Molecular Biology: DNA Replication & Repair

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Questions and Answers

What is the primary role of DNA polymerase during replication?

It assists in DNA packaging after replication.

It proofreads each nucleotide for accuracy. (correct)

It catalyzes the formation of hydrogen bonds.

It alters the structure of the DNA strand.

Which type of repair mechanism is specifically mentioned for fixing mismatched base pairs?

Non-Homologous End Joining

Nucleotide Excision Repair (NER) (correct)

Homologous Recombination Repair

Base Excision Repair (BER)

What initiates the process of Nucleotide Excision Repair (NER)?

Teams of enzymes detect mismatched base pairs. (correct)

DNA polymerase bonds nucleotides.

The damaged strand is directly replicated.

Reactive chemicals cut the DNA strand.

Which enzyme is responsible for cutting the damaged strand during DNA repair?

Nuclease enzyme Signup and view all the answers

What is a significant factor that contributes to the high accuracy of DNA replication?

The high specificity of base pairing and proofreading Signup and view all the answers

How often does a mistake occur during DNA replication, according to the information provided?

Once every ten billion nucleotides Signup and view all the answers

What is one of the roles of the exonuclease activity of DNA polymerase?

It cleaves off mismatched nucleotides. Signup and view all the answers

Which of the following is NOT a cause of DNA damage mentioned?

Metabolic byproducts Signup and view all the answers

What characterizes the process of transcription in eukaryotes compared to prokaryotes?

Eukaryotes need to modify pre-mRNA before it can exit the nucleus. Signup and view all the answers

Which statement accurately describes the synthesis of RNA during transcription?

RNA nucleotides pair with DNA template strands T:A and A:U. Signup and view all the answers

What distinguishes the transcription units in prokaryotic genes from eukaryotic genes?

The transcription unit in prokaryotes does not require post-transcriptional modifications. Signup and view all the answers

What is the main outcome of the process of translation?

Formation of a polypeptide based on mRNA information. Signup and view all the answers

Which role does RNA polymerase play in the transcription process?

It catalyzes the formation of a polynucleotide strand in the 5’ to 3’ direction. Signup and view all the answers

What happens to chromatin during prophase?

It condenses and coils. Signup and view all the answers

Which type of chromatin is characterized by its accessibility to transcriptional machinery?

Euchromatin Signup and view all the answers

What is the highest level of DNA packaging during metaphase?

700 nm fibers Signup and view all the answers

What is the primary function of the attachments of looped chromatin domains to the nuclear envelope during interphase?

To organize regions of active genes. Signup and view all the answers

Which process allows DNA to dictate the synthesis of proteins?

Transcription Signup and view all the answers

Which statement is true regarding chromatin organization within the nucleus?

Each chromosome occupies a specific area within the nucleus. Signup and view all the answers

How do chemical modifications of histones affect gene expression?

They lead to a decrease in chromatin condensation, allowing transcription. Signup and view all the answers

During which phase is chromatin in a highly extended state?

Interphase Signup and view all the answers

The process of gene expression involves which two main stages?

Transcription and Translation Signup and view all the answers

What describes heterochromatin?

It is highly condensed and largely inaccessible to transcription. Signup and view all the answers

What mechanism allows E.coli to differentiate between parental and daughter DNA during mismatch repair?

Daughter DNA is less methylated than parental DNA Signup and view all the answers

Which of the following correctly describes the cellular response to UV-induced DNA damage?

Repair machinery identifies distortions within the DNA structure Signup and view all the answers

Which condition results from a defect in nucleotide excision repair mechanisms?

Xeroderma pigmentosum Signup and view all the answers

How long would a completely stretched eukaryotic chromosome measure?

About 4 cm Signup and view all the answers

What is the primary unit of DNA packaging in eukaryotic cells?

Nucleosome Signup and view all the answers

What effect does UV light have on adjacent pyrimidines in DNA?

It covalently crosslinks them, forming thymine dimers Signup and view all the answers

What structure in bacteria contains the densely packed region of DNA?

Nucleoid Signup and view all the answers

Which of these statements about eukaryotic DNA is accurate?

Eukaryotic chromosomes contain linear DNA double helices Signup and view all the answers

What type of proteins are histones?

Proteins with a high content of positively charged amino acids Signup and view all the answers

In which scenario can children with xeroderma pigmentosum develop skin cancer?

Without any sun protection, even low UV exposure can lead to cancer Signup and view all the answers

What does the one gene – one enzyme model suggest about the relationship between genes and enzymes?

One gene is responsible for encoding one specific enzyme. Signup and view all the answers

What limitation was found in the one gene – one enzyme model?

Some genes do not result in any protein formation. Signup and view all the answers

What hypothesis was developed by Beadle and Tatum regarding the relationship between genetic mutants and enzymes?

Each mutant class had a defective gene responsible for one specific enzyme. Signup and view all the answers

What does the term 'alternative splicing' refer to in relation to eukaryotic genes?

A method by which a gene can produce multiple related polypeptides. Signup and view all the answers

Which of the following is true about genetic mutants identified by Beadle and Tatum?

Each class of mutant required arginine due to a defective gene. Signup and view all the answers

Which statement reflects a major issue with the one gene – one polypeptide model?

Some genes produce a variety of polypeptides from a single mRNA transcript. Signup and view all the answers

What role does transcription play in the process of gene expression?

It copies DNA into RNA for protein synthesis. Signup and view all the answers

What is the fundamental problem with the statement 'one gene – one enzyme'?

It does not account for proteins that do not have enzymatic activity. Signup and view all the answers

What defines the primary structure of a protein?

The sequence of amino acids in a polypeptide chain. Signup and view all the answers

What was the primary method used by Beadle and Tatum to generate mutant strains of Neurospora?

X-ray bombardment was utilized to induce mutations. Signup and view all the answers

Signup and view all the answers

Study Notes

DNA Damage and Repair

DNA replication achieves high accuracy with only about one error per 10 billion nucleotides.
Base pairing specificity is crucial for this accuracy.
Proofreading and error-checking mechanisms ensure near-perfect matching of base pairs during replication.
Other enzymes further correct errors left behind by DNA polymerase or created after DNA synthesis.

DNA Proofreading and Repair

DNA polymerase proofreads each nucleotide against its template immediately after bonding.
If a mistake is found, the wrong nucleotide is replaced with the correct one.
DNA polymerase has exonuclease abilities to remove incorrect nucleotides.

Nucleotide Excision Repair (NER)

Reactive chemicals, radioactivity, X-rays, ultraviolet light, and other harmful chemicals can damage DNA.
Mismatched nucleotides can sometimes evade DNA polymerase proofreading.
Mismatch repair removes and replaces incorrectly paired nucleotides.
Repair mechanisms include nucleases, DNA polymerase, and DNA ligase.

DNA Mismatch Repair

Parental DNA is methylated, daughter DNA is not.
Repairing errors is crucial for organism survival.
Specific enzymes catalyze DNA repair.

UV light covalently crosslinks two adjacent pyrimidines, most commonly creating thymine dimers.
This distorts the DNA molecule.
Repair machinery detects the distortion and initiates the appropriate repair pathways.

Repair: UV Damage

Xeroderma pigmentosum (XP) is an inherited disease involving defects in nucleotide excision repair mechanisms, causing extreme sensitivity to sunlight.
Mutations in skin cells from uncorrected UV damage often lead to skin cancer.
Without sun protection, children with XP can develop skin cancer by age 10.

DNA Packaging

Stretched out, E. coli DNA would be about a millimeter long, 500 times longer than the cell.
Proteins cause the chromosome to coil and supercoil, packing the DNA densely.
Unlike eukaryotic cells, the dense DNA region called the nucleoid in prokaryotes is not enclosed in a membrane.

DNA Packaging: Eukaryotes

Each eukaryotic chromosome contains a single linear DNA double helix.
If stretched out, a human chromosome would be approximately 4 cm long.
Eukaryotic DNA is precisely combined with a large amount of protein, forming chromatin.

DNA Packaging: Chromatin

Chromatin undergoes changes in its degree of packing during the cell cycle.
Interphase chromatin is highly extended.
Prophase chromatin coils/folds (condenses)
Metaphase chromosomes are short and thick.

Chromatin: Spatial Organization

Looped domains of chromatin are attached to the nuclear envelope during interphase.
These attachments organize regions of active chromatin.
Chromatin of each chromosome occupies a specific area within the nucleus.

Heterochromatin vs Euchromatin

Some chromatin regions are more/less condensed than others.
Heterochromatin is highly condensed, DNA largely inaccessible to transcriptional machinery.
Euchromatin is less tightly packed, DNA in these regions is more easily transcribed, usually associated with actively transcribed genes.
Chemical modifications of histones influence chromatin condensation and gene activity.

Transcription: Gene → Protein

DNA inherited by an organism dictates protein synthesis and RNA molecule synthesis.
This produces specific traits of an organism.
Proteins link genotype and phenotype.
Gene expression is the process of DNA directing the synthesis of proteins (or, in some cases, just RNAs).

Individual Genes Specify Individual Enzymes

Neurospora has modest food requirements.
It can grow in minimal nutrients solution incorporated into agar medium
Neurospora uses the minimal media and its own metabolic pathways to produce needed molecules.
Experiments by Beadle and Tatum demonstrated a one-gene-one-enzyme model. Each enzyme is encoded by a specific gene.

One Gene - One Enzyme

Beadle and Tatum bombarded Neurospora cells with X-rays to generate mutants needing arginine.
They isolated mutants unable to grow in minimal medium without arginine into three classes.
This demonstrated that each mutant was defective in one gene and produced one specific enzyme.

One Gene - One Enzyme: Flaws & Revisions

Not all genes encode enzymes.
Many genes encode proteins without enzymatic properties.
Many proteins are constructed from multiple polypeptide chains.
A more accurate model is one gene - one polypeptide.
Many eukaryotic genes code for a set of closely related polypeptides via alternative splicing.
Some genes code for RNA molecules not translated into proteins.

Transcription & Translation

Genes have hundreds or thousands of nucleotides.
Each polypeptide of a protein has amino acids arranged in a specific linear order (primary structure).
Transcription synthesizes RNA using information in DNA.
Different RNA types can be produced via transcription.
Translation synthesizes a polypeptide using information in mRNA.
Translation changes the language from nucleic acids to amino acids.

Transcription & Translation (Bacteria vs Eukaryotes)

Bacteria lack nuclear membranes, thus translation can begin before transcription is finished.
Eukaryotic transcription occurs in the nucleus, producing pre-mRNA that subsequently undergoes post-transcriptional modification before translation in the cytoplasm.
All types of initial RNAs are transcribed (primary transcripts).

Transcription

RNA nucleotides match with the DNA template strand sequence.
RNA polymerase synthesizes RNA in the 5' to 3' direction.

Gene Components

Prokaryotic genes have regulatory sequences (including promoter) and coding regions (exons).
Eukaryotic genes have regulatory sequences (including promoter), coding regions (exons), and noncoding regions (introns).
Transcribing into an RNA molecule is called the transcription unit.

Steps of Transcription

Transcription involves RNA polymerase.
RNA polymerase synthesizes in the 5' to 3' direction.
RNA polymerase does not require a primer to begin.
Prokaryotes have one type of RNA polymerase, while eukaryotes have three or more.
Transcription occurs in initiation, elongation, and termination steps.

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Description

Test your knowledge on DNA replication and repair mechanisms with this quiz. Explore the roles of DNA polymerase, various repair methods, and transcription processes in eukaryotes and prokaryotes. Challenge yourself with questions that cover the accuracy of these fundamental biological processes.