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Independent Study Guide – The Blueprint of Life, from DNA to Protein (Chapter 7)

I. General Principles (Chapter 7 introduction) a. Morse code – distinct series of dots and dashes encode the 26 letters of the alphabet

i. Letters strung together make words → sentences → stories b. DNA – distinct series (triplets) of the four nucleotides encode the 20 amino acids

i. Amino acids strung together make proteins (structural/ functional) → cells → organisms

II. Overview (section 7.1) a. Central Dogma of Molecular Biology (fig. 7.1)

i. DNA replication ii. Transcription iii. Translation

b. Characteristics of DNA (p. 32-34; p.162-164) i. Composed of deoxyribonucleotides (figure 2.22)

1. Basic structure - base, phosphate group, deoxyribose 2. Four different bases - adenine, guanine, cytosine, thymine (figure 2.23)

ii. Deoxyribonucleotides are covalently bonded in chains (figure 7.3) 1. 5’ end (phosphate) 2. 3’ end (hydroxyl) 3. Double–stranded 4. Strands are anti-parallel 5. Strands are complementary 6. Base-pairing rules:

a. A-T b. G-C

iii. Double helix iv. Sugar-phosphate backbone

c. Characteristics of RNA (p. 34, 164) i. Composed of ribonucleotides (ribose not deoxyribose); uracil replaces thymine ii. Sequence is "identical" to a stretch of one strand of DNA; complementary to other

(figure 7.7) iii. Three functional types of RNA, all single stranded:

1. Messenger RNA (mRNA) 2. Ribosomal RNA (rRNA) 3. Transfer RNA (tRNA)

III. DNA Replication (section 7.2)

a. Bi-directional, semi-conservative (figure 7.4) b. DNA polymerase adds proper nucleotide to the 3’ end of the new chain (figure 7 .5)

i. Synthesis is 5’ → 3’ c. DNA polymerases generally correct errors during replication (“proofreading”)

i. Error rate = 1/billion nucleotides d. Second round of replication can start before first is complete e. DNA polymerases require a primer (they can only add nucleotides onto an existing chain) f. Bacterial DNA replication is initiated at a single distinct region (origin of replication = ori)

i. A short stretch of RNA (complementary to DNA) is synthesized

IV. The Replication Fork (figure 7.6) a. Leading strand (continuous synthesis) b. Lagging strand (discontinuous synthesis)

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V. Replication vs. Transcription a. DNA polymerase vs. RNA polymerase b. deoxyribonucleotides vs. ribonucleotides c. thymine vs uracil

Gene Expression – Overview:

transcription translation Coded by DNA: RNA transcripts protein molecules

Protein A Protein B Protein C Protein D Protein E

VI. Bacterial Gene Expression - Transcription (p. 168 - 170)

a. Transcription is initiated at a promoter b. Transcription stops at a terminator c. Initiation - RNA polymerase binds to promoter (guided by sigma factor) d. Elongation - RNA polymerase synthesizes RNA 5’ → 3’ (no primer needed) e. Termination -

f. Terms to note: i. Monocistronic

ii. Polycistronic (prokaryotes only)

iii. Upstream iv. Downstream

v. Plus strand vi. Minus strand

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g. Orientation of the promoter determines which strand serves as the template

VII. Bacterial Gene Expression – Translation (p. 170 - 173)

a. Ribosomes “read” mRNA; facilitate conversion of the encoded information into proteins b. The role of mRNA - carries encoded instructions for synthesis of a polypeptide

i. Genetic code correlates codon to amino acid (figure 7.10) ii. Genetic code is degenerate iii. Genetic code encodes "start" and "stop" signals iv. Three possible reading frames; only one is generally used (figure 7.11)

c. The role of ribosomes i. "Workbench" of translation; "read" the mRNA one codon at a time (proper reading

frame is critical; see figure 7.11) ii. Ribosome moves along RNA in the 5' to 3' direction iii. Ribosome structure (figure 7.12) iv. Eukaryotes (monocistronic messages) – translation starts at first AUG v. Prokaryotes (monocistronic and polycistronic messages) – translation begins at first

AUG after a ribosome-binding site d. The role of tRNA

i. tRNAs are the “keys” that decipher the code ii. Each tRNA carries a specific amino acid (figure 7.13) iii. The anticodon, complementary to a codon, binds mRNA

e. Initiation of translation i. In prokaryotes, ribosome-binding site, first AUG after that (critical because of

polycistronic messages) ii. In eukaryotes, first AUG (moncistronic messages)

VIII. Process of Translation

a. Initiation b. Elongation

i. Translocation ii. Elongation factors

c. Termination - stop codon

Figure 7.8

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IX. Eukaryotic Gene Expression (section 7.4)

X. Regulation of Bacterial Gene Expression (section 7.5) a. Constitutive enzymes b. Inducible enzymes c. Repressible enzymes

XI. Sensing and Responding to Environmental Fluctuations (section 7.7)

a. Signal transduction i. Two-component regulatory systems

b. Quorum sensing

c. Natural selection

XII. Mechanisms of regulation (in prokaryotes) a. Alternative sigma factors b. DNA-binding proteins - lac operon as an example (part of figure 7.19)

i. Negative control - repressors bind, blocking transcription ii. Positive control - activators bind, facilitating transcription iii. Activity of repressors/activators can be controlled (allosteric)

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XIII. Review Question

1. What is the Central Dogma of Molecular Biology? 2. Distinguish between replication, transcription, and translation. 3. Describe the basic structure of a deoxynucleotide (i.e. name the three general parts). 4. Which 4 bases are found in DNA? 5. What are the "base pairing rules"? 6. Describe the basic structure of a DNA molecule. 7. How is RNA different from DNA? 8. What are the three functional types of RNA? 9. DNA replication is semi-conservative. What does this mean? 10. Where is DNA synthesis initiated on a bacterial chromosome, and how many of these sites are on a

bacterial chromosome? 11. How does a cell that takes 40 minutes to replicate the chromosome divide every 20 minutes? 12. Nucleotides are added onto which end of a DNA (or RNA chain), and what chemical group is found at

that end? 13. What is the name of an enzyme that synthesizes DNA? 14. What is a primer? 15. With respect to DNA synthesis, what is "proofreading"? 16. Describe the difference between leading and lagging strand synthesis, and why this difference is

necessary. 17. What two general processes are involved in gene expression? 18. Where does transcription begin, and where does it end? 19. What is a sigma factor? 20. How is a polycistronic message different from a monocistronic one? 21. Is a promoter upstream, or downstream, of the terminator? 22. What is the significance of the 3'OH on a nucleotide? 23. What is a codon vs. an anticodon? 24. In prokaryotes where does translation begin and where does it end? 25. Describe the key differences between prokaryotic and eukaryotic gene expression. 26. Give an example of the function of the following types of enzymes: constitutive, inducible, and

repressible. 27. Compare and contrast the roles of activators and repressors. 28. Describe the mechanism of two-component regulatory systems. 29. Describe the mechanism of quorum sensing. 30. Describe how some cells use natural selection as a means of responding to environmental fluctuations.