Chapter 16 Bio

What does DNA stand for?

Deoxyribonucleic Acid

Where is DNA found?

In chromosomes within the cell nucleus.

What is the primary role of DNA?

To carry genetic information that determines traits.

What is a gene?

A unit of heredity consisting of a specific DNA sequence.

What experiment provided evidence that DNA is genetic material?

The Hershey-Chase Experiment.

What were the main components labeled in the Hershey-Chase experiment?

Radioactive sulfur (35S) for protein and radioactive phosphorus (32P) for DNA.

What type of virus was used in the Hershey-Chase experiment?

Bacteriophage T2.

What did the results of the Hershey-Chase experiment conclude?

DNA, not protein, serves as the genetic material.

What is the structure of DNA described as?

A double helix.

What forms the backbone of DNA?

A sugar-phosphate backbone.

Which bases pair together in DNA?

Adenine (A) pairs with Thymine (T) and Guanine (G) pairs with Cytosine (C).

What did Chargaff’s rules state?

The amount of A is roughly equal to T, and G is roughly equal to C.

Where is heterochromatin found

in regions like centromeres & telomeres & its formation can be influenced by histone modifications

What is semiconservative replication?

Each new DNA molecule consists of one original strand and one newly synthesized strand.

What did the Meselson-Stahl experiment provide evidence for?

The semiconservative model of DNA replication.

What are the steps of DNA replication

Initiation, Unwinding & Stabilization, Primer Synthesis, Elongation, Finishing touches

Initiation

Proteins bind to the origin of replication to begin the process of DNA synthesis. They separate the 2 strands of DNA, creating a replication bubble.

How many origins of replication does bacteria have?

Replication proceeds in both directions from the single origin until the entire circular chromosome is copied

How many origins of replication do eukaryotes have?

multiple replication bubbles form and eventually fuse, speeding up the replication process

Unwinding and Stabilization

Enzymes involved are helicases, single-strand binding proteins, topoisomeres

Helicases; unwind the double-stranded DNA at the replication forks by breaking hydrogen bonds between the base pairs & separating the 2 parental strands

Single-strand binding proteins;  Bind to the unpaired DNA strands, preventing them from re-pairing.

Topoisomerases: Relieve the strain ahead of the replication fork caused by unwinding, by breaking, swiveling, and rejoining DNA strands.

Primer Synthesis

Primase: Synthesizes short RNA primers (5-10 nucleotides long) that are complementary to the DNA template strands. These primers provide a free 3' OH group, which is essential for DNA polymerase to begin adding DNA nucleotides.

What happens during the initiation step of DNA replication?

Proteins bind to the origin of replication and separate the DNA strands.

What enzyme unwinds the DNA at the replication fork?

Helicase.

What role do single-strand binding proteins play during replication?

They prevent the unpaired DNA strands from re-pairing.

What function does primase serve in DNA replication?

It synthesizes short RNA primers complementary to the DNA template.

What are Okazaki fragments?

Short segments of DNA synthesized discontinuously on the lagging strand.

How does DNA Polymerase I contribute to DNA replication?

It removes RNA primers and replaces them with DNA nucleotides.

What is the role of DNA ligase?

It joins Okazaki fragments into a continuous strand.

What is the trombone model of DNA replication?

A mechanism where the DNA moves through a stationary replication complex.

What is proofreading in DNA replication?

The ability of DNA polymerases to correct errors during nucleotide addition.

What is mismatch repair?

A set of enzymes that correct mismatched nucleotides in newly synthesized DNA.

What is nucleotide excision repair?

A mechanism to repair DNA damage by removing and replacing damaged segments.

What challenge does DNA replication face at chromosome ends?

The end replication problem, leading to shorter DNA strands after replication.

What are telomeres and their function?

Repetitive DNA sequences at chromosome ends that protect against loss of genetic information.

What is telomerase?

An enzyme that lengthens telomeres in germ cells and some stem and cancer cells.

What is chromatin?

A complex of DNA and proteins that organizes DNA within the nucleus.

What is a nucleosome?

The basic unit of chromatin structure consisting of DNA wrapped around histone proteins.

What are euchromatin and heterochromatin?

Euchromatin is loosely packed and accessible to transcription factors (gene expression), while heterochromatin is tightly packed and less accessible to transcription factors (gene silencing).

What is the importance of chromatin condensation during mitosis?

It allows for proper segregation of chromosomes into daughter cells.

What type of proteins play a role in DNA replication and repair?

DNA binding proteins such as histones, helicases, and DNA polymerases.

How does DNA replication differ between prokaryotes and eukaryotes?

Prokaryotes have a single origin of replication, while eukaryotes have multiple origins.

Which nitrogenous base pairs with Adenine?

Thymine.

What is the function of topoisomerases in DNA replication?

To relieve the strain ahead of the replication fork.

What does the 5' end of a DNA strand contain?

A phosphate group.

What are the products of DNA replication?

Two identical DNA molecules, each containing one parental and one new strand.

What does DNA ligase do at the end of replication?

It connects the sugar-phosphate backbones of adjacent DNA fragments.

What indicates a successful proofreading event by DNA polymerase?

An incorrect nucleotide is removed and replaced with the correct one.

What can cause DNA damage that nucleotide excision repair might fix?

Ultraviolet (UV) radiation, leading to thymine dimers.

What is the consequence of telomere shortening?

It can contribute to aging and cell death.

In what cells is telomerase active?

Germ cells, some stem cells, and cancer cells.

What is the major function of histones in chromatin?

They help package DNA into nucleosomes.

Which layer of chromatin allows gene expression?

Euchromatin.

During which stage of the cell cycle is DNA most condensed?

During mitosis.

What happens to DNA structure during transcription?

Euchromatin becomes more accessible.

Why is DNA replication described as directional?

Nucleotides are added only to the 3' end, running in the 5' to 3' direction.

How does chimera formation relate to DNA replication?

It occurs when mispaired bases lead to genetic diversity.

What occurs during the elongation phase of DNA replication?

DNA polymerase adds nucleotides to the growing DNA strand complementary to the template strand.

What direction does DNA elongation occur?

Elongation occurs in the 5' to 3' direction.

What are leading and lagging strands during elongation?

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

What is the role of DNA polymerase III in elongation?

It extends the RNA primer by adding DNA nucleotides in the elongation process.

What is the importance of the 3' OH group in DNA elongation?

It provides a site for DNA polymerase to add nucleotides.

How does the lagging strand elongate discontinuously?

It is synthesized in small segments (Okazaki fragments) that are later joined together by DNA ligase.

What role does the sliding clamp play during elongation?

It helps hold the DNA polymerase in place, increasing its efficiency.

What initiates the process of elongation after primer synthesis?

DNA polymerase begins adding nucleotides at the 3' end of the RNA primer.

What is the consequence of errors during the elongation phase?

Errors can lead to mutations, but proofreading by DNA polymerase helps correct them.

What role do helicases play in DNA replication?

Helicases unwind the double-stranded DNA by breaking hydrogen bonds between base pairs.

What are single-strand binding proteins and their function during DNA replication?

They bind to unpaired DNA strands, preventing them from re-pairing.

What is the function of topoisomerases in the unwinding phase?

Topoisomerases relieve strain caused by unwinding by breaking, swiveling, and rejoining DNA strands.

What is a replication fork?

A Y-shaped region where the DNA double helix is unwound during replication.

Why is unwinding considered a critical step in DNA replication?

It allows the DNA strands to be accessible as templates for new strand synthesis.

What is the function of primase in DNA replication?

Primase synthesizes short RNA primers needed for DNA polymerase to begin replication.

What is the typical length of RNA primers synthesized by primase?

The RNA primers are typically 5-10 nucleotides long.

Why are RNA primers necessary for DNA synthesis?

They provide a free 3' OH group for DNA polymerase to add DNA nucleotides.

What occurs immediately after primer synthesis?

DNA polymerase binds to the primer to begin adding DNA nucleotides.

How does primer synthesis differ on leading and lagging strands?

On the leading strand, one primer is sufficient, while multiple primers are needed for the lagging strand.

What happens to RNA primers after DNA replication?

They are removed and replaced with DNA nucleotides by DNA polymerase I.

In what direction does primase synthesize RNA primers?

Primase synthesizes RNA primers in the 5' to 3' direction.

What is the relationship between primers and Okazaki fragments on the lagging strand?

Okazaki fragments are initiated by primers, which allow discontinuous synthesis of the lagging strand.

What are the finishing touches in DNA replication?

They involve the removal of RNA primers, replacement with DNA, and joining of DNA fragments by DNA ligase.

What happens to the DNA strands after finishing touches are completed?

They are connected to form two continuous double strands.

What is the role of exonuclease activity in finishing touches?

It allows DNA polymerase I to remove RNA primers and proofread the DNA during replacement.

Once finishing touches are completed, what happens to the DNA strands?

They become fully separated and can be packaged into chromatin.

What is telescoping in the context of DNA finishing touches?

The process of ligating fragmented DNA into a singular, continuous structure.