Bio Lecture 16
What is a gene? What does it mean to express a gene?
A gene is a specific sequence of DNA that contains the information to make a product; a polypeptide or functional RNA; Gene expression is using the information stored in DNA to make that specific products
Two cells have exactly the same amount of DNA (same number of base pairs), but one cell has 1,000 genes and the other cell has 3,000 genes. Will the difference in the number of genes affect DNA replication? Explain your answer.
In DNA replication all chromosomes are replicated. If both chromosomes have the same amount of DNA , then DNA replication will not differ despite the amount of genes in a cell. DNA replication is unrelated to the amount of genes in a cell.
Identify the feature of DNA's structure that allows a DNA helix to be copied in cells to form two new, identical DNA helices.
The feature of DNA's structure that allows it to be copied is the nucleotides that pair up in specific ways. A DNA helix can be copied because the nucleotides on each strand are complementary to one another; they run in opposite directions. Something like an amino acid does not have this specific feature.
A cell is treated with a drug that prevents formation of RNA primers. How will this affect DNA replication?
Without RNA primers, DNA polymerase cannot bind to the template strands and thus cannot replicate DNA. This is because DNA polymerases, the enzymes that form new strands in DNA replication, are not able to start a DNA strand "from scratch" - they need both a template DNA strand to copy AND an RNA primer to add on to.
Draw a picture to show the process of DNA replication, focusing on one replication fork (one side of a replication bubble). Label the ORI and include a DNA helicase, DNA polymerases, and a DNA ligase. Draw arrows to indicate which direction each DNA polymerase is moving along the template strand.
........ Draw on piece of paper.....
Describe the roles of the DNA replication enzymes that we discussed. Explain why there are two DNA polymerases at each replication fork.
DNA helicase: unwinds DNA strands by breaking hydrogen bonds and helps keep strands separated; This puts a lot of strain on the molecule so single strand binding proteins come in and protect single stranded DNA from being degraded by cellular enzymes that break phosphodiester bonds. DNA polymerase: forms new strands with 2 @ each replication form because there are two template strands to copy; it can only add nucleotides to the hydroxyl group end; highly accurate and able to proof read by removing and replacing incorrect nucleotides added during replication process RNA primer: short piece of RNA; formed by specific enzyme ( different types in prokaryotic vs eukaryotic cells); gets replaced and removed with DNA by other enzymes after a new strand is started DNA ligase: links pieces of this new strand together by forming phosphodiester bonds (strand in chunks). NOT needed for other strand that is being built continuously
In what direction are DNA strands read/written by scientists? In what direction do DNA polymerases form new DNA strands? Why is one strand built continuous while the other strand is built in Okazaki fragments?
DNA helices are antiparallel and the two template strands go in opposite directions. Because strands are always built from P end to OH, the two strands must be formed in the opposite directions. One strand is formed continuously as the DNA unwinds, and the other is formed in pieces DNA strands are read and written from the 5' end (phosphate group) to the 3' end (hydroxy group). DNA polymerase can only form strands in one direction, phosphate to hydroxyl end. One strand is built continuously because the hydroxyl end is towards the replication fork. The other strand is built in fragments because the hydroxyl end is away from replication fork. This requires for RNA primer to create multiple starting points to allow for DNA polymerase to attach the complimentary nucleotides. At the end the RNA primers are removed and DNA polymerase fills those gaps before DNA ligase seals the strand.
Explain/describe how the structural differences of DNA and RNA relate to their respective roles in biological information processing.
DNA is is double stranded and more stable molecule with more hydrogen bonds in comparison to RNA. It is harder to break it down because it is stronger. Molecule that holds information is rationalized as more stable RNA is single stranded and less stable. Easier to break down because its primary role in cells is to temporarily hold information for access and then is broken down
Is DNA permanent or temporary information storage? what about RNA?
DNA is permanent information storage and must be passed on to the next generation RNA is a temporary message and only needed when expressing a particular gene and does not need to exist forever
Describe the basic mechanism by which DNA is replicated in cells. Include in your description an explanation of how and why formation of two new strands at a replication fork differ from each other.
DNA replication starts at the origin(s) of replication. DNA helicase binds to the ORI site and unwinds/unzips the DNA strands by keeping them separated creating a replication fork. Single strand binding proteins come in to protect single stranded DNA from being degraded by cellular enzymes that break phosphodiester bonds. The separated strands each provide a template for creating a new strand of DNA. RNA primase then attaches to template nucleotides on strands marking the starting point for the construction of new strand of DNA. DNA polymerase then binds to the primer and begins to copy the DNA strand. It can only form strands in ONE direction (phosphate group to hydroxy). One new strand is formed continuously (the one that starts away from the ORI) and the other new strand is formed in multiple pieces (Okazaki fragments) away from replication fork (towards the ORI). DNA ligase then seals/links pieces of new strand together by forming phosphodiester bonds to form a continuous double strand. https://www.youtube.com/watch?v=TNKWgcFPHqw
If a change in the DNA sequence of a prokaryotic chromosome occurred that introduced an additional origin of replication (ORI), how would that affect DNA replication?
ORI: Origin of replication having multiple ORIs allow a chromosome to be replicated more quickly because there are more places to start = gets copied faster
A cell is treated with a drug that decreases the activity of DNA ligases in a cell. Will replication of both strands of a DNA helix at a replication fork be equally affected? Why or why not? What if a drug decreased the ability of DNA polymerases to function? Decreased the activity of DNA helicases? Reduced the ability of the enzymes that form RNA primers to function? Explain your answers Explain your answers.
Only one strand of a DNA helix at a replication fork will be affected by this drug because DNA ligase is only used on the new DNA strand that gets built in pieces. If a drug decreased the ability of DNA polymerases to function, new DNA would be formed more slowly or there would be more mistakes in DNA replication. If DNA helicases were impaired, the DNA would be unzipped more slowly. If RNA primers were not formed, then the DNA polymerase would not have a place to start attaching new nucleotides to the template strand.
A change in the DNA sequence of the ORI in the chromosome of a prokaryotic cell alters the sequence so that DNA replication proteins can no longer interact with the ORI. How will this affect the cell? What if the sequence of an ORI was altered on a chromosome in a eukaryotic cell? Explain how and why the outcomes would be different.
Prokaryotic cells have one origin of replication so if proteins can no longer interact with the ORI the cell would not be able to multiply Eukaryotic cells have multiple/many origins of replication so if proteins were no longer able to interact with one ORI there would still be others present to interact with; Would decrease efficiency and rate
If a drug was added to a cell that inhibited the proofreading ability of DNA polymerases, what would happen?
The new DNA strand would have various errors creating faulty DNA
Why do the two strands of a DNA helix need to be separated in order for DNA to be copied?
The nucleotides on the template strands must be accessible to the DNA polymerase, and they are not accessible when they are locked in a helix via hydrogen bonds. Also the two strands of a DNA molecule have complimentary base pairs and the nucleotide sequence of each strand automatically supplies the information needed to produce its partner.
What correctly describes the three main processes involved in cellular information processing? OVERVIEW...
There is DNA replication, transcription, and translation to go from DNA strand to RNA strand to Polypeptide(protein) DNA replication: making a copy of all genetic information (DNA) ONCE prior to cell division Transcription: Making an RNA copy of a gene (first step in expressing all genes) Translation: Making an RNA message (mRNA) to direct the formation of a polypeptide and is only required for expression of genes that contain information to make proteins NOTE: most of the time when we are expressing a gene we are making protein Mastering Bio Input: In DNA replication, all DNA in a cell is copied once prior to cell division In Transcription, only some DNA is copied.... Makes an RNA copy of a gene. Transcription is the first step in expression of all genes. Translation is only involved in expression of genes that contain information to produce proteins. Uses mRNA to direct formation of polypeptide
