LDI Final Study Guide PDF

Quiz 1: What is science? Explain the Scientific Method and its parts (Observations, questions, hypothesis, predictions, experiments, independent/dependent/controlled variables, results, conclusions). Be able to recognize and generate each part on yo...

Quiz 1: What is science? Explain the Scientific Method and its parts (Observations, questions, hypothesis, predictions, experiments, independent/dependent/controlled variables, results, conclusions). Be able to recognize and generate each part on your own. What are the limitations of scientific inquiry? How do these contribute to the changes in our understanding of the natural world over time? What are the features of reliable scientific information? That is, how is scientific information validated? Explain what is meant by “Correlation does not equal Causation” and why this is important to keep in mind when reading scientific information. What is public health? Be able to give examples. What are major characteristic of life? What are the three parts of the cell theory? What are the four main structural components of all cells? What other characteristics or behaviors do they share? What is a model organism? What are benefits of using a model organism in research? What are the similarities and differences between prokaryotic and eukaryotic cells? Explain the hierarchical classification of life from Domains to Species. Be able to list and describe the 3 domains and 6 kingdoms. List the major chemical components of all cells. List and explain the 4 properties of water that result from its unique chemical structure. Describe the four groups of biomolecules from which all cells are made, including the names of the monomers and polymers of each biomolecule type. What are the key structural and functional features of each type of biomolecule and where is each found in cells? Be able to give examples of each type of biomolecule and their role in cells. Quiz 2: Describe the structure and function of each of the cellular organelles and other cellular structures (e.g. ribosomes, cytoskeleton). Be able to identify these structures and their correct locations in cells. Explain how scientists classify organisms composed of these different types of cells (Kingdom-Phylum-Class-Order-Family-Genus-Species). Compare/contrast cells from different prokaryotic and eukaryotic kingdoms in terms of their organelle structure and function. Explain why microscopes are needed to observe cell structures and why different types of microscopes (e.g., stereo, compound light, fluorescence, electron) might be better for viewing different cellular features. Explain 3 reasons why cells reproduce. Explain how cells know when to reproduce. Explain why cancer is considered diseases of uncontrolled cell reproduction Define and explain the differences between benign, malignant, and metastatic tumors in terms of their development and relation to cancer. Explain what is meant when we say cells are “immortal”. Define and explain the key steps in signal transduction and its importance to cell reproduction. Describe the major steps that must occur for 1 cell to become 2 daughter cells Explain the differences between prokaryotic and eukaryotic cells and the consequences for cell reproduction (asexual vs. sexual and binary fission vs. mitotic division vs. meiotic division). Explain the difference between sexual and asexual reproduction. Give examples of both types of reproduction. Explain how bacteria reproduce via binary fission. Explain what the mitotic cell cycle is and the two main phases that control both cell growth and cell division during this type of eukaryotic cell reproduction. Explain and be able to recognize and draw the 4 stages of mitosis and how they allow for chromosome separation into daughter cells. Compare and contrast cytokinesis in animal and plant cells. Quiz 3: Explain why progression through the cell cycle must be tightly regulated. Explain cell cycle checkpoints and what they are “checking”. Define the restriction point (in G1) and its relationship to growth factors and signal transduction. Give examples of other “stop” and “go” proteins that govern progression through cell cycle checkpoints. Explain how problems in cell cycle proteins can lead to cancer initiation and progression. Define and distinguish between these terms: somatic cell & gamete; autosome & sex chromosomes; haploid & diploid. Compare/contrast sexual and asexual reproduction. Describe and draw the events that characterize each phase of meiosis. Compare/contrast meiosis I, meiosis II, & mitotic division. Name and explain the three events that contribute to genetic variation in sexually reproducing organisms. Explain the potential consequences of non-disjunction in mitosis, meiosis and meiosis II Define basic cancer terms: benign, malignant, tumor, metastasis Explain the main controls on normal cell reproduction and how they are misregulated in cancer cells. Explain the roles of uncontrolled cell reproduction and invasion in the multistep progression that transforms normal cells into cancerous cells. Define and describe the basic structure of viruses and the two basic types of virus infection cycles. Describe the two ways by which viruses can promote cancer development – direct and indirect. Explain how the HPV virus promotes cancer by deregulating specific cell cycle checkpoints. Explain what a vaccine is and how an HPV vaccine could prevent cervical cancer. Generate, interpret, and explain means and standard deviation when analyzing and comparing data. Define tumor suppressor and (proto) oncogenes and explain their role in the cell cycle and cancer. Distinguish between the DNA code and the epigenome.  Describe how the expression of a gene can be regulated through epigenetic mechanisms. Predict how DNA methylation affects gene expression. Interpret graphical representations of data. Compare and contrast different types of cancer treatment, including surgery, radiation, and chemotherapy. Explain why cancers are so difficult to treat despite these treatments. Quiz 4: Define and be able to explain the current treatment options for cancer (surgery, radiation, and chemotherapy) Explain why one therapy, or combination of therapies, would be beneficial in certain treatment cases but not others. That is, explain the advantages and disadvantages of different types of cancer treatments or combinations of treatment for different therapeutic purposes. Explain the patient-specific factors affecting the potential response to chemotherapy. Explain how cell cycle dependent chemotherapy works including the roles these agents have in affecting cancerous cells over normal cells. Explain how what we know about chemotherapy agents and the cell cycle leads to chemotherapy toxicities. List the major societal groups that experience cancer health disparities and be able to give examples of disparities that could result from inadequate prevention, screening/detection, or treatment. List and be able to explain the reasons why such disparities exist and be able to give examples. Explain how many of the causes of these disparities can be linked to institutional, system racism. Describe some of the key areas where improvements can be targeted to combat the systemic roots of these disparities. Define the following terms: gene, allele, mutation, locus, trait, character, heredity, true breeding. Define and explain the difference between the following terms: dominant/recessive; heterozygous/homozygous; genotype/phenotype.  Explain how meiosis and random fertilization in sexual reproduction account for the ability of each parent to donate one allele per gene to their offspring. Define the terms “virus” and “vaccine”. Describe the three main types of vaccines [Parts of pathogen, killed/weakened version of germ, and blueprint (DNA/mRNA) versions] Distinguish influenza from other infectious diseases and explain why the influenza vaccine does not protect against all illnesses that might be commonly identified as “flu.” Explain why the flu vaccine is not recommended for all people while others are considered “high risk” individuals. Explain why antibiotics are for bacterial, not viral infections—and that secondary bacterial infections (which can be treated with antibiotics) sometimes follow a primary viral infection. Be able to identify and argue against vaccine misinformation. Explain the importance of DNA repair enzymes in protecting cells from UV light Explain how DNA damage is possible even with properly functioning repair enzymes Explain how UV exposure can lead to skin problems and cancers. Evaluate the protective effects of sunscreen components to protect yeast cells from UV-induced damage. Quiz 5: Define the following terms: gene, allele, mutation, locus, trait, character, heredity, true breeding. Define and explain the difference between the following terms: dominant/recessive; heterozygous/homozygous; genotype/phenotype. Explain how meiosis and random fertilization in sexual reproduction account for the ability of each parent to donate one allele per gene to their offspring. Use a Punnett square to predict the results of a cross (mating) and to state the expected phenotypic and genotypic ratios of the offspring. Explain how independent assortment during meiosis accounts for the independent inheritance of traits specified by genes on different chromosomes.  Define and explain how phenotypes in heterozygotes differ with complete dominance, incomplete dominance, and codominance Define and give examples of pleiotropy and polygenic traits. Define and explain sex-linked traits and how they affect transmission of traits from parents to children Explain the importance of DNA repair enzymes in protecting cells from UV light Explain how DNA damage is possible even with properly functioning repair enzymes Explain how UV exposure can lead to skin problems and cancers. Evaluate the protective effects of sunscreen components to protect yeast cells from UV-induced damage. Write scientifically testable hypotheses and predictions. Analyze and interpret qualitative and quantitative scientific data in graphic and/or numeric form. Determine if results support conclusions based on error bar overlap. Quiz 6: Be able to use a pedigree to determine whether a conditions is dominant or recessive, and autosomal or sex-linked. Explain why lethal dominant genes are much rarer than lethal recessive genes and why consanguineous marriages increase the risk of genetic disorders. Explain and give examples of multifactorial diseases that involve genetic and environmental factors. Explain the difference between spontaneous and hereditary cancers. Explain the difference between gatekeeper and caretaker tumor suppressor genes Explain how recessive mutations can lead to dominant cancer syndromes. Define tumor suppressor genes and oncogenes and explain how they relate to cell cycle control. Describe the mechanisms by which mutations in tumor suppressors and oncogenes may arise. Explain the direct versus the indirect role for oncogenes and tumor suppressor genes in causing cancer.  Describe the experimental contributions of the following people to the discovery and characterization of DNA as the genetic material: ○ Chargaff; Watson and Crick; Franklin Describe the structure of DNA in terms of the following: ○ Monomer composition, base-pairing ○ Double-stranded nature (complimentary & antiparallel) Explain the relationship between DNA, genes, and chromosomes, and between coding and non-coding regions of DNA Explain how the semi-conservative model for DNA replication is possible due to the complimentary nature of DNA base pairing. Explain the relationship between DNA replication and chromosome duplication during the cell cycle. Describe the two main sources of DNA mutations, as well as the three main ways that DNA is repaired. Explain the “end-replication problem” that results during DNA replication and how telomeres help to solve it. Describe telomerase and how its activation in certain cell types, including HeLa and other cancer cells, can lead to cellular “immortality” Explain how the transfer of chromosomes during meiosis and fertilization result in offspring with different kinds of traits. Explain how the kinds of alleles (variation) and organism has for various genes (its genotype) translate into the manifestation of the traits (its phenotype). Solve basic Mendelian genetics problems. Explain how DNA extraction works and what else would be needed to distinguish the DNA from different organisms. Define the following terms: locus/loci, allele, short tandem repeats (STRs), DNA profiling/fingerprinting, non-coding vs. coding DNA, allele frequency Know how STRs are used to build genetic profiles that can be used in forensic investigations. Explain that STRs are found across the genome; thus, the more STR loci used to build a genetic profile, the more confident investigators can be of a positive match between samples.  Interpret capillary electrophoresis (electropherograms) results by distinguishing DNA fragments by length and determining whether individuals are homozygous or heterozygous at different STR loci. Calculate allele frequencies and the probability of generating a match, at random, at one or more loci using allele frequency data. Quiz 7: Explain parts of a gene – coding and regulatory sequences & the basic path of information flow from gene to protein. Be able to compare/contrast DNA, RNA, and proteins in terms of their structure and function. Explain the basic structure of proteins and how the amino acid sequence determines protein shape and function Explain where transcription and translation happen in eukaryotic and prokaryotic cells Explain the process of transcription using these terms: ○ mRNA, RNA polymerase, transcription factors, promoter, terminator Explain the process of translation using these terms: ○ mRNA, tRNA, ribosomes, amino acids, codon/anti-codon Explain why the genetic code is universal, redundant, & unambiguous Define and give examples of the two main type of mutations – large chromosomal (block- changes and point mutations; give examples of each type Explain the potential effects of mutations in coding regions on protein structure, function, and expression. Explain the potential effects of mutations in non-coding regions on protein structure, function, and expression. Describe the potential benefits and harm of mutations and explain why many mutations are not passed on to offspring in sexually reproducing organisms. Describe why regulation of gene expression is critical for cellular and organism function. Explain how differential gene expression explains the diversity of cell types in a multi-cellular organism. List and describe the major steps in gene expression at which regulation can happen: i.e., chromatin structure protein degradation Define epigenetics and explain how epigenetic modifications such as DNA methylation and histone modification can impact gene expression.  Be able to use epigenetics to explain how identical twins (with identical genes) can have very different health outcomes. Explain the basics of planarian regeneration and ecological developmental biology Explain why planarians are a useful model system for studying regeneration Develop a testable hypothesis related to regeneration. Design a well-controlled quantitative experiment to test that hypothesis Collect, analyze, interpret and share both quantitative and qualitative data.