MODULE 2

What is the chromosomal configuration of the phiX174 virus?

-circular -DNA -single stranded

In what ways do the amino acid side chains interact to influence protein function? Name three classes of molecular interaction that can occur between amino acid side chains.

-dictate secondary and tertiarty structures -determine how a protein will fold and how a protein will interact a solution 3 classes: hydrophobic effect, hydrogen bonding, disulfide bonds

What is the chromosomal configuration of the polyoma virus?

-double stranded -circular -DNA

Present two forms of post-translational modification of proteins

-proteolytic cleavage - folding

Which three general characteristics must the genetic material possess?

1. must be able to encode complex informationthat encodes phenotype; must be able to replicate (faithfully); must be able to mutate to generate diversity.

You have a solution of DNA who's absorbance of UV radiation at 260nm is 0.05. What is the concentration of DNA in the sample?

13?

Which of the following are among the major components of prokaryotic ribosomes?

16 5 23

A protein is 300 amino acids long. Which of the following could be the number of nucleotides in the section of DNA that codes for this protein? (Remember: DNA is double-stranded.)

1800

In transcription, nucleotides are always added to the _____end of the elongating strand.

3'

When codons that code for the same amino acid differ in their ________, a single tRNA might bind both of them through wobble base pairing.

3' base

Write the anticodon, with correct polarity, of all tRNAs that will bind to the mRNA codon 5' UCG 3', considering wobble-base pairing rules.

3'-AGC-5'

Use the following table for the questions below: Determine a possible metabolic pathway that would give the results seen for the four mutant strains, A through D. (If necessary, use a separate piece of paper to diagram the pathway). Which supplement (1-4) is needed at position 1a? Which supplement (1-4) is needed at position 1b? Which supplement (1-4) is needed at position 1c? Which supplement (1-4) is needed at position 1d? Which strain's (A-D) gene product would function at position 1e if it were not mutant? Which strain's (A-D) gene product would function at position 1f if it were not mutant? Which strain's (A-D) gene product would function at position 1g if it were not mutant? Which strain's (A-D) gene product would function at position 1h if it were not mutant?

4 2 1 3 C B A D

List the components of a nucleosome. Be sure to list specific protein, not just protein type.

4 different histone molecules, each exists twice so it makes an octomer

discontiunity of DNA replication in vivo is due

5 to 3 polarity restriction

Which of these sequences could form a hairpin?

5' GGGGTTTTCCCC 3'

Select three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes.

5'-capping, 3'-poly(A) tail addition, splicing

Approximately how much of the mammalian genome is composed of repetitive DNA?

5-10 highly 30 moderately

You are producing a heteropolymer of synthetic mRNA using a 1C:5G ratio. In this synthetic mRNA what is the proportion of codons with 2Gs and 1C?

75/216

Which one of the following statements regarding eukaryotic transcriptions is not true?

A group of genes is transcribed into a polycistronic RNA.

In an analysis of the nucleotide composition of double-stranded DNA to see which bases are equivalent in concentration, which of the following would be true?

A+C=T+G

Describe four base triplets that are clearly responsible for punctuation (initiation, termination).

AUG, UAA, UGA, UAG

Name the three major modifications of mRNA of eukaryotes before it is transported to the cytoplasm. In addition, tell why each of the modifications is necessary.

Add 5' cap (protect against degradation, acts as a binding site for the ribosome); Add poly-A tail (possibly protect against degradation, possibly helps in the transfer of the mRNA to the cytoplasm); Remove introns (forms a message that can be translated into a functional protein).

The Meselson and Stahl experiment provided conclusive evidence that DNA replication in E. coli is semiconservative. Imagine that DNA replication were conservative, rather than semiconservative. What pattern of bands would occur in a CsCl gradient after the first generation of replication? What pattern of bands would occur after the second generation of replication?

After one generation in the 14N, there would be two bands, one heavy and one light (no intermedieate). After the second generation in the 14N, there would also be two bands, one heavy and one light (no intermediate).

What is an intron, and what is the relationship between an intron and a heterogeneous nuclear RNA (hnRNA)?

An intron is a section of DNA, which, when transcribed as part of an RNA, is eventually spliced out of that RNA. The entire gene transcript, which may serve as an eventual mRNA (after intron removal and other forms of processing), is called heterogeneous nuclear RNA.

Antisense oligonucleotides are relatively short stretches of nucleotides (usually about 20 nucleotides long) that are likely to bind with sense RNAs in a given cell. Of what importance might such a material have in human health?

Antisense oligonucleotodes can be used in gene therapy. If a genetic sequence is known to cause a particular disorder, an oligonucleotide can be synthesized that will bind to the mRNA coded by the sequence. When the oligonucleotide binds to the mRNA it inactivates it, effectively shutting the gene off.

Briefly define the term "autoradiography". Identify and describe a classic experiment that used autoradiography to determine the replicative nature of DNA in eukaryotes.

Autoradiography is a technique that allows an isotope to be detected within a cell: The Taylor, Woods, and Hughes (1957) experiment used 3H-thymidine

3 forms of DNA

B A Z

Below is a list of terms, each term relating to the replication of chromosomes. Describe the role (relationship) of each in chromosome replication. (a) Okazaki fragment (b) Lagging strand (c) Bidirectional

B. In DNA synthesis, the lagging strand is the strand of original DNA in which DNA Polymerase III must move away from the replication fork, because it synthesizes new DNA only 5' to 3'. DNA synthesis is not continuous on the lagging strand. A. Because synthesis is not continuous and in order for DNA Polymerase III to synthesize in the correct 5' to 3' direction on the lagging strand, short strands of DNA called Okazaki fragments are synthesized. This will later be joined by DNA Ligase. C. There are two replication forks, each withs its own leading and lagging strand, that move away from one another in opposite directions, or bidirectionally.

Describe two ways in which bacterial DNA differs from eukaryotic DNA:

Bacterial DNA found in a large circular and not located with a nucleus. Eukaryotic DNA is organized into linear chromosomes within the nucleus. Eukaryotic DNA is also wrapped around histones. Bacterial gene contains no introns.

Kornberg, in his experiments to demonstrate the function of DNA polymerase I, sought to show that DNA Pol 1 was capable of replicating biologically active DNA. What is the definition of biologically active DNA in this context?

Biologically active DNA is capable of supporting metabolic activities and directs reproduction of the original organism from which it was originally duplicated

Genetic material must replicate faithfully. Describe how the double-stranded structure of DNA gives it this property.

Complementary base-pairing rules mean that, given one strand of DNA, the base sequence of the other strand can be determined. If each strand is used as a template in replication, two DNA molecules of identical sequence are generated.

long term storage

DNA

At what approximate wavelengths do DNA, RNA, and proteins maximally absorb light?

DNA =260 nm RNA=260 Protein=280

Which of the following enzymes are known to be involved in the replication of DNA in bacteria?

DNA polymerase I RNA Primase ligase

In biology, most information flows through which sequence?

DNA to RNA to Protien

Explain at least two reasons why the following definition of a gene is incomplete: "A gene consists of DNA sequences that encode a single polypeptide."

Definition does not include 1. regulatory sequences 2. not all genes are DNA sequences (see RNA virus) 3. not all genes transcribe a single RNA molecule 4. not all RNA molecules encode for a single polypeptide.

To prove DNA Pol I was a viable DNA polymerase, Kornberg and is associates sought to replicate phi X174, a DNA virus, with it. Phi X174 is a doubly stranded DNA virus. How were they able to separate the two strands of the virus?

Double stranded DNA was nicked with a nuclease, and the two strands were separated by denaturation. They are then separated by density sedimentation centrifugation. To assist in this, the minus strands made in vitro were labelled with BrdU, to change their density, and 32P, to distinguish them from the + strands.

To prove DNA Pol I was a viable DNA polymerase, Kornberg and is associates sought to replicate phi X174, a DNA virus, with it. They found that DNA Pol I could replicate biologically active virus. In their experiment, how did they know that the phi X174 that they used to infect bacteria wasn't contaminated with the viral DNA they started with?

Double stranded DNA was nicked with a nuclease, and the two strands were separated by denaturation. They are then separated by density sedimentation centrifugation. To assist in this, the minus strands made in vitro were labelled with BrdU, to change their density, and 32P, to distinguish them from the + strands.

Which of the following statements is NOT true about enhancers?

Enhancers are recognized by and bind directly to RNA polymerase.

Describe the rate of DNA replication in prokaryotes and eukaryotes in approximate kb per minute.

Eukaryotes are 25 times slower

Knowing that the base sequence of any given messenger RNA is responsible for precisely ordering the amino acids in a respective protein, present two mechanisms by which intrinsic properties of mRNA may regulate the "net output" of a given gene.

Final output of a given gene may be influenced by the stability of an mRNA, and stability of an mRNA is determined in part by its base content and sequence. (2) Differential splicing of mRNA (actually mRNA precursors) can influence how much of a given product will be made from a gene.

Two "naked" (without histones or other proteins) double-stranded fragments of DNA are exactly the same length. At 89°C, fragment A has completely denatured, which means that the two strands have separated. At that temperature, fragment B is still double-stranded. How might these fragments differ, to result in different denaturation temperatures?

Fragment A likely has a low Gaunosine/Cytosine content than fragment B. Because Guanosine/Cytosine has 3 h-bonds and Adenine/Thymine only has 2 h-bonds, more energy (higher temperature) is required to break apart the G/C rich fragment.

Why would a given dsDNA molecule that is very GC rich be harder to dissociate into single stranded DNA than another dsDNA molecule of the same length that is very AT rich?

GC have more hydrogen bonds

What is the fundamental difference between Group I and Group II self-splicing introns?

Group I introns require a simple co-factor (guanosine) for intron removal, however Group II introns require NO co-factor for successful intron removal.

How did the work of Hershey and Chase contribute to the model of DNA as the genetic material?

Hershey and Chase designed a series of experiments to determine whether phage protein or DNA is transmitted in phage replication. They used the model system E. coli and its phage T2. They used radioactive forms of Phosphorus (P32) to label the DNA and sulfur (S35) to label the protein. Initially, the infected bacteria were grown in the radioactive media, labeling the phages. In the next generation, the labeled phages were introduced to unlabeled bacteria, infecting them. When the bacteria were washed and centrifuged, the radioactive phosphorus was found to be present in the infected bacteria, and the sulfur was washed away with the protein coats, demonstrating that DNA had been passed on and was the genetic material of E. coli.

Present an overview of two classical experiments that demonstrated that DNA is the genetic material. Can RNA be the genetic material? Explain.

Hershey and chase, Griffith and Avery Yes, RNA can be the genetic material as described for the Tobacco Mosaic Virus (TMV), retroviruses, and many others.

What is unusual about the amino acid composition of histones? How is the function of histones related to the amino acid composition? Of which histones are nucleosomes composed?

Histones contain large amounts of positively charged amino acids such as lysine and arginine. Thus, they can bind electrostatically to the negatively charged phosphate groups of nucleotides. Nucleosomes are composed of all histones except H1.

While mutations have been observed in many different genes, no mutations have been isolated in the genes that code for histones. Why does this seem reasonable? If one wanted to produce antibodies to histones, would it be an easy task? Explain your answer. Keep in mind the process used to produce antibodies.

Histones represent one of the most conserved molecules in nature because they are involved in a fundamental and important function relating to chromosome structure. Mutations are probably lethal. Since all antibody-producing organisms have essentially the same histones, it would be difficult to find an organism that produces histone antibodies, for to do so would be self-destructive.

Below is a list of several phenomena relating to protein structure. Clearly describe each phenomenon, the conditions under which each occurs, and the probable influence each has on protein structure. - Hydrophobic interactions - Hydrogen bonds - Disulfide bridges Clearly separate each of your answers in the box below.

Hydrophobic interactions: Nonpolar side chains of amino acids tend to associate to form hydrophobic clusters usually away from the protein surface. - Hydrogen bonds: Such bonds may occur between the components of the peptide bond, the side chains, or a combination of the two. They are responsible for helical and pleated sheet structures of proteins. - Disulfide bridges: Such bonds are formed between two cysteine side chains and, because of their covalent nature, represent relatively strong attractive forces between different regions (sometimes distant) of proteins.

Describe the role of the various types of nucleic acids in the storage and expression of information in living organisms.

Information contained in the base sequences of DNA is transcribed into a variety of RNAs. Certain RNAs (tRNA) carry amino acids to the site of translation where proteins are assembled. Other RNAs (mRNA and rRNA) provide a mechanism for ordering the sequence of amino acids in proteins.

The TATA-binding protein (TBP) binds to the TATA box sequence in eukaryotic promoters. What is its function in transcriptional initiation?

It bends and partly unwinds DNA at a promoter.

Telomerase is composed of what two types of macromolecules? What is the name for such a combination?

It contains protein and RNA together, a ribonucleoprotein

There is some indication that the code is in some way ordered; a certain pattern exists. Name an observation that supports this view.

It has been observed that amino acids that are chemically similar share the middle base of their respective codons.

There is some indication that the code is in some way ordered; a certain pattern exists. Name an observation that supports this view.

It has been observed that amino acids that are chemically similar share the middle base of their respective codons. Also, codons that share the same two starting nucleotides frequently encode the same amino acid.

In addition to highly repetitive and unique DNA sequences, a third category of DNA sequences exists. What is it called, and what types of elements are involved?

Moderately repetitive DNA, SINEs, LINEs and VNTR

The one-gene, one-enzyme hypothesis emerged from work on which two organisms?

Neurospora and Drosophila

In eukaryotes, what factors (either DNA sequences or proteins) appear to encourage the specific association of RNA polymerase(s) to a specific region of DNA?

Promoters, enhancers, and transcription factors

What are the two major components of the Tobacco Mosaic Virus?

RNA and protein

Which of the following statements is not true concerning RNA and DNA?

RNA is more stable than DNA

Can RNA act as the genetic material? If so, give an example.

RNA is the genetic material in viruses was established by A.Gierer and G.Schramm.in 1956 with the experiments conducted on tobacco plant by TMV virus .

What provides 3 end and what is the enzyme called

RNA primer and RNA primase

An intron is a section of

RNA that is removed during RNA processing

Describe how the sigma subunit of E. coli RNA polymerase participates in transcription.

Recognizes promoter region which differentiates the AUG start codon from other AUG's within the genome that codes for Met

Describe four major functions of DNA in a cell.

Replication = duplication of genetic material. Expression = production of a phenotype. Storage = stable maintenance and passage of information. Variation = capable of alteration.

Regarding the efficient initiation of transcription by RNA polymerase II, what two major types of "upstream" signals appear to be involved?

TATA and CAAT base sequences, and enhancers

A number of scientists have become interested in telomerase as a drug target. Why would they be interested in telomerase? How might cancer drug therapies that target telomerase work?

Telomerase is an enzyme that functions in cells that undergo continuous cell division and may play a role in the lack of cellular aging in these cells. Cells that lack telomerase exhibit progressive shortening of the chromosomal ends or telomeres. This shortening leads to unstable chromosomes and ultimately to programmed cell death. Many tumor cells also express telomerase, which may assist these cells in becoming immortal. If the telomerase activity in these cancer cells could be inhibited, then cell division might be halted in the cancer cells thus controlling cancer cell growth. Chemically modified antisense RNAs or DNA oligonucleotides complementary to the telomerase RNA sequence might block the telomerase activity by base pairing with the telomerase RNA, making it unavailable as a template. A second strategy would be target the DNA synthesis activity of the telomerase protein preventing the telomere DNA from being synthesized

Telomeres regulate the replication of the ends of chromosomes in eukaryotes. Why is this structure implicated in human aging?

Telomeres are structures at the ends of eukaryotic chromosomes that contain tandem DNA sequences added to the 3′ ends by the enzyme telomerase. Telomeres stabilize chromosomes by preventing the loss of genomic information after each round of DNA replication. Human somatic cells contain little or no telomerase, and those that do get progressively shorter and enter premature senescence. People with diseases of premature aging such as Werner syndrome and dyskeratosis congenital have shorter telomeres than healthy people.

Compare and contrast the structure of the genetic material in viruses, bacteria, and eukaryotes. What is the genetic material in each organism? What is the chromosome structure in each organism? In which organisms do the chromosomes include proteins, and how is the genetic material organized around these proteins?

The amount of DNA per structure (virus particle, bacterium, cell) increases as one goes from viruses to eukaryotic cell. Viral chromosomes may be composed of single-stranded or double-stranded RNA or DNA, while bacterial and eukaryotic DNA is double-stranded. Bacterial DNA is considered to be a covalently closed circle, while the "global" structure of eukaryotic chromosomes is uncertain. Although some proteins are associated with viral and bacterial DNA, the regularly spaced histones of eukaryotic chromosomes are unique.

In the classic experiment conducted by Hershey and Chase, why was the pellet radioactive in the centrifuge tube that contained bacteria with viruses, which had been grown on medium containing 32P?

The bacteria were in the pellet, and many contained the radioactive viral DNA.

Which of the following are role(s) of the 5' cap?

The cap protects the RNA from degradation. The cap acts as a binding site for the ribosome. The cap plays a role in the removal of introns.

Nutritional mutants in Neurospora can be "cured" by treating the medium with substances in the defective metabolic pathway. What determines whether the mutant strain (auxotroph) is "cured" by a particular substance? Explain.

The mutant strain will be "cured" if the substance added occurs after the metabolic block in the biochemical pathway. This allows the mutant to effectively bypass the required gene product that is defective/mutant in the strain.

Consider the structure of double-stranded DNA. When DNA is placed into distilled water, it denatures; however, by adding NaCl, the DNA renatures. Why?

The negatively charged phosphates repel each other on the two sides of the helix. In distilled water, these charges are not neutralized (by positively charged ions), and the hydrogen bonds, which hold the double helix together, are broken. In the presence of positive ions, such charges are neutralized.

Describe the basic structure of normal adult hemoglobin and the structural abnormality observed in sickle-cell hemoglobin protein. Which amino acid residue is abnormal in hemoglobin from individuals with sickle-cell anemia? How is this residue different in people with wild-type hemoglobin?

The predominant form of adult hemoglobin is composed of two a and two b chains. In sickle-cell hemoglobin, the sixth amino acid in the b chain is valine instead of glutamic acid.

What is the spliceosome?

The spliceosome is the RNA-protein complex that is responsible for intron-exon splicing in eukaryotes. Following the GU-AG rule, introns are excised and removed from mRNA and the exons are joined to form a mature mRNA molecule ready for translation. The spliceosome is made of five small nuclear ribonucleoproteins (snRNPs) which consists of proteins and one of five snRNAs (U1, U2, U4, U5 and U6) which together with over 100 proteins form the large biological machine used for splicing.

As a ribosome translocates along an mRNA molecule by one codon, which of the following occurs?

The tRNA that was in the A site moves into the P site.

DNA replication is semi-conservative in that

The two stands of the original helix are conserved, but they become part of separate progeny DNAs.

Explain the experimental method of "differential labeling"

This is a method used to differently label 2 molecules of interest in an experiment so that investigators are able to distinguish between the two molecules in the results

Briefly define transformation and describe the relationship between the phenomenon of transformation and the discovery that DNA is the genetic material in bacteria.

Transformation is the process whereby one organism is genetically altered by exposure to DNA from another organism. Since DNA can carry heritable "traits" from one organism to another, it must be the genetic material.

Describe the differential identification with respect to virulence that Griffiths was able to exploit with Diplococcus pneumoniae.

Virulent colonies grow as smooth colonies whereas avirulent organisms grow as rough colonies on agar plates. Therefore Griffiths could tell virulence by just looking at the colonies on an agar plate.

You grow your test organism in 15N for many generations, then switch it to 14N for one or two generations. You harvest DNA at each point and subject it to density centrifugation. Your results appear above. What kind of replication are you seeing? Why? What are the identities of the bands?

You are seeing dispersive replication. 15N and 14N DNA are dispersed within the nucleic acid molecules in the first generation. The second generation still has 15N and 14N DNA dispersed in the same molecules, but there is more 14N DNA because that is what is being synthesized.

Given that the origin of replication is fixed in E. coli, what region signals the location of the origin? Give both the name of this region and a description of the sequences present.

a region called ori C which consists of about 250 base pairs characterized by repeating sequences of 9 and 13 bases

You grow an organism that carries out conservative DNA replication a in 3H containing medium for 50 generations. You add them to medium containing 32P for one or two generations, sampling DNA from the population after each generation of growth. a. What are your expected after one generation? b. What are your expected results after two generations?

a. You expect the first generation will have either 3H or 32P b. in the second generation you will still have either 3H or 32P, but there will be more 32P DNA.

What is the function of the TATA binding protein?

allows eukaryotic RNA polymerase 2 to bind to promoter of genes

In human chromosomes, satellite DNA sequences of about 170 base pairs in length are present in tandem arrays of up to 1 million base pairs. Found mainly in centromere regions, they are called

alphoid familes

nucleoside

base and sugar (no phosphate)

Why are prions like zombies?

because an abnormal prion protein can convert a normal prion protein to the abnormal confirmation if contacted, just like zombies can turn humans to zombies by biting them.

Why does DNA polymerase III exist as a dimer?

because both strands of DNA are replicated simultaneously

In E. coli, which terms accurately reflect the nature of replication of the chromosome?

bidriectional and fixed point of replication

Which of the following traits exemplify plasmid DNA?

both a and b above

The concept that genetic information passes from DNA to RNA to protein is called

central dogma

Strand not used to guide transcription is

coding strand

This form of DNA replication was eliminated during the Meselson-Stahl experiment because the original double-helix did not appear to be preserved during cell division.

conservative

Heterochromatin is characterized by all of the following, EXCEPT that it

contains genes that require high levels of transcription.

The Avery et al. (1944) contribution to an understanding of molecular biology was ________.

demonstration that DNA was the genetic material

2 proteins are the same except for 1 domain..why

differences in pre-mRNA splicing that resulted in altered exons pattern

Until about 1970, mitotic chromosomes viewed under the microscope could be distinguished only by their size, positions of centromeres, and "satellites" in some cases. However, various staining techniques have allowed a different view of chromosomes because they allow the visualization of ________.

distinct bands along the chromosomes

Which protein class directly controls many of the metabolic reactions within a cell?

enzymes

That some organisms contain much larger amounts of DNA than are apparently "needed" and that some relatively closely related organisms may have vastly different amounts of DNA is more typical in

eukaryotes than in prokaryotes

Before DNA was known to be the genetic material, scientists knew that genetic material must do or be all of the following, EXCEPT that

genetic material must be composed of many different units to account for the variability seen in nature.

In eukaryotic replication, there is another fundamental level of complexity because of what proteins?

histones

What term is used to describe genetic exchange at equivalent positions along two chromosomes with substantial DNA sequence homology?

homologous recombination

The relationship between codon and anticodon can be characterized as involving ________ between complementary bases (usually) in typical ________ fashion.

hydrogen bonds antiparallel

What chemical group is found at the 3' end of a DNA molecule?

hydroxyl group

DNA polymerase I is thought to add nucleotides

in the place of the primer RNA after it is removed

The poly(A) tails found in the 3' end of an mRNA are important for all the processes listed below except for ___ and ___.

intron splicing and protein stability

What are histones? How many families of histones exist? Which families are considered linker histones, and which are considered core histones? What is the structural relationship between histones and the nucleosome?

istones are represented by five main classes of relatively small basic proteins containing relatively large amounts of lysine and arginine. The classes are as follows: H1, H2A, H2B, H3, H4. Each nucleosome is made of 8 histones: 2 from each core family.

What is the function of peptidyl transferase activity?

it forms peptide bonds

Bacterial cells are grown with tritiated thymidine for a very short time. What are your expected results?

labeling on both sides of the orgign

Bacterial cells are grown with 35S for a very short time. What are your expected results?

labeling on both sides of the origin

This new strand of DNA has its 3' end oriented in the opposite direction as that in which the replication fork travels.

lagging strand

All of the following are general purpose translation components and could be used in the translation of any gene, except for one. Which one?

mRNA

relationship between genes and mRNA

mRNA are made from genes

Which of the following statements best describes the messenger RNA?

mRNA is the only type of RNA that carries DNA's protein building instructions

RNA Polymerase II

mRNA snRNA

one exception to genetic universality is

mitochondrial DNA

Sidney Brenner argued that the code was nonoverlapping because he considered that coding restrictions would occur if it were overlapping. A second major argument against an overlapping code involved the effect of a single nucleotide change. In an overlapping code ________ adjacent amino acids would be affected by a point mutation, while in a nonoverlapping code ________ amino acid(s) would be affected.

multiple, one

Which statement is true regarding negative supercoiled DNA?

negative supercoiled DNA is under-rotated and allows for easier strand separation during replication and transcription.

Is DNA pol I the major DNA polymerase in E. coli? If not, what experiment suggested this and what is its function during DNA replication?

no it isn't, as bacterial DNA Pol I mutants are viable. DNA Pol I removes RNA primers and fills the resultant gaps with DNA.

This organic subunit is the monomer from which nucleic acid is formed.

nucleotide

Three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes occur in which cellular organelle?

nucleus

The term peptidyltransferase relates to

peptide bond formation during protein synthesis

end of 5 end of DNA

phosphate group

DNA ligase

phosphodiester bonds at DNA nicks

What enzyme is exploited to produce synthetic mRNAs?

polynucleotide phosphorylase

RNA Polymerase I

rRNA

What is the name of the replication unit in prokaryotes, and how does it differ in eukaryotes?

replicon, one replicon in prokaryotes and multiple in eukaryotes

The complex of proteins that is involved in the replication of DNA is called a ________.

replisome

The discovery of RNA self-splicing by T. Cech (1982) and others in Tetrahymena revealed that RNA can demonstrate autonomous catalytic properties. RNAs that undergo such splicing are often called

ribozymes

In what way are microRNAs (miRNAs) and short interfering RNAs (siRNAs) different?

siRNAs begin as double stranded mRNAs from viruses or transposons, while miRNAs begin as nuclear transcripts. siRNAs have to bind with complete complementarity and can only target the mRNAs from which they're derived, while miRNAs can bind with noncomplimentarity and can bind to a number of mRNAs. miRNAs can also bind to the RITS pathway and silence transcription.

What is the chromosomal configuration of the phiX174 virus?

single stranded circular DNA

Telomeres________________the end of chromosomes

stabilize

Considering the Central Dogma of Molecular Biology, what three general properties are ascribed to DNA?

storage and expression of information, variation through mutation

Reverse transcriptase

synthesis of DNA from RNA template

Of the following three types of nucleic acids-DNA, mRNA, tRNA-which is most likely to contain modified bases?

tRNA

In each round of the elongation cycle of protein synthesis, a new _______ binds to the codon in the _______ site, then the peptide is transferred from the tRNA in the _______ site to the new aminoacyl-tRNA, and finally the entire _______ moves along the mRNA in a 5' to 3' direction.

tRNA A P ribosome

RNA polymerase III

tRNA rRNA snRNA

What are the three sites that tRNAs bind to in the ribosome? What are they're functions during translation?

tRNAs bind to the aminoacyl (A) site, the Peptidly (P) site and the Exit (E) site. tRNAs charged with amino acids bind the A site. After peptide bond formation they move to the P site which is bound to tRNAs with the growing polypeptide chain. The tRNA bind to the E site after the polypeptide chain has been hydrolyzed and before it is released from the ribosome.

RNA polymerase II binds to __________

template strand

packaging of DNA into a confined space is what level

tertiary

When scientists were attempting to determine the structure of the genetic code, Crick and co-workers found that when three base additions or three base deletions occurred in a single gene, the wild-type phenotype was sometimes restored. These data supported the hypothesis that

the code is triplet

Significant in the deciphering of the genetic code was the discovery of the enzyme polynucleotide phosphorylase. What was this enzyme used for?

the manufacture of synthetic RNA for cell-free systems

By their experimentation using the Neurospora fungus, Beadle and Tatum were able to propose the far-reaching hypothesis that:

the role of a specific gene is to produce a specific enzyme.

What two experimental procedures allowed deciphering of the ordered triplet assignments of the genetic code?

the triplet binding assay and the use of repeating RNA polymers with known sequence

A base at the first position of an anticodon on the tRNA would pair with a base at the ________ position of the mRNA

third

In eukaryotes, tRNAs are

transcribed in the nucleus, but function in the cytoplasm

In prokaryotes, translation of an mRNA is coupled to

transcription

The 5' cap on an mRNA is important for all the processes listed below except for the ___ of an mRNA molecule.

transcription

Splicing of eukaryotic pre-mRNA involves ___ reactions and occurs in the ___ .

transesterfication, nuclues

What is the name of the precursor molecule used in nucleic acid synthesis (do not give an abbreviation)?

triphosphonucleocide

rolling circle replication

unidirectional replication

You grow your test organism in 15N for many generations, then switch it to 14N for one generation. You harvest DNA and subject it to density centrifugation. Your results appear above. What kind of replication are you seeing? Are there multiple possibilities? Why? What are they? What results would resolve any ambiguity?

you might be seeing either semi-conservative or dispersive replication, both produce 15N/14N hybrids. If the cultures are allowed to grow one more generation in 14N, the problem can be resolved, as dispersive replication will give one hybrid band, as more 14N is dispersed into the replicating DNA. Semi-Conservative replication will give two bands, a 15N/14N hybrid and 14N/14N DNA.