Chapter+16+&+17+Molecular+Genetics

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Chapter 16 & //Chapter 17// Molecular Genetics LET"S SEE SOME VIDEOS FOR THIS ONE!!!

** DNA as the Genetic Material **
1. Summarize the experiments performed by the following scientists that provided evidence that DNA is the genetic material: a. Frederick Griffith b. Oswald Avery, Maclyn McCarty, and Colin MacLeodc. c. Alfred Hershey and Martha Chased. d. Erwin Chargaff
 * Frederick Griffith** - used pathogenic and non pathogenic bacteria to test for a transformation factor. Discovered that when he killed pathogenic bacteria with heat and mixed the cell remains with living bacteria of the harmless strain, some of the living cells were converted to the pathogenic form. The new trait was inherited by all the descendants of the transformed bacteria. Conclusion: a chemical compound of the dead pathogenic cells caused this change (transformation).

-Monika
 * Oswald Avery, Maclyn McCarty, and Colin MacLeodc -** []

Hershey and Chase added radioactive isotopes of sulfur into one batch of T2 bacteriophages, and radioactive phosphorous into a different batch of bacteriophages. They then blended the contents of each batch in a centrifuge and let the infection run its course. They found that in the batch where sulfur was added, the radioactive isotope was not present in the phage, but was in the liquid. The opposite was true of phosphorus which was present in the phage, but not in the liquid. Since phosphorus is mainly present in DNA, while sulfur is mainly present in the proteins in chromosomes, they determined that DNA was in fact responsible for heredity, not proteins.
 * Alfred Hershey and Martha Chase**

http://www.youtube.com/watch?v=HvJlnujmYcg
 * Erwin Chargaff**

-Gordie

2. Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain the significance of the research of Rosalind Franklin. Watson and Crick were working at Cambridge trying to figure out the structure of DNA when they heard about the work of Rosiland Franklin. She was using a technique called X-Ray Cyrstalography to take actual pictures of DNA molecules. When Watson and Crick saw her X-ray photographs the pieces of their puzzle came together and they realized that the DNA had a double helical structure and were then able to construct a model. Watson and Crick had the idea, but Franklin's work gave them the tangible proof to turn their idea into a tangible model.

[] Jared 3. Describe the structure of DNA. Explain the "base-pairing rule" and describe its significance.

DNA is in the structure of a double-helix and it is comprised of small molecules called nucleotides. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonds between paired bases of adenine (A) with thymine (T), and guanine (G) with cytosine (C). Adenine and Guanine are Purines, and Thymine and Cytosine are Pyrimidines. According to the base pairing rule, hydrogen bonds attach A::T G:::C, with each colon representing the number of H bonds. Base stacking contributes significantly to the stability of the double-helix. This video demonstrates the structure of DNA, and also how the bases are connected: http://www.youtube.com/watch?v=ZGHkHMoyC5I Tom Haile

** DNA Replication and Repair **
4. Describe the semiconservative model of replication and the significance of the experiments by Matthew Meselson and Franklin Stahl.

The Meselson-Stahl experiments proved that DNA replication is semiconservative. With regards to DNA replication, semiconservative refers to the fact that DNA replication produces two double-stranded double helixes, each of which contains an original DNA helix strand and a newly synthesized strand. The Meselson-Stahl experiment involved the growth of E. Coli in a Nitrogen-15 (non-radioactive isotope) rich medium for several generations. After several generations, DNA from E. Coli grown in both Nitrogen-15 and Nitrogen-14 was separated and N-15 cultured E. Coli cells were transferred to an N-14 medium and allowed to divide. When DNA was extracted from the N-15 to N-14 sample and compared to pure N-14 and N-15 samples, it was found to have an intermediate density; this proved that the conservative model of replication could not be accurate because it would not account for a sample of intermediate density. This led Meselson and Stahl to believe that either the semiconservative or the dispersive model held true. DNA was allowed to replicate and further samples were taken; these samples varied in density from the intermediate density initially observed; the dispersive model would have only accounted for an intermediate density but not varying density after further rounds of replication and as such, the Meselson-Stahl experiment successfully proved the semiconservative model of replication. -Kellen

5. Describe the process of DNA replication. Note the structure of the many origins of replication and replication forks and explain the role of DNA polymerase. DNA replication begins at the origin of replication (prokaryotes) where proteins attach to nucleotides and separate the two DNA strands to from a replication "bubble." Two replication forks results in both directions within the DNA strand. In eukaryotes, there are several origins of replication and therefore more than one replication fork. The enzyme helicase begins the process by unwinding the helix structure of the DNA. SSBP and Topoisomerase keep the strands separate. Primase then joins several RNA nucleotides to create a primer that DNA polymerase 3 can connect from 5' to 3'. On the leading strand, the process is continuous however the lagging strand requires okazaki fragments to link due to DNA's antiparallel nature. The DNA becomes continuous when DNA pol I replaces the RNA primer with DNA nucleotides and DNA Ligase joins the sugar phosphate backbones of the fragments. -AHC 6. Define "antiparallel" and explain why continuous synthesis of both DNA strands is not possible. 7. Distinguish between the leading strand and the lagging strand. The leading strand of DNA moves in the 3' to 5' direction, therefore replication can start at the 3' end from 5' to 3 '. The lagging strand moves in the 5' to 3' direction and newly synthesized DNA is laid down at the 5' to 3' in the opposite direction from the leading strand. The lagging strand is synthesized in fragments because the newly replicated DNA is being formed in the direction away from the replication fork and must wait for it to open up, thus producing Okazaki fragments. - Eli

8. Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3' end. The leading strand is synthesized continuously while the lagging strand is synthesized in fragments. This is because DNA polymerase cannot synthesize in the 3' to 5' direction. Primase builds an RNA primer in short bursts and then DNA polymerase is able to synthesize the short bursts of DNA. These pieces are called Okazaki fragments, ligase eventually joins the fragments together creating a seamless strand of synthesized DNA. [|http://www.youtube.com/watch?v=AnNs416Rcws]

9. Explain the roles of DNA ligase, primer, primase, helicase, and the single-strand binding protein.
 * **Ligase** joins the 3' end of one fragment to the 5' end of its neighbor.
 * **Primer** is the starting point of DNA synthesis.
 * **Primase** synthesizes a primer of 5-10 RNA bases to start the new strand.
 * **Helicase**, an enzyme that works at the replication fork, unwinds the helix and separates the strands.
 * **Single-strand binding proteins** support the separated strands while replication takes place. --Sabrina

10. Explain why an analogy can be made comparing DNA replication to a locomotive made of DNA polymerase moving along a railroad track of DNA. During DNA replication, DNA polymerase travels down the DNA template strand to make a new complementary strand of DNA just like a locomotive(DNA polymerase) traveling down a railroad track of DNA. The enzyme moves in 1 direction much like a train and make DNA replication fast and accurate. - Joanne H

** Evolution, Unity, and Diversity **
11. Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair. === Nuclease and DNA Polymerases function as repairing enzymes that fix small nucleotide errors in the DNA sequence during replication. Although these enzymes cannot fix everything. Major DNA or Chromosomal issues remain dysfunctional. Nuclease excels at fixing UV-ray induced mutations in the genetic sequence. ===

Philip
12. Describe the structure and functions of telomeres. Explain the significance of telomerase to healthy and cancerous cells. Telomeres are the ends of chromosomes. They’re only on a 3’ and a 5’ end, the leading strand can’t be completed leaving remaining primer. With every replication, telomeres shorten. With age telomeres will be shorter. Telomerase adds DNA to make up for the shortened telomere. Telomerase is present in healthy and cancer cells, the study of telomerase function is very important in cancer research.

https://www.youtube.com/watch?v=AJNoTmWsE0s

Jason Weiss

**// The Connection between Genes and Proteins //**
// 13. Explain how RNA differs from DNA. // DNA (deoxyribonucleic acid) is double stranded and makes a double helix, while RNA (ribonucleic acid) is made up of only a single strand. Each is comprised of two base pairs of nucleotides, DNA is AT and GC, while NA is AU and GC. DNA codes for everything and carries tons of genetic material. RNA is necessary to DNA because it synthesizes proteins, which is sometimes needed in the duplication of DNA. Also, there are three different types of RNA (rRNA, mRNA, and tRNA), while there is only one type of DNA. Elena Zifkin // 14. Briefly explain the central dogma of protein synthesis // the flow of genetic information goes from DNA to RNA to PROTEIN. - DNA information is transcribed into mRNA - mRNA information is translated into an amino acid chain that becomes a PROTEIN EMILY H.



// 15. Define "codon" and explain the relationship between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide. //

// A codon is a set of 3 adjacent nucleotide bases in a DNA or mRNA strand. The linear sequence of codons on mRNA serve as instructions for the linear sequence of amino acids in a polypeptide; each codon codes for a specific amino acid, so the order of the codons determine the order of the amino acids in a polypeptide. Specifically, the codons in mRNA determine which anticodons of tRNA can bind to the mRNA strand to undergo translation into a polypeptide chain. // [|mRNA to polypeptide video] -Supritha

**// The Synthesis and Processing of RNA //**
// 16. Explain how RNA polymerase recognizes where transcription should begin. Describe the promoter, the terminator, and the transcription unit. // The RNA polymerase binds at the promoter site. This site is where the start point for transcription is. The RNA continues to travel upstream, and the template strand determines the pattern of the sequence. Once the transcription factors bind to the promoter site, the RNA polymerase can begin the transcription initiation complex. It extends past the terminator, where the sequence ending transcription is formed. THe transcription unit is the stretch of DNA that was transcribed into an RNA molecule. http://www.youtube.com/watch?v=cQlA3O39rEQ JLM

// 17 Explain the general process of transcription, including the three major steps of initiation, elongation, and termination. // Transcription is the process by which RNA is synthesized from DNA. RNA polymerase is responsible for this process. In the initiation phase, transcription factors help RNA polymerase bind to the DNA strand at the promoter site. The elongation phase is marked by the addition of nucleotides to the 3' end. Termination is the end of the transcription phase when the sequence has ended, allowing RNA polymerase to be released.

[] Ella P

// 18 Explain how RNA is modified after transcription in eukaryotic cells.. // === Post-transcriptional modification, a process in eukaryotic cells, occurs as the primary transcript RNA is converted into mature RNA. Often times, this process occurs prior to protein synthesis and involves splicing, a modification of RNA after transcription that joins exons while removing introns. Splicing is known to be essential in producing a correct protein in translation to form a mature mRNA and is mediated by spliceosomes. As RNA is modified after transcription, the mature coding RNAs are generated via splicing, which allows for the cell to produce variations of a protein that is encoded by a gene. Overall, the messenger RNA will undergo RNA splicing until it reaches its state of mature mRNA and will continue on to exit the nucleus. As this occurs, introns, known as non-coding RNA regions will be removed, while the coding regions that remain are known as exons and are spliced together thanks to DNA ligase - Daniel Kogan ===

**// The Synthesis of Protein //**
// 19. Describe the structure and functions of tRNA.and rRNA // // tRNA is used to bring the amino acids to the ribosomes. THere they are linked and made into proteins. This video shows a great demonstration of how tRNA works. // [] rRNA is part of the protein-synthesizing ribosome as well as help translate the information in mRNA into proteins. THey are synthesized in the nucleolus of the cell. ribosomal RNA form secondary structures and are very important in recognizing tRNA and mRNA. They provide a mechanism that helps decode mRNA into amino acids and helps tRNA in translation. -Andrew CHang // 20. Describe the process of translation (including initiation, elongation, and termination) and explain which enzymes, protein factors, and energy sources are needed for each stage. // After transcription, ribosomes synthesize proteins using the mRNA just produced to carry out the process of translation. An initiation code starts a genetic message. As the ribosome moves along a mRNA transcript, it won't begin synthesizing proteins until it reaches an initiation code. Next, the ribosomes begin the elongation phase, during which amino acids are added to the growing protein chain. EEFs (Eukaryotic Elongation Factors) are required to speed up the elongation process, as there are a colossal amount of codons to synthesize. The process of elongation in detail is as follows: 1. Amino acid-containing tRNA molecules (aminoacyl-tRNAs, aa-tRNA) are picked up by elongation factor eEF-1 in the presence of GTP. 2. The formed complex enters the empty A-site on a ribosome carrying an initiator Met-tRNAi or a peptidyl-tRNA. 3. On the ribosome, the anticodon of the incoming aminoacyl-tRNA is matched against the mRNA codon positioned in the A-site. As the three bases in the codon can be arranged in 64 different combinations, the translational machinery must be able to select the aminoacyl-tRNA carrying the matching anticodon. During this proof-reading, aminoacyl-tRNAs with non-cognate anticodons are thrown out of the ribosome and replaced by new aa-tRNAs that are to be checked. Finally, termination is completed upon the ribosomes encountering a stop codon. http://www.nobelprize.org/educational/medicine/dna/a/translation/elongation.html http://www.youtube.com/watch?v=1NkLqjQkGHU - JH

// 21 Define "point mutations." Distinguish between base-pair substitutions and base-pair insertions. Give examples of each and note the significance of such changes. // Point mutations are mutations in which a single nucleotide is replaced with another base nucleotide from either RNA or DNA. A base pair insertion is when a nucleotide is inserted into the DNA sequence. An insertion can be one or more nucleotides, and this can sometimes result in a frameshift mutation. For example, if a codon were supposed to signal a stop (i.e. UGA) but a nucleotide is inserted causing the codon to become UCA and coding for tyrosine rather than stop. A base pair substitution is when a nucleotide is simply substituted for another. This can often be harmless due to redundancy of codons. Redundancy means that multiple codons and code for the same amino acid, greatly reducing the chances a major mutation will occur. For example, GGG and GGC both code for the amino acid glycine. -D. Gorelik aka DG3