Lecture 10, 11, 12 Structure, Replication, Transcription

What is the monomer of DNA?

A nucleotide, composed of a phosphate group, deoxyribose sugar, and a nitrogenous base.

What are the four nitrogenous bases in DNA?

Adenine (A), Thymine (T), Cytosine (C), Guanine (G).

Which bases are purines and which are pyrimidines?

Purines: A and G (2 rings); Pyrimidines: C and T (1 ring).

How are DNA strands arranged?

DNA is a double helix with antiparallel strands (one 5'→3', the other 3'→5').

What type of bond holds the two DNA strands together?

Hydrogen bonds between complementary bases.

What are the base pairing rules?

A pairs with T (2 hydrogen bonds); G pairs with C (3 hydrogen bonds).

What type of bond forms between the sugar and phosphate in the DNA backbone?

Phosphodiester bonds.

What does it mean that DNA is antiparallel?

One strand runs 5′→3′ while the complementary strand runs 3′→5′.

What is the diameter of the DNA double helix?

About 2 nanometers (nm).

What direction is DNA synthesized in?

Always in the 5′ to 3′ direction.

What does it mean that DNA replication is semiconservative?

Each new DNA molecule contains one old (template) strand and one newly synthesized strand.

Where does DNA replication begin?

At the origin of replication.

What is the function of helicase?

Unwinds the DNA double helix at the replication fork.

What does single-stranded binding protein (SSBP) do?

Stabilizes and holds the separated DNA strands apart.

What does topoisomerase do?

Relieves supercoiling ahead of the replication fork.

What does primase do?

Synthesizes a short RNA primer to initiate DNA synthesis.

What is the function of DNA polymerase III?

Synthesizes new DNA strands by adding nucleotides to the RNA primer (5′→3′).

What is the leading strand?

The DNA strand that is synthesized continuously in the 5′→3′ direction toward the replication fork.

What is the lagging strand?

The DNA strand synthesized in short fragments (Okazaki fragments) away from the replication fork.

What is the function of DNA polymerase I?

Removes RNA primers and replaces them with DNA nucleotides.

What is the function of DNA ligase?

Joins Okazaki fragments by sealing nicks between fragments.

What are Okazaki fragments?

Short fragments of DNA synthesized on the lagging strand.

What energy source drives DNA synthesis?

The hydrolysis of high-energy phosphate bonds in dNTPs.

What enzyme proofreads DNA during replication?

DNA polymerase III (has 3′→5′ exonuclease activity).

What is transcription?

The process of synthesizing RNA from a DNA template.

What enzyme carries out transcription?

RNA polymerase.

What are the three main stages of transcription?

Initiation, elongation, and termination.

Where does RNA polymerase bind to initiate transcription?

The promoter region upstream of the gene.

What is the TATA box?

A DNA sequence in the promoter that signals where transcription begins.

In what direction is RNA synthesized?

5′ to 3′ direction (just like DNA replication).

What is the template strand?

The DNA strand that is transcribed (read 3′ to 5′) to make RNA.

What is the coding strand?

The non-template DNA strand; its sequence matches the RNA (except T is U in RNA).

What replaces thymine (T) in RNA?

Uracil (U).

What is the function of the sigma factor in bacteria?

Helps RNA polymerase recognize the promoter and initiate transcription.

What happens during elongation in transcription?

RNA polymerase adds complementary RNA nucleotides to the growing RNA strand.

What signals transcription termination in prokaryotes?

A hairpin loop followed by a U-rich sequence or Rho-dependent termination.

What modifications occur to eukaryotic mRNA after transcription?

5′ cap addition, 3′ poly-A tail, and splicing out introns.

What is the function of the 5′ cap?

Protects mRNA from degradation and helps with ribosome binding.

What is the function of the poly-A tail?

Increases mRNA stability and aids in nuclear export.

What are introns and exons?

Introns are non-coding regions removed during RNA splicing; exons are coding sequences that remain.

What enzyme complex carries out RNA splicing?

The spliceosome.