Reference no: EM132857791

Lecture: DNA and genes

1.GUIDING QUESTION: The amount of DNA that organisms possess can be staggering. For example, in humans, it would take a person type 60 words per minute, 8 hours a day, for 50 years to type the entire human genome! Given the rapid pace of biotechnology and computer data processing improvements, scientists can decode an entire species' genome in a relatively short period of time and at relatively low cost. However, analyzing all of those data, letter by letter (A, T, C, G) is a daunting task. One long-used technique known as gel electrophoresis can be used as a sort of shortcut to decipher genetic differences not only among species but among individuals within a species. This is commonly known as DNA fingerprinting. In your own words, describe the process of gel electrophoresis, including the role of restriction enzymes or the mechanism by which DNA is fragmented in this process. How are the results of gel electrophoresis analyzed in order to lead to differentiating between individuals or species? That is, what is the nature of the data being analyzed?

1. Genes are composed of what molecule? Genes code for ___________ and are located on ___________.
2. Discuss the scientific consensus (or lack thereof) regarding the genetic material during the first half of the 1900s.
3. What is a genome? How can it be true that highly distinct species, such as bonobos and chimps or humans and chimps, share nearly identical DNA?
4. Genes commonly code for ________, which have a unique ____________ sequence (and a unique function), that ultimately contributes to producing an individual's __________.
5. What is gene expression, and how does it explain cellular specialization in the human body? Why is the regulation of developmental genes of particular significance?
6. Review the basic structure of DNA.
7. What is a base pair? What is meant by the term "complementary strands?" Who first proposed the idea of base pairing, and when did they propose this?
8. DNA stores information in the order of the __________ in the ___________ chain. One gene is different from another gene because the two have a different ___________.

Lecture: DNA processes: replication, repair, and packaging

 GUIDING QUESTION: Extreme packaging is needed in order to stuff truly enormous amounts of DNA into the nucleus of a eukaryotic cell (including plants, animals, and humans). How much DNA? Well, if all of the 46 different DNA molecules in one of your skin cells were lined up end to end, they would make a double helix nearly 2 meters (about 6 feet) long. Yet the nucleus is tiny, with a diameter slightly less than 5 micrometers (0.005 millimeters). Provide a detailed explanation of how this feat of extreme packaging is accomplished; in your answer, be sure to use the following terms: histones, nucleosomes, chromatin, and chromosome.

1. What was Rosalind Franklin's contribution to understanding DNA structure?
2. What are the four nitrogenous bases found in DNA? Which base pairs are found in DNA, and how many hydrogen bonds are formed between each type of base pair?
3. In the structure of DNA, nucleotides are joined so that the sugars and phosphates alternate, forming a continuous ___________ to the polynucleotide chain? How many polynucleotide chains are found in DNA?
4. Explain the significance of the following terms when discussing DNA structure and replication: antiparallel, 5' à 3', pentose sugar, phosphate group.
5. DNA replication forms ______ double helices from one.
6. What is meant by the term "semiconservative" when describing DNA replication? What is a "parental" strand and a "daughter" strand?
7. What is the function of DNA polymerase? In which direction (3'à 5' or 5' à 3') does DNA polymerase operate? Does DNA polymerase require an RNA primer?
8. What is the difference between the leading and lagging strands? On which strand are Okazaki fragments formed? How long, in base pairs (bp), are Okazaki fragments in eukaryotes and prokaryotes? What is the name of the enzyme that forges a covalent bond between Okazaki fragments?
9. There are four "nucleoside triphosphates" that are used during DNA replication: one for each of the nitrogenous bases (A, T, G, C). What is the significance of the fact that these bases are supplied to the growing polynucleotide chain in the form of a "triphosphate?"
10. In addition to synthesizing the growing polypeptide, DNA polymerase also performs what other function?
11. What is the error rate of DNA polymerase?
12. Of those few errors that occur as a result of DNA synthesis by DNA polymerase, what percentage are corrected by additional special "proofreading" proteins?
13. __________ arise as a result of mutations. What is a mutation? What is a mutagen? Most genetic mutations are ______________.
14. Mutations are the __________ of genetic variation, and genetic variation is the ___________ for natural selection and adaptive evolution.
15. DNA repair requires three steps. What are these steps?
16. Describe the condition known as "xeroderma pigmentosum" (XP). What causes XP? What is a thymine dimer?
17. Each cell of humans has about __________ billion base pairs (bp) of DNA that, outstretched linearly, would reach a length of more than __________ meters, and humans have _________ cells. Therefore, DNA packaging is essential.
18. A gene can not be expressed when packaged compactly. Why not?
19. In meters, how long is a nanometer (nm)? Describe (briefly) the nature of DNA packaging at each of the following spatial scales: 1 nm, 11 nm, 30 nm, 300 nm, 700 nm, and 1,400 nm.

Lecture: Genome organization and "junk" DNA

1. GUIDING QUESTION: Many scientists over the years have noted that many genomes (including that of humans) is made up of apparent "junk DNA," with the actual genes few and far between. It would be like going on a journey of 1,000 miles and having very little of note to see-long stretches where nothing seemed to be happening, and where the roadside was monotonous. Occasionally you would pass through a town, full of activity and purpose, corresponding to a gene. Cities in this journey correspond to families of genes. Discuss at least three reasons (drawn from information discussed in lecture class meetings or obtained when preparing your special topic presentation on this topic or your textbook) why such "junk DNA" might be passed on from generation to generation. These reasons may include the fact that in some cases this DNA is not junk at all but actually serves important functional purposes; if so, what are those purposes? However, other reasons may include explanations involving what are generally called selfish genetic elements (SGEs); if so, name the specific type of SGE and how this DNA achieves propagating itself at the expense of the larger multicellular organism.
2. How many chromosomes do prokaryotes (e.g., bacteria) have? Is the chromosome(s) circular or linear? Are the chromosomes of eukaryotes (e.g., humans) circular or linear? What are the relative amounts of noncoding DNA in prokaryotes and eukaryotes? How do prokaryotes and eukaryotes differ with respect to the organization of genes on the chromosome(s)?
3. Is DNA of unknown function common in eukaryotes? In humans?
4. Compare the genome size of an onion, Amphiuma (an amphibian), a pufferfish, and Euglena (a single-celled protist) to that of a human. Is there a clear trend with respect to genome size and organismal complexity among these eukaryotes?
5. What is an exon? What is an intron? Are either of these portions of a gene protein-coding? If so, which one? What is the spatial arrangement of introns relative to exons?
6. Define spacer DNA.
7. Genes that code for proteins or RNA constitute _________________ of the DNA in most eukaryotes.
8. What is RNA splicing, and how is an RNA primary transcript different from mRNA?
9. What are the consequences (in terms of the diversity of protein types synthesized) of alternative spicing? Is alternative splicing observed in prokaryotes as well as eukaryotes?
10. Regulation of ______________ can generate significant phenotypic variation.
11. Alternative splicing is one way of increasing the diversity of functional gene products (and complexity) without _____________________________.
12. Is there a relationship between the percentage of DNA not coding for protein and organismal complexity? What percentage of humans noncoding DNA is potentially subject to alternative splicing? What is this same percentage in roundworms? Why is this significant?
13. What is a microRNA (miRNA), and how does it act to "silence" gene expression? Name at least four human diseases that are caused by miRNA dysfunction?
14. The relationship between genetic make-up and organism "complexity" is unclear, although more "complex" organisms may have genetic features (such as alternative splicing and microRNAs)                   that generate greater ______________.
15. Humans have approximately ___________ protein-coding genes?

Lecture: Central dogma of biology: transcription, translation

45.  GUIDING QUESTION: Proteins and other non-nucleic acid biomolecules compose and maintain living cells. Yet the information encoding these biomolecules is ultimately stored in DNA. Before biologists could decipher how DNA encodes such information (the central dogma of biology), the molecular structure of DNA first needed to be elucidated. The story of the race to discover the structure of DNA is one of the most famous and interesting tales in the history of science. This took place primarily in the late 1940s and early 1950s, culminating in a series of publications beginning in 1953 by James Watson and Francis Crick. In lecture class, although we briefly discussed Watson and Crick's work, we did not have an opportunity to discuss several other scientists whose work was integrally involved in the ultimate discovery of DNA's true molecular structure. Explain the significance of each of the following historical figures who each played an important role in this story that unfolded in the mid-20^th Century: Rosalind Franklin, Maurice Wilkins, and Linus Pauling.

1. The so-called "central dogma of biology" involves three biomolecules and three biochemical processes. Name these three biomolecules and three processes.
2. Compare and contrast DNA replication and gene transcription with respect to (a) the key enzyme involved, (b) the portion of the chromosome copied, and (c) the biochemical product.
3. DNA is transcribed to make RNA? Name four other types of RNA. Which of these four types of RNA are involved in translation? Which of these types of RNA codes directly for an amino acid sequence?
4. What is the function of the promoter sequence? Transcription by RNA polymerase proceeds in the               __________ direction. What happens in transcription once the terminator sequence is reached?
5. Which four nitrogenous bases are found in RNA? Is this different from the nitrogenous bases found in DNA? Explain.
6. Does RNA processing (= RNA splicing/editing) occur in prokaryotes or eukaryotes, or both? What is the difference between an exon and an intron? Distinguish between the raw primary transcript of RNA and mRNA. Which is longer?
7. What is the function of codons in translation? How many nucleotides are included in each codon? On which biomolecule are codons found?
8. Translation begins at the _______ codon. Translation ends at the _______ codon.
9. Which codon (three letters) correspond to the start codon in all living organisms? List the codons that correspond to the stop codon.
10. After ribosomes bind the mRNA, each specific ____________ is delivered to the ribosome-mRNA complex by a _________ molecule specialized to deliver a specific type of _________.
11. What is the relationship between an anticodon and a codon? Which biomolecule possesses an anticodon?
12. Discuss (briefly) the processes occurring during three major stages of protein synthesis through translation: initiation, elongation, and translation.
13. How does transcription and translation in bacteria differ fundamentally from that of eukaryotes? How does this benefit bacteria?
14. How many different types of amino acids are found in biological proteins? Amino acids are abbreviated with ______ lower-case letters.
15. Where in the eukaryotic cell do the following processes occur: DNA replication, transcription, and translation?
16. Discuss (briefly) what is meant by "the redundancy of the mRNA code."

Lecture: Gene Expression

62.  GUIDING QUESTION: "Evo Devo" is short for Evolutionary Developmental Biology, a cross-disciplinary field that emerged and gained prominence in the 1990s, largely with the highly impactful discovery of homeotic genes (= Hox genes, for short). The discovery of Hox genes was not predicted by biologists and caught essentially everyone off guard. Obviously, this discipline integrates developmental biology and evolutionary biology. In 2-3 sentences, explain how Hox genes direct the large-scale development of animal body plans as disparate as fruit flies and mammals, including humans. Then explain how the ubiquity of Hox genes provides key insights into the evolution of the animal kingdom.

1. What is meant by the term "gene expression?" What is meant by the term "gene regulation?"
2. Different sets of genes are expressed in _______________.
3. Gene expression changes during _____________ and can change in response to ______________ and _______________.
4. Cells generally control gene expression by regulating the ____________ of specific genes.
5. What is the function of regulatory DNA?
6. Gene regulatory proteins are also known as ______________. What is their function?
7. What is an operon? What organism possesses the lac operon? Discuss (briefly) how the lac operon works.
8. What important field of biology is referred to as "evo devo," for short? What is the primary aim of evo devo?
9. What is a homeotic gene? What is the shorthand name for homeotic genes that is commonly used in animal species?
10. Discuss (briefly) the genic and chromosomal organization of homeotic genes when comparing fruit flies and mice.
11. Altering how and when a homeotic gene is expressed in the developing embryo can _____________________.
12. Evo-devo has demonstrated that gene regulatory patterns can bring about dramatic changes in organism form without _____________________.
13. Discuss (briefly) how differing patterns of homeotic gene regulation provides an explanation for the generation of body plans of very different segmented arthropods, such as grasshoppers and brine shrimp.
14. Homeotic genes and chromosome structure are highly ______________.
15. How is transcription rate of the Hoxc8 gene related to the differential development of thoracic vertebrae in evolutionarily distant vertebrates, such as chicken and mice?
16. Gene expression can be regulated at many stages/levels. List the six corresponding ways that gene expression can be regulated, as discussed in Figure 12.12 of your textbook (and covered in classroom lecture).
17. Which toxic chemical is produced by corn lilies? What abnormal phenotype does ingestion of this toxin by grazing vertebrates generate?
18. Discuss what is meant by the terms "personal genomics" and "personalized medicine."
19. Is a snake simply a legless lizard? What is the relationship between legless lizards and regulation of homeotic gene expression?
20. Differences in patterns of gene expression explain many of the differences between ________ and humans. Name two phenotypic traits that differ between this species and humans that is linked with gene regulatory differences.

Attachment:- DNA and genes.rar