Mod+9+Reading+Guide

__**Mod 9 Summary**__ The main idea of module 9, nucleic acids, is to understand the composition, replication, transcription, translation, and other uses of DNA and RNA within cells and viruses.

__**21.1 Components of Nucleic Acids**__ Summary: Both **DNA**, dioxyribonucleic acid, and **RNA**, ribonucleic acid, are unbranched polymers of repeating monomer units called nucleotides. Each nucleotide is made of a nitrogenous base, a five-carbon sugar, and a phosphate group. The **nitrogen-containing bases** in nucleic acids are derived from pyrimidine (C,T and U) or purine (A and G). The difference between ribose and deoxyribose is that deoxyribose doesn't have a hydroxyl group on carbon 2', but ribose does. A **nucleoside** is produced when a pyrimidine or a purine forms a glycosidic bond to C1' (carbon 1) of a sugar (deoxyribose or ribose). For example, adenosine is formed with adenine and ribose form a nucleoside. **Nucleotides** are formed from an ester between the C5'--OH group of a sugar and a phosphate group. Naming a nucleotide is done by first giving the name of the nucleoside followed by 5'-monophosphate. For example, an A nucleotide for DNA would be named deoxyadenosine 5'-monophosphate (dAMP).

Struggling Topic 1: ATP is used as a major energy source in the cell, GTP provides energy for protein synthesis, and CTP is used for lipid synthesis. Is there a use for TTP or UTP, and do these compounds exist in the body?

Struggling Topic 2: How does the structure of A,T,U,C, and G cause only A,T, and U to pair together and C and G to pair together? It looked like an NH3 group on C would pair with the C=O group on G. Why couldn't C pair with the C=O group in T or U?

__**21.2 = Primary Structure of Nucleic Acids - Make Quiz Questions on this one**__ Summary: **Nucleic acids** are polymers of many nucleotides (the 3'-OH group of a sugar is bonded to the 5'-carbon atom of the phosphate group). A **phosphodiester bond** is a phosphate link between the sugars in adjacent nucleotides. The **primary structure** of a nucleic acid is its sequence of bases attached to the alternating phosphate and sugar molecule backbone. The base sequence is always read from the free 5'-phosphate group to the free 3'-hydroxyl group. Often this is written as only the letters of the bases (ACTG, etc).

Struggling Topic 1: DNA is well known for its double-helix shape. Is this shape caused by the angles of the phosphodiester bond between the sugars in adjacent nucleotides, or is its shape caused by the attractions between the bases?

Struggling Topic 2: How does the structure of A,T,U,C, and G cause only A,T, and U to pair together and C and G to pair together? It looked like an NH3 group on C would pair with the C=O group on G. Why couldn't C pair with the C=O group in T or U?

__**21.3 DNA Double Helix**__ Summary: Due to hydrogen bonding (2 between A and T and 3 between C and G), the DNA bases only pair with their **complementary base pair** (A with T, and C with G). This forms the **double helix** shape with two polynucleotide strands winding about each other like a staircase. The sugar-phosphate backbones are like the railing, and the base pairs are like the steps. The complementary segment of DNA runs in the opposite direction as the original strand (ex: 5' A C G 3' would pair with 3' T G C 5').

Struggling Topic 1: If strands of DNA/RNA are always read from the 5' end to the 3' end, then how can complimentary strands that are "backwards" code for the same proteins? Or how does the body know to use one side of the DNA strand but not the other?

Struggling Topic 2: Is the twisting in the helix shape caused by the phosphodiester bonds or by the hydrogen bonds in the DNA?

__**21.4 DNA Replication**__ Summary: DNA **replication** is the process where DNA is copied. First, the parent DNA strands separate so that the original strands can make copies by synthesizing complementary strands. A nucleoside triphosphate bonds to a sugar as the complimentary strand is formed by losing two phosphate groups. This loss of phosphate groups provides the needed energy for the reaction. This process is called semi-conservative replication where two new and identical daughter DNA strands are produced from a single parent DNA strand. **Replication forks** are open DNA sections that have begun the replication process. The leading strand may be synthesized continuously from the 5' to the 3' direction, but the lagging strand is synthesized in the opposite direction so that short sections, **Okazaki fragments**, are synthesized at the same time by several polymerases and ligase to eventually form a single 3' to 5' strand.

Struggling Topic 1: What effect does the difference between a leading and a lagging strand of DNA have on the replication of DNA? Is mutation more likely in the lagging strand? Does a difference in rate make a significant difference often?

Struggling Topic 2: How do phosphate groups store energy within their bonds? Is this a popular form of energy within the body? It reminds me of the ATP from cellular respiration. Are there other groups similar to phosphate in this function?

__**21.5 RNA and Transcription**__ Summary: RNA is different from DNA because RNA is made of ribose rather than deoxyribose, the base uracil replaces thymine, RNA is single stranded (not double), and RNA molecules are much smaller than DNA molecules. Three major types of RNA include messenger RNA, **mRNA**, ribosomal RNA, **rRNA**, and transfer RNA, **tRNA**. mRNA is the most abundant type of RNA that is contained in the ribosomes and used for protein synthesis. mRNA carries genetic information from the DNA in the nucleus (or chromosome ring for prokaryotes) to the ribosome for protein synthesis. The length of mRNA depends on the number of nucleotides in that particular gene. tRNA is the smallest of the RNA molecules, and it interprets the genetic information in mRNA and brings specific amino acids to the ribosome for protein synthesis. tRNA is usually drwan as a cloverleaf with a 3' end with the nucleotide sequence ACC which is the aceptor stem. This acceptor stem allows and enzyme to attach an amino acid there with the free hydroxide group. An **anticodon** is a series of three bases found in tRNA that compliment three bases on an mRNA. **Transcription** is the process where DNA copies genetic information onto mRNA. **Translation** is the process where tRNA converts the information in mRNA into amino acids. For eukaryotes, **exons** are sections of genes that code for proteins, and **introns** are sections of genes that do not code for proteins. **Enzyme induction** is a process where the presence of a molecule causes the production of an enzyme that affects it to be made. For example, lactose enters a cell and causes B-galactosidase to be produced so that the lactose can be broken down. For prokaryotes, **operons** are sections of DNA that precede the **structural genes** (that code for proteins) and regulate groups of related proteins by providing a **control site**. A control site contains a promoter and an operator. **Regulator genes** produce mRNA for the synthesis of a **repressor** protein that binds to the operator and blocks synthesis when it is finished. (see pictures and diagrams on p.763 and 764)

Struggling Topic 1: Does transcription turn on and off the same way fro prokaryotes and for eukaryotes? Do both contain sections of genes that code for proteins and others that do not?

Struggling Topic 2: Are exons and introns contained only in eukaryotes and operons and structural genes found in prokaryotes?

__**21.6 The Genetic Code**__ Summary: The genetic code is made of may **codons**, sequences of three bases, that each specify amino acids in a protein. 64 codons are possible in the genetic code. Three of these, UGA, UAA, and UAG, are stop signals that code for the end of protein synthesis. Some amino acids are coded for by several different codons. The triple AUG signals the beginning of protein synthesis, or when it's located in the middle of an exon it codes for the amino acid methionine. See page 766 for which codons code for which amino acid.

Struggling Topic 1: One of the objectives is that we be able to identify the sequence of amino acids given an mRNA segment. Will there be a time when this must be done without using the chart in the book? This doesn't seem like the kind of thing that should be memorized.

Struggling Topic 2: Why make section 21.5 huge and section 21.6 so small?

__**21.7 Protein Synthesis: Translation**__ Summary: After mRNA is synthesized, it moves to the ribosomes where translation involves tRNA. An anticodon in the loop at the bottom of tRNA contains a triplet of bases that complement a codon on mRNA. An amino acid is connected to the acceptor stem of the tRNA by enzymes called aminoacyl-tRNA synthetases. Each amino acid has a different synthetase, and these use ATP for energy to catalyze ester bonds between the carboxylic acid groups on the amino acids and the hydroxyl groups of the acceptor stem. If the wrong amino acid is attached to the tRNA, then it would be placed into the protein and make an incorrect protein. The synthetase checks that attachement of the amino acid and tRNA hydrolyzes any incorrect combinations. Protein synthesis begins with the start codon, AUG anda tRNA anticodon UAC that arries the amino acid methionine. Then translation may begin. After the first tRNA has placed its amino acid, it detaches and returns to the cytoplasm. Then the ribosome shifts to the next codon on the mRNA (**translocation**). The stop codon does not have a tRNA to attach to, so protein synthesis ends and the enzyme releases the complete protein.

Struggling Topic 1: If I understand this correctly, tRNA carries only one amino acid at a time to translate using the mRNA at the ribosome as a pattern or model. Then once the tRNA has placed its amino acid, it gets out of the way for the next codon. Is this correct?

Struggling Topic 2: Is tRNA constantly being refilled with the appropriate amino acid so that it can continuously be reused? Would each cell have all 20 versions of tRNA in its cytoplasm? There would probably be doubles and duplicates so that translation could happen more quickly, right?

__**21.8 Genetic Mutations**__ Summary: A **mutation** is a change in the DNA nucelotide sequence that changes the sequence of amino acids. A **substitution** mutation is the replacement of one base in the coding strand of DNA with another. This change in the codon can lead to the insertion of a different amino acid. Substitution is the most common way mutations occur. **Frameshift mutations** are when bases are added to or deleted from the normal order of bases in the coding strand of DNA. A **genetic disease** is when a protein deficiency is genetic.

Struggling Topic 1: Is cancer a mutation that causes a cell to divide too quickly? I have heard that this could be caused by a DNA mutation that causes the length of time the cell spends in interphase to be significantly shortened. This would explain why tumors of cancer cells can spread relatively quickly.

Struggling Topic 2: Is it common for substitution mutations to go unnoticed or with no effect? It seems like many of the codons of the 64 available have similarities such that a substitution might not have a significant effect. Also, many amino acids seem to function similarly within the proteins they make up, so it seems reasonable that a substitution mutation might cause minimal effect maybe 50% of the time or so.

__**21.9 Recombinant DNA**__ Summary: **Recombinant DNA** are synthetic forms of DNA that contain DNA fragments from different organisms. This is often done with prokaryotes because they have DNA present in several small circular molecules called plasmids. Then because these prokaryotes reproduce very quickly (E. coli cells can reproduce a million times in one day), many cells with new, synthetic DNA can be produced for therapeutic use. RFLP's may be used to create a DNA fingerprint of a person that could be used to screen for many genetic diseases. The human genome project reports that over 30,000 genes are found in human genes but that only about 1% of them actively make protein. This project is working on identifying defective genes that lead to genetic disease. **Polymerase chain reaction (PCR)** is a process that allows us to produce multiple copies of DNA in a short time. Previously DNA could only be studied within living cells.

Struggling Topic 1: How do scientists answer the moral questions about recombinant DNA's use? It is very cool that it has so many good uses such as producing insulin for diabetes. Is there an ethical way to keep the work on recombinant DNA from becoming a search for the "master race" and a screening test for the "ideal genetic code?"

Struggling Topic 2: What makes E. coli the choice bacteria for working with recombinant DNA? Is this related to how quickly E. coli reproduces? I would assume that you need a prokaryote that quickly reproduces so that you can make many copies of DNA in a relatively short amount of time.

__**21.10 Viruses**__ Summary: **Viruses** are small particles of 3 to 200 genes that cannot replicate without a host cell. Usually a virus contains a nucleic acid (DNA or RNA) inside a protein coat. Viruses do not have the ability to synthesize proteins, so DNA is inserted into the host cell and the host cell produces viral RNA that produces new protein coats until so many new viruses are produced that the host cell bursts. Vaccines are inactive forms of viruses that boost the immune response by causing the body to produce antibodies to the virus. A virus that contains RNA is a **retrovirus**. A retrovirus must first make viral DNA using reverse transcription. Retroviruses have an enzyme called reverse transcriptase that uses viral RNA to synthesize complementary strands of DNA. Then the new viral DNA, a provirus, joins the DNA of a host cell. HIV is an example of a virus that causes disease (AIDS), and there are many drugs that have been synthesized to help attack the HIV as it is in its various stages of replication.

Struggling Topic 1: Viruses are not classified as living things because they do not have the ability to grow or reproduce on their own, right?

Struggling Topic 2: Why must a retrovirus use reverse transcription to make a provirus? Couldn't a retrovirus simply use the RNA it carries to produce more protein coats? Or would this process fail because the new protein coats wouldn't have any copies of the viral RNA to carry?

__**Critique**__ A. specifics about how clearly the author communicated individual topics -21.5 - the author's diagrams describing the on and off processes for transcription were much more helpful than the paragraph's words. -21.6 - the author's diagram that identifies mRNA codons and amino acids is useful for identifying proteins that will be synthesized.

B. specifics about the amount of content and whether it was sufficient to help learn the material (did you need more examples?) -21.5 - the paragraph description for transcription turning on and off was very detailed. This was challenging for me to understand and perhaps could have been covered using more examples than only the lactose one that was used. Without the diagram to explain how the vocabulary fit together I probably would not have understood.

C. why did the author place this chapter where she did in the overall text? not later or earlier, transitions with previous chapter, with subsequent chapter(s), did this chapter seem out of place? -21.5 and 21.6 - section 21.5 seemed much larger than 21.6. Perhaps some of the information in 21.5 should have had its own section.