Chapters 10 and 11 Quiz

Identify the location of mRNA, rRNA, and tRNA in the figure.

(i) tRNA (ii) mRNA (iii) rRNA SEE DIAGRAM

Why does it make sense that tRNA and rRNA molecules are more stable than mRNA molecules?

tRNA and rRNA are encoded in the DNA, tRNA carries amino acid until the point of synthesis in the ribosome rRNA is an important component of the ribosomes that ensure the alignment of the mRNA and tRNA while mRNA serves as a "photocopy" of specific info & are short lived

In the chromatin of eukaryotic cells, which regions of the chromosome would you expect to be more compact: the regions that contain genes being actively copied into RNA or those that contain inactive genes?

the regions that contain genes being actively copied into RNA

Predict the effect of a mutation in the -35 region of a bacterial promoter.

the sequence will be recognized and bound by o(sigma)

Why does translation terminate when the ribosome reaches a stop codon? What happens?

Translation terminates when the ribosome reaches a stop codon because it does not code for a tRNA. Release factors cause the polypeptide to be released, and the ribosomal complex dissociates.

When a new base is added to a strand of DNA, to which end is it added? (5' or 3')

When a new base is added, it gets added to the 5'- end (NOT ENTIRELY SURE IF THIS IS CORRECT)

What are some differences in chromosomal structures between prokaryotes and eukaryotes?

Prokaryotes = circular chromosomes, single chromosome within, haploid (1 copy of each gene) Eukaryotes - linear, multiple distinct chromosomes, diploid (2 copies of each chromosome)

Speculate on why it can be problematic to copy and express genes from Bacteria into Eukarya.

Prokaryotes = mRNA can code for multiple genes all at once, and have one single RNA polymerase Eukaryotes = mRNA can only code for gene at a time, there are 3 types of RNA polymerase that each encode for specific subset of RNA

What is the purpose of RNA processing in eukaryotes? Why don't prokaryotes require similar processing?

RNA processing in eukaryotes is required because it gets information into the cytoplasm in order for information to be translated into proteins, (mRNA may las serval hours). Prokaryotes do not have membrane bound nuclei, so mRNA lasts no more than 5 seconds.

Draw and label the general structure of a mRNA paired to a tRNA with the appropriate amino acid attached.

SEE FIGURE

Why was nucleic acid disregarded for so long as the molecule responsible for the transmission of hereditary information?

Scientists thought it was structurally too simple to encode such complex genetic information (they thought protein was capable of doing so

Explain why supercoiling is important and the role DNA gyrase plays.

Supercoiling is important because it extensively wraps the chromosomal DNA that is wrapped around histones, which makes the information in the DNA molecule inaccessible. DNA gyrase is used to relax the supercoiled DNA strands.

Briefly describe two ways in which chromosomal DNA from a donor cell may be transferred to a recipient cell during the process of conjugation.

1) Conjugation of the F plasmid : conjugation pilus bringing the two cells into contact. A single strand of the F plasmid is transferred to the F− cell, which is then made double stranded. 2) Conjugation of F' and HFr : The F plasmid can occasionally integrate into the bacterial chromosome, producing an Hfr cell. Imprecise excision of the F plasmid from the chromosome of an Hfr cell may lead to the production of an F' plasmid that carries chromosomal DNA adjacent to the integration site. This F' plasmid can be transferred to an F− cell by conjugation

A certain DNA sample is found to have a makeup consisting of 22% thymine. Use Chargaff's rules to fill in the percentages for the other three nitrogenous bases.

22% Adenine; 78% Guanine & 78% Cytosine; A=T while G=C

There are 64 possible codons. How many amino acids are coded for with those codons and do all codons code for an amino acid?

61 of the 64 possible triplets code for amino acids, three of the 64 codons do not code for an amino acid; they terminate protein synthesis, releasing the polypeptide from the translation machinery.

Bacteriophages inject their genetic material into host cells, whereas animal viruses enter host cells completely. Why was it important to use a bacteriophage in the Hershey-Chase experiment rather than an animal virus?

A bacteriophage was used instead of an animal cell because the phage DNA makes multiple copies of itself using the host machinery, and eventually the host cell bursts, releasing a large number of bacteriophages.

Describe what happens when a nonsense mutation is introduced into the gene encoding transposase within a transposon.

A nonsense mutation will have thrown in a random stop codon in a gene.

Why is primase required for DNA replication?

A primase is required for DNA replication because it synthesizes RNA primers needed to start replication

Label the following in the figure: ribosomal E, P, and A sites; mRNA; codons; anticodons; growing polypeptide; incoming amino acid; direction of translocation; small ribosomal unit; large ribosomal unit.

A. Growing polypeptide B. Incoming amino acid C. Ribosomal E, P, and A sites D. Codons E. Small ribosomal unit F. direction of translocation G.mRNA H. Anticodons I. Large ribosomal unit

Finish this string of DNA with its complementary antiparallel strand. Use lines to indicate the number of bonds between nucleic acids.

AACGTATGCATCAGGA TTGCATACGTAGTCCT

Why do you think the Ames test is preferable to the use of animal models to screen chemical compounds for mutagenicity?

Because no one cares if you kill a bunch of bacteria, but testing/killing animals is controversial

What is the role of single-stranded binding protein in DNA replication?

Bind to single-stranded DNA to prevent hydrogen bonding between DNA strands, reforming double-stranded DNA

What are the differences between DNA nucleotides and RNA nucleotides?

DNA molecules are typically long and double stranded, more suitable for storage RNA molecules are much shorter and are typically single stranded, suitable for short term functions DNA nitrogenous bases = ATGC, RNA nitrogenous bases = AUGC

Describe the function of the following enzymes in DNA replication: DNA polymerase, helicase, primase, DNA ligase, binding proteins.

DNA polymerase:The three main types have different duties. DNA pol III is the enzyme required for DNA synthesis while DNA pol II and DNA pol I are primarily required for repair. Helicase: Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases Primase: Synthesizes RNA primers needed to start replication DNA Ligase: Seals the gaps between the Okazaki fragments on the lagging strand to create one continuous DNA strand. Binding Proteins: Bind to single-stranded DNA to prevent hydrogen bonding between DNA strands, reforming double-stranded DNA

Why is DNA with a high GC content more difficult to denature than that with a low GC content?

DNA with high GC content have additional hydrogen bonding between the C=G base pair, making it harder to denature.

How is the information stored within the base sequence of DNA used to determine a cell's properties?

DNA→ RNA→ Amino acid sequence→ Protein shape→ Shape determines function→ Function determines cell

What is the central dogma of molecular biology and what three informational macromolecules are involved?

DNA→ RNA→ Protein; the central dogma states that DNA encodes messenger RNA, which in turn, encodes protein.

How do prokaryotes and eukaryotes manage to fit their lengthy DNA inside of cells? Why is this necessary?

Eukaryotes - DNA supercoiling is necessary for the genome to fit within the prokaryotic cell. Supercoiling and DNA packaging using DNA binding proteins allows lengthy molecules to fit inside a cell. Prokaryotes - The DNA in the bacterial chromosome is arranged in several supercoiled domains. DNA gyrase is a type of topoisomerase, found in bacteria and some archaea, that helps prevent the overwinding of DNA.

Is the following statement TRUE or FALSE? Explain why you think so."Proteins are the only biomolecules capable of catalyzing bond formation."

False: False - RNA serves as a catalyst for proteins , inorganic compounds like montmorillonite clay

Explain the difference between a gene, a chromosome, a plasmid and a genome.

Gene = segments of DNA molecules that code for proteins or stable RNA molecules Chromosome = discrete DNA structure within a cell that controls cellular activities Plasmid = small, circular, double-stranded DNA molecule that is typically independent from the bacterial chromosome Genome = entire genetic content of a cell A genome contains the full complement of DNA within a cell and is organized into smaller, discrete units called genes that are arranged on chromosomes and plasmids.

If deoxyribonucleotides that lack the 3'-OH groups are added during the replication process, what do you expect will occur?

If the 3' OH group was missing, the replication process will stop. As each nucleoside triphosphate is added to the growing polynucleotide chain, two phosphates are removed from the 5' end of the nucleotide. The remaining phosphate is linked to the 3'-OH of the RNA molecule to form the phosphodiester bond.

How does the process of translation differ between prokaryotes and eukaryotes?

In prokaryotes, transcription and translation may be coupled, with translation of an mRNA molecule beginning as soon as transcription allows enough mRNA exposure for the binding of a ribosome, prior to transcription termination. Transcription and translation are not coupled in eukaryotes because transcription occurs in the nucleus, whereas translation occurs in the cytoplasm or in association with the rough endoplasmic reticulum.

What are the three basic steps of transcription? Be able to describe what happens during each.

Initiation - the RNA polymerase unzips the DNA double helix Elongation - RNA Nucleotides are formed from the nucleotides in the DNA template strand Termination the mRNA that is formed leaves the nucleus

What are the three basic steps of translation (protein synthesis) and what occurs during each?

Initiation - transition complex forms, and the tRNA brings first amino acid in polypeptide chain to bind to start codon on mRNA Elongation - tRNA's bring amino acids one by one to add to the polypeptide chain Termination - release factor recognizes stop codon, translation complex dissociates, and completed polypeptide is released.

Describe the role of promoters and sigma factors in transcription.

It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.

Why is DNA replication considered semiconservative?

It is semi-conservative because in replication, each original strand is paired with a new strand, leaving each of the new DNA strands with one original and one new strand.

Why does double-stranded RNA (dsRNA) stimulate RNA interference?

It's presence serves as an indicator of viral infection

Prior to the elucidation of the genetic code, prominent scientists, including Francis Crick, had predicted that each mRNA codon, coding for one of the 20 amino acids, needed to be at least three nucleotides long. Why is it not possible for codons to be any shorter?

Least three nucleotides long allows for total 64 possible combinations , with 4 different nucleotides possible at each of 3 different positions within codon= a greater number than the number of amino acids=each amino acid encoded by more than 1 codon

What are some functions of noncoding DNA?

Noncoding DNA is not fully understood but scientists contribute to the regulation of transcription or translation through the production of small noncoding RNA molecules, DNA packaging, and chromosomal stability.

. What is the role of phosphodiester bonds within the sugar-phosphate backbone of DNA?

Phosphodiester bonding between nucleotides forms the sugar-phosphate backbone, the alternating sugar-phosphate structure composing the framework of a nucleic acid strand The 5'-3' phosphodiester bonds combine individual nucleoside triphosphates with each other by covalent bonding, it is also the linkage between the phosphate group attached to the 5ʹ carbon of the sugar of one nucleotide bonding to the hydroxyl group of the 3ʹ carbon of the sugar of the next nucleotide.

What is polycistronic mRNA and what makes it useful?

Polycistronic mRNA are found in prokaryotic mRNAs of bacteria and archaea and they are useful because they encode multiple polypeptides.

A new type of bacteriophage has been isolated and you are in charge of characterizing its genome. The base composition of the bacteriophage is A (15%), C (20%), T (35%), and G (30%). What can you conclude about the genome of the virus?

The bacteriophage consist of DNA not RNA, base pairs of ATCG.

How do complementary base pairs contribute to intramolecular base pairing within an RNA molecule?

The complementary base pairs, even though single stranded, create a predictable 3D structure essential for their function by extensive intramolecular base pairing

What is meant by the genetic code being nearly universal?

The genetic code is nearly universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis, which is powerful evidence that all extant life on earth shares a common origin.

Explain why GC-rich DNA requires a higher temperature to denature or melt than AT-rich DNA and hypothesize as to why the GC content of chromosomes in microorganisms from different environments varies widely.

The overall increase in stability of G-C pairing should be emphasized over A-T binding. A DNA strand with high GC content (low AT) has more triple H bonds compared to an AT rich (low GC) strand of the same length contains mostly double H bonds. More energy is therefore required to break more H bonds, and thus GC rich DNA is more heat resistant to denaturation.

What is the role of a primer in DNA replication? Why is it important?

The primer is a short strand of DNA that serves as a starting point for DNA synthesis and it is important for DNA replication because the when DNA polymerases catalyzes the process, it can only add new nucleotides to an existing strand of DNA.

How does the ribosome know where to start translation? (two components to this) How does it know when to stop?

The ribosome knows to start translation once the untranslated region of the mRNA passes and it encounters the start codon (AUG). The ribosome continues translation until it reaches a stop codon. The translation of mRNA begins with the formation of a complex on the mRNA. Three initiation factor proteins bind to the subunit of the ribosome along with a Met (carrying the tRNA) bind to the mRNA near the start of the AUG start codon, forming the initiation complex. Initiation of translation occurs when the small ribosomal subunit binds with initiation factors and an initiator tRNA at the start codon of an mRNA, followed by the binding to the initiation complex of the large ribosomal subunit.

.What is meant by the term "antiparallel?"

The two DNA strands are antiparallel, such that the 3ʹ end of one strand faces the 5ʹ end of the other

.Why do bacteria and viruses make good model systems for various genetic studies?

They are propagated more easily in the laboratory, can grow to high population densities in a small amount of space and in a short amount of time, and they are structurally simplistic (microbes and viruses are readily manipulated genetically).

Can two observably different cells have the same genotype? Explain.

Yes they can. Although multiple cells may have the same genotype, they may exhibit a wide range of phenotypes resulting from differences in patterns of gene expression in response to different environmental condition.

Why is it more likely insertions or deletions are more detrimental to a cell than point mutations?

frameshift mutations, caused by insertions or deletions of a number of nucleotides that are not a multiple of three are extremely problematic because a shift in the reading frame results Because ribosomes read the mRNA in triplet codons, frameshift mutations can change every amino acid after the point of the mutation.