Chapter 5 - Nucleic Acid Structure, DNA Replication, and Chromosome Structure

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Questions and Answers

What is the primary purpose of transformation in bacteria?

To protect against viral infections

To replicate bacterial DNA for division

To create new bacterial species

To take up environmental DNA and incorporate it into the cell (correct)

Which component is NOT part of a nucleotide in DNA?

Ribose (correct)

Deoxyribose

Phosphate group

Nitrogenous base

What key discovery did Rosalind Franklin contribute to the understanding of DNA?

Establishment of DNA's role in heredity

X-ray diffraction pattern indicating a helical structure (correct)

Chargaff's rule on base pairing

The process of DNA replication

What is Chargaff's rule concerning DNA base composition?

A = T and C = G Signup and view all the answers

What characterizes the double helix structure of DNA?

Nitrogenous bases form hydrogen bonds to stabilize the structure Signup and view all the answers

How do the two strands of the DNA double helix run?

In opposite directions (antiparallel) Signup and view all the answers

Which of the following nucleobase pairs are connected by three hydrogen bonds?

Cytosine and Guanine Signup and view all the answers

What structural feature defines the sugar-phosphate backbone of DNA?

Linking of deoxyribose sugars via phosphodiester bonds Signup and view all the answers

Which scientist(s) proposed the double helix model of DNA in 1953?

James Watson and Francis Crick Signup and view all the answers

What is the role of the 3’ –OH group in DNA strands?

It links nucleotides together Signup and view all the answers

What type of replication allows parental strands to separate and serve as templates for new strands?

Semiconservative replication Signup and view all the answers

What is the role of DNA helicase during DNA replication?

To unwind DNA strands at the origin of replication Signup and view all the answers

What enzyme is responsible for synthesizing complementary DNA strands?

DNA polymerase Signup and view all the answers

Why is it necessary for RNA primers to be replaced with DNA later in replication?

DNA replication requires a pure DNA sequence in the final product Signup and view all the answers

What are Okazaki fragments?

Short DNA segments synthesized on the lagging strand Signup and view all the answers

Which statement about bidirectional replication is true?

It begins at a single origin and proceeds in both directions Signup and view all the answers

How does DNA polymerase ensure the accuracy of DNA synthesis?

Through complementary base-pairing rules Signup and view all the answers

What prevents the single-stranded DNA from re-forming a double helix during replication?

Single-strand binding proteins Signup and view all the answers

Which of the following accurately describes the leading strand during DNA replication?

Synthesis occurs in the same direction as the fork movement Signup and view all the answers

Which process occurs first at the origin of replication?

Unwinding of the DNA helix Signup and view all the answers

What is the function of DNA topoisomerase during DNA replication?

To prevent supercoiling ahead of the replication fork Signup and view all the answers

Which direction does DNA synthesis occur in relation to the template strand?

5' to 3' Signup and view all the answers

What activity allows DNA polymerase I to remove RNA nucleotides during DNA replication?

5' to 3' exonuclease activity Signup and view all the answers

What role does DNA ligase play in DNA replication?

Sealing phosphodiester bonds between DNA fragments Signup and view all the answers

Which aspect of DNA polymerase contributes to its high fidelity during DNA replication?

Correct hydrogen bonding is more stable than mismatched pairs Signup and view all the answers

What does telomerase do to prevent chromosome shortening?

Adds repeat sequences to chromosome ends Signup and view all the answers

Which problem arises from the end replication issue during DNA synthesis?

Formation of single-stranded DNA Signup and view all the answers

What are telomeres primarily composed of?

Short DNA sequences repeated many times Signup and view all the answers

What methodology does DNA polymerase use to detect mispaired bases?

Exonuclease activity in the 3' to 5' direction Signup and view all the answers

Which proteins are responsible for sealing DNA fragments stemming from multiple origins of replication on the lagging strand?

DNA ligases Signup and view all the answers

Why is DNA replication considered very accurate?

Cells contain repair enzymes for fixing DNA abnormalities Signup and view all the answers

Which of the following statements is true regarding the synthesis direction of DNA polymerase?

It can only synthesize DNA in the 5’ to 3’ direction after an RNA primer Signup and view all the answers

What was the primary conclusion of Avery, MacLeod, and McCarty's experiments?

DNA is the genetic material. Signup and view all the answers

Which of the following criteria must genetic material meet?

Must allow for variation. Signup and view all the answers

What characteristic of smooth (S) strains of Streptococcus pneumoniae contributes to their pathogenicity?

They secrete a polysaccharide capsule. Signup and view all the answers

Why did Griffith's experiments demonstrate the role of genetic material in bacterial transformation?

He observed that R type bacteria could acquire traits from S type bacteria. Signup and view all the answers

What was the main focus of biochemical identification of genetic material in the early 20th century?

To determine whether chromosomes contain hereditary information. Signup and view all the answers

What happened to the rough (R) type bacteria when exposed to heat-killed smooth (S) type bacteria in Griffith's experiment?

They transformed into smooth (S) type bacteria. Signup and view all the answers

What role did DNase play in Avery, MacLeod, and McCarty's experiments?

It prevented the transformation from occurring. Signup and view all the answers

Which strain of Streptococcus pneumoniae cannot cause disease?

Rough (R) Signup and view all the answers

Which of the following substances did not prevent transformation in Avery, MacLeod, and McCarty's experiments?

Protease Signup and view all the answers

Study Notes

Chapter 11 Outline

Biochemical Identification of the Genetic Material
Nucleic Acid Structure
Overview of DNA Replication
Molecular Mechanism of DNA Replication
Molecular Structure of Eukaryotic Chromosomes

Genetic Material

Functions as a blueprint for the construction of living organisms.
Enables organisms to survive in their environments.
Must meet criteria of: Information, Replication, Transmission, Variation

Identification of the Genetic Material

In the late 1800s, scientists hypothesized a chemical substance within cells responsible for traits transmission.
Researchers believed chromosomes were the hereditary material, observed doubling and dividing during cell division and containing DNA and protein.
In the 1920s to 1940s, scientists anticipated proteins to be the genetic material.

Griffith's Bacterial Transformation

In the late 1920s, Frederick Griffith studied Streptococcus pneumoniae strains.
Smooth (S) strain: secretes a polysaccharide capsule, causing fatal infections in mice, pathogenic.
Rough (R) strain: does not secrete a capsule, unable to cause infections in mice.
Griffith discovered transformation, where non-virulent (R) bacteria were transformed into virulent (S) bacteria by a substance in heat-killed (S) bacteria.

Avery, MacLeod, and McCarty

Followed up on Griffith's work in the 1940s
Isolated DNA, RNA, and protein from the S type bacteria
Only purified DNA converted type R bacteria to type S.
DNA is the genetic material.

Levels of DNA Structure

Nucleotides form a single strand of DNA.
Two strands form a double helix.
In living cells, DNA is combined with proteins to form chromatin, packaged into chromosomes.
A genome is the complete complement of an organism's genetic material.

Nucleotides of DNA

Three components: phosphate group, Deoxyribose, nitrogenous base
Purines: Adenine (A), Guanine (G)
Pyrimidines: Cytosine (C), Thymine (T)

Nucleotides of RNA

Three components: phosphate group, Ribose, nitrogenous base
Purines: Adenine (A), Guanine (G)
Pyrimidines: Cytosine (C), Uracil (U)

Conventional Numbering System

In the sugar ring, carbon atoms are numbered 1' to 5'.
1' carbon is to the right of the ring oxygen.
Phosphate group is attached to 5' carbon.
3'-OH group is crucial for linking nucleotides.

A DNA Strand

Nucleotides are linked by covalent phosphodiester bonds to form a strand (polymer)
Strand has a specific directionality
Sequence: 5' – TACG – 3'

DNA Structure

In 1953, Watson, Crick, and Wilkins proposed DNA's double helix structure.
Key contributions: Rosalind Franklin's X-ray diffraction results, Chargaff's base composition studies, Linus Pauling's methods
Using ball-and-stick models
DNA structure has been proposed by many scientists.

Rosalind Franklin's X-Ray Diffraction

Atoms in a substance scatter X-rays.
Repeating structures create diffraction patterns related to atomic arrangements.
X-shaped diffraction is characteristic of a helix.

DNA Base Composition

Erwin Chargaff analyzed DNA base composition from different species.
Results show similar amounts of adenine (A) and thymine (T), and cytosine (C) and guanine (G).
Chargaff's rule: A=T and C=G.

Watson & Crick

Compiled existing knowledge (from colleagues' experimental approaches)
Tested several DNA structure models
Identified the correct model consistent with known findings.
Published DNA structure in 1953.
Awarded the Nobel Prize in 1962.

Structure of DNA Double Helix

Two deoxyribonucleotide strands form a helical structure with a sugar-phosphate backbone on the outside and bases on the inside.
The two strands are antiparallel (opposite directionality).
Stabilized by hydrogen bonding between nitrogenous bases (A-T, G-C pairs)
Base sequences of two strands are complementary (e.g., 5'-GCGGATTT-3' pairs with 3'-CGCCTAAA-5'

Three proposed mechanisms for DNA Replication

Semiconservative: Each new DNA molecule includes one original and one newly synthesized strand.
Conservative: One new molecule includes both original strands while the other molecule contains two newly synthesized strands.
Dispersive: New DNA molecules have segments of original and newly synthesized DNA interspersed.

Experiments of Meselson & Stahl

In 1958, Matthew Meselson and Franklin Stahl differentiated between the three replication models.
Used isotopic labeling (N15 and N14) to distinguish between parental and new DNA strands.
Used density gradient centrifugation to observe resulting DNA bands in each generation.
Their results supported semiconservative replication.

Semiconservative DNA Replication

During replication, parental strands separate and serve as templates for new strands.
New nucleotides are added based on complementary base-pairing rules (AT/GC).
Result is two identical double-helix DNA molecules each with one original and one new strand.

Bidirectional Replication

DNA replication begins at an origin of replication.
Base-pairing is disrupted allowing strands to unwind.
Replication proceeds outward in both directions from the origin (bidirectional replication).

Single Origin of Replication (Bacteria)

DNA replication starts from a single origin.
Replication proceeds outward in both directions until the entire chromosome is replicated.

Multiple Origins of Replication (Eukaryotes)

Replication begins at multiple origins (replication forks).
Replication forks move outward in both directions until the entire chromosome is replicated.

Molecular Events of DNA Replication

Origin of replication is bound by proteins that unwind DNA to create a replication bubble.
Two DNA helicases move in opposite directions to separate the DNA strands, requiring ATP energy.
A replication fork, in each direction, is created where the strands have been separated.
Unwinding DNA creates tightened coils ahead of the replication fork. DNA topoisomerase alleviates that strain.

Molecular Events of DNA Replication (Cont.)

Single-strand binding proteins prevent single strands from re-forming a double helix.
This ensures the parental strands' nitrogenous bases remain exposed so DNA polymerase uses them as templates.

DNA Synthesis

The enzyme DNA polymerase synthesizes DNA, using a DNA template strand.
Slides along template DNA, covalently linking new nucleotides to the 3'-OH of the last nucleotide.
Correct hydrogen bonding between incoming dNTPs and the template strand is required for accurate synthesis.
Incorporating dNTPs breaks high-energy bonds, which is exergonic.

Primers

DNA polymerase needs a primer to start DNA synthesis. This process occurs in a 5' to 3' direction.
An enzyme called DNA primase makes an RNA primer.
The RNA primer must be removed and replaced with DNA later.

Leading and Lagging Strands

The replication fork moves unidirectionally. Newly synthesized strands will be made at the replication fork.
The two template strands have opposite directions
New daughter strands must be synthesized antiparallel to its template
DNA polymerase works in the 5' to 3' direction only.
Leads to different replication methods for each strand: Leading and Lagging strands.

Leading Strand Synthesis

A single RNA primer is initially created at the origin.
DNA polymerase extends the primer, moving in the same direction as replication fork.
DNA synthesis occurs continuously from the primer, forming a single long molecule.

Lagging Strand Synthesis

Requires multiple RNA primers near the replication fork.
Short DNA segments are synthesized (Okazaki fragments) in the opposite direction of the replication fork.
RNA primers between Okazaki fragments are later removed and joined.

Primer Removal and Replacement

A specific DNA polymerase removes RNA primers and fills gaps with DNA.
The enzyme DNA ligase connects the RNA primer-free DNA segments.

DNA Ligase

Seals DNA fragments after RNA primers have been removed and replaced with DNA.
Joins Okazaki fragments on the lagging strand and adjacent DNA strands from multiple origins.

Proteins involved in leading and lagging strand synthesis in E. coli

Several proteins carry out different steps in DNA synthesis.
DNA polymerase III, DNA primase, DNA polymerase I, and DNA ligase are essential for both leading and lagging strand synthesis.

DNA Replication is Very Accurate

DNA polymerase has high fidelity due to correct hydrogen bonding.
The polymerase's active site prefers correct matches over mismatches.
Polynucleotide proofreading removes incorrectly paired bases
Cells and additional repair enzymes are used to ensure DNA accuracy.

Telomeres

Regions at ends of linear eukaryotic chromosomes.
Consist of short repeated DNA sequences (e.g., TTAGGG repeats).
Special telomeric proteins bind to these sequences, protecting chromosome ends from damage or fusion.

End Replication Problem

Linear DNA molecules encounter problems at the ends.
DNA polymerase can only work from 5' to 3' but cannot replicate the very end of the lagging strand.
The result is progressive shortening of chromosomes in each DNA replication cycle

Telomerase

Telomerase is an enzyme with a protein and RNA component.
It attaches many new copies of the DNA repeat sequence to the ends of chromosomes to prevent chromosome shortening.
It binds and synthesizes new telomeric DNA, then moves down and repeats this process to lengthen the 3' end.

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