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50 Essential Questions on the Structure & Functions of DNA & RNA – Strengthen Your Molecular Biology Foundations
Conceptual Foundations Before Higher-Order Thinking!
Dear Students,
Before we dive into higher-order, case-based questions, let’s take a step back and solidify our fundamental understanding of key molecular biology concepts. Mastering the structure and functions of DNA & RNA, DNA packaging, and chromosome structure is crucial for tackling complex applications in genetics and medicine. This post contains 50 essential questions that will help you conceptualize the core principles before advancing to more challenging problem-solving scenarios. Take your time to reflect, revise, and strengthen your grasp of these foundational topics.
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1. What are the three components of a nucleotide?
A nucleotide is made up of a sugar (deoxyribose or ribose), a phosphate group, and one of four nitrogenous bases.
2. Name the four nitrogenous bases found in DNA.
The four nitrogenous bases in DNA are adenine (A), thymine (T), guanine (G), and cytosine (C).
3. What is the primary structural difference between DNA and RNA?
DNA is double-stranded, while RNA is mainly single-stranded. Also, DNA contains deoxyribose, while RNA contains ribose.
4. Describe Chargaff’s rules.
Chargaff’s rules state that in DNA, the number of guanine units equals the number of cytosine units, and the number of adenine units equals the number of thymine units. Also, the relative amounts of these bases vary from one species to another. These rules suggested that DNA has a specific base pairing, which helped Watson and Crick determine the double helix structure.
5. Why is DNA more stable than RNA?
DNA is more stable than RNA because it lacks a 2′-OH group, which makes it resistant to alkali action and spontaneous degradation.
6. What is the role of tRNA?
tRNA transfers amino acids from the cytoplasm to the protein-synthesizing machinery.
7. What is the function of microRNAs (miRNAs)?
MicroRNAs (miRNAs) cause inhibition of gene expression by decreasing specific protein production.
8. What type of bonds hold the DNA strands together?
Hydrogen bonds between complementary base pairs
9. What is the role of mRNA?
mRNA carries genetic information from DNA to the ribosomes for protein synthesis.
10. What is the role of tRNA?
tRNA transfers amino acids from the cytoplasm to the protein-synthesizing machinery.
11. How do the nucleotides differ between DNA and RNA?
A nucleotide consists of a sugar (deoxyribose in DNA, ribose in RNA), a phosphate group, and a nitrogenous base. DNA uses adenine (A), guanine (G), cytosine (C), and thymine (T), while RNA uses A, G, C, and uracil (U). These components form the building blocks of nucleic acids.
12. Describe the primary and secondary structure of DNA.
The primary structure of DNA is the linear sequence of nucleotides linked by phosphodiester bonds. The secondary structure is the double helix, where two antiparallel strands are held together by hydrogen bonds between complementary base pairs (A with T, and G with C).
13. What are the key differences between A-DNA, B-DNA, and Z-DNA?
B-DNA is the most common physiological form, a right-handed helix with 10.4 base pairs per turn. A-DNA is a right-handed helix with 11 base pairs per turn and is wider and shorter than B-DNA, while Z-DNA is a left-handed helix with 12 base pairs per turn and a zigzag backbone.
14. How is DNA organized and packaged within eukaryotic cells, starting with the double helix and ending with chromosomes?
DNA is first wound around histone proteins to form nucleosomes. Nucleosomes are arranged into a 10-nm fibril, which is further supercoiled into a 30-nm chromatin fiber. This fiber is organized into loops anchored to a scaffolding, ultimately forming chromosomes during metaphase.
15. What are the four major types of RNA, and what are their primary functions?
The four major types of RNA are messenger RNA (mRNA), which carries genetic information from DNA to the ribosomes; transfer RNA (tRNA), which transfers amino acids to the ribosomes for protein synthesis; ribosomal RNA (rRNA), which forms part of the ribosome structure; and small nuclear RNAs (snRNAs; miRNAs, siRNAs) which help process mRNA.
16. Describe the structure and function of tRNA, including the acceptor arm, anticodon arm, DHU arm, and TΨC arm.
tRNA has a cloverleaf secondary structure and an L-shaped tertiary structure. The acceptor arm contains the CCA sequence where amino acids attach. The anticodon arm recognizes and binds to the mRNA codon. The DHU arm serves as the recognition site for the enzyme, and the TΨC arm is involved in binding tRNA to the ribosomes.
17. What are miRNAs and siRNAs, and how do they regulate gene expression?
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are small RNA molecules involved in gene regulation. They inhibit gene expression by decreasing specific protein production through distinct mechanisms, often by binding to mRNA and blocking translation or causing degradation.
18. How does the absence of a 2′-OH group in DNA contribute to its stability compared to RNA?
The absence of a 2′-OH group in deoxyribose makes DNA more resistant to hydrolytic cleavage compared to RNA, which has a 2′-OH group that can attack the neighboring phosphate diester. This difference makes DNA a more stable molecule for long-term storage of genetic information.
19. What is the significance of major and minor grooves in DNA’s structure?
Major and minor grooves are indentations in the DNA double helix. Proteins can interact specifically with exposed atoms of the nucleotides in these grooves via specific hydrophobic and ionic interactions, which allows proteins to bind to DNA and regulate gene expression without disrupting the base pairing of the double-helical DNA molecule.
20. Explain the concept of complementary base pairing in DNA replication.
Each DNA strand serves as a template for the synthesis of a new strand. Adenine (A) pairs with Thymine (T), and Cytosine (C) pairs with Guanine (G), ensuring accurate copying of genetic information.
21. Why is RNA generally single-stranded, while DNA is double-stranded?
RNA’s structure allows it to be more flexible for various functions like protein synthesis (mRNA), catalysis (rRNA), and amino acid transport (tRNA). DNA’s double-stranded nature provides stability for long-term genetic storage.
22. What is the significance of hydrogen bonding in the structure of DNA?
Hydrogen bonds between complementary bases stabilize the DNA double helix and allow for easy separation during replication and transcription.
23. What is the role of the sugar-phosphate backbone in nucleic acids?
The sugar-phosphate backbone provides structural integrity to DNA and RNA molecules, protecting the genetic code and linking nucleotides via phosphodiester bonds.
24. Differentiate between purines and pyrimidines with examples.
Purines (larger, two-ring structures): Adenine (A) and Guanine (G).
Pyrimidines (smaller, single-ring structures): Cytosine (C), Thymine (T) (in DNA), and Uracil (U) (in RNA).
25. What is the importance of the 5′ and 3′ ends in DNA and RNA molecules?
DNA and RNA have directionality: the 5′ end has a phosphate group, and the 3′ end has a hydroxyl (-OH) group. This polarity is crucial for replication and transcription, as enzymes like DNA and RNA polymerases synthesize new strands in the 5′ to 3′ direction.
26. How does the presence of uracil in RNA instead of thymine in DNA impact its function?
Uracil (U) is structurally simpler than thymine (T) and allows RNA to be more transient and flexible for its role in protein synthesis. Thymine (T) in DNA increases stability for long-term genetic storage.
27. What is the significance of the antiparallel arrangement of DNA strands?
The two strands of DNA run in opposite directions (5′ to 3′ and 3′ to 5′), which is essential for proper base pairing, replication, and enzymatic function during processes like transcription and DNA replication.
28. What type of bond connects nucleotides in a single strand of DNA or RNA?
Phosphodiester bonds connect nucleotides in a single strand of DNA or RNA by linking the 3′ hydroxyl group of one sugar to the 5′ phosphate group of the next sugar.
29. Why is DNA considered a more stable molecule than RNA?
DNA is more stable because it lacks the 2′ hydroxyl (-OH) group found in RNA, making it less susceptible to hydrolysis. Additionally, its double-stranded structure provides extra stability and protection from degradation.
30. How does DNA compact itself to fit inside a cell nucleus?
DNA wraps around histone proteins to form nucleosomes, which further coil into chromatin fibers and condense into chromosomes during cell division.
31. How do histone acetylation and deacetylation affect gene expression?
Histone acetylation adds acetyl groups to histone proteins, reducing their positive charge and loosening DNA-histone interactions. This makes DNA more accessible to transcription factors, promoting gene expression. Histone deacetylation removes acetyl groups, leading to tighter DNA packing and gene repression.
32. What is the role of histone methylation in gene regulation?
Histone methylation can either activate or repress gene expression, depending on which lysine (K) or arginine (R) residues are modified and the number of methyl groups added. For example, H3K4 methylation is associated with active transcription, while H3K9 and H3K27 methylation are linked to gene repression.
33. What is DNA denaturation, and what causes it?
DNA denaturation is the process in which the double-stranded DNA unwinds and separates into single strands due to the breaking of hydrogen bonds between base pairs. It can be caused by heat, extreme pH, or chemical agents such as urea or formamide.
34. How does the GC content of DNA affect its denaturation temperature (Tm)?
DNA with a higher GC content has a higher melting temperature (Tm) because guanine (G) and cytosine (C) form three hydrogen bonds, compared to adenine (A) and thymine (T), which form only two hydrogen bonds. More hydrogen bonds require more energy (heat) to break, making GC-rich DNA more thermally stable.
35. What are base stacking interactions, and why are they important in DNA stability?
Base stacking interactions are non-covalent hydrophobic interactions between adjacent nitrogenous bases in the DNA double helix. They stabilize the DNA structure by minimizing exposure of the hydrophobic bases to water and contributing to the overall helical conformation.
36. How do base stacking interactions differ between GC and AT base pairs?
GC base pairs exhibit stronger base stacking interactions than AT base pairs due to their planar structure and increased π-electron overlap. This contributes to the greater stability of GC-rich DNA regions, in addition to the extra hydrogen bond in GC pairs.
37. What is the primary function of small nuclear RNA (snRNA) in the cell?
snRNA plays a crucial role in RNA splicing, where it helps form the spliceosome, a complex that removes introns from pre-mRNA and joins exons together to produce mature mRNA.
38. Which snRNA molecules are involved in the spliceosome, and how do they function?
The major spliceosome contains U1, U2, U4, U5, and U6 snRNAs, which recognize splice sites, catalyze the excision of introns, and facilitate exon ligation. These snRNAs work in coordination with proteins to ensure precise mRNA processing.
39. What is the function of the anticodon arm of tRNA?
The anticodon arm contains the anticodon sequence, which base-pairs with the complementary codon on mRNA during translation, ensuring the correct amino acid is incorporated into the growing polypeptide chain.
40. What is the role of the aminoacyl (acceptor) arm of tRNA?
The aminoacyl (acceptor) arm carries the 3′-CCA sequence, where a specific amino acid is attached by aminoacyl-tRNA synthetase. This enables the tRNA to deliver the correct amino acid to the ribosome during protein synthesis.
41. What is the function of the 5′ cap in eukaryotic mRNA?
The 5′ cap (a modified guanine nucleotide) protects mRNA from degradation, aids in ribosome recognition for translation initiation, and facilitates nuclear export of the mRNA.
42. How does the poly(A) tail affect mRNA stability and translation?
The poly(A) tail, a stretch of adenine nucleotides at the 3′ end, enhances mRNA stability by preventing exonuclease degradation and plays a role in efficient translation by facilitating ribosome binding.
43. What is the primary function of rRNA in the ribosome?
rRNA is a structural and catalytic component of the ribosome, providing a scaffold for ribosomal proteins and catalyzing peptide bond formation during protein synthesis (peptidyl transferase activity).
44. How do the large and small ribosomal subunits contribute to translation?
The small subunit (40S in eukaryotes, 30S in prokaryotes) binds mRNA and ensures correct codon-anticodon pairing, while the large subunit (60S in eukaryotes, 50S in prokaryotes) contains peptidyl transferase activity, catalyzing peptide bond formation between amino acids.
45. How do euchromatin and heterochromatin differ in structure and function?
Euchromatin is loosely packed, transcriptionally active chromatin that allows gene expression, while heterochromatin is tightly packed, transcriptionally inactive chromatin that primarily functions in gene silencing and structural support of chromosomes.
46. What are the two types of heterochromatin, and how do they differ?
Constitutive heterochromatin remains permanently condensed and contains repetitive sequences (e.g., centromeres, telomeres), while facultative heterochromatin can switch between condensed and relaxed states depending on cellular needs (e.g., X chromosome inactivation).
47. What are the key structural components of a chromosome?
A chromosome consists of chromatin, which is made up of DNA wrapped around histone proteins. The main structural components include the centromere (which links sister chromatids), telomeres (which protect chromosome ends), and chromatid arms (which contain genetic information).
48. What is the function of the centromere in a chromosome?
The centromere is the region where sister chromatids are held together and serves as the attachment site for kinetochore proteins, which help in chromosome movement during cell division (mitosis and meiosis).
49. How do telomeres contribute to chromosome stability?
Telomeres are repetitive nucleotide sequences at the ends of chromosomes that prevent degradation and fusion with other chromosomes. They protect genetic information during DNA replication and are maintained by the enzyme telomerase in certain cells.
50. What are ribozymes, and how do they contribute to biological processes?
Ribozymes are RNA molecules with enzymatic activity capable of catalyzing specific biochemical reactions, such as RNA splicing, peptide bond formation, and RNA cleavage or ligation. They play essential roles in biological processes, including protein synthesis (as part of the ribosome’s large subunit), RNA processing, viral replication, and transfer RNA biosynthesis. Ribozymes demonstrate that RNA can function both as genetic material and as a biological catalyst.
