GEN 371 - Exam 2 Study Material

Study Guide 

Genetic Mapping & Recombination 

• Three-point crosses reveal gene order and distances by analyzing parental, single crossover, and double crossover offspring. 

• Genes on the same chromosome may behave independently if they are far apart, allowing frequent crossing over. 

• Map units (centimorgans) reflect crossover frequency; 1% recombination = 1 map unit. 

• Linkage analysis uses recombinant frequencies to infer distances. 

• Gene order is determined by comparing double crossover offspring to parental types. 

Bacteriophage and Bacterial Genetics 

• Phage plaques are clear zones on bacterial lawns caused by lysis from viral infection. 

• Plasmids (F, ColE1, R factors) are circular DNA molecules carrying genes such as antibiotic resistance or fertility factors. 

• Conjugation transfers DNA between bacteria through cell contact mediated by an F plasmid. 

• Transformation involves uptake of free DNA; transduction transfers genes via bacteriophages. 

• Integrated viral DNA in a host chromosome is called a prophage. 

Structure and Composition of Nucleic Acids 

• Nucleotides contain a phosphate, pentose sugar, and nitrogenous base. 

• DNA is double-stranded, antiparallel, and held by hydrogen bonds (A–T, G–C). 

• Chargaff’s rule: A pairs with T, G pairs with C; total purines = total pyrimidines. 

• E. coli DNA is circular and double-stranded; eukaryotic chromosomes are linear and double-stranded. 

• RNA contains ribose, uracil, and is usually single-stranded. 

DNA Replication 

• Replication is semiconservative and bidirectional from a fixed origin. 

• Leading strand is synthesized continuously; lagging strand forms Okazaki fragments. 

• DNA polymerase III extends the 3′ end; DNA polymerase I removes RNA primers and fills gaps. 

• Helicase unwinds the double helix; gyrase relieves supercoiling; ligase seals nicks; primase synthesizes primers. 

• Telomerase extends chromosome ends in eukaryotes. 

• DNA strands run 5′ to 3′; 5′ ends have phosphate groups, 3′ ends have hydroxyl groups. 

Gene Expression and the Genetic Code 

• The genetic code is triplet, universal, non-overlapping, and degenerate. 

• The wobble hypothesis explains flexibility at the third codon position. 

• Codon–anticodon pairing occurs via complementary base pairing between mRNA and tRNA. 

• Promoters, enhancers, and transcription factors help RNA polymerase bind specific DNA regions.

Molecular Techniques 

• Gel electrophoresis separates DNA fragments by size; smaller fragments move faster toward the positive electrode. 

• VNTRs were used in early DNA fingerprinting methods. 

• Microsatellites and RFLPs are common genetic markers for gene mapping. 

Chromatin and Histones 

• Histone acetylation neutralizes charge and loosens chromatin structure, promoting gene expression. 

• Histones are rich in lysine and arginine, giving them a positive charge to bind DNA. 

• Nucleosomes contain histones H2A, H2B, H3, and H4; H1 links nucleosomes. 

DNA and RNA Processing 

• Eukaryotic genes contain introns removed during RNA splicing, making mRNA shorter than the original gene. 

• mRNA carries coding information; tRNA and rRNA are involved in translation; snRNA aids in splicing. 

Experimental Foundations 

• Avery, MacLeod, and McCarty identified DNA as the transforming principle. 

• Hershey and Chase confirmed that DNA is the genetic material using radioactive sulfur and phosphorus labeling. 

• Proteins were once believed to be genetic material due to their complexity and variability. 

Functional Properties of Genetic Material 

• Stores information for cellular function and inheritance. 

• Replicates accurately to ensure faithful transmission. 

• Expresses information as phenotypic traits. 

• Allows mutation and variation to enable evolution. 

Eukaryotic Genome Features 

• A small portion of the genome codes for proteins; most is noncoding DNA. 

• Repetitive DNA makes up about 5% of the human genome. 

• Genome size does not correlate with organism complexity. 

Bacterial and Viral Systems 

• Auxotrophs require supplemental nutrients; prototrophs can grow on minimal media. 

• Lytic phages cause cell lysis; lysogenic phages integrate into the host genome as prophages. 

Quantitative Examples 

• Recombination frequency = (recombinants / total offspring) × 100. 

• Double crossover frequency = product of two single crossover rates. 

• Map distances help determine gene order and linkage relationships.

Quiz

Flashcards

Genetic Mapping & Recombination

1. Front: What do three-point crosses reveal?
   Back: Gene order and distances by analyzing parental, single, and double crossover offspring.

2. Front: What does 1% recombination equal?
   Back: 1 map unit (centimorgan).

3. Front: What type of offspring reveals gene order in a three-point cross?
   Back: Double crossover offspring.

4. Front: What does linkage analysis infer?
   Back: Gene distances based on recombinant frequencies.

5. Front: When can genes on the same chromosome behave independently?
   Back: When they’re far apart, allowing frequent crossing over.

Bacteriophage & Bacterial Genetics

6. Front: What are phage plaques?
   Back: Clear zones on bacterial lawns caused by viral lysis.

7. Front: What are plasmids?
   Back: Small circular DNA molecules carrying accessory genes like antibiotic resistance.

8. Front: Define conjugation.
   Back: DNA transfer between bacteria through direct cell contact via F plasmid.

9. Front: Define transformation.
   Back: Uptake of free DNA from the environment.

10. Front: Define transduction.
    Back: Gene transfer mediated by bacteriophages.

11. Front: What is a prophage?
    Back: Viral DNA integrated into a host chromosome.

Structure & Composition of Nucleic Acids

12. Front: What are the three components of a nucleotide?
    Back: Phosphate group, pentose sugar, nitrogenous base.

13. Front: DNA strands are ______ and ______.
    Back: Double-stranded and antiparallel.

14. Front: Chargaff’s rule states?
    Back: A = T and G = C; purines equal pyrimidines.

15. Front: E. coli DNA structure?
    Back: Circular and double-stranded.

16. Front: Eukaryotic chromosomes structure?
    Back: Linear and double-stranded.

17. Front: RNA differs from DNA by containing what sugar and base?
    Back: Ribose and uracil.

DNA Replication

18. Front: Type of replication in DNA?
    Back: Semiconservative.

19. Front: Leading vs. lagging strand synthesis?
    Back: Leading is continuous; lagging forms Okazaki fragments.

20. Front: DNA polymerase III role?
    Back: Extends 3′ end during replication.

21. Front: DNA polymerase I role?
    Back: Removes RNA primers and fills gaps.

22. Front: Helicase function?
    Back: Unwinds the double helix.

23. Front: Gyrase function?
    Back: Relieves supercoiling.

24. Front: Ligase function?
    Back: Seals nicks between fragments.

25. Front: Primase function?
    Back: Synthesizes RNA primers.

26. Front: Telomerase function?
    Back: Extends chromosome ends in eukaryotes.

27. Front: DNA runs in what directions?
    Back: 5′ to 3′ with phosphate at 5′ and hydroxyl at 3′.

Gene Expression & Genetic Code

28. Front: The genetic code is ______.
    Back: Triplet, universal, non-overlapping, and degenerate.

29. Front: What does the wobble hypothesis explain?
    Back: Flexibility of tRNA pairing at the third codon position.

30. Front: What forms codon–anticodon pairing?
    Back: mRNA codon with tRNA anticodon.

31. Front: Role of promoters and enhancers?
    Back: Help RNA polymerase bind to specific DNA regions.

Molecular Techniques

32. Front: Purpose of gel electrophoresis?
    Back: Separates DNA fragments by size.

33. Front: Direction smaller DNA fragments move?
    Back: Toward the positive electrode faster.

34. Front: VNTRs were used in what?
    Back: Early DNA fingerprinting.

35. Front: Common markers for mapping genes?
    Back: Microsatellites and RFLPs.

Chromatin & Histones

36. Front: Why are histones positively charged?
    Back: Rich in lysine and arginine.

37. Front: What do nucleosomes contain?
    Back: Histones H2A, H2B, H3, H4 with DNA.

38. Front: Role of histone H1?
    Back: Links nucleosomes.

39. Front: Effect of histone acetylation?
    Back: Loosens chromatin; promotes expression.

DNA & RNA Processing

40. Front: What are introns?
    Back: Noncoding sequences removed during RNA splicing.

41. Front: What is mRNA’s role?
    Back: Carries coding information to ribosomes.

42. Front: tRNA and rRNA function?
    Back: Involved in translation.

43. Front: snRNA function?
    Back: Aids in RNA splicing.

Experimental Foundations

44. Front: Avery, MacLeod, and McCarty discovered what?
    Back: DNA is the transforming principle.

45. Front: Hershey–Chase confirmed what?
    Back: DNA, not protein, is genetic material.

46. Front: Why were proteins once suspected as genetic material?
    Back: Greater complexity and variability.

Functional Properties & Genome Features

47. Front: Four functions of genetic material?
    Back: Stores info, replicates, expresses traits, allows mutation.

48. Front: Coding portion of human genome?
    Back: Small; most is noncoding.

49. Front: Repetitive DNA makes up about what percent of human genome?
    Back: ~5%.

50. Front: Does genome size correlate with organism complexity?
    Back: No, it does not.

Multiple Choice

Select the best answer.

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1. In a three-point cross, gene order is determined by:
   A. Parental types
   B. Double crossover offspring
   C. Single crossover frequency
   D. Map units between genes

2. One map unit (centimorgan) corresponds to:
   A. 10% recombination
   B. 1% recombination
   C. 0.1% recombination
   D. 5% recombination

3. Which of the following allows gene transfer between bacterial cells via physical contact?
   A. Transformation
   B. Conjugation
   C. Transduction
   D. Translation

4. A prophage is:
   A. Free DNA in the environment
   B. Bacterial DNA integrated into a viral genome
   C. Viral DNA integrated into a host genome
   D. A plasmid carrying antibiotic resistance genes

5. DNA and RNA differ because:
   A. DNA has uracil; RNA has thymine
   B. RNA has deoxyribose
   C. RNA has uracil instead of thymine
   D. Both contain deoxyribose

6. DNA polymerase III functions to:
   A. Remove RNA primers
   B. Join Okazaki fragments
   C. Extend the 3′ end during replication
   D. Unwind DNA strands

7. Which enzyme relieves supercoiling during replication?
   A. Ligase
   B. Helicase
   C. Gyrase
   D. Primase

8. The wobble hypothesis explains:
   A. How tRNA recognizes multiple codons
   B. How ribosomes bind promoters
   C. Mutation frequency in DNA
   D. Stop codon recognition

9. A nucleosome consists of:
   A. DNA wrapped around histones H1 and H2A only
   B. DNA plus histones H2A, H2B, H3, and H4
   C. Only histone H1
   D. RNA wrapped around histones

10. Histone acetylation generally results in:
    A. Condensed chromatin and gene silencing
    B. Loosened chromatin and increased gene expression
    C. DNA methylation
    D. Protein degradation

11. In Avery, MacLeod, and McCarty’s experiment, DNA was identified as the:
    A. Enzyme of transcription
    B. Genetic material
    C. Viral protein coat
    D. Structural protein of the cell

12. The Hershey–Chase experiment used:
    A. Radioactive calcium and potassium
    B. Radioactive sulfur and phosphorus
    C. Radioactive nitrogen and carbon
    D. Radioactive hydrogen and oxygen

13. Gel electrophoresis separates DNA fragments based on:
    A. Sequence
    B. Shape
    C. Size
    D. Charge type

14. Eukaryotic genes are often interrupted by:
    A. Exons
    B. Promoters
    C. Introns
    D. Start codons

15. The E. coli genome is:
    A. Linear and double-stranded
    B. Circular and single-stranded
    C. Circular and double-stranded
    D. Linear and single-stranded

True/False

Short Answer

Answer concisely in 1–3 sentences.

21. Explain how double crossover events help determine gene order in a three-point cross.

22. Describe two main differences between DNA and RNA.

23. What is the role of DNA ligase in replication?

24. Why was protein once thought to be the genetic material instead of DNA?

25. Write the formula for recombination frequency and explain what it measures.

Answer Key

Multiple Choice

1. B

2. B

3. B

4. C

5. C

6. C

7. C

8. A

9. B

10. B

11. B

12. B

13. C

14. C

15. C

True/False

16. True

17. False

18. False

19. True

20. False

Short Answer

21. Double crossovers swap the middle gene relative to the outer two, revealing which gene lies in between.

22. DNA has deoxyribose and thymine; RNA has ribose and uracil and is usually single-stranded.

23. DNA ligase seals nicks between Okazaki fragments on the lagging strand.

24. Proteins were thought to be genetic material because they are more complex and variable than DNA.

25. Recombination frequency = (recombinants ÷ total offspring) × 100; it measures crossover frequency between genes.