chapter 7 study guide

6. Describe four differences between prokaryotic and eukaryotic gene expression.

1. In eukaryotes, one mRNA = one protein.(in bacteria, one mRNA can be polycistronic, or code for several proteins). 2. DNA in eukaryotes forms a stable, compacted complex with histones. In bacteria, the chromatin is not in a permanently condensed state. 3. Eukaryotic DNA contains large regions of repetitive DNA, whilst bacterial DNA rarely contains any "extra" DNA. 4. Much of eukaryotic DNA does not code for proteins (~98% is non-coding in humans); in bacteria often more than 95% of the genome codes for proteins

1. DNA Replication: a. At what site does DNA replication begin? b. Draw a replication fork, labeling key components of the replication process: leading strand, lagging strand, RNA primer, DNA Polymerase III (DNA Pol. III), Okazaki fragments.

A: The specific site where replication of DNA begins is origin of replication. Prokaryotes have only 1 point of origin, replication occurs inside the cell cytoplasm at two opposing directions at the same time. Eukaryotic cells have multiple points of origin, and it occurs inside nucleus by using undirectional replication

1. Compare and contrast the characteristics of DNA and RNA.

DNA and RNA are different from their structure, functions, and stabilities. DNA has four nitrogen bases adenine, thymine, cytosine, and guanine and for RNA instead of thymine, it has uracil. Also, DNA is double-stranded and RNA is single-stranded which is why RNA can leave the nucleus and DNA can't.

4. Explain why DNA replication is semi-conservative

Each of the two DNA molecules created through replication contain one of the original strands paired with a newly synthesized strand. Because one strand of the original molecule is conserved in each molecule, replication is said to be semiconservative.

2. Explain why gene regulation is important to a cell.

Gene regulation is an important part of normal development. Genes are turned on and off in different patterns during development to make a brain cell look and act different from a liver cell or a muscle cell, for example. Gene regulation also allows cells to react quickly to changes in their environments.

4. Coupled transcription-translation: What does it mean to say that coupled transcription and translation occurs in prokaryotes? Please explain in terms of what happens and how this differs from eukaryotes.

In a prokaryotic cell, transcription and translation are coupled; that is, translation begins while the mRNA is still being synthesized. In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs in the cytoplasm.

5. Describe the process of transcription, focusing on the role of RNA polymerase, sigma factors, promoters, and terminators.

In transcription, the enzyme RNA polymerase synthesizes single-stranded RNA molecules from a DNA template. Specific nucleotide sequences in the DNA direct the polymerase where to start and where to end. The DNA sequence to which RNA polymerase can bind and initiate transcription is called a promoter; one that stops the process is a terminator. Like DNA polymerase, RNA polymerase can add nucleotides only to the 3′ end of a chain and therefore synthesizes RNA in the 5′ to 3′ direction. Unlike DNA polymerase, however, RNA polymerase can start synthesis with-out a primer. Sigma (σ) factor Component of RNA polymerase that recognizes the promoter regions. A cell can have different types of σ factors that recognize different promoters, allowing the cell to transcribe specialized sets of genes as needed.

5. Gene expression: What are the key differences between eukaryotic and prokaryotic gene expression? In your description, explain why each is a difference.

Prokaryotic gene expression (both transcription and translation) occurs within the cytoplasm of a cell due to the lack of a defined nucleus; thus, the DNA is freely located within the cytoplasm. Eukaryotic gene expression occurs in both the nucleus (transcription) and cytoplasm (translation).

1. Transcription: B. How does a promoter dictate which DNA strand is used as the template in transcription? Please explain any other details or molecules involved in this decision.

Promoters identify the regions of a DNA molecule that will be transcribed into RNA. In doing so, they also orient the direction of the RNA polymerase on the DNA molecule, thereby dictating which strand will be used as a template

3. Describe the DNA replication process, including its initiation and the events that occur at the replication fork

The process of DNA replication requires the coordinated action of many different enzymes and other component. Many of the proteins involved exist together in DNA-synthesizing "assembly lines" called replisomes. Enzymes called DNA polymerases synthesize DNA in the 5′ to 3′ direction, using one parent strand as a template to make the complement (figure 7.6). To do this, a DNA polymerase adds nucleotides onto the 3′ end of the new strand, powering the reaction with the energy released when a high-energy phosphate bond of the incoming nucleotide is hydrolyzed. DNA polymerases add nucleotides only onto an existing nucleotide strand, so they cannot initiate synthesis. The progression of bidirectional replication around a circular DNA molecule creates two advancing forks where DNA synthesis is occurring. These regions, called replication forks, ultimately meet at a terminating site when the process is complete. To initiate replication of a DNA molecule, specific proteins recognize and bind to the origin of replication (a certain DNA sequence). Bacterial chromosomes and plasmids typically contain only one of these initiating sites, and a DNA molecule that lacks the sequence will not be replicated. The proteins that bind to the bacterial origin of replication include DNA gyrase and helicases, which temporarily break and unwind the DNA helix at that site.

1. Transcription: a. Describe the process of transcription in prokaryotes (provide details for the 3 steps: initiation, elongation, and termination). In your response, describe any key molecules and events, including the sigma () factor, promoter, and RNA polymerase.

Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. The DNA sequence onto which the proteins and enzymes involved in transcription bind to initiate the process is called a promoter. Initiation RNA polymerase binds to the promoter and melts a short stretch of DNA. Elongation Sigma factor often dissociates fromRNA polymerase, leaving the core enzyme to complete transcription.RNA is synthesized in the 5 to 3direction as the enzyme adds nucleotides to the 3 end of the growing chain. Termination When RNA polymerase encounters a terminator, it falls off the template and releases the newly synthesized RNA. The part of RNA polymerase that recognizes the promoter is a loosely attached subunit called sigma (σ) factor.

1. Translation: b. What is the role of tRNA in the process? Could two mRNAs have different nucleotide sequences and yet code for the same protein? Please explain describing the role of tRNAs in this situation.

Transfer ribonucleic acid (tRNA) is a type of RNA molecule that helps decode a messenger RNA (mRNA) sequence into a protein. tRNAs function at specific sites in the ribosome during translation, which is a process that synthesizes a protein from an mRNA molecule Yes, because the genetic code is degenerate

1. Translation: a. Describe the process of translation in prokaryotes (provide details for the 3 steps: initiation, elongation, and termination). In your response, describe any key molecules and events.

Translation involves translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis. It is the process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA During initiation, the small ribosomal subunit binds to the start of the mRNA sequence. During the elongation stage, the ribosome continues to translate each codon in turn. Each corresponding amino acid is added to the growing chain and linked via a bond called a peptide bond. Elongation continues until all of the codons are read termination occurs when the ribosome reaches a stop codon (UAA, UAG, and UGA). Since there are no tRNA molecules that can recognize these codons, the ribosome recognizes that translation is complete. The new protein is then released, and the translation complex comes apart.

5. Describe the process of translation, focusing on the role of mRNA, ribosomes, Ribosome-binding site , rRNAs, tRNAs, and codons.

Translation is the process of decoding the information carried in the mRNA to synthesize the specified protein. The process requires three major structures—mRNA, ribosomes (which contain rRNA), and tRNAs An mRNA molecule is a temporary copy of the information in DNA; it carries encoded instructions for synthesis of a specific protein, or in the case of a polycistronic message, a specific group of proteins. Ribosome: 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 a 50S subunit. Ribosome-binding site: 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. tRNAs: Type of RNA molecule involved in interpreting the genetic code; each tRNA molecule carries a specific amino acid dictated by its anticodon. codons: 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 codons.

1. DNA Replication: c. Describe the differences between leading strand and lagging strand replication and role of DNA Polymerase I and DNA Ligase in the completion of the lagging strand.

leading strand: Synthesis of one new strand proceeds continuously as fresh template is exposed, because DNA polymerase simply adds nucleotides to the 3′ end. Synthesis of the other strand, the lagging strand, is more complicated. This is because DNA polymerases cannot add nucleotides to the 5′ end of a nucleotide chain, so synthesis must be reinitiated as additional template is exposed. Each time synthesis is reinitiated, another RNA primer must be made first. synthesis restarts many times as the helix unwinds, resulting in many short fragments called "Okazaki fragments." DNA ligase joins the Okazaki fragments together into a single DNA molecule.