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Questions and Answers
What distinguishes heterochromatin from euchromatin?
What distinguishes heterochromatin from euchromatin?
Which statement accurately describes the structure of a nucleosome?
Which statement accurately describes the structure of a nucleosome?
What is the main role of telomeres in chromosomes?
What is the main role of telomeres in chromosomes?
Which type of chromosomal centromere position is described as being at the end?
Which type of chromosomal centromere position is described as being at the end?
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What is the primary feature of polytene chromosomes?
What is the primary feature of polytene chromosomes?
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Which of the following statements about cytogenetics is true?
Which of the following statements about cytogenetics is true?
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What characterizes G banding patterns in chromosomes?
What characterizes G banding patterns in chromosomes?
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What is the approximate length of a haploid set of human chromosomes in terms of DNA?
What is the approximate length of a haploid set of human chromosomes in terms of DNA?
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What initiates homologous recombination during meiosis?
What initiates homologous recombination during meiosis?
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What are the ends left after the specialized nuclease processes the broken DNA?
What are the ends left after the specialized nuclease processes the broken DNA?
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What are the two ways to resolve the double Holliday junction during homologous recombination?
What are the two ways to resolve the double Holliday junction during homologous recombination?
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What primarily dictates the shape and chemical properties of proteins?
What primarily dictates the shape and chemical properties of proteins?
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Which statement best describes the arrangement of coding DNA in most multicellular organisms?
Which statement best describes the arrangement of coding DNA in most multicellular organisms?
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How does the genome determine the features of each species on Earth?
How does the genome determine the features of each species on Earth?
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Where are proteins that work closely together in a cell usually located?
Where are proteins that work closely together in a cell usually located?
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What are the consequences of a crossover event in homologous recombination?
What are the consequences of a crossover event in homologous recombination?
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What is the primary role of RNA in the process of gene expression?
What is the primary role of RNA in the process of gene expression?
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What is the central dogma of molecular biology?
What is the central dogma of molecular biology?
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What is a crucial processing step that RNA undergoes in eukaryotic cells?
What is a crucial processing step that RNA undergoes in eukaryotic cells?
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Which of the following statements accurately describes the complexity of gene identification in genomes?
Which of the following statements accurately describes the complexity of gene identification in genomes?
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How does the processing of RNA affect the resulting protein?
How does the processing of RNA affect the resulting protein?
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Why can cells synthesize a large amount of protein rapidly?
Why can cells synthesize a large amount of protein rapidly?
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What typically hinders the identification of the beginning and end of genes in complex genomes?
What typically hinders the identification of the beginning and end of genes in complex genomes?
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What is true about RNA molecules produced from genes?
What is true about RNA molecules produced from genes?
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What happens during the process of alkylation to DNA bases?
What happens during the process of alkylation to DNA bases?
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What type of DNA damage is caused primarily by UV radiation?
What type of DNA damage is caused primarily by UV radiation?
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Which repair mechanism directly undoes UV-induced DNA damage?
Which repair mechanism directly undoes UV-induced DNA damage?
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What is the role of O6-methylguanine methyltransferase in DNA repair?
What is the role of O6-methylguanine methyltransferase in DNA repair?
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What does base excision repair primarily address?
What does base excision repair primarily address?
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What is the first step in the base excision repair process?
What is the first step in the base excision repair process?
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What commonly occurs after alkylation that can cause DNA replication to stall?
What commonly occurs after alkylation that can cause DNA replication to stall?
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Which type of radiation causes the most energetic and damaging effects on DNA?
Which type of radiation causes the most energetic and damaging effects on DNA?
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Which of the following statements about DNA damage and mutations is true?
Which of the following statements about DNA damage and mutations is true?
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What is the primary goal of excision repair mechanisms?
What is the primary goal of excision repair mechanisms?
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What is the primary function of DNA polymerase I in base excision repair?
What is the primary function of DNA polymerase I in base excision repair?
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Which enzyme is responsible for proofreading in eukaryotic base excision repair?
Which enzyme is responsible for proofreading in eukaryotic base excision repair?
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What type of DNA damage is primarily addressed by nucleotide excision repair?
What type of DNA damage is primarily addressed by nucleotide excision repair?
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Which process involves the binding of Ku and DNA-PKcs to treat double-strand breaks in eukaryotes?
Which process involves the binding of Ku and DNA-PKcs to treat double-strand breaks in eukaryotes?
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What is the main challenge posed by double-strand DNA breaks in eukaryotic cells?
What is the main challenge posed by double-strand DNA breaks in eukaryotic cells?
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What role does chromatin remodeling play in double-strand break repair?
What role does chromatin remodeling play in double-strand break repair?
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How does the mismatch repair system differentiate between parental and progeny strands?
How does the mismatch repair system differentiate between parental and progeny strands?
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What best describes the process of recombination repair after DNA replication?
What best describes the process of recombination repair after DNA replication?
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What is the outcome of the error-prone bypass mechanism during DNA replication?
What is the outcome of the error-prone bypass mechanism during DNA replication?
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What is a special case of base excision repair involving oxoG sites?
What is a special case of base excision repair involving oxoG sites?
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What is the primary structure of DNA composed of?
What is the primary structure of DNA composed of?
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What is the function of introns in eukaryotic genes?
What is the function of introns in eukaryotic genes?
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Which statement about the nitrogenous bases in DNA is correct?
Which statement about the nitrogenous bases in DNA is correct?
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What role does DNA play during cell division?
What role does DNA play during cell division?
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How are genes typically organized in prokaryotic genomes?
How are genes typically organized in prokaryotic genomes?
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Which of the following is true regarding plasmids?
Which of the following is true regarding plasmids?
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What best describes the composition of viral genomes?
What best describes the composition of viral genomes?
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What are exons in the context of genes?
What are exons in the context of genes?
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Which component of a DNA nucleotide provides identity to the nucleotide?
Which component of a DNA nucleotide provides identity to the nucleotide?
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Which of the following is NOT a mechanism that leads to gene mutations?
Which of the following is NOT a mechanism that leads to gene mutations?
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How does the process of transcription relate to genes?
How does the process of transcription relate to genes?
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What is meant by genome size in genomics?
What is meant by genome size in genomics?
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What do major and minor grooves in DNA signify?
What do major and minor grooves in DNA signify?
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Which type of genetic element is primarily responsible for providing genetic diversity in a population?
Which type of genetic element is primarily responsible for providing genetic diversity in a population?
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Study Notes
Genes and Evolution
- Darwin recognized the role of hereditary variation in evolution but was unaware of the mechanism of heredity.
- Genetic variation (product of mutation) is the raw material for evolutionary change.
- Natural selection is the differential reproduction of individuals with different alleles.
- Random genetic drift is the change in frequencies of genetic variants resulting from random, non-selective processes.
Evolution
- Evolution was an accepted fact among many scholars prior to Darwin.
- Darwin provided a plausible explanation for evolution: natural selection.
- All living organisms are related through a common ancestor.
- Homologous features have the same developmental origin inherited from a common ancestor.
- Analogous features have independent origins.
- Similarities of DNA and protein sequences allow inferences about evolutionary origins.
Darwinian Evolution
- Variation exists among individuals in a population in morphology, physiology, and behavior.
- Offspring resemble their parents more than they resemble unrelated individuals.
- Some variants are more successful at surviving and reproducing than others in a given environment. This natural selection leads to the selection of individuals.
Evolutionary History
- Phyletic evolution is change within a continuous line of descent
- Diversification involves many contemporaneous species evolving from a common ancestor (branching).
- Natural selection converts heritable variation among members of a population into heritable differences among populations.
Synthesis of Evolutionary Forces
- Adaptive evolutionary change is a balance between forces of breeding structure, mutation, migration, and selection.
- Forces that increase or maintain variation within populations prevent differentiation of populations (e.g., migration, mutation, balancing selection).
- Divergence of populations is a result of forces that make each population homozygous (e.g., inbreeding, founder effect, directional selection).
- Evolution requires genetic variation in order to occur; direction of change is unpredictable.
Genetics and Human Affairs
- Over 1000 inherited genetic diseases exist in humans.
- Cancer is caused by mutations in somatic cells.
- Genetics plays a role in social policy (e.g., debate over role of genetics in IQ, sexual orientation ).
- Biotechnology and genetic engineering have led to new pharmaceuticals and new varieties of plants and animals.
- Ethical concerns surround these fields and advances.
The Structure of Genes and Genomes
- DNA's structure is a double helix
- DNA is comprised of nucleotides
- A gene is a segment of DNA that is transcribed into a functional RNA molecule.
- Introns interrupt many eukaryote genes.
- Viral genomes consist of either DNA or RNA.
Nature of DNA
- Transformation (uptake of foreign DNA) shows DNA is hereditary material in prokaryotes and eukaryotes.
- DNA is accurately replicated prior to each cell division.
- DNA encodes proteins needed by the cell..
- DNA is capable of mutation, providing raw material for evolutionary change.
Prokaryotic and Eukaryotic Genomes
- Prokaryotic genomes are mostly single circular chromosomes
- Eukaryotic genomes consist of one or two sets of linear chromosomes confined to the nucleus.
- Eukaryotes have a larger amount of non-coding DNA interspersed with genes.
Viral Genomes
- Viruses are non-living particles.
- Viral genomes consist of nucleic acid (DNA or RNA) and protein.
- Viral genomes are compact with little spacer DNA.
- Some viruses are sometimes referred to as bacteriophages in prokaryotes.
Prokaryotic Genomes
- Typically circular double helix DNA
- Occupies nucleoid region and attached to membrane
- Genes in operons- coordinately regulated genes transcribed as a single molecule of mRNA
- Introns are rare
Eukaryotic Nuclear Genomes
- Each species has a characteristic chromosome number
- Ploidy refers to the number of complete chromosome sets.
- Haploid (1n) has one complete set, Diploid (2n) has two, Polyploid (≥3n) has three or more.
- In diploids, chromosomes come in homologous pairs (homologs)
- Homologous pairs share the same gene loci but can have different alleles causing different expressions of traits.
Eukaryotic Chromosomes
- Cytogenetics is the microscopic study of chromosomes/
- Chromosomes vary in size and number of genes.
- Centromere position varies (telocentric, acrocentric, metacentric).
- Telomeres are chromosome ends
- Nucleolar organizers are regions of DNA for rRNA.
Heterochromatin and Euchromatin
- Heterochromatin is densely stained, highly compact non-coding DNA.
- Euchromatin is poorly stained, less compact, contains transcribed genes.
Organization of DNA in the Nucleus
- Highly organised, various degrees of coiling
- Fundamental unit of chromatin is the nucleosome
- DNA wound around a histone core (octamer) composed of H2A, H2B, H3, and H4.
- 10 nm fiber (DNA coiled around histones).
- 30 nm fiber (solenoid structure)
- Higher order attachments to scaffolding containing topoisomerase II, forms larger diameter fibres
Comparative Genomics
- Study of similarities and differences among genomes.
- Genes are often shared among living things
- Study of "model" organisms provides info about genes.
- Large-scale genome projects yield significant biological information and require extensive computer analysis.
Nature of Genomes
- Genomics is the study of the structure and function of genomes
- Genome size can vary widely, impacting the number of genes, with a general trend of larger genomes correlated with higher complexity.
Viral Genomes
- Nonliving particle with genetic material (DNA or RNA) and proteins
- Compact genomes with little spacer DNA
- In prokaryotes, viruses are sometimes referred to as bacteriophages.
Cell Proliferation:
- Cell proliferation is critical for development and homeostasis.
- Stem cells divide in response to signals to replace dead cells.
- Cell death (apoptosis) is regulated by internal and external signals.
- Cancer arises from mutations and uncontrolled proliferation in one cell clone.
Cell proliferation and Elimination:
- Proliferation is regulated by the cell cycle checkpoints and protein kinases/phosphatases.
- Apoptosis is a programmed cell death activated by various signals.
- Proliferation and apoptosis pathways can be interrelated through phosphorylation, allosteric interactions, and interactions of protein subunits.
Extracellular Signals
- Mitogens (growth factors) stimulate cell cycle progression.
- Ligands can negatively regulate the cell cycle.
- Apoptosis-positive signals can come from neighboring cells.
- Survival factors can inhibit apoptosis.
Cancer
- Cancer results from aberrant cell cycle control.
- Cancer cells differ from normal cells.
- The genetic basis of cancer includes oncogenes, tumor suppressor genes, chromosomal abnormalities, and susceptibility genes.
- Mutations can alter the structure/function of oncogenes and tumor suppressor genes.
Mutations in Cancer Cells
- Mutations in oncogenes are typically dominant, while mutations in tumor suppressor genes are typically recessive.
- Chromosomal abnormalities can create oncogenes.
- Cells that lose ability to undergo apoptosis have longer time to accumulate proliferation-promoting mutations.
Oncogenes
- Oncogenes usually encode proteins that regulate cell proliferation or apoptosis.
- Normal cell regulation can lead to inappropriate protein activity if mutations build up in proto-oncogenes.
- Mutations in proteins, caused by changes (deletions, point mutations, etc.) in DNA sequences, can generate oncogenes.
Tumor Suppressor Genes
- These genes usually encode proteins that act as negative regulators for the cell cycle or as positive regulators for apoptosis.
- Tumor suppressor genes typically need loss-of-function mutations to have an effect.
Cancer Complexities
- Different cancers have unique phenotypes related to proliferation, metastasis, etc.
- Cancer types differ, based on somatic cell progenitors, mutations, etc
- Cancer research spans a wide array of disciplines to develop cures.
Cell Cycle regulation
- Cell cycle phases include G1(gap 1), S(synthesis), G2(gap 2), and M(mitosis).
- Cyclical protein expression and degradation regulate cell cycle activities.
- Cyclin-dependent kinases (CDKs) have substrate specificity, activity controlled by bound cyclins and regulate the cell cycle.
Steps of Mitosis
- The stages of the cell cycle before mitosis are called interphase
- Prophase to Telophase detail the process of nuclear and cell division
Meiosis
- A type of cell division producing haploid gametes (sex cells)
- Prophase I to Telophase II details the process of meiosis
- Genetic variation occurs through the process of homologous recombination
Viral Genomes
- Viruses consist of nucleic acid (DNA or RNA) and protein and are considered non-living
- Viral genomes are compact with little spacer DNA
- Viruses are sometimes referred to as bacteriophages
DNA Replication
- DNA strands are replicated with high fidelity.
- DNA replication errors can occur, but error-checking and repair systems are in place.
- Accurate replication is crucial for producing identical daughter cells- a key requirement for cell division
- DNA replication proceeds in the 5'-to3' direction
- DNA is continuously copied from the leading strand, via Okazaki fragments on the lagging strand.
- DNA helicases and single-stranded binding proteins help in opening and stabilizing the DNA template.
- DNA topoisomerases resolve stress caused by unwinding.
- DNA polymerases are needed for continuous synthesis
- Primers are produced by primase and are RNA
- Repair mechanisms aid in correcting mistakes and repairing damaged DNA.
- Replicated DNA is composed of one original strand and a newly synthesized strand (semiconservative)
- Replication forks, are where replicaton proceeds at each side of the unwound template.
DNA Damage and Repair
- DNA can be damaged in multiple ways (e.g. radiation, chemicals, alkylation, etc).
- Damage types vary in their effects (e.g., base modifications, pyrimidine dimers).
- Repair processes handle damage and include direct reversal, excision repair, and others.
Base Excision Repair
- Begins by removing damaged bases from DNA.
- DNA repair enzymes remove/replace the damaged region.
Nucleotide Excision Repair
- This system removes bulky DNA damages such as UV radiation-induced pyrimidine dimers.
- Damaged DNA region is excised and replaced by a new fragment.
Double-Strand Break Repair
- Double strand DNA breaks can be extraordinarily damaging to cells and requires specialized repair mechanisms.
- Homologous recombination and nonhomologous end joining are common methods eukaryotic cells use to repair double strand breaks after DNA replication.
Mismatch Repair
- Detection and correctino of incorrect base pairings during or after DNA replication
- The process recognizes the newly synthesized strand from the methylated parent strand
Coping with DNA Damage Without Repairing
- Some cellular damage is too severe for successful repair and requires methods such as damage bypass or replication of a damaged region
Recombination Repair
- Recombination allows for the copying of unreplicated DNA template across a repair gap
- Allows for the repair of damages that occur before the DNA is replicated
Error-Prone Bypass
- Cells use error-prone mechanisms that can introduce additional mutations during DNA replication to produce a complete copy of DNA when no other methods are able to.
Homologous Recombination
- Homologous recombination is crucial for: accurately repairing double-strand breaks, rearranging DNA segments, generating genetic variation during meiosis.
- Crossing over in meiosis involves the exchange of genetic material between homologous chromosomes.
Holiday Junction
- Transient four-stranded structure, a key intermediate, formed within recombining DNA strands during homologous recombination
How cells read the genome:
- Genetic information flows from DNA to RNA to protein
- Transcription and translation are the two primary processes needed to achieve this flow of information within the genes.
- RNA intermediates and various processing steps are used to produce functional protein products.
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Description
This quiz tests your understanding of cytogenetics and the structures of chromosomes, including differences between heterochromatin and euchromatin, nucleosome structure, and centromere positions. Assess your knowledge about telomeres, polytene chromosomes, G banding patterns, and the DNA length of human chromosomes.
