Curriculum Map 137 - BIOLOGY JUNCTION

AP Lecture Guide 16 – The Molecular Basis of Inheritance

AP Biology: CHAPTER 16

THE MOLECULAR BASIS OF INHERITANCE

1. After Morgan and fellow scientists developed the Chromosomal Theory of Inheritance, the

search was on for the chemical mechanism of inheritance. What are the two components of the chromosome?

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2. From initial logic, which component would be the most likely candidate for the genetic

material and why?

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3. What did Griffith, Avery, and others accomplish with bacteria?

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4. Define transformation. _______________________________________________________

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5. What did the experiments done by Alfred Hershey and Martha Chase show?

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6. What are Chargaff’s rules?

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7. If a species has 35% adenine in its DNA, determine the percent of the other three bases.

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8. What was the role of Maurice Wilkins and Rosalind Franklin in determining the structure of

DNA?

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9. Use the diagram to describe the structure of DNA. Include several comments.

10. What is the advantage of the double stranded aspect of the DNA? ____________________

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11. Which model of DNA replication is accepted? ____________________________________

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12. What happens at the DNA replication fork?

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13. Make a list of the enzymes involved in replication and their role.

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14. Why does the DNA have to add nucleotides in the 5’ to 3’ direction?

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15. Label the diagram of DNA replication. Include the directions and the terms.

16. Describe the “priming of the DNA” before replication. _______________________________

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17. List some of the steps involved in DNA repair. ____________________________________

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18. What is the problem that occurs at the ends of the chromosome during replication?

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19. What is a telomere and its role in cell division. ____________________________________

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20. Why was there no selection pressure for prokaryotes to evolve a telomere-like solution on

their chromosome? _________________________________________________________

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21. Why is telomerase an active area in cancer research? _____________________________

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AP Lecture Guide 25 – Phylogeny and Systematics

AP Biology: CHAPTER 25: PHYLOGENY AND SYSTEMATICS

1. What is phylogeny?

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2. How are fossils significant to our study of biology?

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3. Review these key points in the study of fossils:

a. Sedimentary rocks are the richest source of fossils.

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b. Paleontologists use a variety of methods to date fossils.

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c. The fossil record is a substantial, but incomplete, chronicle of evolutionary history.

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d. Phylogeny has a biogeographic basis in continental drift.

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e. The history of life is punctuated by mass extinctions.

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4. List examples of fossils. ______________________________________________________

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5. What techniques do relative dating use to place fossils in their place in geologic time?

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6. What marks the separation between the major eras in the geologic time scale?

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7. How does absolute dating compare to relative dating?

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8. Describe the two main characteristics of the Linnaean system of classification.

a. _______________________________________________________________________

b. _______________________________________________________________________

9. What modern techniques are used as the basis for grouping creatures with modern

phylogenetic systematics?

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10. What does a phylogenic tree show?

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11. When classifying organisms in a cladistic diagram, identify three pitfalls scientists might

encounter classifying creatures.

a. _______________________________________________________________________

b. _______________________________________________________________________

c. _______________________________________________________________________

12. What do scientists use when placing an organism on a cladistic diagram?

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13. How have molecular clocks influenced our thoughts on evolutionary paths?

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14. Why is the four chamber heart a poor choice of structure to place creatures on a phylogenic

tree?

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15. Why are crocodiles now thought to be closer to birds than other reptiles?

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AP Lecture Guide 17 – From Gene to Protein

AP Biology: CHAPTER 17

FROM GENE TO PROTEIN

1. How did diseases involving metabolic pathways lead to hypotheses about the nature of

genes?

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2. Identify some genetic diseases that occur along metabolic pathways.

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3. What was Beadle and Tatum’s hypothesis regarding enzymes?

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4. How has that hypothesis been modified?

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5. What occurs during transcription?

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6. What occurs during translation?

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7. How does the protein process differ in prokaryotes and eukaryotes?

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8. Briefly explain how Marshall Nirenberg and Heinrich Matthaei “cracked the genetic code?”

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9. What is the genetic code and why is said to be universal?

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10. List several features about the genetic code.

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11. Give an example of what happens if reading frames are altered?

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12. List the highlights of the three stages of transcription.

a. Initiation _______________________________________________________________

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b. Elongation ______________________________________________________________

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c. Termination _____________________________________________________________

13. What happens to the transcript RNA before it leaves the nucleus?

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14. What is the advantage of the 5’ cap and poly A tail?

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15. Distinguish between exons and introns.

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16. Describe the mechanism for splicing RNA.

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17. What does alternative RNA processing do for cells?

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18. Identify the roles of the players of the translation process.

a. Transfer RNA ___________________________________________________________

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b. Aminoacyl-tRNA synthetase _______________________________________________

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c. Ribosomes _____________________________________________________________

19. Identify and briefly describe the steps of translation. Initiation Elongation Termination

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20. What is the advantage of polyribosomes?

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21. Give an example of how a polypeptide gets into the ER for additional processing.

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22. How does protein synthesis differ between prokaryotes and eukaryotes?

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23. Define point mutations. ______________________________________________________

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24. Define mutations that are:

a. Missense ______________________________________________________________

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b. Nonsense ______________________________________________________________

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c. Insertion or deletion ______________________________________________________

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25. Use the diagram to trace the flow of chemical information from the gene to the protein product.

AP Lecture Guide HGP

HUMAN GENOME PROJECT
INSIGHTS LEARNED FROM THE SEQUENCE

What has been learned from analysis of the working draft sequence of the human genome? What is still unknown?

By the Numbers

• The human genome contains 3164.7 million chemical nucleotide bases (A, C, T, and G).

• The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.

• The total number of genes is estimated at 30,000 to 35,000, much lower than previous estimates of 80,000 to 140,000 that had been based on extrapolations from gene-rich areas as opposed to a composite of gene-rich and gene-poor areas.

• The order of almost all (99.9%) nucleotide bases are exactly the same in all people.

• The functions are unknown for over 50% of discovered genes.

The Wheat from the Chaff

• Less than 2% of the genome encodes for the production of proteins.

• Repeated sequences that do not code for proteins (“junk DNA”) make up at least 50% of the human genome.

• Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, thereby creating entirely new genes or modifying and reshuffling existing genes.

• During the past 50 million years, a dramatic decrease seems to have occurred in the rate of accumulation of repeats in the human genome.

How It’s Arranged

• The human genome’s gene-dense “urban centers” are predominantly composed of the DNA building blocks G and C.

• In contrast, the gene-poor “deserts” are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on chromosomes.

• Genes appear to be concentrated in random areas along the genome, with vast expanses of noncoding DNA between.

• Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the “junk DNA.” These CpG islands are believed to help regulate gene activity.

• Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231).

How the Human Genome Compares with That of Other Organisms

• Unlike the human’s seemingly random distribution of gene-rich areas, many other organisms’ genomes are more uniform, with genes evenly spaced throughout.

• Humans have on average three times as many kinds of proteins as the fly or worm because of mRNA transcript “alternative splicing” and chemical modifications to the proteins. This process can yield different protein products from the same gene.

• Humans share most of the same protein families with worms, flies, and plants, but the number of gene family members has expanded in humans, especially in proteins involved in development and immunity.

• The human genome has a much greater portion (50%) of repeat sequences than the mustard weed (11%), the worm (7%), and the fly (3%).

• Although humans appear to have stopped accumulating repeated DNA over 50 million years ago, there seems to be no such decline in rodents. This may account for some of the fundamental differences between hominids and rodents, although gene estimates are similar in these species. Scientists have proposed many theories to explain evolutionary contrasts between humans and other organisms, including those of life span, litter sizes, inbreeding, and genetic drift.

Variations and Mutations

• Scientists have identified about 1.4 million locations where single-base DNA differences (SNPs) occur in humans. This information promises to revolutionize the processes of finding chromosomal locations for disease-associated sequences and tracing human history.

• The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females. Researchers point to several reasons for the higher mutation rate in the male germline, including the greater number of cell divisions required for sperm formation than for eggs.

What We Still Don’t Know: A Checklist for Future Research

• Exact gene number, exact locations, and functions

• Gene regulation

• DNA sequence organization

• Chromosomal structure and organization

• Noncoding DNA types, amount, distribution, information content, and functions

• Coordination of gene expression, protein synthesis, and post-translational events

• Interaction of proteins in complex molecular machines

• Predicted vs experimentally determined gene function

• Evolutionary conservation among organisms

• Protein conservation (structure and function)

• Proteomes (total protein content and function) in organisms

• Correlation of SNPs (single-base DNA variations among individuals) with health and disease

• Disease-susceptibility prediction based on gene sequence variation

• Genes involved in complex traits and multigene diseases

• Complex systems biology, including microbial consortia useful for environmental restoration

• Developmental genetics, genomics

http://genome.gsc.riken.go.jp/hgmis/project/journals/insights.html

AP Lecture Guide 19 – Control of Eukaryotic Genome

AP Biology: CHAPTER 19

CONTROL OF EUKARYOTIC GENOME

1. Outline the levels of DNA packing within the eukaryote nucleus.

2. What is the difference between heterochromatin and euchromatin? Which is transcribed?

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3. Which regions of the chromosome will typically be in the form of hererochromatin?

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4. How do the coding regions and genome sizes of prokaryotes and eukaryotes compare?

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5. Much of mammalian non-coding DNA is in the form of ______________________________

6. What is the cause of Fragile X?

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7. What is the cause of Huntington’s disease?

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8. Discuss an example of interspersed repetitive DNA?

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9. What is a multigene family?

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10. Multigene families are hypothesized to have evolved from…

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11. How is the globulin multigene family an adaptive to mammals?

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12. Explain how gene amplification can regulate gene expression.

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13. How can transposons alter gene expression?

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14. How do immunoglobulin genes code for a seemingly infinite variety of antibodies?

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15. Review the opportunities for gene regulation in eukaryotes in the diagram.

16. Where is the most important step in gene regulation?

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17. Describe the effect of each of the following control mechanisms.

a. DNA methylation ________________________________________________________

b. Histone acetylation _______________________________________________________

c. Transcription factors ______________________________________________________

d. Control elements ________________________________________________________

e. Enhancers _____________________________________________________________

f. Activators ______________________________________________________________

g. DNA-binding domain _____________________________________________________

18. How does alternative RNA splicing affect gene expression?

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19. How does RNA degradation affect gene expression?

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20. How does protein processing and degradation affect gene expression?

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21. Identify the opportunities to regulate gene expression in eukaryotes.

22. Typically, what happens to cell function when cells become cancerous?

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23. What is a proto-oncogene? What happens to them when cancer occurs?

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24. List the three events that can turn proto-oncogenes into oncogenes.

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25. Identify and describe mutations in specific proteins that can lead to cancer.

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26. What is p53?

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27. Why is it said that cancer formation is a multi-step process?

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