GENOME ORGANIZATION
- Chloroplast DNA is also circular and present in multiple copies.
- Early studies of chloroplast DNA utilized isodensity centrifugation as the main tool for its isolation.
- Although this approach works well with unicellular plants in higher plants most of the isolated DNA components initially believed to be chloroplast DNA turned out not to be chloroplast DNA at all.
- These early experiments, in which DNA prepared from isolated chloroplast was analyzed by cesium chloride isodensity centrifugation, revealed the presence of three DNA components: a major component with a density of about 1.696g/cm that was thought to represent contaminating nuclear DNA, and two minor DNA components denser than nuclear DNA that were thought to represent chloroplast DNA.
- But in 1971 the chloroplast DNA of the alga Euglena was isolated as a single large circle, suggesting that the linear typical plant leaf cell contains about 10,000 chloroplast DNA circles distributed among 50 to 100 chloroplasts, giving each chloroplast between 100 to 200 DNA molecules.
- Depending on the organism. chloroplast DNA contains anywhere from 70,000 to more than 5,00,000 base pairs, with an average of 1,50,000 base pairs being typical for the chloroplasts of higher plants; the presence of DNA in chloroplasts is not indisputable evidence that this DNA contains genes governing chloroplast traits.
- Independent support for the existence of circular DNA in chloroplasts has come from the genetic studies of Ruth Sagar, who employed the antibiotic streptomycin to induce mutations in chloroplast genes of the green alga Chlamydomonas.
Inverted repeats
- Many chloroplast DNAs contain two inverted repeats, which separate a long single copy section (LSC) from a short single copy section (SSC).
- The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 base pairs long each. in plants, each being 20,000–25,000 base pairs long.
- The inverted repeat regions usually contain three ribosomal RNA and two tRNA genes, but they can be expanded or reduced to contain as few as four or as many as over 150 genes.
- While a given pair of inverted repeats are rarely completely identical, they are always very similar to each other, apparently resulting from concerted evolution.
- The inverted repeat regions are highly conserved among land plants, and accumulate few mutations.
- Similar inverted repeats exist in the genomes of cyanobacteria It is possible that the inverted repeats help stabilize the rest of the chloroplast genome, as chloroplast DNAs which have lost some of the inverted repeat segments tend to get rearranged more.
Linear structure
- Chloroplast DNAs have long been thought to have a circular structure, but some evidence suggests that chloroplast DNA more commonly takes a linear shape.
- Over 95% of the chloroplast DNA in corn chloroplasts has been observed to be in branched linear form rather than individual circles.
Nucleoids
- New chloroplasts may contain up to 100 copies of their DNA, though the number of chloroplast DNA copies decreases to about 15–20 as the chloroplasts age.
- They are usually packed into nucleoids which can contain several identical chloroplast DNA rings. Many nucleoids can be found in each chloroplast.
- Though chloroplast DNA is not associated with true histones, in red algae, a histone-like chloroplast protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast DNA ring into a nucleoid has been found.
- In primitive red algae, the chloroplast DNA nucleoids are clustered in the center of a chloroplast, while in green plants and green algae, the nucleoids are dispersed throughout the stroma.
1. What is the structure of chloroplast DNA?
a) Linear
b) Circular
c) Double helix
d) Single-stranded
Answer: b) Circular
2. How many copies of chloroplast DNA are typically found in higher plant cells?
a) 1000
b) 10,000
c) 50,000
d) 1,00,000
Answer: b) 10,000
3. What technique was initially used to isolate chloroplast DNA?
a) Gel electrophoresis
b) Isodensity centrifugation
c) PCR
d) Northern blotting
Answer: b) Isodensity centrifugation
4. Which type of DNA was first mistaken for chloroplast DNA in higher plants?
a) Mitochondrial DNA
b) Nuclear DNA
c) Viral DNA
d) Plasmid DNA
Answer: b) Nuclear DNA
5. What density value (g/cm³) was initially thought to represent contaminating nuclear DNA?
a) 1.696
b) 1.700
c) 1.800
d) 1.500
Answer: a) 1.696
6. In which organism was chloroplast DNA first observed as a single large circular molecule?
a) Chlamydomonas
b) Euglena
c) Cyanobacteria
d) Arabidopsis
Answer: b) Euglena
7. What is the approximate number of chloroplasts per plant cell?
a) 10-50
b) 50-100
c) 100-500
d) 500-1000
Answer: b) 50-100
8. How many DNA molecules are found per chloroplast?
a) 1-10
b) 50-100
c) 100-200
d) 500-1000
Answer: c) 100-200
9. What is the typical base pair size of chloroplast DNA in higher plants?
a) 10,000 bp
b) 70,000 bp
c) 150,000 bp
d) 500,000 bp
Answer: c) 150,000 bp
10. Who provided genetic evidence for the presence of circular DNA in chloroplasts?
a) Barbara McClintock
b) Ruth Sagar
c) Gregor Mendel
d) Thomas Morgan
Answer: b) Ruth Sagar
11. What antibiotic did Ruth Sagar use to induce chloroplast mutations?
a) Penicillin
b) Tetracycline
c) Streptomycin
d) Rifampicin
Answer: c) Streptomycin
12. What structural feature separates LSC and SSC in chloroplast DNA?
a) Operons
b) Inverted repeats
c) Telomeres
d) Exons
Answer: b) Inverted repeats
13. What is the range of inverted repeat lengths in chloroplast DNA?
a) 1,000–5,000 bp
b) 4,000–25,000 bp
c) 50,000–1,00,000 bp
d) 500–2,000 bp
Answer: b) 4,000–25,000 bp
14. What genes are commonly found in the inverted repeat regions?
a) Photosynthetic genes
b) Ribosomal RNA and tRNA genes
c) Structural proteins
d) Enzymatic genes
Answer: b) Ribosomal RNA and tRNA genes
15. In plants, how long are inverted repeat regions typically?
a) 4,000–10,000 bp
b) 10,000–15,000 bp
c) 20,000–25,000 bp
d) 50,000–60,000 bp
Answer: c) 20,000–25,000 bp
16. Why are inverted repeat regions highly conserved?
a) They prevent chloroplast mutations
b) They facilitate gene expression
c) They stabilize the chloroplast genome
d) They promote recombination
Answer: c) They stabilize the chloroplast genome
17. What organism’s genome contains similar inverted repeats as in chloroplast DNA?
a) Fungi
b) Cyanobacteria
c) Viruses
d) Bacteria
Answer: b) Cyanobacteria
18. What happens to chloroplast DNA when inverted repeats are lost?
a) Becomes unstable and rearranges
b) Increases in size
c) Gains more genes
d) Converts into nuclear DNA
Answer: a) Becomes unstable and rearranges
19. What is the most common structural form of chloroplast DNA?
a) Circular
b) Linear
c) Branched linear
d) Double-stranded
Answer: c) Branched linear
20. In which plant was over 95% of chloroplast DNA found in a linear form?
a) Wheat
b) Corn
c) Arabidopsis
d) Pea
Answer: b) Corn
21. Where is chloroplast DNA located within the chloroplast?
a) Thylakoid membrane
b) Stroma
c) Grana
d) Inner membrane
Answer: b) Stroma
22. What is a nucleoid in chloroplasts?
a) DNA-protein complex
b) Photosynthetic pigment
c) RNA storage site
d) Membrane organelle
Answer: a) DNA-protein complex
23. What is the role of histone-like chloroplast protein (HC)?
a) Regulates photosynthesis
b) Compacts chloroplast DNA into nucleoids
c) Acts as an enzyme
d) Repairs DNA damage
Answer: b) Compacts chloroplast DNA into nucleoids
24. In which algae is histone-like chloroplast protein (HC) found?
a) Brown algae
b) Green algae
c) Red algae
d) Diatoms
Answer: c) Red algae
25. How many chloroplast DNA copies are found in young chloroplasts?
a) 10-50
b) 50-100
c) Up to 100
d) More than 500
Answer: c) Up to 100
26. How many copies of chloroplast DNA are present in older chloroplasts?
a) 5-10
b) 15-20
c) 50-100
d) 200-300
Answer: b) 15-20
27. In which part of primitive red algae are chloroplast DNA nucleoids located?
a) Scattered in the stroma
b) Inside the thylakoid membrane
c) Clustered in the center of the chloroplast
d) Attached to ribosomes
Answer: c) Clustered in the center of the chloroplast
28. Where are chloroplast DNA nucleoids located in green plants and green algae?
a) Clustered in the center
b) Dispersed throughout the stroma
c) Attached to the thylakoid membrane
d) Found in vacuoles
Answer: b) Dispersed throughout the stroma
29. What is the function of the chloroplast genome?
a) Code for photosynthetic pigments
b) Encode genes necessary for chloroplast function
c) Regulate stomatal opening
d) Store carbohydrates
Answer: b) Encode genes necessary for chloroplast function
30. What percentage of chloroplast DNA in corn exists as a branched linear form?
a) 50%
b) 75%
c) 90%
d) 95%
Answer: d) 95%
31. What is the main function of tRNA genes found in chloroplast DNA?
a) Encode proteins
b) Facilitate photosynthesis
c) Assist in protein translation
d) Regulate cell division
Answer: c) Assist in protein translation
32. What does the term “concerted evolution” refer to in chloroplast DNA?
a) Mutation accumulation
b) Stability of inverted repeats
c) Expansion of genome size
d) DNA recombination
Answer: b) Stability of inverted repeats
33. What is the key difference between chloroplast DNA and nuclear DNA?
a) Chloroplast DNA is single-stranded
b) Nuclear DNA is linear, while chloroplast DNA is mostly circular
c) Nuclear DNA lacks genes for photosynthesis
d) Chloroplast DNA has more chromosomes
Answer: b) Nuclear DNA is linear, while chloroplast DNA is mostly circular
34. What is the primary role of ribosomal RNA genes in chloroplast DNA?
a) Encode proteins
b) Assist in DNA replication
c) Form ribosomes for protein synthesis
d) Act as a genetic switch
Answer: c) Form ribosomes for protein synthesis
35. What process is most affected by mutations in chloroplast DNA?
a) DNA replication
b) Protein synthesis
c) Photosynthesis
d) Cell division
Answer: c) Photosynthesis
36. What molecule is primarily responsible for stabilizing chloroplast DNA structure?
a) Histones
b) Inverted repeats
c) RNA polymerase
d) Topoisomerase
Answer: b) Inverted repeats
37. What is the primary evidence supporting chloroplast DNA’s circular structure?
a) PCR analysis
b) Restriction enzyme mapping
c) DNA sequencing
d) Electron microscopy
Answer: d) Electron microscopy
38. What type of inheritance is typically observed for chloroplast DNA?
a) Maternal inheritance
b) Paternal inheritance
c) Biparental inheritance
d) Dominant inheritance
Answer: a) Maternal inheritance
39. Why is chloroplast DNA maternally inherited in most plants?
a) Pollen lacks chloroplasts
b) Male gametes contain degraded chloroplast DNA
c) Female gametes have more organelles
d) All of the above
Answer: d) All of the above
40. What technique is commonly used to analyze chloroplast DNA variations?
a) Southern blotting
b) Western blotting
c) ELISA
d) Mass spectrometry
Answer: a) Southern blotting
41. Which of the following organisms have a chloroplast genome similar to cyanobacteria?
a) Fungi
b) Green algae
c) Animals
d) Viruses
Answer: b) Green algae
42. Which of the following is NOT found in the chloroplast genome?
a) Photosynthetic genes
b) Ribosomal RNA genes
c) tRNA genes
d) Hemoglobin genes
Answer: d) Hemoglobin genes
43. What is the primary function of chloroplast ribosomes?
a) ATP synthesis
b) Protein synthesis
c) DNA replication
d) Cell signaling
Answer: b) Protein synthesis
44. How does chloroplast DNA replication differ from nuclear DNA replication?
a) Chloroplast DNA replicates independently of the cell cycle
b) Chloroplast DNA replication follows mitosis
c) Chloroplast DNA does not replicate
d) Chloroplast DNA replicates only in dividing cells
Answer: a) Chloroplast DNA replicates independently of the cell cycle
45. Which type of DNA repair mechanism is most active in chloroplasts?
a) Base excision repair
b) Nucleotide excision repair
c) Homologous recombination
d) Direct repair
Answer: c) Homologous recombination
46. How does streptomycin affect chloroplast DNA?
a) Causes mutations in chloroplast genes
b) Inhibits DNA replication
c) Destroys ribosomal RNA
d) Blocks nuclear DNA expression
Answer: a) Causes mutations in chloroplast genes
47. What is the significance of the LSC and SSC regions in chloroplast DNA?
a) Encode all chloroplast proteins
b) Separate the inverted repeat regions
c) Maintain mitochondrial function
d) Regulate photosynthetic pigments
Answer: b) Separate the inverted repeat regions
48. Which molecule primarily controls gene expression in chloroplasts?
a) DNA polymerase
b) RNA polymerase
c) Histone proteins
d) Ribosomes
Answer: b) RNA polymerase
49. How do mutations in chloroplast DNA affect plant phenotypes?
a) Alter leaf color and photosynthesis efficiency
b) Change flower shape
c) Modify root growth
d) Affect seed size
Answer: a) Alter leaf color and photosynthesis efficiency
50. Why is chloroplast DNA highly conserved among plant species?
a) Low mutation rates in chloroplast genes
b) High rates of recombination
c) Frequent horizontal gene transfer
d) Rapid genome expansion
Answer: a) Low mutation rates in chloroplast genes