Chapter 7 - Exam III

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The Blueprint of Life, from DNA to Protein
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Define these term: Codon, DNA polymerase, Gene, Messenger RNA (mRNA), Primer, Promoter, Replication, Ribosomal RNA (rRNA), Ribosome, RNA polymerase, Transcription, Transfer RNA (tRNA), and Translation.

Codon - A series of three nucleotides that code for a specific amino acid.

DNA polymerase - Enzyme that synthesizes DNA, using an existing strand as a template to' synthesize the complementary strand.

Gene - The functional unit of the genome.

Messenger RNA (mRNA) - Type of RNA molecule that is translated during the process of protien synthesis.

Primer - Fragment of nucleic acid to which DNA polymerase can add nucleotides.

Promoter - Nucleotide sequence to which RNA polymerase binds to iitiate transcription.

Replication - Duplication of DNA so that its encoded information can be passed on to future generations.

Ribosomal RNA (rRNA) - Type of RNA molecule present in ribosome.

Ribosome - Structure that facilitates the joining of amino acids during the process of translation; it is composed of ribsomal RNA (rRNA) and protein.

RNA polymerase - Enzyme that synthesizes RNA using one strand of DNA as a template.

Transcription - The processthat copies the information envoded by DNA into RNA.

Transfer RNA (tRNA) - Type of RNA molecule that acts as a key, interpreting the genetic code; each tRNA molecule carries a specific amino acid.

Translation - The process that interprets the information carried by mRNA to synthesize the encoded protein.


Compare and contrast the characteristics of DNA and RNA.

DNA - A single strand of DNA has a 5' end and a 3' end; the two strands of DNA in the double helix are antiparallel

RNA - A single-stranded RNA fragment is transcribed from one of the two strands of DNA. There are three different functional groups of RNA molecules: messenger RNA (mRNA), ribosomal RNA (rRNA), and transer RNA (tRNA).


Explain why it is important that a cell be able to regulate the expression of certain genes.

Not all proteins are required by a cell in the same quantity at all times; therefore, mechanisms that determine the extent and duration of their synthesis are needed.


How does a 5' end of DNA differ from the 3' end?

A single strand of DNA will always have a 5'PO4 at one end and a 3'OH at the other.


If the nucleotide sequence of one strand of DNA is 5' ACGTTGCA 3', what is the sequence of the complementary strand?



Why is a short-lived RNA important in cell control mechanisms?

If transcription of a gene ceases, the level of gene expression rapidly declines.


Describe the process of replication, focusing on initiation of replication and the events that occur at the replication fork.

DNA replication begins at the origin of replication. DNA polymerase synthesizes DNA in the 5' to 3' direction, using one strand as a template to generate the complementary strand.

The Replication Fork- 1. Primase synthesizes an RNA primer, 2. DNA polymerase adds nucleotides onto the 3' end of the fragment. 3. DNA polymerase replaces the RNA primer with deoxynucleotides. 4. DNA ligase seals the gaps between adjacent fragments.


Why is a primer required for DNA synthesis?

A Primer - is a fragment of nucleic acid to which DNA polymerase can add nucleotides (the enzyme can oly add nucleotides to a preexisting fragment).


How does synthesis of lagging strand differ from that of the leading strand?

Synthesis of the leading strand proceeds continuously.

Synthesis of the lagging strand is discontinuous; synthesis is reinitiated periodically, generating a series of fragments that are later joined. `


If DNA replication were shown to be "conservative", what would this mean?



Describe the process of transcription, focusing on the role of RNA polymerase, sigma (σ) factor, promoters, and terminators.

RNA polymerase - Enzyme that synthesizes RNA using single-stranded DNA as a template; synthesis always occurs in the 5' to 3' direction.

Sigma (σ) factor - Component of RNA polymerase that recognizes the promoter regions. A cell may have different types of σ factors that recognize different promoters. These may be expressed at different stages of cell growth, enabling the cell to transcribe specialized sets of genes as needed.

Promoters - Nucleotide sequence to which RNA polymerase binds to initiate transcription.

Terminators - Sequence at which RNA synthesis stops; the RNA polymerase falls off the DNA template and releases the newly synthesized RNA.


Describe the process of translation, focusing on the role of mRNA, ribosomes, ribosome-binding sites, rRNAs, and codons.

mRNA - Type of RNA molecule that contains the genetic information deciphered during translation.

Ribosomes - Structure that facilitates the joining of amino acids during the process of translation; composed of protein and ribosomal RNA. The prokaryotic ribosome (70S) consists of a 30S and 50S subunit; it is the target of several groups of antibacterial drugs.

Ribosome-binding sites - Sequence of nucleotides in mRNA to which a ribosome binds; the first time the codon for methionine (AUG) appears after that site, translation generally begins.

rRNAs - Type of RNA molecule present in ribosomes.

Start codon - Codon at which translation is initiated; it is typically the first AUG after a ribosome-binding site.

Stop codon - Codon that terminates translation, signaling the end of the protein; there are three stop codon.


How does the orientation of the promoter dictate which strand is used as a template for RNA synthesis?

The promoter orients the RNA polymerase in one of two possible directions. Thish dictates which of the two DNA strands is used as a template.


Explain why it is important for the translation machinery to recognize the correct reading frame.

If translation occurs in the wrong reading frame, a very different, and generally non-functional, polypeptide would be synthesized.


Could two mRNAs have different nucleotide sequences and yet code for the same protein?

-More than one codon can code for a specific amino acid.

-Two different amino acids are never coded for by the same codon.


Describe four differences between prokaryotic and eukaryotic gene expression.

Prokaryotes - (1) MRNA is not processed. (2) mRNA does not contain introns. (3) Translation of mRNA begins as it is being transcribed. (4) mRNA is often polycistronic; translation usually begins at the first AUG that follows a ribosome-binding site.

Eukaryotes - (1) A cap is added to the 5' end of mRNA, and a poly A tail is added to the 3' end. (2) mRNA contains introns, which are removed by splicing. (3) The mRNA transcript is transported out of the nucleus so that it can be translated in the cytoplasm. (4) mRNA is monocistronic; translation begins at the first AUG.


What is an intron?

An intron is part of the eukaryotic chromosome that does not code for a protein; removed from the RNA transcript before the mRNA is translated.


Explain the mechanism of action of diphtheria toxin.

The Diphtheria toxin selectively kills eukaryotic but not prokaryotic cells. The toxin produced by Corynebacterium diphtheriae; binds to and inactivates one of the elongation factors of eukaryotes. Since this protein is required for translocation of the ribosome, translation ceases and the eukaryotic cell dies, resulting in the typical symptons of diphtheria. pg181


Would a deletion of two base pairs have a greater consequence if it occured in an intron or in an exon?

An exon, because the introns are removed form the pre-RNA.


Give a functional example of a constitutive enzyme, an inducible enzyme, and a repressible enzyme.

Constitutive enzymes- are constantly synthesized; i.e. the enzymes of glycolysis are constitutive.

Inducible enzymes - are not regularly produced; i.e. β-galactosidase, whose sole function is to break down the disaccharide lactose into its two component monosaccharides, glucose and galactose.

Repressible enzymes - are routinely synthesized but can be turned off by certain conditions; i.e. generally involved with biosynthetic pathways, such as those that produce amino acids. pg 182


Using the lac operon as a model, explain the role of inducers and repressors.

The lac operon employs a repressor that prevents transcription of the genes when lactose is not available.

Catabolite repression prevents transcription of the lac operon when glucose is available.


Explain the difference between a constitutive enzyme and an inducible enzyme.

The synthesis of inducible enzymes can be turned on by certain conditions.

The synthesis of repressible enzymes can be turned off by certain conditions.


Explain the mechanism by which glucose represses the lactose operon.

The mechanism by which cells decrease the expression of genes that encode certain degradative enzymes in the presence of a compound such as glucose. pg 185

Glucose present, No lactose - Transcription not activated And blocked

Glucose present, Lactose present - Transcription not activated

No Glucose, No lactose - Transcription activated but blocked

No Glucose, Lactose present - Transcription activated. pg.185


Why would it be advantageous for a cell to control the activity of an enzyme as well as its synthesis?

It forces cells to first use the carbon source that is most easily metabolized. Then when the first supply is exhausted do the cells begin degrading a carbon source that requires additional enzymatic steps to metabolize.



Describe how two-component regulatory systems and quorum sensing allows cells to adapt to fluctuating environmental conditions.

Two-component systems utilize a sensor that recognizes changes outside the cell and then transmits that information to a response regulator.

Bacteria that utilize quorum sensing synthesize a soluable compound that can move freely in and out of a cell. Only when that compound reaches a critical concentration does it activate specific genes.


Compare and contrast antigenic variation and phase variation.

Antigenic variation- is a routine change in the expression of surface proteins.

Phase variation - is the routine switching on and off of certain genes.


Explain the mechanism by which certain bacteria can "sense" the density of cells.

They use quorum sensing; they synthesize an extracellular signaling molecule. The concentration of that molecule reflects the cell density. pg186


Why would it be advantageous for a bacterium to synthesize more than one type of homoserine lactone?



Explain how protein-encoding regions are found when analyzing a DNA sequence.

Since either strand of the DNA could be the template strand, two entirely different mRNA molecules could potentially code for the protein. In turn, each of those two molecules has three reading frames, for a total of six reading frames. Yet only one of these actually codes for the protein.


What is an open reading frame?

Open reading frame (ORF) - Stretch of DNA, generally longer than 300 base pairs, that has a reading frame beginning with a start codon and ending with a stop codon; it suggests that the region encodes a protein.


Describe two things that can be learned by searching a computerized database for sequences that have homologies to a newly sequenced gene.

Proteins that bind DNA share amino acid sequences in certain regions.

Regulatory regions in DNA such as promoters can sometimes be identified based on the nucleotide homologies to known sequences.


There are some characteristic differences in the nucleotide sequences of the leading and lagging strands. Why might this be so?

Sequences in the lagging strand direct the replication machinery to reinitiate DNA synthesis.

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