True or False: Most cancers involve mutations in the germ-line
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genomic instability, DNA repair failure, chromatin modifications
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Which of the following general mechanisms appear to be involved in the formation of cancer cells?
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False
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True or False: A single mutation is capable of rendering a cell malignant.
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True
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True or False: Oncogenes, not proto-oncogenes, contribute to the development of cancer.
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Oncogene
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If Ras gains a mutation such that the protein product is always activated, then that gene is a(n)
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the accumulation of several mutations
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The genetic basis for cancer is usually
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failure to undergo apoptosis, genomic instability, the inability to control cell division, reduced ability to repair DNA damage
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Hallmarks of many cancer cells inculde
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Tumor-suppressor gene
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You have identified a mutation in your cell line in the lab that causes unregulated growth of the cells. This mutation is dominant and, when transfected into other cells, causes the unregulated growth phenotype. Further, you now know it produces a protein product. What type of gene has this mutation most likely effected?
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is a normal response to severe DNA damage. (Programmed cell death)
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Apoptosis
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may stimulate either apoptosis or the arrest of the cell cycle
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Protein p53
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that metastatic tumors are caused by malignancy genes
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Calling cancer a "genetic disease" means what?
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Abnormal proliferation, and capable of metastasis
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Fundamental properties of cancerous cells
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Abnormal cell growth and division
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Proliferation
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defects in the normal restraints that keep cells from spreading and colonizing other parts of the body
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Metastasis
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when a cell loses genetic control over cell growth and it grows into a multicellular mass
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benign tumor
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a life threatening tumor that has the ability to break loose, enter the blood stream, and form secondary tumors
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Malignant tumor
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give growth advantage to tumor cells
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Driver mutations
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mutations that may be acquired over time and have no direct contribution to cancer phenotype
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passenger mutations
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all cells in 1er and 2er tumors, ALL originated from a single ancestral cell that had many cancer-causing mutations
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Clonal
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encode transcription factors that stimulate expression of other genes, signal transduction molecules that stimulate cell division, and cell cycle regulators that move the cell through the cell cycle
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Proto-oncogenes
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abnormally mutated proto-oncogene that causes cancer
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Oncogene
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genes whose products normally regulate cell cycle checkpoints or initiate the process of apoptosis
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tumor suppressor genes
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RNA virus that causes cancer in animals
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Retrovirus
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integrated DNA copy of the retroviral RNA
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provirus
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DNA created by joining pieces of DNA together that come from different sources
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Recombinant DNA
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gene of interest, a plasmid, some restriction enzymes
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To use recombinant DNA technology you need...
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produced by bacteria as a defense against bacteriophages, Recognize and bind to DNA at specific nucleotide sequences
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restriction enzymes
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DNA molecules that accept DNA fragments and replicate these fragments when the vector is introduced into a host cell.
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DNA vector (cloning vector)
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Independently replicates in host cell, Number of restriction sites that allow insertion of DNA, Contain a selectable marker to determine if host cell has taken up vector, Easy to recover vector from host cell, because you might want to do something with the DNA that you inserted.
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Properties of a vector
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same version of a given gene (allele) (# of eyeballs)
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Monomorphic
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different versions of a given gene (color of eyeballs)
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Polymorphic
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gene exists in more than one form
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Genetic variation
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they can arise spontaneously: through error in DNA replication, can be induced by something in the environment (mutagen)
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What causes gene mutations?
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study of patterns of genetic variation in natural population
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Population genetics
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if allele frequencies are changing in a population form one generation to the next, it's evolving
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Microevolution
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p^2+ 2pq+q^2=1
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Hardy-Weinberg equation
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one generation to the next allele frequencies are not changing and gene frequency is not changing
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in a non evolving population
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the population is not evolving
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if a population is in Hardy-Weinberg equilibrium
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natural selection
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adaptive evolutionary mechanism
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process in which individuals with certain heritable traits survive and reproduce more than those individuals lacking those traits
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Natural selection
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a population is able to adapt to its environment through genetic variation for fitness-related traits
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Evolution can only occur if
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no possibility to adapt to the environment
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no variation=
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FALSE: you will never have a genotype that allows you to survive in every environment
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true or false: Certain genotypes can survive in every environment
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characterized by random changes in the genetic conditions of a population. It can lead to genetic divergence between populations
effects tend to be strongest in small populations
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Genetic drift
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involves transfer of alleles into and out of a population which occurs when the individuals are moving between populations that have different allele frequencies
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Gene flow
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Genetic drift, gene flow
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non-adaptive evolutionary mechanisms
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decrease in genetic variation
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What does genetic drift lead to?
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a population is suddenly reduces to a small number of individuals and alleles are lost from the population as a result
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Bottle neck effects
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a small group of settlers or "founders" break off from the main population and establish a new one in a new territory
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founder effects
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increase i genetic variation and reduces difference in allele frequencies across populations.
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What does gene flow lead to?
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genetic variation
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The most important concept in the field of population genetics is
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all alleles for every gene in a population.
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A gene pool is
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Allele and genotype frequencies are stable from generation to generation.
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If a population is in Hardy-Weinberg Equilibrium, we'd expect
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false
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TRUE or FALSE: A population with primarily monomorphic genes has a greater potential to adapt to environmental stressors, and thus evolve, than a population with polymorphic genes.
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false
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TRUE or FALSE: All evolutionary mechanisms result in populations becoming better adapted to their environments.
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Frequency of the genotype (bc it has to have two copies) so it is Squared
p^2+ 2pq+ q^2=1
q^2= 0.0064..........√q^2=0.08
p+q=1
p=0.92
2pq= 2(0.08)(0.92)
=0.147
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Consider rare disorder in a population caused by an autosomal recessive mutation. From the frequencies of the disorder in the population given, calculate the percentage of heterozygous carriers:
A.0.0064
B.0.000081
What must be assumed in order to validate the answers in this problem?
In a population where only the total number of individuals with the dominant phenotype is known, how can you calculate the percentage of carriers and homozygous recessives?
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the first vectors developed: extrachromosomal: DNA that replicate independently from bacterial chromosome
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Bacterial plasmids
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•similar structure to lactose,
•when it is cleaved it is blue. if lacZ is transcribed/translated β-galactosidase will cleave it and it will be blue.
•if DNA is successfully inserted lacZ will be disrupted and it will turn white
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X-gal
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Bacterial colonies with recombinant plasmids will be white
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What color will X-gal be if successfully inserted
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collection of cloned DNA sectioned into Genomic library or cDNA library
* must screen the libraries. can do this using probes
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DNA libraries
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a collection of the total genomic DNA from a single organism, contain all coding and non-coding regions of DNA
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Genomic Library
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contain only expressed genes, made through reverse transcription
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cDNA library
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rapid method of cloning that extends power of recombinant DNA technology, and sometimes eliminates need to use host cells: Target DNA sequences present in low amounts in sample, amplify in presence of DNA polymerase, Mg2+ , dNTP's, and primers
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Polymerase chain reaction (PCR)
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Short sequences of DNA that are complementary to the target DNA
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primers
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1)Need to know about target sequence to design primers
2)Amplifies small sections (< 4kb)
3)Contamination problems
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Limitations to PCR
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go from mRNA to cDNA
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RT-PCR (reverse transcriptase PCR)
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how many transcripts
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qRT-PCR(quantitative real-time PCR)
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Dideoxynucleotide chain termination sequencing
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Sanger sequencing
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1) No mutation introducing new alleles into the population
2)No survival or reproductive advantage for any genotype
3)An infinitely large population size
4)No influx of alleles from neighboring populations
5)Random mating
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Five conditions of Hardy-Weinberg Equilibrium
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change in base pair sequence
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What is a gene mutation?
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can be spontaneous or induced
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How do gene mutations arise?
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Beneficial: usually phenotypic to be better suited for an environment
Neutral: doesn't really effect the individual
Harmful: like tumors
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How can mutations be sometimes beneficial, while others can be harmful, and still others be neutral?
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•change in one base pair to another.
•a mutation that can be mapped to a single locus. •A mutation that results in substitution of one nucleotide for another.
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Point mutation
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Mismatch repair: Involves correction of replication errors not caught by proofreading. Original DNA is methylated, new strand not yet
Base and nucleotide excision repair: Glycosylase realizes that uracil shouldn't be there and removes it.Polymerase and ligase fill in.
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How does your body fix mutations (DNA repair mechanisms...)?
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investigates patterns of genetic variation wihtin and among groups of inbreeding individuals.
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Population Genetics
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If it is not in Hardy-Weinberg equilibrium then it is evolving
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How do you know if a population is evolving (it has to do with HW equilibrium...)?
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random (error in DNA replication)
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Spontaneous mutations
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resulting from external or artificial source
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Induced Mutations
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NOT heritable
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Mutations in the Somatic cell
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IS heritable
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Mutation in the germ cell
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if a pyrimidine replaces a pyrimidine or a purine replaces a purine
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transition mutation
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if purine replaces pyrimidine or vice versa
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transversion mutation
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the frame of triplet reading is altered due to the addition or loss of a single nucleotide
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frameshift mutation
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a change of one nucleotide of a triplet within a protein-coding portion of a gene may result in the creation of a new triplet that codes for a different amino acid in the protein product
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missense mutation
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triplet is changed into a stop codon resulting in the termination of translation of protein
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nonsense mutation
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Bases can exist in several chemical forms, that differ only in a single proton shift
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tautomeric shift
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frameshift
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A class of mutations that results in multiple contiguous amino acid changes in proteins is likely to be which of the following?
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True
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TRUE or FALSE: Not all mutations results in negative phenotypic consequences.
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false
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TRUE or FALSE Gene mutations in somatic cells are heritable.
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phosphodiester
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Ionizing radiation is capable of breaking __________ bonds in the DNA.
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false
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TRUE or FALSE All errors made by DNA polymerases are corrected by proofreading mechanism
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passenger mutations
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Driver mutations provide a growth advantage to a tumor cell. Which type of mutation is known to accumulate in cancer cells but has no direct contribution to the cancer phenotype?
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oncogenes
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Mutant versions of genes that are normally involved in promoting the cell cycle are known as
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p53
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What is the name of the protein that appears to regulate the entry of cells into an S phase? This protein is also known as the "guardian of the genome."
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Ras
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Example of a proto-oncogene
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p53
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example of tumor suppressor gene
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false
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TRUE or FALSE Cancer can be caused by a single gene mutation.
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false
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TRUE or FALSE A cell in a benign tumor has the ability to start a secondary tumor.
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single-stranded complementary tails
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Restriction endonucleases are especially useful if they generate "sticky" ends. What makes an end sticky?
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multiple cloning site
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Some vectors such as pUC18 and others of the pUC series contain a large number of restriction enzyme sites clustered in one region. Which term is given to this advantageous arrangement of restriction sites?
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assembling a DNA sequence from an mRNA
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In the context of molecular genetics, reverse transcription PCR (RT-PCR) refers to
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OH; 2′; 3′
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A ddNTP, used often in DNA sequencing, lacks a(n) ________ at the ________ and ________ carbons
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FALSE
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TRUE or FALSE The antibiotic resistance gene located in the cloning vector ultimately allows you to determine whether the gene of interest was successfully inserted into said vector.
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TRUE
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TRUE or FALSE If the lac Z gene is disrupted in the vector, then X-gal will not be cleaved.
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FALSE
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TRUE or FALSE A genomic DNA library contains only the expressed genes in a cell.
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false
answer
TRUE or FALSE Natural populations choose to adapt to their environment by way of natural selection.
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true
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TRUE or FALSE Having a phenotype (with a heritable genetic basis) that makes you fitter in one environment will not necessarily make you fitter in every environment.
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false
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TRUE or FALSE Gene flow is an example of an adaptive evolutionary mechanism.
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reduce genetic variation within a population, and lead to divergence between populations
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genetic drift can
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heterozygous
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In the Hardy-Weinberg equation:
p2 + 2pq + q2
2pq represents the frequency of ______________________ in the population?
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Genetic diversity may better adapt a population to inevitable changes in the environment.
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A number of mechanisms operate to maintain genetic diversity in a population. Why is such diversity favored?
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evolutionary change within populations of a species
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microevolution
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