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Questions and Answers
What describes the process of denaturation of DNA?
Which factor does NOT contribute to the denaturation of DNA?
What is the melting temperature (Tm) of DNA primarily influenced by?
What enzyme cuts within nucleic acids to generate fragments?
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Which nucleotide is NOT part of DNA?
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The width of B-form DNA double helix is approximately how many nanometers?
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How many hydrogen bonds are formed between guanine and cytosine base pairs in DNA?
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What is the main outcome of removing denaturing conditions from DNA?
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How many hydrogen bonds form between adenine and thymine in DNA?
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What is the helical diameter of B-form DNA?
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How many base pairs are present in a single turn of B-form DNA?
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Which type of DNA has a left-handed double helix structure?
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If thymine concentration in a DNA molecule is 30%, what would the concentration of guanine be?
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In a DNA molecule where guanosine content is 40%, what is the expected content of adenine?
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Which statement about double-stranded DNA is correct?
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What is the most likely source of a nucleic acid sample with 10% adenine, 40% cytosine, 30% thymine, and 20% guanine?
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What type of bond links a base to the 1 carbon of a sugar in the formation of a nucleoside?
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What structural feature distinguishes the primary structure of DNA?
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Which statement best describes Chargaff's rules concerning DNA base pairing?
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In a nucleic acid strand, what does the term 'polarity' refer to?
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What type of bond connects nucleotides within a DNA strand?
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What is the orientation of the two strands in a DNA double helix?
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Which of the following correctly describes a characteristic of nucleoside di- and tri-phosphates?
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In the Watson and Crick model of DNA, where are the bases located?
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What is the basic packaging unit of chromatin?
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How many base pairs of DNA are typically found in a nucleosome core?
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What is the role of histone H1 in nucleosome structure?
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Which type of chromatin is generally more transcriptionally active?
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What characterizes heterochromatin?
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What is the structure termed when a series of nucleosomes is observed together?
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What type of DNA is mitochondrial DNA classified as?
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Which of the following is a characteristic of euchromatin?
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What does a base compositional analysis that deviates from Chargaff’s rules indicate?
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Which type of DNA has only a few viruses, such as parvovirus, as examples?
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Which histone molecule is typically NOT found in nature?
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Which structure in an apoptotic cell would be degraded first by endonucleases?
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What factor is most likely to increase the melting temperature of DNA?
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Study Notes
Mitochondrial DNA
- Mitochondrial DNA has a mutation rate 5-10 times higher than nuclear DNA
- Mitochondrial DNA is maternally inherited because the ovum contains hundreds or thousands of mitochondria compared to the sperm
Denaturation/Renaturation of DNA
- Double-stranded DNA can be denatured by conditions that disrupt hydrogen bonding, resulting in the separation of the double strand into two single strands.
- Denaturing conditions include: heat, alkaline pH, chemicals such as formamide and urea
- The covalent 3-5 phosphodiester bonds are not broken during denaturation, so the sugar phosphate backbone is maintained.
- The temperature at which 50% of the DNA molecule exists as single strands is called the melting temperature (Tm).
- The Tm varies according to the base composition of the DNA molecule. Higher Tm values are seen in DNA molecules rich in C-G base pairs.
- Denatured single-stranded DNA can be renatured (annealed) if the denaturing condition is slowly removed.
- The renaturation of complementary DNA strands is an important step in the polymerase chain reaction.
Enzymes
- Nucleases are enzymes that hydrolyze nucleic acids.
- Exonucleases remove nucleotides from the 5′ or the 3′ end of a nucleic acid.
- Endonucleases cut within the nucleic acid and release nucleic acid fragments.
DNA Structure
- The primary structure of DNA refers to the sequence of bases in the nucleic acid chain.
- DNA is formed of polymers of nucleotides (dNTPs): d.AMP, d.GMP, d.TMP, d.CMP
- The nucleotides are covalently linked by 3
,5phosphodiester bonds. - Each DNA strand has two ends: a 5
end with a free phosphate and a 3end with a free (OH). - The base sequence of a nucleic acid strand is written by convention in the 5′→3′ direction.
- The secondary structure of DNA refers to the double-stranded linear structure formed by the annealing of two DNA strands according to base pairing complementarity.
- Base complementarity (Chargaff’s rules) means that A always pairs with T (2 hydrogen bonds), and G always pairs with C (3 hydrogen bonds).
- The two strands are antiparallel (opposite in direction). One strand is 5′→3′, and the other is 3′→5′.
- The Watson and Crick double helix model describes the two DNA strands winding around each other to form a right-handed double helix (B form).
- The hydrophilic sugar-phosphate backbone of each chain is on the outside of the helix, while the hydrophobic bases are stacked inside the helix.
Nucleosome Structure
- The nucleosome is the basic packaging unit of chromatin and results from binding DNA to histones.
- It generates a 10 nm structure.
- It consists of:
- DNA core: 140-150 Base pair (bp) of supercoiled DNA and 8 histones (2 molecules of H2A, H2B, H3, H4).
- Linking region: 20-200 bp of DNA that joins one nucleosome core to the next and one molecule of histone (H1) which protects the linker DNA from digestion by nucleases.
Chromatin Structure
- A series of nucleosomes is sometimes called “beads on a string” or a 10nm chromatin fiber.
- This fiber is then coiled again to form the 30 nm fiber.
- This 30 nm fiber is organized into loops to form a 300 nm fiber.
- Further condensation occurs to eventually form the 700 nm chromatid.
- Finally, the 1400 nm chromosome is formed.
- Each eukaryotic chromosome contains one linear molecule of double-stranded DNA.
Types of Chromatin
- Heterochromatin:
- More compact structure.
- Stains densely.
- Gene poor (AT-rich).
- Transcriptionally less active.
- Genes are silenced by methylation.
- Seen in interphase and mitotic chromosomes.
- Not sensitive to digestion by DNAase (nuclease).
- Euchromatin:
- Less compact structure.
- Stains lightly.
- Transcriptionally more active.
- Gene rich (CG-rich).
- Generally corresponds to the nucleosomes (10-nm fibers) loosely associated with each other or to looped 300-nm fibers.
- Sensitive to digestion by DNAase (nuclease).
Types of DNA
- Double-stranded linear: Eukaryotic nuclear chromosome.
- Double-stranded circular: Mitochondrial, bacterial chromosome, plasmid, viral, and chloroplast DNA.
- Single-stranded circular DNA: Small viruses.
Mitochondrial DNA
- It's a circular double-stranded DNA of about 16 kb length.
- It codes for a few genes involved in energy production and the electron transport chain.
Chargaff’s Rules
- A base compositional analysis that deviates from Chargaff's rules (%A = %T, %C = %G) is indicative of a single-stranded, not double-stranded nucleic acid molecule.
- All the options listed except the viral genome are examples of circular (A, B, and C) or linear (D) DNA double helices.
- Parvovirus is an example of a virus with single-stranded DNA.
Histones
- There are five types of histone molecules found in nature.
Mutations in Mitochondrial DNA
- Mutations in mitochondrial DNA can result in:
- Defects in enzymes of the respiratory chain I and IV.
- Maternal pattern of diseases.
- Non-Mendelian inheritance for diseases.
Chromatin Fragmentation During Apoptosis
- Endonuclease activation and chromatin fragmentation are characteristic features of eukaryotic cell death by apoptosis.
- The 10-nm fiber is most likely to be degraded first in an apoptotic cell due to its open structure, making it more susceptible to enzyme attack.
Factors Affecting DNA Melting Temperature
- The melting temperature of DNA is increased by its G and C content.
Nucleosides and Nucleotides
- Nucleosides are formed by covalently linking a base to the number 1 carbon of a sugar by an N-glycosidic bond.
- Nucleotides are formed when one or more phosphate groups are attached to the 5′ carbon of a nucleoside by a phospho-ester bond.
- Nucleoside di- and triphosphates are high-energy compounds, such as ATP and GTP.
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Description
Explore the fascinating world of mitochondrial DNA and its unique mutation rate, as well as the processes of DNA denaturation and renaturation. This quiz covers key concepts such as the maternal inheritance of mitochondrial DNA and the conditions affecting the melting temperature of DNA. Test your knowledge and deepen your understanding!
