Bio Exam 2 study guide answers

How did the work of Meselson and Stahl support the semiconservative model of DNA replication?

They used isotope labeling of nitrogen in DNA and density gradient centrifugation to show that each new DNA molecule consists of one old and one new strand.

What is a replication bubble?

A region where the DNA double helix is unwound to allow replication.

What do initiator proteins do?

They bind to the replication origin and help separate the DNA strands to initiate replication.

What does helicase do during DNA replication?

Unwinds the DNA double helix at the replication fork.

What does topoisomerase (gyrase) do?

Relieves supercoiling tension ahead of the replication fork by cutting and rejoining DNA strands.

What is a replication fork?

The Y-shaped region where the DNA strands are separated and replication occurs.

Where does DNA primase build an RNA primer?

On the leading strand once and on the lagging strand multiple times to provide a starting point for DNA polymerase.

Where does DNA polymerase attach, and why?

It attaches to the RNA primer to begin synthesizing the new DNA strand.

What is the direction of DNA synthesis?

5’ to 3’ direction, since nucleotides can only be added to the 3’ end of the growing strand.

What is the leading vs. lagging strand during replication?

The leading strand is synthesized continuously, while the lagging strand is synthesized in short Okazaki fragments.

What problem occurs with the lagging strand, and how does telomerase help?

The lagging strand shortens over time; telomerase extends the ends of chromosomes to prevent genetic loss.

What are the key enzymes in DNA replication and their functions?

Helicase (unwinding), Topoisomerase (relieves tension), Primase (makes primers), DNA Polymerase III (elongates strands), DNA Polymerase I (replaces RNA primers), Ligase (joins fragments), Telomerase (extends chromosome ends).

What provides energy for building DNA?

The cleavage of phosphate bonds in deoxynucleoside triphosphates (dNTPs).

Define Okazaki fragments.

Short DNA fragments synthesized on the lagging strand during replication.

What effect does UV light have on DNA?

It causes thymine dimers, which can lead to mutations.

Define depurination.

The loss of a purine base (adenine or guanine) from DNA, leading to mutations.

Define deamination.

The removal of an amino group from cytosine, converting it to uracil.

How does mismatch repair work?

It corrects base-pair mismatches by excising incorrect nucleotides and replacing them with the correct ones.

How are double-stranded breaks repaired?

By non-homologous end joining (NHEJ) or homologous recombination.

What is the central dogma of molecular biology?

DNA → RNA → Protein.

How does RNA differ from DNA?

RNA has ribose sugar, uracil instead of thymine, and is single-stranded.

Define ssRNA.

Single-stranded RNA, as opposed to double-stranded DNA.

What is RNA polymerase and how does it function?

It synthesizes RNA from a DNA template; unlike DNA polymerase, it does not require a primer.

How is transcription initiated and terminated?

Initiated at a promoter sequence and terminated by a stop signal or hairpin loop structure.

What are enhancer and silencer sequences?

Enhancers increase transcription, silencers decrease transcription.

What is a codon?

A three-nucleotide sequence that codes for an amino acid.

What is the start codon?

AUG (Methionine).

What are the stop codons?

UAA, UAG, UGA.

What are the A, P, and E sites in the ribosome?

A (accepts tRNA), P (holds growing peptide), E (exit for empty tRNA).

What is a ribozyme?

An RNA molecule with enzymatic activity.

What is an operon?

A cluster of genes controlled by a single promoter.

How does the Lac operon work?

It is activated when lactose is present and glucose is low.

What does a repressor protein do?

Blocks RNA polymerase from transcribing genes.

How do regulatory elements control gene expression?

By interacting with transcription factors and RNA polymerase.

What role do restriction enzymes play?

They cut DNA at specific sequences for cloning and analysis.

What is recombinant DNA?

DNA composed of sequences from different sources.

What is PCR used for?

Amplifying DNA sequences.

How does CRISPR-Cas9 work?

It uses guide RNA and the Cas9 enzyme to edit DNA.

What is next-generation sequencing?

A method for high-throughput DNA sequencing.