Nucleic acids Review

Flashcards covering DNA structure, replication, RNA differences, RNA types, and key molecular details from the lecture notes.

Who identified the DNA double helix and who modeled its structure?

Rosalind Franklin identified the structure; James Watson and Francis Crick modeled it.

What two characteristics describe the DNA double helix strands?

They are complementary and antiparallel.

How many kinds of nucleotides compose DNA?

Four kinds.

What type of bonds join nucleotides within a DNA strand?

Covalent phosphodiester bonds.

How many polynucleotide chains come together to form the DNA double helix?

Two chains.

Despite its simple structure, what is DNA described as?

A complex informational molecule.

What are the three components of a DNA nucleotide?

A sugar (deoxyribose), a nitrogenous base, and up to three phosphate groups.

What sugar is present in DNA nucleotides?

Deoxyribose.

To which carbon of deoxyribose is the base attached?

The 1' carbon.

Which carbon of deoxyribose bears the 3'-OH group?

3' carbon.

Where are the phosphate groups attached on the deoxyribose?

5' carbon.

Name the two types of DNA bases and their ring structures.

Pyrimidines (thymine and cytosine) have a single ring; Purines (adenine and guanine) have two rings.

What are dNMPs?

Deoxynucleotide monophosphates; single phosphates within a polynucleotide chain; N refers to any of the four bases.

Are deoxynucleotide triphosphates (dNTPs) part of a polynucleotide chain?

No.

Give examples of deoxynucleotide monophosphates: dAMP, dGMP, dTMP, dCMP.

5'-monophosphates of adenine, guanine, thymine, and cytosine in DNA.

Which enzyme catalyzes the formation of phosphodiester bonds during DNA synthesis?

DNA polymerase (primarily DNA polymerase III).

During DNA chain elongation, which groups form the phosphodiester bond?

The 3' hydroxyl group of the growing nucleotide and the 5' phosphate of the adjacent nucleotide.

What is released when a phosphodiester bond forms during nucleotide addition, and what happens to it?

Pyrophosphate (PPi) is released and subsequently hydrolyzed.

What forms the backbone of a polynucleotide chain?

Sugar-phosphate backbone (alternating sugar and phosphate).

What are the ends of a nucleic acid strand called?

5' end and 3' end.

What are the complementary base-pairings in DNA?

A pairs with T; G pairs with C.

Are the two DNA strands antiparallel?

Yes; they run in opposite 5' to 3' directions.

What is the diameter of B-form DNA?

About 20 Å.

What two forms of DNA did Franklin reveal?

A-form and B-form.

Which DNA form is more common?

B-form.

What is the base-pair spacing along the DNA duplex in B-form?

3.4 Å per base pair.

What effect does base stacking have on the DNA helix?

It leads to base planes being parallel and twists the helix.

What are the approximate widths of the major and minor grooves in B-form DNA?

Major ~12 Å; Minor ~6 Å.

Why are DNA grooves important?

They are regions where DNA-binding proteins can contact nucleotides.

How many forms of DNA exist?

Three forms: B-form (most common), A-form, Z-form.

What is distinctive about Z-form DNA?

Left-handed twist and a zigzag sugar-phosphate backbone.

What is a common RNA secondary structure motif?

Stem-loop (hairpin) structure.

What is the sugar in RNA?

Ribose.

What nitrogenous base replaces thymine in RNA?

Uracil.

Is RNA typically single-stranded or double-stranded?

Single-stranded.

What is the difference at the 2' carbon between DNA and RNA sugars?

DNA has a hydrogen at the 2' position; RNA has a hydroxyl group (2'-OH).

What are the RNA bases?

Cytosine, Uracil, Guanine, Adenine.

What are the DNA bases?

Cytosine, Thymine, Guanine, Adenine.

Which bases are common to both DNA and RNA?

C, G, A.

What are the main categories of RNA and their roles?

mRNA (coding and translation), rRNA (ribosome structure), tRNA (amino acid delivery), plus regulatory and other RNAs (miRNA, siRNA, snRNA, telomerase RNA).

What is the role of mRNA?

Transcribed from DNA and translated into protein; short-lived intermediary.

What is the role of rRNA?

Forms ribosomes together with proteins for protein synthesis.

What is the role of tRNA?

Binds amino acids and delivers them to the ribosome for incorporation into protein.

What do miRNA and siRNA do?

Involved in posttranscriptional regulation of mRNA.

What is telomerase RNA?

Provides a template for the synthesis of telomere repeats.

What is snRNA's role?

In the nucleus, participates in mRNA processing.

Do functional RNAs have complex secondary and tertiary structures?

Yes, with non-Watson-Crick base interactions and multi-base interactions.

What is a key structural characteristic of RNA that enables its diverse functions beyond coding?

Folding into complex secondary and tertiary structures with non-Watson-Crick interactions.