria after being treated with DNAase?

No

If molecule of heredity is protein, will it still transform bacteria after being treated with protease?

No

At what site on DNA does DNA replication start?

Origin of replication and they add a primer to it!

Name two ways in which RNA differs chemically from DNA

RNA has ribose sugar; DNA has deoxyribose sugar RNA has uracil base that is complementary to adenine; DNA has thymine base complementary to adenine RNA is single stranded, DNA is double stranded

RNA polymerase always begins transcription of a gene at a DNA sequence called what? It will stop transcription at a place on the DNA known as what?

RNA polymerase begins transcription at the promoter of a DNA sequence (TATA box). It stops transcription at the terminator of a DNA.

Distinguish these terms: replication, transcription, translation. Tell how these processes fit into the flow of genetic information known as the "central dogma"?

Replication: DNA → more DNA Transcription: DNA → RNA Translation: mRNA → protein synthesis The central dogma is the simplified process of going DNA -> RNA-> Protein

Some proteins bind to regulatory DNA sequences and act like repressors of transcription, while other proteins act like activators. What is the effect of each of those on the rate of transcription initiation?

Repressor proteins can bind DNA at the promoter and stop RNA polymerase action. Activator proteins, on the other hand, can bind at control regions of the DNA and increase RNA polymerase binding.

Tell how a human gene can be inserted into a bacterial plasmid and expressed by bacterial cells. In order to get bacteria to produce protein from a human gene, that "recombinant plasmid" must include what?

Restriction enzyme cuts the plasmid and that same restriction enzyme cuts the human gene of interest so that the human gene and plasmid can form complementary base pairs by forming hydrogen bonds. DNA Ligase connects the sugar phosphate backbones. Bacterial (prokaryotic) promoter needed

What are restriction enzymes, and at what types of base pair sequences do they bind and cut DNA? Why do some restriction enzymes produce so-called "sticky ends" when they cut DNA?

Restriction enzymes ("cutters"): only cut the DNA at particular base sequences base pair sequence: "palindromic base sequence" make staggered cuts on the DNA backbone, leaving sticky ends - no longer paired bases once cut by restriction enzymes, leave potential to form H bonds with complementary bases

What are Genetically Modified Organisms (GMO foods)? How are they different from agricultural crops developed over the years through selective plant breeding?

Selective plant breeding is a form of artificial selection, choosing the most favorable plant traits that naturally appear within plants. GMOs are genetically modified to have improved nutrition, shelf life, drought, pesticide, and pathogen resistance

Name two examples of post-translational processing of a new protein (putting it into its fully functional form)

Signal sequence removed First amino acid (met) removed Individual amino acids phosphorylated Sugar chains added Polypeptide chain cleaved (cut) (insulin) Non-protein added (metal) (Hemoglobin)

What is somatic cell gene therapy and how does that differ from making a transgenic animal?

Somatic cell gene therapy only involves body cells. In Somatic Cell Gene Therapy, cloned normal genes are inserted into a recombinant virus as a carrier. The virus then infects the cells of a patient that have been removed from the patient. The viral DNA carrying the normal gene is inserted into the chromosome. Then the engineered cells are injected back into the patient. Offspring of a recipient of somatic gene therapy will still have the diseased version. However, transgenic animals can pass on modified genes because the change occurred in a reproductive cell/egg instead of a somatic (body) cell.

Why is cDNA complimentary to mRNA if it is made from RNA?

That's why it's called cDNA because it's DNA made from a messenger RNA template.

What are 3' and 5' ends of DNA? What is meant by the "anti - parallel" structure of DNA?

The 3' and 5' designations refer to the number of carbon atom in a deoxyribose sugar molecule to which a phosphate group bonds. The two strands of the DNA are oriented in opposite directions.

Examine the mRNA codon chart and explain what is meant by the term "redundant code".

The genetic code is considered a "redundant code" because the same amino acid can be specified by multiple codons.

What is the "signal peptide" and how does it get the new protein into the rER?

The signal peptide is like the luggage tag of the mRNA The signal recognition particle recognizes the signal peptides and it moves it to the RER, pulling the new protein. The lead end of the protein goes into the space of the rER.

In DNA profiles comparing family members, a person has two copies of each STR (short tandem repeat) gene locus, but they often are not identical. Why not?

The two are from their two different parents

An operon has three protein‐coding genes (proteins A, B, C) that are usually turned off (How?)

These are usually turned off because a repressor protein is usually bound to the regulatory DNA

What is the difference between hybridization probes and marked nucleic acid probe?

They are the same in that they are specific nucleic acid strands that are perfectly complementary to, and thus will hybridize with/bind to, specific target sequences. Probes don't copy anything they just bind to a specific sequence.

Genes in a certain bacterial operon are generally turned off, except when a certain food source is present. Is this a repressible operon or an inducible operon? Name a specific example of this type.

This is an inducible gene because it's usually off. An example of an inducible gene is the lac operon. It is usually off, but is turned on when lactose appears.

In eukaryotic cells, RNA polymerase cannot begin transcription at the promoter until what proteins are present and bound to the DNA in the region of the promoter?

Transcription factors (ie. TATA binding protein)

What is a transgenic organism? Tell how a foreign gene could be introduced to make a transgenic plant or animal.

Transgenic organisms have DNA from another organism (ie. foreign gene) inserted into a reproductive cell, so all cells in plant/animal that develop from the egg contain the inserted gene. Modified bacterial plasmid genes can be put into plants to create genetically modified crops (transgenic plants).

Compare the processes of transcription and translation between prokaryotic and eukaryotic cells in terms of location within the cell. Prokaryotic cells can have coupled transcription and translation, simultaneously on the same mRNA. Why can't eukaryotes do that?

Translation in eukaryotes: cytoplasm Translation in prokaryotes: cytoplasm Transcription in eukaryotes: nucleus - Transcription in prokaryotes: cytoplasm Prokaryotic cells have no nuclear envelope, no mRNA processing, and no genes with introns. Eukaryotic cells, on the other hand, do have a nuclear envelope and their mRNA needs to be processed before it's translated, so transcription and translation can't happen at the same time.

What is translation? How does translation begin? Tell what happens in translation elongation to synthesize the protein.

Translation is the formation of proteins from mRNA. It begins by the 5' end of mRNA binding to a small ribosomal unit. The first tRNA arrives at the P site (with "met" amino acid attached) and binds its anticodon to the start codon on mRNA. The large ribosomal subunit binds and translation elongation begins. Translation elongation: new tRNA arrives at the A site, peptide bond forms between 2 adjacent amino acids, mRNA-tRNA complex slides across the ribosome, new triplet mRNA codon becomes exposed at the A site.

What happens during translation when the mRNA stop codon appears at the A site on the ribosome?

Translation terminates! No tRNA binds! A "release factor" frees the last tRNA from the P site and releases the polypeptide. mRNA separates from the ribosome and the two ribosomal subunits separate.

(b) DNA with nucleotide bases that are methylated or DNA that is un-methylated;

Unmethylated: it is packed less close because methyl groups are not binded to the nucleotide bases

What were some specific types of data used by Watson & Crick to determine the structure of DNA?

Watson and Crick knew that DNA changed slightly when heated, which indicated there were hydrogen bonds involved. They also knew that the percent of adenine equaled the percent of thymine and the percent of cytosine equaled the percent of guanine (Chargaff's rule).

How does cDNA work and why is it necessary?

We use cDNA version of a gene in recombinant DNA when we want bacteria to express human genes, because bacteria don't have spliceosomes.

Eukaryotic genes that will be transcribed a great deal have enhancer DNA. What is the role of the enhancer? Explain how transcription factors and activator proteins interact with promoter and enhancer regions of the DNA to initiate the process of transcription (major control of eukaryote gene expression)

When activator proteins bind to enhancer regions on the DNA, they attract transcription factors and then when other proteins fold the DNA, the transcription factors move to the promoter region and increase transcription

If molecule of heredity is DNA, will it still transform bacteria after being treated with protease?

Yes

If molecule of heredity is protein, will it still transform bacteria after being treated with DNAase?

Yes

How does alternate splicing work? Does it cut out exons along with introns?

Yes, and cells in different tissues cut out different exons (alternate splicing makes alternate forms)

If there is a mutation in the promoter, the DNA can't be transcribed but if the DNA is not transcribed can it still be replicated?

Yes, because the promoter is just for transcription, making RNA, not DNA replication, which is a separate process.

How can alternative splicing of a certain tmRNA in different body cells produce slightly different proteins from the same gene?

You can use one gene and splice out different exons in order to form slightly different proteins.

If the daughter DNA molecule after one replication consisted of one all heavy and one all light DNA, which model would that support?

a) Conservative model

If DNA is the genetic material...Which radioactive label shows up inside the bacterial cells?

a) Phosphorus

which is the function of the poly-A tail on mRNA?

a) helps resist breakdown by hydrolytic enzymes

Which of these is/are necessary to explain the specific complementary base pairing in DNA?

a) one purine and one pyrimidine b) specific positions for either 2 or 3 hydrogen bonds

DNA contains - which?

a) phosphorus but not sulfur

DNA polymerase adds the new nucleotide to:

a) the 3' sugar of the growing chain

Operon DNA with 1 regulatory region and 3 protein‐coding genes will contain how many promoters?

b) 1

If a person's DNA consists of 20% cytosine bases, then how much of it is adenine?

b) 30%

In a certain cell there is a mutation in the promoter for a gene. Because of that particular mutation, the gene

b) Cannot be transcribed

Watson and crick were getting close to realizing their double helix model was correct because:

b) Chargaff's ratios involved one purine and one pyrimidine c) DNA changed form slightly when heated, suggesting that weak bonds were involved

What is the role of DNA ligase in the elongation of the lagging strand during DNA replication?

b) It joins Okazaki fragments together

Which amino acid (abbreviation) is specified by the start codon?

b) Met

If DNA is the genetic material...Which label was left in fluid outside the bacterial cell?

b) Sulfur

The genetic code is considered "redundant" because:

b) the same amino acid can be specified by multiple codons

How do the genomes of bacteria and eukaryotes differ?

bacteria: small, mostly coding genes eukaryotes: large, mostly non-coding genes organelle (chloroplasts and mitochondria) : even smaller than bacteria

If primers in cells are RNA, why don't we have segments of RNA in our DNA?

c) A second DNA polymerase exchanged them for DNA

Which best describes the action of DNA ligase?

c) Joins a 3' sugar to a 5' phosphate without adding a new nucleotide

Which one is true about the lagging strand of DNA (and is not true of the leading strand)?

c) Okazaki fragments are formed

Which amino acids (abbreviations) does the codon CCC code for?

c) Pro

Which of these two RNA primers could DNA polymerase extend?

c)Right AGGU add to A end

How is a cDNA molecule made from mRNA?

cDNA is perfectly complementary to the mRNA, so it has no introns. We make this by performing reverse transcription (RNA -> DNA) with the enzyme reverse transcriptase (from retroviruses) in a lab. So, we use a primer that's complementary to the mRNA's poly-A tail (basically TTTTT), and reverse transcriptase is able to make complementary DNA by reading the mRNA sequence.

Repressor proteins...

can bind DNA at the promoter and stop RNA polymerase action

Activator proteins...

can bind at control regions of DNA and increase RNA polymerase binding.

1 base per word - info for 4 amino acids 2 bases per word (4 bases taken at 2 at a time gives how many combinations?)

d) 16 amino acids

Which of the following is the same for both RNA polymerase and DNA polymerase?

d) Adds to the 3' end of the growing chain

What is an intron?

d) non-expressed part cut out of the mRNA

where does mRNA splicing occur?

mRNA processing (cap tail, splicing) is only in Eukaryotes and all occurs before mRNA's leave the nucleus

Which of these proteins will be produced (a) if the promoter ahead of gene A is mutated?(b) if the start codon of gene C is deleted?(c) if a repressor binds to the operator for this operon?(d) if the regulatory gene is mutated and no longer makes a repressor?

none, A & B, none, all

Distinguish the functions of each of the following types of RNA: rRNA, tRNA, mRNA, snRNA. Remember that each is made in the nucleus by transcription from the DNA.

rRNA (ribosomal RNA): forms part of the ribosome, which is exported to cytoplasm to help translate information in mRNA → protein tRNA (transfer RNA): brings correct amino acid to the mRNA, complementary base pairing (mRNA codon - tRNA anticodon) mRNA (messenger RNA): carries protein blueprint from DNA to ribosomes; product of transcription, used in translation snRNA (small nuclear RNA): part of the snRNP; recognize splice sites in the mRNA

Give examples of how analysis of DNA samples of the same individually variable part of the genome (STRs short tandem repeats) from different individuals can be used for forensic analysis and paternity testing. Why is non-coding short tandem repeat DNA more useful for comparative DNA profiling than DNA coding for proteins?

short tandem repeats (STR) in a NON-CODING genome is used for "DNA profiling" and "DNA fingerprinting" because the specific combination of number of repeats tends to be unique for each individual compared to DNA coding for proteins

What's the difference between snRNA and snRNP?

snRNA is the name for the small nuclear RNA in the spliceosome. snRNP stands for small nuclear ribonuclear protein, and it includes snRNA plus a tightly associated specific protein.

What is the general function of a tRNA? How does a tRNA become bonded to its specific amino acid? Does this occur at the mRNA or before the tRNA arrives at the mRNA? How do the mRNA codon and the tRNA anticodon interact with each other?

tRNA brings correct amino acid to the mRNA, complementary base pairing (mRNA codon - tRNA anticodon). An enzyme matches the tRNA to its specific amino acid by recognizing both of them; this occurs before the tRNA arrives at the mRNA. The mRNA codon and tRNA anticodon are complementary to each other and held together by hydrogen bonds.