Lecture 10 - Nucleic Acids

What are nucleic acids made of?

Polymers of Nucleotides.

What is the function of DNA?

Storage of genetic information.

What is the function of mRNA?

Transmission of genetic information.

What is the function of ribozymes?

Processing of genetic information.

What are tRNA and rRNA used for?

Protein Synthesis.

Name three cellular functions of nucleotides in monomer form.

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

What are the three components of a nucleotide?

Nitrogenous base, pentose sugar, and phosphate group.

What are the two components of a nucleoside?

Nitrogenous base and pentose sugar.

How are carbon and nitrogen atoms numbered in the nitrogenous base?

In cyclic format.

How are the carbons of the pentose numbered?

With a prime (′) to distinguish them from base carbons.

What is the charge of the phosphate (PO₄) group at neutral pH?

Negatively charged.

To which carbon is the phosphate usually attached?

The 5′ position of the pentose.

What form of nucleotides are used to build nucleic acids?

5′-triphosphate versions (e.g., ATP, GTP, TTP, CTP).

How many phosphate groups remain per nucleotide in a completed nucleic acid?

One phosphate group.

Can phosphate be attached to positions other than 5′?

Yes, for specialized functions.

What pentose form is found in RNA?

β-D-ribofuranose.

What pentose form is found in DNA?

β-2′-deoxy-D-ribofuranose.

What are nitrogenous bases derived from?

Pyrimidine or purine.

What kind of molecules are nitrogenous bases?

Nitrogen-containing heteroaromatic molecules.

What is the shape of nitrogenous bases?

Planar or almost planar.

What wavelength do nitrogenous bases absorb UV light at?

Around 250–270 nm.

Which bases are found in both DNA and RNA?

Cytosine, adenine, and guanine.

Which base is found only in DNA?

Thymine.

Which base is found only in RNA?

Uracil.

Are the nitrogenous bases good hydrogen bond donors and acceptors?

Yes.

What is the charge of nitrogenous bases at pH 7?

Neutral.

What wavelength is commonly used for UV absorption measurements of nucleotides?

260 nm

What does the molar extinction coefficient (ε) represent in UV absorption of nucleobases?

It represents how strongly a substance absorbs light at a given wavelength, measured in M⁻¹cm⁻¹.

Which nucleotide has the highest molar extinction coefficient at 260 nm?

AMP (Adenosine monophosphate) with ε = 15,400 M⁻¹cm⁻¹.

Rank the nucleotides by their molar extinction coefficient at 260 nm (highest to lowest).

AMP (15,400) > GMP (11,700) > UMP (9,900) > dTMP (9,200) > CMP (7,500).

Why is 260 nm chosen for nucleotide absorption measurements?

Because nucleobases strongly absorb UV light around 260 nm, making it ideal for quantifying nucleic acids.

Which nucleotide absorbs the least at 260 nm?

CMP (Cytidine monophosphate) with ε = 7,500 M⁻¹cm⁻¹.

What is the difference between a nucleoside and a nucleotide?

A nucleoside consists of a base + sugar, while a nucleotide consists of a base + sugar + phosphate group.

What are the two main classes of nitrogenous bases in nucleic acids?

Purines and Pyrimidines.

Which bases are purines?

Adenine and Guanine.

Which bases are pyrimidines?

Cytosine, Thymine, and Uracil.

What nucleic acid contains thymine?

DNA.

What nucleic acid contains uracil?

RNA.

What is the nucleoside name for adenine?

Adenosine (or deoxyadenosine in DNA).

What is the nucleotide name for adenine?

Adenylate (or deoxyadenylate in DNA).

What is the nucleoside name for guanine?

Guanosine (or deoxyguanosine in DNA).

What is the nucleotide name for guanine?

Guanylate (or deoxyguanylate in DNA).

What is the nucleoside name for cytosine?

Cytidine (or deoxycytidine in DNA).

What is the nucleotide name for cytosine?

Cytidylate (or deoxycytidylate in DNA).

What is the nucleoside name for thymine?

Thymidine or deoxythymidine.

What is the nucleotide name for thymine?

Thymidylate or deoxythymidylate.

What is the nucleoside name for uracil?

Uridine.

What is the nucleotide name for uracil?

Uridylate.

What is the abbreviation for adenosine monophosphate?

AMP.

What is the abbreviation for guanosine monophosphate?

GMP.

What is the abbreviation for uridine monophosphate?

UMP.

What is the abbreviation for cytidine monophosphate?

CMP.

What is the abbreviation for deoxyadenosine monophosphate?

dAMP.

What is the abbreviation for deoxyguanosine monophosphate?

dGMP.

What is the abbreviation for deoxythymidine monophosphate?

dTMP.

What is the abbreviation for deoxycytidine monophosphate?

dCMP.

What structural difference distinguishes ribonucleotides from deoxyribonucleotides?

Ribonucleotides OH group at the 2′ carbon of the pentose sugar and deoxyribonucleotides have an H (no OH) at the 2′ carbon

At what pH are nucleotides shown in their free form?

pH 7.0.

Which nucleotide is unique to RNA and not found in DNA?

Uridylate (Uridine).

Which nucleotide is unique to DNA and not found in RNA?

Thymidylate (Thymidine).

What type of bond attaches the pentose ring to the nitrogenous base in nucleotides?

An N-glycosidic bond.

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

Position N1.

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

Position N9.

How stable is the N-glycosidic bond toward hydrolysis?

It is quite stable, especially in pyrimidines.

What is the configuration of the N-glycosidic bond in nucleotides?

β-configuration.

What type of rotation can occur around the N-glycosidic bond in free nucleotides?

Relatively free rotation.

What does an angle near 0° correspond to in N-glycosidic bond conformation?

Syn conformation.

What does an angle near 180° correspond to in N-glycosidic bond conformation?

Anti conformation (1)

Which conformation is found in normal B-DNA?

Anti conformation (2)

Give an example of a nucleotide in syn conformation.

Syn-Adenosine.

Give an example of a nucleotide in anti conformation.

Anti-Adenosine or Anti-Cytidine.

How many bonds affect the conformation of a nucleotide in DNA?

Seven different bonds.

Which bond limits the angle of torsion for the N-glycosidic bond?

Ring pucker (bond 4).

What is the sugar pucker in A-DNA?

C3′-endo.

What is the sugar pucker in B-DNA?

C2′-endo.

What is the approximate distance between phosphates in A-DNA?

5.9 Å.

What is the approximate distance between phosphates in B-DNA?

7.0 Å.

Which conformation (A or B) has a more compact structure?

A-DNA (C3′-endo).

The difference between a ribonucleotide and a deoxyribonucleotide is:

a deoxyribonucleotide has an —H instead of an —OH at C-2.

The chemical difference between a nucleotide and a nucleoside is that:

nucleosides do not contain phosphate groups.

When are minor nucleoside modifications in DNA introduced?

After DNA synthesis.

Which minor nucleoside is common in eukaryotes and bacteria?

5-Methylcytosine.

Which minor nucleoside is found only in bacteria?

N6-Methyladenosine.

What is an epigenetic marker?

A chemical modification that marks DNA for specific purposes, such as:

• Marking own DNA so cells can degrade foreign DNA.

• Marking which genes should be transcribed.

Where is inosine commonly found in RNA?

In the wobble position of the anticodon in tRNA.

How is inosine formed?

By de-aminating adenosine.

What is the function of inosine in tRNA?

Provides a richer genetic code by allowing flexible base pairing.

Where is pseudouridine (Ψ) found?

Widely in tRNA and rRNA, more common in eukaryotes.

How is pseudouridine formed?

From uridine by enzymatic isomerization after RNA synthesis.

What roles does pseudouridine play?

• May stabilize tRNA structure.

• May help in folding of rRNA.

What type of covalent bond links nucleotides in DNA and RNA?

Phosphodiester linkage.

Which carbons are involved in a phosphodiester bond?

The 3′ carbon of one sugar and the 5′ carbon of another.

What type of interaction forms base pairs in DNA?

Hydrogen bonding.

Which base pairs are found in Watson-Crick DNA?

• A pairs with T.

• C pairs with G.

Why do purines pair with pyrimidines?

To maintain uniform width of the DNA double helix.

What do Chargaff’s rules state?

DNA from any cell has a 1:1 ratio of purines to pyrimidines:

• Amount of A = T.

• Amount of G = C.

Who first isolated “nuclein” from cell nuclei?

Friedrich Miescher (1868–1935).

What components were identified after hydrolysis of nuclein?

Phosphate, pentose, and nitrogenous base.

What did chemical analysis of nuclein reveal?

• Phosphodiester linkages.

• Pentose is ribofuranoside.

What did Rosalind Franklin and Maurice Wilkins discover from X-ray diffraction?

• “Cross” pattern indicates helix.

• “Diamonds” indicate phosphate-sugar backbone outside.

• Calculated helical parameters.