1.1: The Structure of DNA

Flashcards covering nucleotide structure, nitrogenous base classification, phosphodiester bonding, Chargaff's rules, major and minor groove recognition, and double helix geometry based on the lecture transcript.

What are the two main types of nucleic acids and what is their primary function?

The two main types are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). They carry the genetic blueprint of a cell and contain instructions for cellular functioning.

How is DNA organized into chromatin within eukaryotic cells?

DNA forms a complex with histone proteins to form chromatin, which is the substance that makes up eukaryotic chromosomes.

What is the primary function of messenger RNA (mRNA)?

Because DNA never leaves the nucleus, mRNA acts as an intermediary to communicate genetic instructions from DNA to the rest of the cell for protein synthesis.

What three basic components make up a nucleotide monomer?

A nitrogenous base, a pentose (five-carbon) sugar, and one or more phosphate groups.

What structural feature distinguishes purines from pyrimidines, and which bases belong to each group?

Purines (adenine and guanine) have a double carbon-nitrogen ring structure. Pyrimidines (cytosine, thymine, and uracil) have a single carbon-nitrogen ring structure.

What chemical difference distinguishes deoxyribose from ribose at the 2′ carbon position?

Deoxyribose has a hydrogen atom ($H$) at the 2′ position instead of a hydroxyl group ($OH$), meaning deoxyribose is missing an $-OH$ group compared to ribose.

To which carbon positions of the pentose sugar are the nitrogenous base and phosphate group attached in a nucleotide?

The nitrogenous base is attached to the 1′ carbon, and the phosphate group is attached to the 5′ carbon.

How is a 5′–3′ phosphodiester linkage formed between adjacent nucleotides?

A phosphate residue connects the hydroxyl group on the 5′ carbon of one sugar to the hydroxyl group on the 3′ carbon of the next sugar, involving the removal of two phosphate groups.

According to Chargaff's rules, if a bacterial DNA sample contains $15.5\%$ adenine, what is the expected percentage of guanine?

The expected percentage of guanine is $34.5\%$. Because adenine pairs with thymine, $T = 15.5\%$ and $A + T = 31\%$. The remaining $G + C = 100\% - 31\% = 69\%$, meaning $G = 34.5\%$.

What directional orientation do the two strands of a DNA double helix maintain relative to each other?

The two strands run anti-parallel (in opposite directions), with the 5′ end of one strand adjacent to the 3′ end of the complementary strand.

Using the rules of base pairing, what is the sequence of the complementary strand for the DNA sequence AATTGGCC?

The complementary sequence is TTAACCGG.

Why can DNA sequence-recognizing proteins distinguish all base pairs in the major groove, but NOT in the minor groove?

In the major groove, each base pair displays a unique pattern of exposed hydrogen bond donors, acceptors, hydrogens, and methyl groups. In the minor groove, AT and TA appear identical, and GC and CG appear identical.

If a mutation replaces a cytosine base with an adenine, what impact will this have on the DNA double helix structure?

Adenine is a larger two-ring purine than single-ring cytosine and cannot base-pair properly with guanine, causing the DNA double helix to bulge at that location.

What functional problem would occur if the two strands of DNA were held together by covalent bonds instead of hydrogen bonds?

Covalent bonds are much stronger than hydrogen bonds and are difficult to break. This would prevent the double helix from unwinding easily during essential processes like DNA replication and transcription.