Nucleic Acid Structure

Question 1

What are the three core components of a nucleotide?

Answer 1

A phosphate backbone, a pentose sugar, and nitrogenous bases.

Question 2

How does the number of phosphate groups vary in nucleotides?

Answer 2

The number of phosphate groups can range from 1 to 3 phosphates.

Question 3

How does the 2’ carbon of a pentose sugar differentiate between RNA and DNA?

Answer 3

In RNA, the 2’ carbon is attached to a hydroxyl group (-OH), while in DNA, it is attached to a hydrogen (-H).

Question 4

What is the significance of the base attached to the 1’ carbon in a nucleotide?

Answer 4

The chemistry of the nucleotide is largely dependent on the base attached to the 1’ carbon, which is critical from a molecular information perspective.

Question 5

How are pyrimidines and purines different structurally?

Answer 5

Pyrimidines have one ring, while purines have two rings.

Question 6

Which bases are purines and which are pyrimidines?

Answer 6

Purines are Adenine (A) and Guanine (G), while pyrimidines are Cytosine (C), Thymine (T), and Uracil (U).

Question 7

Why is uracil not found in DNA?

Answer 7

Uracil is not found in DNA because of the spontaneous deamination of cytosine, which would convert it to uracil.

Question 8

What are the chemical properties of nitrogenous bases?

Answer 8

Nitrogenous bases are weakly basic, aromatic molecules. Pyrimidines are planar, while purines have a slight pucker due to their two-ring structure.

Question 9

What is the role of the sugar’s pucker in nucleotides?

Answer 9

The pucker of the sugar impacts the orientation of the phosphate group and the base, which influences DNA and RNA structures.

Question 10

What is the difference between 2’-exo and 3’-exo conformations in nucleotide sugars?

Answer 10

2’-exo conformation is favored by deoxyribose (DNA), and 3’-exo conformation is favored by ribose (RNA).

Question 11

What type of bond forms between the nitrogenous base and the pentose sugar?

Answer 11

A 1’ N-glycosidic bond forms between the nitrogenous base and the pentose sugar.

Question 12

How does the N-glycosidic bond influence nucleotide conformation?

Answer 12

Bases usually adopt an anti conformation around the N-glycosidic bond in DNA. Pyrimidines cannot rotate into syn conformation due to steric hindrance, but purines can.

Question 13

How are phosphate groups typically linked in nucleotides?

Answer 13

Phosphate groups are most commonly linked at the 5’ carbon on the pentose sugar, which is central in the formation of nucleotide polymers.

Question 14

What roles do cyclic nucleotide structures like cAMP and cGMP play?

Answer 14

Cyclic nucleotides like cAMP and cGMP play important roles in cell signaling.

Question 15

What type of bond links nucleotides in a nucleic acid polymer, and what is its directionality?

Answer 15

Phosphodiester bonds link nucleotides in a 5’ to 3’ direction, forming the sugar-phosphate backbone.

Question 16

What is the structural difference between the 5’ and 3’ ends of a nucleotide chain?

Answer 16

The 5’ end has a free phosphate group, while the 3’ end has a free hydroxyl group.

Question 17

In DNA, what causes the negatively charged backbone?

Answer 17

The negatively charged backbone is due to the free 3’ OH group at the end of the nucleotide chain and the phosphate groups along the backbone.

Question 18

According to the Watson-Crick model, where are the sugar-phosphate backbone and nitrogenous bases located in the DNA structure?

Answer 18

The polar sugar-phosphate backbone is on the outside, and the nitrogenous bases are on the inside of the DNA helix.

Question 19

What is the significance of the major groove in the DNA helix?

Answer 19

The major groove provides space for proteins, like transcription factors, to interact with the nitrogenous bases of the DNA.

Question 20

How do the strands of DNA align with each other in the double helix?

Answer 20

The strands of DNA are antiparallel, meaning the 5’ end of one strand aligns with the 3’ end of the complementary strand.

Question 21

What are the base-pairing rules according to Chargaff’s rules?

Answer 21

Adenine (A) pairs with Thymine (T) in DNA or Uracil (U) in RNA, and Guanine (G) pairs with Cytosine (C). Purines equal pyrimidines.

Question 22

How many hydrogen bonds are formed between G-C and A-T base pairs in DNA?

Answer 22

G-C pairs form 3 hydrogen bonds, and A-T pairs form 2 hydrogen bonds.

Question 23

What is the role of base stacking in DNA stability?

Answer 23

Base stacking, through delocalized electron sharing in the z-dimension, provides the main stabilization of the double helix.

Question 24

How does the hydrophobic effect contribute to DNA structure?

Answer 24

The hydrophobicity of the nitrogenous bases drives them inward, away from water, promoting the formation of the helical structure.

Question 25

What is Hoogsteen base pairing, and when can it occur?

Answer 25

Hoogsteen base pairing is non-canonical base pairing that occurs when purines rotate around the N-glycosidic bond, presenting a new face for hydrogen bonding, often due to damage or modification.

Question 26

What are the three main structural forms of DNA, and which is the most common in RNA and DNA?

Answer 26

The three forms of DNA are A, B, and Z. A-form is favored in RNA, B-form is most common in DNA, and Z-form is a rare left-handed helix.

Question 27

How does the sugar pucker in the pentose affect DNA and RNA structure?

Answer 27

In DNA, the C2’ endo pucker leads to the B-form structure, while in RNA, the C3’ endo pucker leads to the A-form structure.

Question 28

What impact do metal ions have on DNA structure?

Answer 28

Metal ions stabilize the DNA structure by shielding the negative charges on the phosphate backbone.

Question 29

How does the antiparallel arrangement of DNA strands contribute to the copying mechanism of DNA?

Answer 29

The antiparallel arrangement allows each separated strand to attract complementary nucleotides, enabling accurate replication.

Question 30

What are the 3 main types of RNA, and what is their general function?

Answer 30

The main types of RNA include:

mRNA: codes for peptides and proteins.
rRNA: the most abundant RNA, a catalyst for replication.
tRNA: adaptive molecule for protein transfer, involved in regulatory processes.

Question 31

What structural features characterize mRNA?

Answer 31

mRNA is single-stranded, forms a right-handed helix, and is stabilized by base-stacking due to the hydrophobic effect. It can base pair with complementary DNA or RNA regions and interacts with RNA-protein complexes to prevent unwanted base interactions.

Question 32

What drives the secondary structure formation in RNA, and what are some examples?

Answer 32

RNA secondary structure is driven by intramolecular complementarity, forming right-handed A-form helices. Examples include hairpins, bulges, and internal loops.

Question 33

What causes bulges and internal loops in RNA secondary structure?

Answer 33

Bulges and internal loops occur due to mismatched or unmatched bases which will repel each other, where complementary base pairing fails, leading to structural disruptions

Question 34

What are the 3 hierarchical levels of RNA structure?

Answer 34

RNA structure is organized into three levels:

Primary structure: the linear sequence of nucleotides.
Secondary structure: the 2D arrangement, including loops and bulges.
Tertiary structure: the 3D fold (e.g., ribozymes), influencing RNA’s functional shape.

Question 35

What are the three key features of tRNA structure?

Answer 35

tRNA has a canonical 3D fold, allowing it to:

Be charged with an amino acid at the 3’ end.
Interact with ribosomes during peptide synthesis.
Line up its anticodon loop with mRNA for translation.

Question 36

How does tRNA’s cloverleaf secondary structure relate to its 3D conformation?

Answer 36

The cloverleaf secondary structure folds into a hockey-stick 3D conformation, crucial for its interaction with ribosomes and mRNA.

Question 37

How do base modifications affect RNA structure and function?

Answer 37

Base modifications, such as 5-methylcytidine, inosine, and pseudouridine, alter hydrogen bonding and structure. They can impact H-bond potential, codon recognition, and RNA folding.

Question 38

What is the role of 5-methylcytidine in gene regulation?

Answer 38

5-Methylcytidine involves the methylation of cytosine, marking DNA or RNA for protein recognition, but it does not alter the base’s attraction properties.

Question 39

Why is inosine important in tRNA, and how does it function in codon recognition?

Answer 39

Inosine, a modified form of guanine, allows flexibility in codon recognition by interacting with multiple bases, enhancing the versatility of tRNA during translation.

Question 40

What is pseudouridine, and how does it impact RNA structure?

Answer 40

Pseudouridine is a modified uracil with an altered N-glycosidic linkage, which affects RNA folding by changing hydrogen bonding interactions, thus influencing the 3D structure.

Question 41

How does tRNA achieve its 3D hockey-stick conformation?

Answer 41

tRNA’s 3D conformation is achieved through atypical hydrogen bonding with the 2’OH group, Hoogsteen interactions, Watson-Crick base pairing, and base modifications, such as methylation.

Question 42

What are the key structural features of nucleotide bases?

Answer 42

Nucleotide bases are weakly basic, aromatic molecules. Pyrimidines are planar, while purines have a slight pucker due to partial double-bond character in their rings.

Question 43

How does the solubility of nucleosides and nucleotides differ?

Answer 43

Nucleosides are hydrophobic and relatively insoluble in water at pH 7.0, while nucleotides (which include a phosphate group) are more soluble in water. The sugar-phosphate backbone enhances solubility.

Question 44

What role does the sugar-phosphate backbone play in the structure and solubility of nucleic acids?

Answer 44

The sugar-phosphate backbone provides stability to nucleic acids by giving them polarity and increasing their solubility in water.

Question 45

How do nucleotide bases absorb UV light, and how is this property used in laboratory techniques?

Answer 45

Nucleotide bases absorb UV light, especially around 260 nm. The absorption spectra are influenced by the base’s structure. This property is used to monitor nucleic acids, for example, in spectrophotometry and detecting DNA denaturation.

Question 46

What is the hypochromic effect?

Answer 46

The hypochromic effect refers to the decrease in UV light absorption when complementary strands of nucleic acids pair, due to the stacking interactions in the double-stranded form.

Question 47

What is the hyperchromic effect?

Answer 47

The hyperchromic effect is the increase in UV light absorption observed when double-stranded nucleic acids are denatured, as the single-stranded form absorbs more light.

Question 48

What factors affect the melting temperature (Tm) of DNA?

Answer 48

The Tm, or melting temperature, of DNA increases with the G≡C content due to stronger base stacking and more hydrogen bonds between G and C compared to A and T.

Question 49

What structural features are seen in partially denatured DNA, and where do these regions typically occur?

Answer 49

Partially denatured DNA forms “bubbles” where double-stranded regions come apart. These regions are often rich in A=T base pairs and can serve as origins for DNA replication.

Question 50

How do RNA duplexes compare to DNA duplexes in terms of stability to heat denaturation?

Answer 50

RNA duplexes are more stable to heat denaturation than DNA duplexes due to stronger base stacking interactions in the A-form RNA structure. RNA-DNA hybrids have intermediate stability.

Question 51

What conditions can cause the denaturation of double-helical DNA or RNA?

Answer 51

Denaturation of double-helical DNA or RNA can be caused by extreme pH or high temperatures, which disrupt hydrogen bonds and base-stacking interactions.

Question 52

What is the process of annealing in nucleic acids?

Answer 52

Annealing is the process by which two complementary strands of nucleic acids spontaneously rebind when the temperature or pH is returned to normal after denaturation.

Question 53

What is the polymerase chain reaction (PCR), and how does it amplify DNA?

Answer 53

PCR is a method for amplifying DNA segments. It relies on DNA polymerases to synthesize DNA from a template. Through cycles of heating and cooling, the DNA denatures and re-anneals, allowing exponential replication of a segment of interest.