Molecular Genetics Block 1

What are the components of a DNA nucleotide?

A phosphate group, a deoxyribose sugar, and a nitrogenous base.

What bond connects nucleotides in DNA?

Phosphodiester bonds linking the 5' phosphate to the 3' hydroxyl group.

Which bases pair in DNA and how many hydrogen bonds do they form?

A-T pair with 2 hydrogen bonds, C-G pair with 3 hydrogen bonds.

Why is DNA negatively charged?

Because of the phosphate groups in its backbone.

What is the directionality of DNA?

DNA strands run antiparallel

What is the major and minor groove?

Structural features of the DNA helix created by twisting of the strands.

What are the three forms of DNA?

A-form, B-form (most common), and Z-form.

What defines RNA as less stable than DNA?

The 2'-OH group on ribose can attack the backbone, causing strand breakage.

Why does DNA use thymine instead of uracil?

Uracil in DNA would mask cytosine deamination damage; thymine allows repair.

What is the RNA world hypothesis?

The idea that RNA was the original genetic and catalytic molecule.

Why is DNA more suitable for long-term storage?

It is chemically more stable and has better repair mechanisms.

How is the eukaryotic genome organized?

DNA is wrapped around histones to form chromatin.

How is the prokaryotic genome organized?

Circular supercoiled DNA without histones.

What are chromosomes?

Complete DNA molecules; circular in bacteria, linear in eukaryotes.

What is the central dogma?

DNA → RNA → Protein; information generally does not return from protein to nucleic acid.

What experiment identified transforming principle?

Griffith’s experiment showing trait transfer between bacterial strains.

What did Avery, MacLeod, and McCarty show?

Destroying DNA prevented transformation, proving DNA carries genetic information.

What did the Hershey-Chase experiment demonstrate?

DNA, not protein, enters bacteria during phage infection and carries genetic info.

What is a gene?

A DNA sequence transcribed into functional RNA.

What is DNA helicase?

An enzyme that unwinds DNA at the replication fork.

What is primase?

An enzyme that synthesizes short RNA primers for DNA polymerase.

What is DNA polymerase?

An enzyme that extends DNA from a primer in the 5'→3' direction.

What is the leading strand?

The continuously synthesized strand during replication.

What is the lagging strand?

The discontinuously synthesized strand forming Okazaki fragments.

What does DNA ligase do?

Joins Okazaki fragments by sealing phosphodiester bonds.

What differs between prokaryotic and eukaryotic replication origins?

Prokaryotes use a single origin; eukaryotes use many.

What is the end-replication problem?

Lagging-strand synthesis cannot fully replicate chromosome ends.

What is telomerase?

An enzyme that extends telomeres using an internal RNA template.

What is a bacterial promoter?

A DNA sequence where RNA polymerase and sigma factor bind to start transcription.

What is the role of sigma factors?

They guide bacterial RNA polymerase to specific promoter sequences.

What is the TATA box?

A conserved element in many eukaryotic promoters used for RNA polymerase II initiation.

What are enhancers?

DNA regions that bind activators to increase transcription, sometimes far from the promoter.

What is intrinsic (Rho-independent) termination?

Termination caused by a hairpin loop followed by U-rich RNA.

What is Rho-dependent termination?

Termination requiring the Rho helicase to release RNA from DNA.

What is alternative splicing?

A process where different exon combinations produce multiple mRNAs from one gene.

What is tRNA’s function?

Carries specific amino acids and matches them to codons during translation.

What enzyme charges tRNAs?

Aminoacyl-tRNA synthetases, which attach amino acids to tRNAs.

What is wobble pairing?

Flexibility at the third codon position allowing one tRNA to recognize multiple codons.

What is a ribosome?

A complex of rRNA and proteins that synthesizes polypeptides.

How does translation initiation differ between prokaryotes and eukaryotes?

Prokaryotes use the Shine-Dalgarno sequence; eukaryotes scan from 5’ cap to first AUG.

What is the function of the poly-A tail?

Helps stabilize mRNA and enhance translation initiation.

What is conjugation?

Direct DNA transfer between bacteria via an F pilus.

What is an F plasmid?

A fertility plasmid containing genes for pilus formation and DNA transfer.

What is an Hfr strain?

A bacterium where the F plasmid is integrated into the chromosome, enabling chromosomal gene transfer.

What is generalized transduction?

Random bacterial DNA fragments are packaged into phages and transferred to new cells.

What is a prophage?

Phage DNA integrated into the bacterial chromosome during the lysogenic cycle.

What is depurination?

Loss of a purine base, leaving an AP site.

What is deamination?

Removal of an amino group (e.g., C → U), potentially causing mutations.

What is nucleotide excision repair?

Repair of bulky DNA lesions such as thymine dimers.

What is mismatch repair?

A repair system that fixes replication errors by recognizing unmethylated new DNA in bacteria.

What is translesion synthesis?

Error-prone replication across DNA damage when normal polymerases stall.