Untitled Flashcards Set

How can you work from a sequencing an autoradiogram to transcription to translation of protein?4 BACK: You should be able to work from a sequencing an autoradiogram to transcription to translation of protein for the exam4.

FRONT: How will mutation impact protein function?4 BACK: You should understand how mutation will impact protein function4.

FRONT: Review mono- and dihybrid crosses4 BACK: You should review mono- and dihybrid crosses4.

FRONT: Various types of dominance4 BACK: You should review the various types of dominance4.

FRONT: Multiple alleles4 BACK: You should review multiple alleles4.

FRONT: Epistasis4 BACK: You should review epistasis4.

FRONT: Design a drug or experiment to test gene function4 BACK: You should be able to design a drug or experiment to test gene function4.

FRONT: How would you regulate gene expression?4 BACK: You should understand how you would regulate gene expression4.

FRONT: How do cells inherit genetic material?5 BACK: You should understand how cells inherit genetic material5.

FRONT: What are steps of mitosis?5 BACK: You should understand the steps of mitosis5. (Note: Steps are listed in source20...).

FRONT: What are steps of meiosis?5 BACK: You should understand the steps of meiosis5. (Note: Steps are listed in source23...).

FRONT: How do changes to process result in disease?5 BACK: You should understand how changes to the process of cell division result in disease5.

Molecular Analysis and Biotechnology

Terminology

FRONT: Recombinant DNA7 BACK: Recombinant DNA7. (Note: Definition is provided in source27: techniques for locating, isolating, altering, and studying DNA segments, combining DNA from two organisms).

FRONT: Restriction enzymes7 BACK: Restriction enzymes7. (Note: Definition is provided in source27...: recognize and cut DNA at specific nucleotide sequences, produced by bacteria).

FRONT: Restriction sites7 BACK: Restriction sites7. (Note: Definition is provided in source28: Sequence recognized and cut by restriction enzymes, often palindromic sequences).

FRONT: Cohesive ends7 BACK: Cohesive ends7. (Note: Definition is provided in source28: fragments with short, single-stranded overhanging ends, also called sticky ends).

FRONT: Blunt ends7 BACK: Blunt ends7. (Note: Definition is provided in source28: even-length ends from both single strands).

FRONT: Engineered nucleases7 BACK: Engineered nucleases7. (Note: Definition is provided in source28...: protein consisting of part of a restriction enzyme that cleaves DNA, combined with another protein that recognizes and binds to a specific DNA sequence, custom designed to cut specific sequences).

FRONT: Zinc-finger nucleases7 BACK: Zinc-finger nucleases7. (Note: Defined as a type of engineered nuclease29: array of zinc-finger domains attached to a restriction enzyme, pairing of two ZFns increases specificity).

FRONT: Transcription activator like effector nucleases (TALEN)7 BACK: Transcription activator like effector nucleases (TALEN)7. (Note: Defined as a type of engineered nuclease29: protein of a type that normally binds to sequences in promoters is attached to a restriction enzyme).

FRONT: CRISPR7 BACK: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)7. (Note: Defined in source30: series of palindromic sequences separated by unique spacers).

FRONT: Effector complex7 BACK: Effector complex7. (Note: Defined in source30: cRNA and tracer RNA combined with Cas9 protein, recognizes protospacer-adjacent motif (PAM), unwinds DNA, and sgRNA pairs with and cuts DNA31).

FRONT: Homologous recombination7 BACK: Homologous recombination7. (Note: Described in source31 as a CRISPR-Cas9 system repair mechanism that occurs when a template is used, allowing insertion of donor DNA, although highly inefficient).

FRONT: Nonhomologous end joining7 BACK: Nonhomologous end joining7. (Note: Described in source31 as a CRISPR-Cas9 system repair mechanism where ends are joined without a template, which can introduce duplications and deletions, leading to frameshift mutations).

FRONT: Gel electrophoresis7 BACK: Gel electrophoresis7. (Note: Defined in source32: technique for separating charged molecules based on molecular size or charge, or both, nucleic acids stained with ethidium bromide or labeled prior).

FRONT: Probe7 BACK: Probe7. (Note: Defined in source33: DNA or RNA molecule with a base sequence complementary to a sequence of interest, pairs with the target sequence).

FRONT: Polymerase chain reaction (PCR)7 BACK: Polymerase chain reaction (PCR)7. (Note: Explained in source34: process with repeated steps of heating, primer annealing, and DNA synthesis by DNA polymerase).

FRONT: Gene cloning7 BACK: Gene cloning7. (Note: Uses listed in source35: amplify, alter, or manipulate sequences).

FRONT: Cloning vector7 BACK: Cloning vector7. (Note: Defined in source36: DNA molecule to which a foreign DNA fragment can be attached, allows foreign DNA into cells). Requirements: restriction enzyme site, origin of replication, selectable marker36.

FRONT: Linkers7 BACK: Linkers7. (Note: Defined in source36: small synthetic DNA fragment with one or more restriction sites, attach to ends of DNA to insert into a vector).

FRONT: Expression vectors8 BACK: Expression vectors8. (Note: Defined in source37: vector containing DNA sequences like promoters, ribosome-binding sites, and transcription initiation/termination sites, allows inserted DNA to be transcribed and translated).

FRONT: Transformation8 BACK: Transformation8. (Note: Screening cells for transformation success involves using a selectable marker in the plasmid and exposing cells to antibiotics37).

FRONT: In situ hybridization8 BACK: In situ hybridization8.

FRONT: Dideoxy sequencing8 BACK: Dideoxy sequencing8. (Note: Explained in source37...: uses a template to make new DNA with dNTPs and ddNTPs, synthesis stops when a ddNTP is used, products separated by gel electrophoresis).

FRONT: Illumina sequencing8 BACK: Illumina sequencing8. (Note: Explained in source38...: a type of next-generation sequencing similar to dideoxy, uses fluorescent tags attached to dNTPs (color indicates base), and chemical terminators that can be reversed).

FRONT: DNA fingerprinting8 BACK: DNA fingerprinting8. (Note: Uses microsatellites (STRs) and PCR to identify individuals39. Fragments separated by electrophoresis39. Homozygotes show one peak, heterozygotes two peaks40).

FRONT: Forward genetics8 BACK: Forward genetics8. (Note: Defined in source40: begins with a mutant phenotype and determines the gene causing it, traditional genetics study).

FRONT: Reverse genetics8 BACK: Reverse genetics8. (Note: Defined in source40: begins with a gene of unknown function and induces mutations to determine effect on phenotype).

FRONT: Targeted mutagenesis8 BACK: Targeted mutagenesis8. (Note: Defined in source41: mutations are induced at specific locations to study effects, can use CRISPR-Cas9).

FRONT: Site directed mutagenesis8 BACK: Site directed mutagenesis8. (Note: Defined in source41: short sequence cut out with restriction enzymes and replaced with a short sequence with mutation, requires restriction sites around the target).

FRONT: Oligonucleotide directed mutagenesis8 BACK: Oligonucleotide directed mutagenesis8. (Note: Defined in source42: oligonucleotide used to introduce a mutant sequence when restriction sites are not available, acts as a primer for replication, results in a percentage of cells with the mutated plasmid).

FRONT: Transgene8 BACK: Transgene8. (Note: Defined in source42: foreign gene or DNA fragment carried in germ-line DNA, a form of reverse genetics).

FRONT: Gene therapy8 BACK: Gene therapy8. (Note: Defined in source43: direct transfer of genes into human patients to treat disease, can use vectors like retroviruses, adenoviruses, AAV, or CRISPR-Cas9).

Concepts and Topics

FRONT: What are the four innovations since Watson and Crick’s discovery?8 BACK: The four key innovations since Watson and Crick's discovery are Recombinant DNA technology, Polymerase chain reaction (PCR), DNA sequencing technology, and Genome editing methods27.

FRONT: Can you calculate fragment sizes?8 BACK: You should be able to calculate fragment sizes8.

FRONT: Can you draw fragments on a gel?8 BACK: You should be able to draw fragments on a gel8.

FRONT: Can you explain the CRISPR-Cas9 system?8 BACK: You should be able to explain the CRISPR-Cas9 system8. (Note: Explanation involves CRISPRs, Cas9 protein, sgRNA, PAM, unwinding, cutting, and repair mechanisms like nonhomologous end joining and homologous recombination30...).

FRONT: Can you compare homologous recombination to nonhomologous end joining?8 BACK: You should be able to compare homologous recombination (uses a template, less efficient, allows insertion of donor DNA) to nonhomologous end joining (no template, can introduce indels) as repair mechanisms in the CRISPR-Cas9 system8....

FRONT: What are the advantages and limitations of CRISPR-Cas9 system?8... BACK: Advantages: precise editing due to sgRNA length, ability to multiplex, applicable to multiple species44. Limitations: mismatches lead to off-target cuts, mosaics in multicellular organisms, ethical concerns of editing germ cells, off-target cuts can lead to disease44.

FRONT: How has CRISPR-Cas9 been modified?9 BACK: CRISPR-Cas9 modifications include: single cuts for homology directed repair, staggered cuts for sticky ends (increase precision), single nucleotide insertions, modified Cas proteins to recognize different PAMs, inactivated Cas proteins to alter transcription, study experimental evolution, virus detection, monitor cell events (CAMERA)32.

FRONT: How are probes used to locate DNA fragments?9 BACK: Probes are DNA or RNA molecules complementary to a sequence of interest33. They pair with the target sequence33. Fragments (DNA or RNA) are cut with restriction enzymes, denatured, transferred to a membrane (Southern/Northern blotting)33, the membrane is placed in a solution with the probe, washed to remove unbound probe, and bands indicate size, abundance, or transcription location34.

FRONT: What is needed to run a PCR?9 BACK: PCR requirements are: DNA template, DNA Polymerase, Two RNA primers, dNTPs, and Buffer34.

FRONT: What are the steps of PCR?9 BACK: PCR steps are: 1) Heating (breaks hydrogen bonds), 2) Primers anneal, 3) DNA polymerase synthesizes new DNA. This cycle is repeated 20-30 times34.

FRONT: What are applications of PCR?9 BACK: PCR applications include: Virus detection, Environmental DNA, Population genetics, Criminal Investigation, and qPCR35.

FRONT: What are the limitations of PCR?9 BACK: PCR limitations are: must know part of the target sequence, high likelihood of contamination, no proofreading, fragments must be <2000 bp35.

FRONT: What are the three requirements for a plasmid to be a cloning vector?9 BACK: Requirements for a cloning vector: Restriction enzyme site, Origin of replication, and Selectable marker36.

FRONT: How can cells be screened for transformation success?9 BACK: Cells can be screened for transformation success because cells with the plasmid contain a selectable marker; exposing cells to an antibiotic allows measurement of growth37.

FRONT: Can you explain how ddNTPs are used for sequencing?9 BACK: In dideoxy sequencing, ddNTPs are used along with dNTPs. When a ddNTP is incorporated into a growing DNA strand, synthesis stops because it lacks the 3'-OH group needed to add the next nucleotide37. This creates fragments of different lengths ending in a specific ddNTP37....

FRONT: How do dideoxy sequencing and illumina sequencing differ?9 BACK: Both use templates and dNTPs/ddNTPs (or modified dNTPs)37.... Dideoxy sequencing separates fragments by gel electrophoresis after polymerization38. Illumina sequencing uses fluorescently tagged dNTPs with chemical terminators that are reversible; the color indicates the base, and fragments are amplified and sequenced on a flow cell38....

FRONT: Can you determine if someone is heterozygous or homozygous given a DNA fingerprint?9 BACK: In DNA fingerprinting using STRs and PCR, heterozygotes show two peaks (indicating two different fragment sizes), while homozygotes show one peak (indicating the same fragment size for both alleles)40.

FRONT: Can you determine which two DNA fingerprints are same from a group of DNA fingerprints?9 BACK: You should be able to determine which two DNA fingerprints are the same from a group9. (This is done by comparing the pattern and sizes of peaks/bands).

FRONT: How are transgenic mice developed?10 BACK: To develop transgenic mice, 100s of copies of DNA are injected into pronuclei of a fertilized egg42. The DNA randomly integrates into the chromosome via nonhomologous recombination42. Zygotes are implanted, and surviving offspring (and future generations) are studied for gene function45.

FRONT: How are knockout mice developed?10 BACK: Knockout mice have a normal gene fully disabled45. The gene is cloned, disabled (e.g., by inserting 'neo'), and linked to another gene (e.g., Herpes tk)45. The disabled gene is transferred to embryonic cells45. Homologous recombination may occur, replacing the normal gene46. Cells are screened with antibiotics46. Screened cells are injected into embryos, implanted, producing chimeric mice (wild-type and knockout cells)46. Chimeric mice are crossed to produce homozygotes46.

FRONT: What are the different ways gene function can be determined?10 BACK: Gene function can be determined using: Forward genetics (mutant phenotype -> gene), Reverse genetics (gene -> mutations -> phenotype)40, Targeted mutagenesis (mutations at specific locations)41, Creating Transgenic organisms (adding foreign DNA)42, Creating Knockout mice (disabling a gene)45..., and Silencing genes with RNAi46....

FRONT: What are advantages of silencing genes with siRNA?10 BACK: Advantages of silencing genes with siRNA are that a single copy of an siRNA gene will disable gene expression of both copies of the target gene47. The target gene remains intact, so silencing is reversible47.

FRONT: How has biotechnology been used to increase human well-being (medical, agricultural)?10 BACK: Biotechnology has been used for medical and agricultural improvements6. Medical: gene therapy to treat disease43, producing pharmaceutical products like proteins (e.g., human protein produced by bacteria transformed with a plasmid)48, RNAi to treat disease (e.g., reducing ApoB to lower cholesterol)48. Agricultural: plants resistant to viruses, pests, herbicides; increased size of animals used for food; modifying animals to produce human proteins43....

FRONT: What are the challenges of gene therapy?10 BACK: Gene therapy challenges include: transferring foreign genes, getting foreign genes to be expressed, limiting immune responses, only used in somatic cells, and ethical concerns43.

Epigenetics

Terminology

FRONT: Epigenetics11 BACK: Epigenetics11. (Note: Defined in source49: changes in gene expression or phenotype that are potentially heritable but do not alter the underlying DNA sequences).

FRONT: Epigenesis11 BACK: Epigenesis11. (Note: Defined in source49: how an embryo develops, creation).

FRONT: Epigenome11 BACK: Epigenome11. (Note: Defined in source49: epigenetic modifications within the genome of an individual).

FRONT: Methylation11 BACK: Methylation11. (Note: Refers to addition of a methyl group (CH3)50. DNA methylation (on cytosine) represses transcription51.... Histone methylation can activate or repress transcription depending on location50).

FRONT: Acetylation11 BACK: Acetylation11. (Note: Refers to addition of an acetyl group (CH3CO)51. Histone acetylation accelerates transcription by destabilizing chromatin, making DNA more available51).

FRONT: Epigenetic marks11 BACK: Epigenetic marks11. (Note: Induced pluripotent stem cells retain some epigenetic marks53).

FRONT: X inactivation center11 BACK: X inactivation center11.

FRONT: Xist11 BACK: Xist11. (Note: Transcription stimulated by Jpx on the inactive X chromosome53. Coats the X chromosome, inactivating it, suppressed in the active X54).

FRONT: lncRNA11 BACK: lncRNA11. (Note: lncRNAs can attract miRNAs so they are not available to bind to mRNA55).

FRONT: Tsix11 BACK: Tsix11. (Note: Expression stimulated by xite on the active X chromosome53).

FRONT: Jpx11 BACK: Jpx11. (Note: Jpx stimulates the transcription of Xist on the inactive X chromosome53).

FRONT: PRC211 BACK: PRC211.

FRONT: Pluripotency11 BACK: Pluripotency11. (Note: Defined in source53: property of being undifferentiated with the capacity to form every type of cell in an organism).

FRONT: Induced pluripotent stem cells11 BACK: Induced pluripotent stem cells11. (Note: Defined in source53: somatic cells artificially induced to dedifferentiate and revert to pluripotent stem cells, retain some epigenetic marks).

FRONT: Paramutation11 BACK: Paramutation11. (Note: Defined in source53: one allele of a genotype alters the expression of another allele, potentially heritably).

FRONT: Epialleles11 BACK: Epialleles11.

FRONT: Genomic imprinting11 BACK: Genomic imprinting11. (Note: Refers to differential expression of genetic material depending on whether it is inherited from the male or female parent56.... It evolved to influence gene expression in offspring based on parent's diet/environment13...).

FRONT: Genetic conflict hypothesis11 BACK: Genetic conflict hypothesis11. (Note: Hypothesis related to why genomic imprinting evolved12).

Topics and Concepts

FRONT: How is DNA modified? What happens when a methyl or acetyl group is added?12 BACK: DNA is modified by methylation (adding a methyl group)12.... Acetyl groups are added to histones, not DNA51. DNA methylation (on CpG islands) reduces/represses transcription51....

FRONT: How are histones modified? What happens when a methyl or acetyl group is added?12 BACK: Histones are modified by acetylation (adding an acetyl group), methylation (adding a methyl group), phosphorylation, and ubiquitination50. Histone acetylation accelerates transcription by destabilizing chromatin51. Histone methylation can activate or repress transcription depending on which tail and amino acid are methylated50.

FRONT: How is DNA methylation maintained during replication?12 BACK: During replication, the template strand remains methylated52. Methyltransferase recognizes the hemimethylated strand and methylates the newly synthesized strand52.

FRONT: What are the two hypotheses as to how histone modification is maintained during replication?12 BACK: You should understand the two hypotheses for how histone modification is maintained during replication12. (Note: The study guide does not detail these hypotheses).

FRONT: How is DNA methylation detected?12 BACK: DNA methylation is detected by treating genomic DNA with bisulfite, which converts unmethylated cytosine to uracil52. The DNA is then sequenced, and uracil is detected as thymine, revealing the original methylation status52.

FRONT: How does X inactivation occur?12 BACK: X inactivation is random54. Xist coats the X chromosome, inactivating it; Xist is suppressed in the active X chromosome54. Jpx stimulates Xist transcription on the inactive X53.

FRONT: What is the relationship between Tsix and Xist? What about Xist and Jpx?12 BACK: Tsix and Xist have a relationship in X inactivation12. Xist coats the inactive X54. Jpx stimulates Xist transcription on the inactive X53. Tsix expression on the active X (stimulated by xite) suppresses Xist53....

FRONT: Why aren’t iPSCs as good as stem cells?12 BACK: Induced pluripotent stem cells (iPSCs) retain some epigenetic marks from their original differentiated state53, which may make them less versatile or stable compared to embryonic stem cells.

FRONT: What is the process of paramutation?12 BACK: Paramutation is a process where one allele of a genotype alters the expression of another allele in a potentially heritable way53.

FRONT: Why did genomic imprinting evolve?12 BACK: The genetic conflict hypothesis is related to why genomic imprinting evolved12. It allows parents to influence gene expression in offspring based on their diet/environment13....

FRONT: What are examples of behavioral epigenetics?13 BACK: Behavioral epigenetics refers to epigenetic changes related to behavior13. Methylation and acetylation levels can change over a lifetime, affecting memory (less acetylation or increased methylation linked to reduced memory)58.

FRONT: How can environmental chemicals change gene expression?13 BACK: Environmental chemicals can change gene expression13.

FRONT: How does a parent diet impact the metabolic characteristics of offspring?13 BACK: A parent's diet can influence the metabolic traits of offspring via epigenetics13. For example, a low-protein diet in male parents led to offspring with increased expression of genes associated with cholesterol metabolism58.

Developmental Genetics and Immunology

Terminology

FRONT: Totipotent cell14 BACK: Totipotent cell14. (Note: Defined in source59: cell that has the potential to develop into any cell type).

FRONT: Determination14 BACK: Determination14. (Note: Defined in source59: cell becomes committed to a particular cell fate (what the cell becomes)).

FRONT: Egg-polarity genes14 BACK: Egg-polarity genes14. (Note: Transcribed into mRNA during oogenesis60, establish morphogen concentration gradients in the embryo60, involved in establishing dorsal-ventral and anterior-posterior axes60...).

FRONT: Segmentation genes14 BACK: Segmentation genes14. (Note: Control differentiation of the embryo into individual segments62). Include Gap genes, Pair-rule genes, and Segment-polarity genes62.

FRONT: Homeotic genes15 BACK: Homeotic genes15. (Note: Determine the identity of segments63, activated by protein concentrations from genes associated with segmentation63).

FRONT: Morphogen15 BACK: Morphogen15. (Note: Egg-polarity genes establish morphogen concentration gradients in the embryo60).

FRONT: Gap genes15 BACK: Gap genes15. (Note: Segmentation genes that divide the embryo into broad regions62). Mutation eliminates a group of segments62.

FRONT: Pair-rule genes15 BACK: Pair-rule genes15. (Note: Segmentation genes that develop alternate segments63). Mutations cause deletion of either even or odd numbered segments63.

FRONT: Segmentation-polarity genes15 BACK: Segmentation-polarity genes15. (Note: Segmentation genes that develop individual segments63). Mutations cause deletion and replacement with a mirror image63.

FRONT: Homeobox genes15 BACK: Homeobox genes15. (Note: Encode DNA-binding proteins with a regulatory role in transcription64. Hox genes are a type of homeobox gene64).

FRONT: Hox genes15 BACK: Hox genes15. (Note: Encode transcription factors that help determine the identity of body regions64. Similar in fruit flies and mammals16).

FRONT: Sepals15 BACK: Sepals15. (Note: Parts of a flower, whorl 164, controlled by Class A genes65).

FRONT: Petals15 BACK: Petals15. (Note: Parts of a flower, whorl 265, controlled by Class A and Class B genes65).

FRONT: Carpels15 BACK: Carpels15. (Note: Parts of a flower, female reproductive whorl 465, controlled by Class C genes65).

FRONT: Stamen15 BACK: Stamen15. (Note: Parts of a flower, male reproductive whorl 365, controlled by Class B and Class C genes65).

FRONT: Class A genes15 BACK: Class A genes15. (Note: Control flower development, expressed in whorl 1 (sepals) and whorl 2 (petals)65).

FRONT: Class B genes15 BACK: Class B genes15. (Note: Control flower development, expressed in whorl 2 (petals) and whorl 3 (stamen)65).

FRONT: Class C genes15 BACK: Class C genes15. (Note: Control flower development, expressed in whorl 3 (stamen) and whorl 4 (carpels)65).

FRONT: Apoptosis15 BACK: Apoptosis15. (Note: Defined in source65: controlled, programmed cell death. DNA is degraded, nucleus/cytoplasm shrink, cell engulfed by macrophage, no release of contents65. Involves caspases66. Triggers include viral infection, DNA damage, mitochondrial damage, improperly folded proteins66. Survival factors inhibit caspases66).

FRONT: Necrosis15 BACK: Necrosis15. (Note: Defined in source66: injured cells dying in an uncontrolled manner. Cell swells, bursts to release contents, causes inflammatory response67).

FRONT: eyeless gene15 BACK: eyeless gene15. (Note: Controls eye development in fruit flies67. Similar to small eye in mice and Aniridia in humans67).

FRONT: Antigen15 BACK: Antigen15. (Note: Defined in source68: molecules that elicit an immune reaction).

FRONT: Antibodies15 BACK: Antibodies15. (Note: Defined in source68: proteins that bind to antigens and mark them for determination by phagocytosis). Produced by B cells68. Have heavy and light chains, constant and variable regions, binding sites69.... Diversity generated by somatic recombination and alternative splicing70....

FRONT: Humoral immunity15 BACK: Humoral immunity15. (Note: Defined in source68: production of antibodies by B cells).

FRONT: Cellular immunity15 BACK: Cellular immunity15. (Note: Defined in source68: depends on T cells).

FRONT: Clonal selection15 BACK: Clonal selection15. (Note: Process where appropriate lymphocytes (B/T cells) recognizing an antigen divide, leading to a primary immune response. Memory cells remain for a faster secondary response upon re-exposure68...).

FRONT: Primary immune response15 BACK: Primary immune response15. (Note: Production of antigen-specific B and T cells following the first exposure to an antigen, part of clonal selection69).

FRONT: Secondary immune response15 BACK: Secondary immune response15. (Note: Faster and stronger response upon re-exposure to an antigen due to memory cells69).

FRONT: Memory cells15 BACK: Memory cells15. (Note: Cells that remain in circulation after the primary immune response, allowing a faster response if the same antigen reappears69).

FRONT: T cells15 BACK: T cells15. (Note: Involved in cellular immunity68. Have receptors that bind both histocompatibility antigens (MHC) and specific foreign antigens72. Release molecules to destroy target cells72).

FRONT: B cells15 BACK: B cells15. (Note: Involved in humoral immunity, produce antibodies68).

FRONT: Autoimmune disease15 BACK: Autoimmune disease15. (Note: Examples listed are Multiple sclerosis, Lupus, Insulin dependent diabetes mellitus16).

FRONT: Multiple sclerosis15 BACK: Multiple sclerosis15. (Note: An autoimmune disease where the body attacks its own tissues16...).

FRONT: Lupus15 BACK: Lupus15. (Note: An autoimmune disease where the body attacks its own tissues16...).

FRONT: Insulin dependent diabetes mellitus16 BACK: Insulin dependent diabetes mellitus16. (Note: An autoimmune disease where the body attacks its own tissues16...).

FRONT: T cell receptors16 BACK: T cell receptors16. (Note: Have alpha and beta chains held by disulfide bonds, variable region binds antigen71. Alpha chain has V, J, C segments; Beta chain has V, D, J, C segments71. Undergo somatic recombination71).

FRONT: Immunoglobulin16 BACK: Immunoglobulin16. (Note: Another name for antibody69).

FRONT: Somatic recombination16 BACK: Somatic recombination16. (Note: Process in mature lymphocytes where V segments move to a new location near J segments, generating antibody and T cell receptor diversity70...).

FRONT: Immune rejection16 BACK: Immune rejection16. (Note: Can occur with organ transplants if MHC antigens don't match, immune cells attack the foreign organ72).

FRONT: MHC antigens16 BACK: MHC antigens16. (Note: Major Histocompatibility Complex antigens. Proteins that provide identity to an individual's cells71. T cell receptors bind both MHC and foreign antigens72. Matching MHC antigens is important for organ transplants72).

FRONT: Histocompatibility16 BACK: Histocompatibility16. (Note: Related to MHC antigens, compatibility between donor and recipient cells16...).

Topics and Concepts

FRONT: Can you identify when and where the various genes/proteins are expressed that lead to the proper development?16 BACK: You should be able to identify when and where developmental genes/proteins are expressed, including egg-polarity genes (oogenesis, concentration gradients)60, segmentation genes62, and homeotic genes (after fertilization, activated by segmentation genes)63.

FRONT: What happens when there is a mutation in segmentation or homeotic genes?16 BACK: Mutations in segmentation genes lead to problems with segment formation (e.g., Gap mutations eliminate groups of segments, Pair-rule mutations delete alternate segments, Segment-polarity mutations delete/replace parts of segments)62.... Mutations in homeotic genes lead to incorrect segment identities (e.g., Antennapedia complex affects head/anterior thorax, Bithorax complex affects posterior thorax/abdomen)64, such as legs growing on the head64.

FRONT: How are Hox genes similar in fruit flies and mammals?16 BACK: Hox genes are a type of homeobox gene64 and encode transcription factors that determine body region identity64. They are similar across fruit flies and mammals16, reflecting common ancestry and conserved developmental roles.

FRONT: What happens to flowers when there are mutations in the homeotic genes (Class A, B, C)?16 BACK: Mutations in flower homeotic genes (Class A, B, C) cause misplacement or absence of flower parts16. (Note: The study guide lists gene expression patterns for normal development: Class A (whorls 1 & 2), Class B (whorls 2 & 3), Class C (whorls 3 & 4)65. Mutations would alter these patterns, e.g., A mutation affects sepals/petals, B mutation affects petals/stamen, C mutation affects stamen/carpels).

FRONT: How do apoptosis and necrosis differ in terms of cell death?16 BACK: Apoptosis is controlled, programmed cell death involving DNA degradation and cell engulfment without releasing contents65. Necrosis is uncontrolled cell death from injury, where the cell swells, bursts, and releases contents, causing inflammation66....

FRONT: How do developmental genes differ across species? How are they similar?17 BACK: Developmental genes can differ across species, but many core genes, like homeobox/Hox genes, are similar (conserved) across diverse animals (fruit flies, mammals), indicating common ancestry and conserved roles in fundamental processes like body plan development16.... Differences in expression or function of these genes contribute to species diversity67.

FRONT: For the autoimmune diseases listed above (Multiple sclerosis, Lupus, Insulin dependent diabetes mellitus), what tissues are attacked?17 BACK: For autoimmune diseases listed (Multiple sclerosis, Lupus, Insulin dependent diabetes mellitus), the body's own tissues are attacked16.... (Note: Specific tissues are not listed in the provided sources).

FRONT: Can you compare somatic recombination and alternative splicing?17 BACK: Both somatic recombination and alternative splicing are processes that increase diversity in the immune system17. Somatic recombination occurs in mature lymphocytes to rearrange DNA segments (V, J, C, D) for antibody and T cell receptor genes70.... Alternative splicing occurs on the pre-mRNA transcript of the light chain gene, allowing different combinations of segments to be included, further increasing antibody diversity71.

FRONT: Why do organ donors have to be a “match” for the recipient? What happens if they do not match?17 BACK: Organ donors have to be a "match" (as many MHC antigens as possible) because MHC proteins provide identity to an individual's cells71.... If the organs do not match, the recipient's immune system recognizes the foreign MHC antigens, and immune cells attack the foreign organ, leading to immune rejection72. Anti-rejection medications are used to inhibit this response72.

Cancer Genetics

Terminology

FRONT: Benign tumor17 BACK: Benign tumor17. (Note: Defined in source73: groups of cells that cannot spread to other parts of the body).

FRONT: Malignant tumor17 BACK: Malignant tumor17. (Note: Defined in source73...: tumor consisting of cells that invade other tissues, serious cancers).

FRONT: Metastasis17 BACK: Metastasis17. (Note: Defined in source73: movement of cells that separate from malignant tumors to other sites, where they form new tumors).

FRONT: Oncogenes17 BACK: Oncogenes17. (Note: Defined in source74: mutated proto-oncogenes that contribute to cancer development75). Often encode proteins in signal transduction pathways76.

FRONT: Proto-oncogenes17 BACK: Proto-oncogenes17. (Note: Defined in source74: normal cellular genes that are important for cell division and growth, can mutate into oncogenes). Drivers that contribute to cancer development75.

FRONT: Tumor-suppressor genes17 BACK: Tumor-suppressor genes17. (Note: Defined in source74: normal cellular genes that inhibit cell division or promote apoptosis). Mutation or loss contributes to cancer development73.... Examples include p53 and RB76.

FRONT: Aneuploidy17 BACK: Aneuploidy17. (Note: Abnormal number of chromosomes).

FRONT: Translocation18 BACK: Translocation18. (Note: Chromosomal rearrangement where a segment of one chromosome is moved to another). Can be a type of chromosomal abnormality associated with cancer73.

FRONT: Duplication18 BACK: Duplication18. (Note: Chromosomal abnormality where a segment of a chromosome is repeated).

FRONT: Deletion18 BACK: Deletion18. (Note: Chromosomal abnormality where a segment of a chromosome is lost).

FRONT: Inversion18 BACK: Inversion18. (Note: Chromosomal abnormality where a segment of a chromosome is reversed).

FRONT: Clonal evolution18 BACK: Clonal evolution18. (Note: Process where tumor cells accumulate mutations over time, and those with advantageous mutations (drivers) outgrow others, leading to increased proliferation and malignancy74).

FRONT: Loss of heterozygosity18 BACK: Loss of heterozygosity18. (Note: When an individual is heterozygous for a tumor suppressor gene, but the normal allele is lost or inactivated in a somatic cell, leaving only the mutated allele).

FRONT: Haploinsufficiency18 BACK: Haploinsufficiency18. (Note: When a single functional copy of a gene is not sufficient to maintain normal function, often relevant for tumor suppressor genes where one mutated copy can increase cancer risk).

FRONT: Cyclin18 BACK: Cyclin18. (Note: Proteins that regulate the cell cycle77. Their concentration increases during specific cell cycle stages77. They combine with CDKs to activate cell cycle transitions77).

FRONT: Cyclin-dependent kinases (CDKs)18 BACK: Cyclin-dependent kinases (CDKs)18. (Note: Enzymes that bind to cyclins to regulate cell cycle transitions77. They phosphorylate target proteins77).

FRONT: Signal transduction pathway18 BACK: Signal transduction pathway18. (Note: Defined in source76: external signals trigger a cascade of intracellular reactions producing a specific response. In cancer, proteins encoded by oncogenes are often involved76. Steps involve receptor components: extracellular, transmembrane, and intercellular domains76).

FRONT: Angiogenesis18 BACK: Angiogenesis18. (Note: Formation of new blood vessels, which tumors require to grow and metastasize).

FRONT: Telomerase18 BACK: Telomerase18. (Note: An enzyme that extends telomeres. Telomerase activity is high in cancer cells, contributing to their immortality19). A driver mutation75.

FRONT: Passengers18 BACK: Passengers18. (Note: Defined in source75: mutations that arise randomly during tumor development but do not contribute to cancer progression, often in untranscribed or untranslated regions).

FRONT: Drivers18 BACK: Drivers18. (Note: Defined in source75: mutations that directly contribute to cancer development, including proto-oncogenes, tumor suppressor genes, telomerase genes, etc.).

FRONT: Retroviruses18 BACK: Retroviruses18. (Note: A type of virus that can contribute to cancer19. They integrate their RNA genome into the host DNA19). Used as a vector in gene therapy43.

Topics and Concepts

FRONT: What evidence is there for the genetic theory of cancer?18 BACK: Evidence for the genetic theory of cancer includes: specific cancers consistently associated with particular chromosome abnormalities (e.g., translocation, duplication, deletion, inversion)18..., some cancers running in families (though cancer itself isn't inherited, predispositions are)73, and the discovery of mutations in genes (like p53 mutations) associated with cancer73.

FRONT: Can you explain Knudson’s multistep model?18 BACK: Knudson's multistep model states that cancer is a multistep process requiring multiple mutations in the same cell73. For some cancers, like retinoblastoma, this involves at least two mutations (the "two-hit hypothesis"), often affecting both copies of a tumor suppressor gene73. Tumors develop through clonal evolution, accumulating driver mutations74....

FRONT: How do tumors develop?18 BACK: Tumors develop through a process of clonal evolution74. Cells acquire initial mutations (drivers) that give them a selective advantage (like increased proliferation)75. These cells expand, accumulating additional driver mutations and random passenger mutations75. Clones with the most advantageous mutation combinations outcompete others, leading to uncontrolled growth and potentially malignancy and metastasis73....

FRONT: What environmental factors show the strongest link to cancer development?18 BACK: The study guide mentions environmental factors influence cancer development18, but does not list specific factors with the strongest link.

FRONT: How do environmental factors influence the development of cancers?18 BACK: Environmental factors influence cancer development18. (Note: The study guide does not provide details on how, but such factors often cause mutations or epigenetic changes).

FRONT: Can you explain how each step of the cell cycle is regulated? What do mutations in this pathway lead to?19 BACK: Cell cycle steps are regulated by checkpoints and proteins like cyclins and CDKs19.... The G1 to S transition involves RB binding transcription factors; increased cyclins combine with CDKs to phosphorylate RB, releasing the transcription factor needed for replication genes77. The G2 to M transition involves cyclins binding CDKs to form inactive MPF, which is activated by dephosphorylation and phosphorylates proteins for mitosis77. Mutations in this pathway, like in RB or cell cycle checkpoint genes (p53), can lead to unregulated cell proliferation and cancer76.

FRONT: What are the steps of a signal transduction pathway?19 BACK: Steps of a signal transduction pathway involve an external signal binding to a receptor with an extracellular domain, triggering reactions via a transmembrane and intercellular domain, leading to a specific intracellular response76. Proteins encoded by oncogenes are often involved76.

FRONT: What is the relationship between DNA repair gene and cancer?19 BACK: DNA repair genes maintain genome integrity19. Mutations in DNA repair genes lead to an increased accumulation of mutations, which increases the likelihood of mutations in proto-oncogenes and tumor suppressor genes, thereby increasing cancer risk19.

FRONT: How do microRNAs regulate cancer?19 BACK: MicroRNAs (miRNAs) regulate gene expression78. Less miRNA is associated with higher cancer rates, especially in late-stage tumor development19.... They can regulate translation by inhibiting initiation or causing ribosome stalling/premature termination55.... They can also help degrade mRNA78....

FRONT: What is the relationship between telomerase activity and cancer?19 BACK: Telomerase prevents chromosome shortening in germ cells80. In somatic cells, telomeres shorten with each division80. Cancer cells often have high telomerase activity, which maintains telomere length, allowing them to divide indefinitely and contributing to immortality19. Telomerase genes are considered drivers75.

FRONT: What role does epigenetics play in cancer?19 BACK: Epigenetics plays a role in cancer19. Evidence includes mutations in genes that regulate epigenetic changes in chromatin75. Epigenetic modifications like DNA methylation and histone modifications can alter gene expression of proto-oncogenes and tumor suppressor genes, contributing to cancer50....

FRONT: Can you describe the most common pathway for colorectal cancer?19 BACK: The study guide lists the most common pathway for colorectal cancer as a concept to study19, but does not describe the specific steps in the provided source.

FRONT: How do DNA viruses and retroviruses differ?19 BACK: DNA viruses and retroviruses differ in how they replicate and interact with the host genome19. Retroviruses (like HIV) have an RNA genome that is reverse transcribed into DNA and integrated into the host DNA18. DNA viruses (like HPV) have a DNA genome that replicates in the host cell.

FRONT: How do viruses contribute to cancer?19 BACK: Viruses (both DNA viruses and retroviruses) can contribute to cancer19. They can insert oncogenes into the host genome or disrupt host tumor suppressor genes, leading to uncontrolled cell growth.