Unit 4 Genetics 3000
Positive assortative
similar genotypes more likely to mate than dissimilar ones
Restriction endonucleases are especially useful if they generate "sticky" ends. What makes an end sticky?
single-stranded complementary tails
Female spiders are usually significantly larger than male spiders. This phenomena is called
Sexual dimorphism
What are carcinogens?
Any substances or process that damages DNA has the potential to be carcinogenic
Programmed cell death or self destruction is called what?
Apoptosis
What are differentiated cells?
Are specialized for specific functions and are typically in a nondividing state (terminally differentiated)
What are the uses of PCR
Genetic testing Forensics Molecular pathology
Height in a species of plant is controlled by 4 genes with additive alleles. Which of the following is a genotype you would expect for a plant of average height?
aaBBCcDd
Proliferation
abnormal cells growth and division, loss of cell cycle regulation
Which of the following factors is typically monitored during the M checkpoint?
attachment of spindle fibers to kinetochores
Variance
average squared distance of all measurements from mean; provides information about spread of data around mean
Directional selection
extreme phenotype is favored - Traits at one end of spectrum of phenotypes become selected for or against (usually result in changes in environment) - Population mean shifts in direction of one extreme phenotype
G1/S:
checkpoints monitor cell size and determine whether DNA has been damaged; after G1 before S
Gene pool:
genetic information carried by members of population, most populations contain high degree of heterozygosity
Quantitative inheritance
genetic phenomenon; continuous variation can be measured in quantitative terms
Low fitness
genotypes of low rates of reproductive success
Additive variance (VA)
genotypic variance due to additive action of alleles at quantitative trait loci
Driver mutations
give growth advantage to tumor cells and facilitate cancerous growth - tumor suppressor and proto-oncogenes
Heritability estimate
gives proportion of phenotypic variation attributed to genetic variation within a certain population in a particular environment
White clover plants produce hydrogen cyanide gas in response to herbivore insects feeding on them, deterring or even killing them. Recently white clover in urban areas was found to lack this mechanism. Its thought that since there are less herbivore insects in urban areas, the plant can save energy and resources by not producing hydrogen cyanide. This would be considered an instance of ______.
microevolution
Transformation:
plasmids are introduced into bacteria via this
Prezygotic
prevent mating from taking place; individuals may not find each other or see each other as suitable mates
Realized heritability
selective breeding estimates potential success for artificial selection
CDK/cyclin complex
selectively phosphorylates and activates proteins to bring about necessary changes for cell cycle to continue
Origin of Replication
sequence that allows copies of plasmid to be made
Caspases
series of proteases responsible for initiating apoptosis and digesting intracellular components
genetic drift can arise through
the founder effect and a genetic bottleneck
Bioinformatics includes all of the following except
using enzymes to combine DNA from two different sources in a test tube.
Polygenic and polygenes
varying phenotypes result form input of genes at more than one loci
Cladogenesis
when a species splits into two new species
temporal/seasonal
when species breed at different times
Ecological
when two populations occupy different habitats
Multiple Cloning Site
where the gene of interest is inserted
How are restriction fragments put together?
DNA Ligase
what does the hardy-weinberg law assume?
- Equal rate of survival and reproduction (no selection) - No new alleles arise (no mutations) - No migration into or out of population (no gene flow) -Population is infinitely large (no genetic drift) - Random mating occurs (no sexual selection)
Plasmids used in DNA cloning:
- Genetically modified bacterial plasmids - first vectors developed - Engineered to contain: Multiple cloning sites: short sequences with restriction sites for common restriction enzymes
Glycomics:
complete set of carbohydrates
Proto-oncogenes
genes whose products promote cell growth and division
Migration (gene flow)
occurs when individuals move between populations
How does a BLAST search work?
- Calculates: --Identity value: determines sum of identical matches between aligned sequences divided by total number of bases aligned --E-value (expected value): a parameter that described the number of hits one can expect to see by chance when searching a database of a particular size -Genome sequences statistically similar to genes with known function likely encode for proteins with a similar function -Similarity searched can identify homologous genes --Orthologs and Paralogs
Benign Tumors
- Cell loses genetic control over cell growth - Result in multicellular mass - Removed by surgery, usually causing no serious harm
Pharmacogenomics
- Comparing genomic data and response to groups -Key parts of personalized medicine -Identifies genes involved in drug response and metabolism, which an be used to predict a patient's response to a drug - Tumor DNA sequencing can be used to find the best treatment options
What was the Human Genome Project?
- Coordinated effort to sequence and identity all genes of human genome - Project began in 1990 under James Watson - Francis Collins led project under coordination of NCHGR - $3 billion budget and 15-year plan - all human genes were to be sequenced and mapped (took 11 years and $1 billion)
Cloning vectors
- DNA molecules that accept DNA fragments - Can replicate cloned DNA fragments in host cell -Must be able to replicate independent of hist chromosome - Have several restriction enzyme sites to allow insertion of DNA fragment - Carry selectable gene marker/reporter gene to distinguish host cells that have taken them up from those that have not
Expression vectors:
- Designed to ensure mRNA expression of cloned gene - to produce many copies of encoded protein in host cell - Some plasmids only carry DNA and do not signal for protein - Available for prokaryotic and eukaryotic host cells: Ti plasmid and soil bacterium can be used for introducing genes in plants
Phenotypic variance
- Divided between genotypic and environmental variance - Genotype by environment interaction variance - Heritability estimates obtained using experimental and statistical methods -- Partitions Vp into genotypic variance (Vg) and environmental variance (Ve)
How is a PCR different from natural replication?
- Don't need initiator proteins, helicase, ss Binding proteins, gyrase: because heat denatures and keeps strands single - Don't need primase: artificial, premade primers are used - DNA polymerase III is still needed - Don't DNA polymerase I: primers are DNA, don't need to be replaced - Don't need ligase: only one primer attached to one strand, so there is no lagging strand or Okazaki fragments
What ingredients does a PCR reaction require
- Double strands target DNA - DNA polymerase - Mg2+ (cofactor of DNA polymerase) - Four deoxyribonucleoside triphosphates - Primers: Short, single-stranded sequences One complementary to 5' end and another complementary to 3' end
Epigenomics:
- Epigenetic marks can also be sequenced - Bisulfite sequencing for DNA methylation - Mass spectroscopy of histones
Individual Variation in the Human Genome
- Human genomic sequence is 99.9% the same with most genetic differences resulting from: --single-nucleotide polymorphisms (SNPs) → single base changes in genome, variations associated with disease conditions --Copy number variations (CNVs) → segment of DNA duplicated or deleted
How does artificial selection work? Why is it important?
- Humans choosing specific individuals with preferred phenotypes from initially heterogeneous populations for future breeding - purpose is to develop with a high frequency of individuals with desired traits - Artificial trait selection: --Can be polygenic and multifactorial (slower and more complex) --Traits for economic importance: ---Crops and livestock ---Grain yield in plant
What is natural selection
- Individuals exhibit variations in phenotype, variations are heritable, some phenotypes are more successful at survival and reproduce at higher rates - Traits that confer reproductive advantage will increase in frequency: --Will cause population to become better adapted to current environment --Natural selection doesn't produce better organisms, just organisms better adapted to the environment --Over time can result in appearance of new species
What is a molecular clock?
- Measure rate of evolutionary change - Measured in terms of amino acid or nucleotide sequences to estimate time of divergence from common ancestor
Broad sense heritability:
- Measures contribution of genotypic variance to total phenotypic variance (H ^2 = Vg/ Vp) - Estimates assume that the genotype by environment variance component is negligible
What are the uses of RT-PCR
- Methodology for studying gene expression (mRNA production by cells or tissues) - Reverse transcriptase is used to generate cDNA (c= complementary) from RNA (useful because DNA is more stable and easier to work with than RNA) - Method used to test for Covid
What are the steps for apoptosis?
- Normal cell gains irreparable DNA damage - Nuclear DNA becomes fragmented - Disruption of internal cellular structures - Dissolution of cell into small, spherical apoptotic bodies (prevents contents of the cell from damaging nearby cells) - Engulfing of apoptotic bodies by phagocytic white blood cells that recycle the cell's components -Caspases
How are gene annotated
- Once important sequences (enhancers, splice sites, etc.) are identified in the lab, genomic data can be analyzed to find other instances of that sequence - Sequences for similar or related genes can be compared to identify potential important sequences
What are the four major points of the multiple-gene hypothesis
- Phenotypic traits show continuous variation and can be quantified by measuring, weight, so on - Two or more loci show an additive effect on the expression of phenotype (polygenic inheritance) - Each gene loci is occupied by either additive or non additive allele - Additive alleles contribute to a single qualitative trait to produce substantial phenotypic variation
What is apoptosis? When does it happen?
- Programmed cell death - cells in a multicellular organism - Genetically controlled process - cell self destructs --Occurs when DNA damage is too severe to repair ---Prevents cancer --Eliminates cells not contributing to final adult organism ---Occurs during embryogenesis --Infected cells can also enter apoptosis
limitations of estimating heritability
- Provide no information on genes involved in traits - Measured in populations - limited application to individuals - Measured heritability: depends on environmental variation present in population being studied: --Cannot be used to estimate differences between populations - Future changes in environmental factors can affect heritbability
define PCR variants
- RT-PCR: reverse transcriptase; makes DNA complement using RNA - qPCR (quantitative PCR): amplification of different genes; can figure out how much is in an original sample; gene expression.
What is PCR (Polymerase Chain Reaction)
- Rapid method of DNA cloning - Extends power of recombinant DNA - Copies specific DNA sequence via in vitro (in glass) reactions: Amplifies target DNA sequences present in very small quantities in population of molecules; Sources include dried blood, semen, hair → forensics
How does migration affect genetic variation
- Reduces genetic differences between populations - Increases level of genetic variation within a population - Hardy Weinberg assumes that this does not take place
How does Next-Gen Sequencing use DNA synthesis to sequence DNA?
- Simultaneous reaction synthesize NDA from tens of thousands of identical strands - Use fluorescence imaging techniques to detect new strands - Generate massive amounts of DNA sequence data rapidly and at reduced costs
What is p53? What role does it play in cancer?
- TP53: Tumor suppressor gene -Most frequently mutated gene (50% of all cancers) --Encodes transcription factor p53: this represses or stimulates transcription of 50 different genes --Continuously synthesized but rapidly degraded - present at low levels --Increased levels due to posttranslational modifications made in response to DNA damage -Cells lacking p53 are unable to arrest at cell-cycle checkpoints or enter apoptosis -Cellular stress events increase p53 levels: --DNA damage --Double-stranded breaks in DNA --Presence of DNA - repair intermediates due to UV light
major findings of Human Genome Project
- There are less than 2% genome codes for proteins - There are probably only about 20,000 protein coding genes - Number of genes lower than the number of predicted proteins --Over 50% of genes undergo alternative splicing: produces multiple transcripts and proteins
What is shotgun sequencing and how does it work
- This is Whole-genome sequencing/ cloning - Current tech can only sequence short segments, so the genomic DNA is fragmented in short enough pieces. The pieces are then put back together using overlap - Most widely used strategy for sequencing and assembling an entire genome: --Genomic DNA cut with restriction enzymes to create series of overlapping fragments --Overlapping fragments aligned using computer programs to assemble entire chromosome --Fragments are aligned based on identical DNA sequences - creates contig
How can restriction enzymes be used in the laboratory?
- Used to construct and amplify DNA molecules - DNA-cutting enzymes; restrict or prevent infection by degrading DNA of invading virus
Metagenomics (environmental Genomics)
- Whole genome sequencing approaches used to sequences genome from communities of microbes in environmental sample of water, air, and soil - Oceans, glaciers, desserts, and so on are being sampled for this - many new species have been identified - Metagenomics used to create the microbiome - catalog of the microbes living in the human gut
Nutrigenomics
- field of nutritional science -Considers genetics and diet -Focuses on understanding interactions between nutrition and genes -Tests analyze your genome: -Provides customized nutritional report on nutritional metabolism based on genes associated with medical conditions
How does Sanger (dideoxy) sequencing work
- most common method of DNA sequencing; small amount of dideoxynucleotides are added - Dideoxynucleotides: deoxynucleotide with a H at 3' instead of hydroxyl group; causes DNA synthesis to terminant (terminated by ddNTP)
What is a restriction enzyme? How does it work?
- restriction enzymes: -DNA-cutting enzymes -Ligase: paste -Produced by bacteria as defense mechanism against infection by bacteriophage -Restrict to prevent infection by degrading DNA of invading virus -Bind to DNA at specific recognition sequence (restriction site) and cuts DNA to produce restriction fragments -Enzyme cleaves both strand of DNA (digestion) -They do not recognize methylated DNA, so they don't cut bacteria's methylated chromosomes
Accessing Human Genome Project
-Can access databases on internet that display maps for all human chromosomes -Most valuable contribution: --Identification of disease genes --Development of new treatment strategies --Extensive maps developed for genes implicated in human disease conditions
Mutated tumor-suppressor genes:
-Cells unable to respond to cell cycle checkpoints of undergo apoptosis -Leads to more mutations and development of cancer --When both alleles are inactivated, cells may become tumorigenic
What are some natural and artificial examples of carcinogens?
-Chemicals, radiation, some viruses, and chronic infections - natural: aflatoxin, Nitrosamines, Pesticides and antibiotics, Alkylating agents - Environmental agents also contribute to cancer development
applications of bioinformatics
-Comparing DNA sequences - Identify genes in genomic DNA sequence - Finding genes-regulatory regions (promoters and enhancers), identify telomeric sequences, predicting amino acid sequences, deducing evolutionary relationships
Passenger mutations
-Have no direct contribution to cancer phenotype - After the initial mutation that cause cancer, more mutations accumulate as the tumor develops and DNA regulation and repair breaks down
What is the role of mutations in the gene pool and changing allele frequencies?
-Mutation acts to create new alleles (changes allele frequencies) - Conditions must be met for accuracy when measuring significant force of changing allele frequencies: --Allele must produce distinctive phenotype that can be distinguished from similar phenotypes produced by other alleles --Trait must be fully expressed or completely penetrant so that mutants can be identified --Identical phenotype must never be produced by non genetic means
What types of genomic alternations are found in cancer cells?
-Single nucleotide substitutions -Large scale chromosome rearrangement Amplifications and deletions -Cancer caused by mutations in somatic cells --Only 5% of cancers are associated with germ-line mutations
Proto-oncogenes
-Transcription factors that stimulate expression of other genes related to growth and division -Signal transduction proteins that stimulate cell division -Cell-cycle regulators that move cell through cell cycle -Oncogenes are proto-oncogenes that have experiences gain of function alterations: --Promoter mutations that cause growth to be expressed continuously --Coding sequence mutations that cause growth factors to be always active -Only one allele of a proto-oncogene needs to be mutated of misexpressed to contribute to cancer (dominant cancer phenotype)
Opossums can be grey or white, with the grey allele being dominate. If the frequency of the grey allele is 0.6, what frequency do you expect for white opossums?
0.16
The frequency of a genetic disorder caused by a recessive allele is 0.01 in a population. What is the frequency of carriers are in the population?
0.18
In snapdragons, the red and white flower alleles exhibit incomplete dominance. If the frequency of the red alleles is 0.3, what frequency of pink flowers do you expect in the population?
0.42
How many gametes are involved in the formation of dizygotic twins?
4
Eye color in humans is a polygenic trait influenced by 16 genes. How many phenotypic classes of eye color would you expect?
33
A population of fish has and variety of body colors and patterns. After an oil spill, only white fish with red stripes remain. What is this an example of?
A genetic bottleneck
What is an open reading frame (ORF)?
A nucleotide sequence that is translated into a protein
Which of the following is used to calculate Narrow-sense heritability?
Additive variance
_______ tumors grow uncontrollably but do not metastasize..
Benign
Malignant tumors
Cells break loose, enter bloodstream invade other tissue - form secondary tumors (metastases) - life threatening
What can plasmid vectors be used for?
Cloning DNA with plasmid vector: - Plasmid DNA and DNA to be cloned are cut with the same restriction enzyme -DNA restriction fragments from DNA to be closed are added to linearized vector in presence of DNA ligase - Sticky ends anneal - Recombinant DNA is produced and introduced into bacterial host cells by transformation
What is metastasis?
Controlled by larger number of gene products: cell-adhesion molecules, cytoskeleton regulators, and proteolytic enzymes - ex: E- cadherin *Malignant cells not susceptible to normal controls conferred by regulatory molecules such as tissue inhibitors of metalloproteinases (TIMPs)
With regard to the critical checkpoints used to regulate the progression of the cell cycle, which of the following events occurs first?
Cyclins bind to and activate kinase enzymes.
All of these are known to cause cancer EXCEPT
DNA Repair
Extension:
DNA polymerase synthesizes DNA strands
What is the usefulness of estimating heritability?
Describes proportion of total phenotypic variation in population due to genetic factors - multifactorial traits -- High heritability attributed to genetic factors -- Low heritability attributed to environmental factors - Does not indicate how much of the trait is genetically determined of the extent to which an individual's phenotype is due to genotype
What is the Hardy-Weinberg law?
Describes what happens to allele and genotype frequencies in "ideal" populations *Genes that do not fit the model have one or more of these forces acting on them
In a species of Galapagos finch, thick beaked individuals excel at cracking nuts, while thin beaked individuals excel at picking out grubs from trees. Individuals with intermediate beaks aren't good at either task. This is an example of what?
Disruptive selection
The PCR (polymerase chain reaction) protocol that is currently used in laboratories was facilitated by the discovery of a bacterium called Thermus aquaticus in a hot spring inside Yellowstone National Park, in Wyoming. This organism contains a heat-stable form of DNA polymerase known as Taq polymerase, which continues to function even after it has been heated to extremely high temperatures. Why would such a heat-stable polymerase be beneficial in PCR?
Each cycle includes a "hot" denaturation phase (95°C), which separates the hydrogen bonds that hold the strands of the template DNA together.
Describe the steps in a PCR cycle,
First, the DNA is denatured at high temperature around 95 degrees C, which separates the DNA strands. Then, the DNA is annealed and the primers bind to the DNA strands around the temperatures of 40-60 degrees C. Lastly, the DNA is extended with the attachment of DNA polymerase off of primers, this is around 72 degrees C.
oncogenes
Gain of function mutations in Proto-oncogenes converting them into
Eukaryotic genes often contain introns, which are not present in prokaryotes, presenting an obstacle in expressing eukaryotic genes in bacteria. How is this issue dealt with?
Generating cDNA from a mature mRNA
The sequencing of the human genome led to the realization that chromosome 19 contains many genes while chromosomes 13 and Y contain relatively few. What does this finding imply about the density of genes in a genome?
Genes are not uniformly distributed and appear in clusters separated by gene deserts.
species
Groups of actually or potentially interbreeding organisms that can produce fertile offspring
Which is the correct order of experiments for creating recombinant bacteria? I. Use PCR to amplify a gene of interest.II. Transform bacteria with the plasmidIII. Perform a ligation reaction with the gene of interest and the plasmid.IV. Digest the gene of interest and a plasmid with restriction enzymes.
I -> IV -> III - > II
Briefly explain a topic you studied for this exam but weren't asked about. OR briefly explain your favorite topic from this unit
I enjoyed learning about the Human Genome project, which was a coordinated effort to sequence and identify all of the genes within a human genome. This began in 1990 under James Watson, with Francis Collins then leading the project with a $3 billion budget and a 15 year plan. It was discovered that 99.9% of the human genome is the same with the differences resulting from single-nucleotide polymorphisms and copy number variations. In addition, there are less than 2% of genome codes for proteins, only about 20,000 of protein coding genes, and the number of expected proteins was actually lower. I also thought it was interesting that anyone can access the database on the internet, and that this contributed to identifying disease genes and led to new treatment strategies.
The Philadelphia chromosome is a translocation between chromosomes 22 and 9 that leads to translation of a BCR-ABL fusion protein. The normal ABL gene is a proto-oncogene that codes for a kinase involved in a cell signaling pathway. How does this chromosome abnormality lead to cancer?
In the fusion protein, the ABL protein is always active.
A new gene is discovered during the sequencing of a bacterial genome. After a BLAST analysis, the new gene aligns with a known sequence from the same bacterium. The sequence identity is 95%. Which of the following statements best describes the relationship of the newly discovered gene and the known gene?
It is a paralog to the known gene and is a result of a recent gene duplication.
Which of the following describes an expression quantitative trait loci (eQTL)?
Lactose tolerance level is determined by lactase enzyme alleles with different mutations in the promoter that influence the gene's mRNA levels
Which of the following is an example of G x E interaction?
Lobsters with allele A grow larger than lobsters with allele a in cold water environments. In warm tropical waters lobsters with allele a grow larger.
All of the following are checkpoints in the cell cycle EXCEPT
M/G1
Which technique would be used to sequence the amino acids in a protein?
Mass spectrometry
You find the heritability of height of in a population water oak trees in upstate South Carolina to be 0.67. Your colleague finds the heritability of height of in a population water oak trees in south Alabama to be 0.44. How is this possible?
Measured heritability depends on environmental variation present in population being studied
Which of the following is not true about bisulfite sequencing?
Methylated cytosines are removed an replaced with artificial bases
The why is heritability of having two eyes very low?
Most of the variation in eye number is due to accidents and injuries
You are studying the Virginia opossum, Didelphis virginiana. You find 11 genes that influence the weight of newborn joeys, and that the mother's diet also influences birth weight. What term best describes this trait?
Multifactorial
What are the parts of a plasmid vector
Multiple cloning sites: short sequences with restriction sites for common restriction enzymes
How are restriction sites typically added to the ends of a gene?
PCR with primers containing restriction sites
Which of the following is an example of sexual selection?
Peahens prefer peacocks with large and colorful tails, so those peacocks get to mate more frequently.
Which of the following is NOT a major point of the multiple-gene hypothesis?
Phenotypic traits show discontinuous variation and can be cannot be quantified, only qualified
Which technique can make cDNA from RNA?
Reverse Transcriptase PCR (RT-PCR)
During what stage of the cell cycle is DNA replicated?
S
In which of the following biochemical reactions is it common to use ddNTPs (dideoxyribonucleoside triphosphates)?
Sanger sequencing
The human genome is predicted to have approximately 20,000 genes while the human proteome is predicted to have approximately 290,000 proteins. Which of the following is not an explanation for why the human proteome is so much larger than the human genome?
Some genes are duplicated in the genome.
What is the difference between standard deviation and standard error?
Standard error takes sample size into account
A species of beetles have different horn shapes. A group of two-pronged horn beetles are in log that floats to a remote island. A population of beetles form on the island and they all have two-pronged horns. What is this an example of?
The founder effect
Why are most replication proteins not needed for PCR?
The only replication protein needed for PCR is DNA polymerase III. This is because for the initiator proteins, DNA helicase, and single strand binding proteins, the heat used for PCR denatures the DNA and keeps the strands separate. DNA primase is not used because artificial, premade primers are used instead. DNA polymerase I is not used because primers are DNA, and therefore do not need to be replaced. DNA ligase is not used because only one primer attaches to one strand, so there is not lagging strand or Okazaki fragments.
Why isn't DNA polymerase I not needed for PCR?
The primers are made of DNA
You attempt to insert a gene into a plasmid and transform bacteria with the result using blue-white screening. All of the resulting colonies are blue. What happened?
The transformation worked, but the gene insertion didn't
How do heat shock and electroporation allow for transformation of bacteria?
These techniques destabilize the bacterial membrane, causing pores to open that foreign DNA can pass through.
Which of the following is an example of behavioral isolation?
Two groups of jumping spider don't mate because of differences in their courtship dances
How are viruses related to cancer?
Viral infection alone not sufficient to trigger human cancers, there needs to be additional mutations in oncogenes and tumor suppressor genes - HIV/AIDS
What is a cDNA molecule
a DNA copy of an RNA molecule produced by reverse transcription
Cancer is:
a genetic disease caused by an accumulation of mutations in somatic cells.
Quantitative trait loci (QTLs)
a locus that contains a gene or genes contributing to quantitative trait; are mapped by finding associations between DNA markers and phenotypes
Which statement best describes an example of a cancer causing mutation in a tumor-suppressor gene?
a mutation that makes a cell unable to undergo programmed cell death
Anagenesis
a period of no change when one species is transformed into another
Hybrid unviability:
an embryo is produced, but cannot survive developments
Fitness
an individual's genetic contribution to future generations
Reproductive isolation mechanisms
biological barriers that prevent or reduce interbreeding between populations
disruptive selection
both extremes are favored; reduction in intermediate - Selection against intermediate phenotypes - Results in population increasingly bimodal distribution for a trait - Two distinct populations form as a result of bidirectional selection
How does one target specific DNA sequences of the template to be amplified by polymerase chain reaction?
by designing primers complementary to regions on both sides of the specific target
Narrow-sense heritability and genetic variance
can be divided into subcomponents (additive, dominance, interactive variance)
Continuous variation
can be measured in qualitative terms
correlation coefficient 'r'
can standardize covariance, indicates if two traits both increase (r is +) or decrease (r is -) together
Correlation coefficient (r)
can standardize covariance, indicates if two traits both increase or decrease together (r is positive), or if one increases and the other decreases (r is negative)
Any agent that causes damage to DNA is a potential
carcinogen
Inbreeding
commonly affects genotype frequencies in population genetics - Mating among closely related individuals -- Increases proportion of homozygotes in population -- Completely inbred population theoretically will consist of only homozygous genotypes -- Detrimental recessive alleles can become more common, and the likelihood of being homozygous for those alleles also increases
Aligning genome sequences from different organisms to study gene and genome evolution is referred to as
comparative genomics
Toxicogenomics:
comparing genomic data and response to toxins
Comparative genomics:
comparing the genomes of different organisms to determine evolutionary relationships
Lipidomics:
complete set of lipids
Metabolomics
complete set of metabolites
Proteomes
complete set of proteins encoded by genome in a given cell type and/ord condition
Broad-sense heritability and Genetic variance
component includes all types of genetic variation in population
Genotypic variance
component includes all types of genetic variation in population -Can be divided into subcomponents --Additive variance --Dominance variance --Interactive variance
Using modern techniques of sequencing by synthesis and the shotgun approach, sequences are assembled into contigs by
computer analysis looking for sequence overlaps
Contigs
continuous fragments
Behavioral
courtship behavior unique to species are effective barriers to mating
Postzygotic
creates reproductive isolation even when members of two population mate with each other; hybrids are sterile or have lower fitness - hybrid unviability, sterility, and breakdown
Metastasis
defects in normal restraints that keep cells from spreading and colonizing other parts of body
What are the steps in PCR
denaturation, hybridization/annealing, extension - Each cycle results in amplification - products of previous cycle serve as templates for each subsequent cycle (chain reaction) (usually 30-35 cycles)
Which of the following correctly lists the processes in order for one cycle of polymerase chain reaction (PCR)?
denature DNA; anneal primers; extend primers
Standard error of the mean (SE)
described errors between mean determined for multiple samples of the same group, value always smaller than standard deviation, accounts for sample size
Standard error of the mean (SE)
describes errors between means determined for multiple sample of the same group, value always smaller than standard deviation, accounts for sample size
Tumorigenesis
development of a malignant tumor
A genetic bottleneck
develops when large population remains in place yet undergoes drastic but temporary reduction in numbers; populations may recover but with greatly reduced genetic diversity
Interactive variance (V1)
deviation from additive components that occurs when 2+ loci behave epistatically
Dominance Variance (VD)
deviation from additive components that results when phenotypic expression in heterozygotes is not precise
Hybrid sterility
difference species can produce a viable offspring, but the offspring cannot reproduce
Negative assortative
dissimilar genotypes are more likely to mate
Denaturation
dsDNA is denatured into single strands, heat up
mechanisms for reproductive isolation (these are also prezygotic)
ecological, behavioral, temporal/seasonal, mechanical
Microevolution
evolutionary changes within populations of species
Macroevolution
evolutionary events leading to emergence of new species and other taxonomic groups
Phylogeny
evolutionary history, genetic differences among present-day species can be used to reconstruct their evolutionary histories
Hybrid breakdown
first generation hybrids are viable, but subsequent generations have lower fitness
Speciation:
formation of new species caused by mutation, migration, and drift
M
formation of spindle fiber system and attachment of spindle fibers to kinetochores associated with centromeres are monitored; in metaphase of mitosis
Dizygotic (DZ)
fraternal twins, derived from two separate fertilization events
Paralogs
gene duplication events
Selectable Marker
gene that allows the identification of bacteria that have successfully been transformed and taken up the plasmid
High fitness
genes associated with high rates of reproductive success have this
loss of function mutations in tumor suppressor genes
genes for DNA repair enzymes (BRCA1), genes whose products regulate cell-cycle checkpoints and initiate process of apoptosis (TP53)
Polygenes
genes involved referred to as polygenes
Orthologs
genes separated by speciation
Population
group of individuals belonging to the same species, live in same geographic area, actually or potentially interbreed
Artificial selection
humans choosing specific individuals with preferred phenotypes from initially heterogeneous population for future breeding
When some varieties of rice are crossed, the hybrids are viable, but subsequent generations are smaller and have less fitness. This is an example of what?
hybrid breakdown
Monozygotic (MZ)
identical twins, derived from single zygote
Proteomics:
identification, characterization, and quantitative analysis of all proteins - Proteins are sequenced using mass spectrometry Proteins are digested into peptide fragments using proteases - The peptides are identified by their mass/charge ratio - Proteins are reconstructed using overlap and amino acid sequences predicted from DNA sequence data
A genetic bottleneck 12,000 years ago led to ______ in cheetahs, causing deleterious recessive alleles to become much more common.
inbreeding
stabilizing selection
intermediate phenotype is favored; reduced diversity -Both extremes are selected against -Reduces population variance over time but not the mean --Favors maximum adaptation to existing environment: reduces phenotypic variation and genetic diversity
One major difference between prokaryotic and eukaryotic genes is that eukaryotic genes can contain internal sequences, called ________, which get removed in the mature message.
introns
Cloning
making copies; making copies of DNA sequences, not whole organisms
Multiple- gene hypothesis
many genes, individually behaving in Mendelian fashion contribute to phenotype in a cumulative/quantitative way
Broad-sense heritability
measures contribution of genotypic variance to total phenotypic variance; estimates assume that the genotype-by-environment variance component is negligible
Covariance
measures how much variation is common to two quantitative traits
When sequencing a genome, coverage is the:
number of times a particular base is found in the same location in multiple reads of a sequence.
The founder effect
occurs when population originates from small number of individuals (usually migration), genesis carried by members of population are derived from founders
Discordant
one expresses trait while the other does not
"Good Genes" Hypothesis
ornamental traits in males are selected by females because they are linked to higher fitness
What is the name of the protein that appears to regulate the entry of cells into an S phase (along with other functions)? This protein is also known as the "guardian of the genome" and is mutated in ~50% of cancers
p53
Which type of mutation is known to accumulate in cancer cells but has no direct contribution to the cancer phenotype?
passenger mutations
G2/M:
physiological condition and DNA integrity are checked prior to mitosis; after G2 before prophase of mitosis
hybridization/annealing
primers bind to ssDNA - starting point for DNA polymerase to synthesize new DNA strands, lower temperature but is still hot
Nonrandom mating (sexual selection)
process in which individuals with certain inherited characteristics are more likely to acquire mates than other individuals of the same sex - Can result in sexual dimorphism: marked differences between the sexes in secondary sexual characteristics - "Good Genes" Hypothesis
What are two fundamental properties of cancer cells?
proliferation and metastasis *Normal cells have functions tightly controlled by genes expressed properly *Uncontrolled cell proliferation and metastatic spread makes cancer dangerous
Narrow-sense heritability
proportion of phenotypic variance due to additive genotypic variance alone
Narrow-sense heritability
proportion of phenotypic variance due to additive genotypic variance alone (h^2 = Va/ Vp)
Cycling
proteins produced at specific times during the cell cycle, the cell's internal clock
What type of gene encodes products that normally promote appropriate cell growth and division?
proto-oncogene
Mean (x-bar)
provides information on where central point lies along range of measurements for quantitative trait; average set of numbers
Multifactorial (complex traits)
quantitative (polygenic) traits, phenotypes result from both gene action and environmental influences
You are studying corn and find that higher stalk height is correlated with larger cob size. Which of the following r values would be expected for this relationship?
r = +0.78
what are the uses for qPCR
real time PCR allows researchers to quantify amplification reactions as they occur in real time
Clones
recovered copies of recombinant DNA
Cyclin-dependent kinases:
regulate synthesis and destruction of cyclin proteins
Genetic drift
significant random fluctuations in allele frequencies in small populations, possible by chance alone
BLAST (basic local alignment search)
software application used to compare DNA sequences
Standard deviation (s)
square root of variance, more than 95% of all values are found within 2 standard deviations to either side of mean, can be interpreted as form of probability
standard deviation (s)
square root of variance; more than 95% of all values are found within 2 standard deviations of either side of the mean, can be interpreted in form of probability
SS individuals have normal hemoglobin and are susceptible to malaria. Ss individuals have mostly normal hemoglobin and are resist to malaria. ss individuals have sickle cell anemia. This is an example of _______.
stabilizing selection
Transcriptomics
studies expression of genes by genome qualitatively and quantitatively - Quantitative: measures varying levels of expression of different genes - Qualitative: identifies which genes are expressed and which are not - RNA sequencing: --Whole transcriptome sequencing ---RT-PCR followed by shotgun sequencing --Allose for quantitative analysis of all RNAs expressed in tissue, organ, cell type, etc --Provides actual sequence data
Expression vectors differ from cloning vectors by ________.
the presence of necessary sequences to initiate transcription and translation (promoter, terminator, etc.)
Nutrigenomics is the study of
the relationship between diet and the genome
Mechanical
the shape of the male reproductive organ varies among species and is only compatible with that female species
Main techniques for transformation
these destabilize the bacterial membrane, causing pores to open that DNA can pass through - Using calcium ions and brief heat shock to pulse DNA into cells - Electroporation: a brief but high-intensity pulse of electricity to move DNA into bacterial cells
Concordant
twins are this for a given trait if either both or neither express trait
Bioinformatics
use of computer hardware and mathematical software applications to organize, share, and analyze biological data, particularly omics data
mean symbol
x- bar
