Nucleic Acids part 1

What are the three components of a nucleotide?

Nitrogenous base + pentose sugar + phosphate group

What are the two components of a nucleoside?

Nitrogenous base + pentose sugar (no phosphate)

What is a nucleobase?

Just the nitrogenous base alone (no sugar, no phosphate)

What are the three nucleotide functions (non-nucleic acid)?

Energy for metabolism (ATP), enzyme cofactors (NAD+), and signal transduction (cAMP)

What are the four nucleic acid functions?

Storage of genetic info (DNA), transmission of genetic info (mRNA), processing of genetic info (ribozymes), and protein synthesis (tRNA and rRNA)

What does mRNA do?

Transmits genetic information from DNA to the ribosome for protein synthesis

What does tRNA do?

Brings amino acids to the ribosome during translation (protein synthesis)

What does rRNA do?

Structural and catalytic component of the ribosome; facilitates protein synthesis

What is a ribozyme?

An RNA molecule that functions as an enzyme; involved in processing genetic information

What are the two types of pentose sugars in nucleotides?

Ribose (in RNA) and deoxyribose (in DNA); deoxyribose lacks the 2'-OH group

What is the charge of the phosphate group at neutral pH?

Negatively charged — this makes the nucleic acid backbone anionic

Where is the phosphate group typically attached on a nucleotide?

The 5' carbon of the pentose sugar

What triphosphate precursors are used to build nucleic acids?

ATP, GTP, TTP (dTTP), and CTP — all 5'-triphosphates

How many phosphate groups are in a finished nucleic acid chain per nucleotide residue?

One phosphate moiety per nucleotide (the other two are released as pyrophosphate during polymerization)

What are the two parent ring structures of the nucleobases?

Pyrimidine (6-membered ring) and purine (fused 6+5-membered bicyclic ring)

Which bases are purines?

Adenine (A) and guanine (G)

Which bases are pyrimidines?

Cytosine (C), thymine (T), and uracil (U)

Which pyrimidine base is found only in DNA?

Thymine (T)

Which pyrimidine base is found only in RNA?

Uracil (U)

Which pyrimidine base is found in both DNA and RNA?

Cytosine (C)

Which purine bases are found in both DNA and RNA?

Adenine (A) and guanine (G)

What wavelength of UV light do nucleobases absorb?

Around 250–270 nm (measured at 260 nm by convention)

What is Beer's law and how does it apply to nucleobases?

A = εbc, where A = absorbance, ε = molar extinction coefficient, b = path length, c = concentration. Used to determine nucleic acid concentration by absorbance at 260 nm

What is the molar extinction coefficient (ε₂₆₀) of AMP?

15,400 M⁻¹cm⁻¹

What is the molar extinction coefficient (ε₂₆₀) of GMP?

11,700 M⁻¹cm⁻¹

What is the molar extinction coefficient (ε₂₆₀) of CMP?

7,500 M⁻¹cm⁻¹

What is the pKa of cytosine at N3, and what does this mean at pH 7?

pKa = 4.5; cytosine is neutral (unprotonated) at pH 7

What is the pKa of thymine at N3, and what does this mean at pH 7?

pKa = 9.5; thymine is neutral (unprotonated) at pH 7

What is the pKa of adenine at N1, and what does this mean at pH 7?

pKa = 3.8; adenine is neutral at pH 7

What is the pKa of guanine at N7, and what does this mean at pH 7?

pKa = 2.4; guanine is neutral at pH 7

What is the N-glycosidic bond in nucleotides?

The covalent bond connecting the anomeric carbon (C1') of the pentose sugar to the nitrogen of the nucleobase

At which nitrogen is the N-glycosidic bond formed in pyrimidines?

N1 of the pyrimidine ring

At which nitrogen is the N-glycosidic bond formed in purines?

N9 of the purine ring

Which is more stable to hydrolysis: the N-glycosidic bond in pyrimidines or purines?

Pyrimidines are more stable; purines are more susceptible to acid-catalyzed hydrolysis

What catalyzes cleavage of the N-glycosidic bond?

Acid catalysis

What is the syn vs. anti conformation of a nucleoside?

Describes rotation around the N-glycosidic bond (χ angle): syn ≈ 0° (base over the sugar); anti ≈ 180° (base away from sugar)

Which conformation predominates in normal B-DNA?

Anti conformation

Why does syn-cytidine not exist?

In the syn conformation, the C2 carbonyl oxygen of cytosine would clash sterically with the 5' oxygen of the sugar ring, making it energetically unfavorable

What is the two-letter symbol and four-letter code for deoxyadenosine nucleotide?

dA (two-letter) and dAMP (four-letter)

What is the two-letter symbol and four-letter code for deoxyguanosine nucleotide?

dG and dGMP

What is the two-letter symbol and four-letter code for deoxythymidine nucleotide?

dT and dTMP

What is the two-letter symbol and four-letter code for deoxycytidine nucleotide?

dC and dCMP

What are the one-letter and three-letter codes for adenosine ribonucleotide?

A and AMP

What are the one-letter and three-letter codes for guanosine ribonucleotide?

G and GMP

What are the one-letter and three-letter codes for uridine ribonucleotide?

U and UMP

What are the one-letter and three-letter codes for cytidine ribonucleotide?

C and CMP

What are minor nucleosides in DNA and when are they added?

Modified bases (e.g., 5-methylcytosine, N⁶-methyladenosine) added after DNA synthesis as epigenetic marks

What is the function of 5-methylcytosine in eukaryotes?

Acts as an epigenetic marker to regulate gene expression (mark which genes should be active)

What is the function of N⁶-methyladenosine in prokaryotes?

Marks the cell's own DNA so restriction enzymes degrade foreign (unmethylated) DNA

What type of bond links nucleotides in a polynucleotide chain?

3',5'-Phosphodiester bond — connects the 3'-OH of one nucleotide to the 5'-phosphate of the next

Why is DNA more stable than RNA?

DNA lacks the 2'-OH group, which in RNA can attack the phosphodiester bond and catalyze its own hydrolysis under alkaline conditions

What is the directionality of polynucleotide sequences?

Sequences are read and written 5' to 3'; the 5' end has a free phosphate and the 3' end has a free hydroxyl

What is base-catalyzed RNA hydrolysis and why doesn't it apply to DNA?

The 2'-OH of RNA attacks the adjacent phosphate, forming a 2',3'-cyclic intermediate that hydrolyzes to a mix of 2'- and 3'-monophosphate products. DNA has no 2'-OH so this pathway is unavailable

What are the Watson-Crick base pairs and how many hydrogen bonds does each form?

A–T: 2 hydrogen bonds; G–C: 3 hydrogen bonds. A purine always pairs with a pyrimidine

What base replaces thymine in RNA base pairing?

Uracil (U) pairs with adenine (A) via 2 hydrogen bonds, just as thymine does in DNA