FINAL EXAM BIO375 VOCAB and QUIZZES
No population
In nature ____ meets all the criteria for HW equilibrium
C) some donor strands will be inserted with an incorrect orientation
In producing a recombinant plasmid to be used to clone a given donor insert, it is possible to cut both the donor and plasmid with the same restriction enzyme, resulting in complementary sticky ends. Assuming plenty of plasmid DNA is available, why is further selection necessary before the introduction of the plasmid into a cellular system? A) Contamination will have introduced other donor inserts. B) Some donor inserts will be single stranded and deteriorate. C) Some donor strands will be inserted with an incorrect orientation. D) Some donor inserts will be sensitive to particular antibiotics. E) Some donor pieces will remain uninserted.
B) identification of a gene of interest followed by screening for mutations in that gene and studies of the phenotypes caused those mutations
In reverse genetics, what is the correct order in which the experimenter proceeds? A) random bombardment of the DNA with a known mutagen, followed by observation of offspring for newly acquired traits B) identification of a gene of interest followed by screening for mutations in that gene and studies of the phenotypes caused those mutations C) screening individuals by PCR/ DNA sequencing to associate altered genes with the trait of interest D) selection of mutants with a phenotype of interest and then mapping to locate the effected gene(S) E) silencing the genes in question using RNAi, followed by mapping to locate the gene
D) the antibiotic resistance gene is encoded in the vector
In selecting recombinant bacteria, cells are chosen that are resistant to a specific antibiotic. How are the bacteria made resistant? A) Resistance is activated by the recombination event. B) The antibiotic resistance gene is encoded on the donor insert. C) Resistance is activated when the cells are provided with the antibiotic D) The antibiotic resistance gene is encoded in the vector. E) They are pre-selected for the experiment on this basis.
C
In the Hershey-Chase experiment, bacteriophages were produced in either 32P-containing or 35S-containing medium. Where were these isotopes eventually detected when the radioactively- labeled bacteriophages were introduced to a fresh bacterial culture? A) Both 32P and 35S were associated with the bacterial cells. B) The 32P was associated with the culture medium and 35S was associated with the phage particles. C) The 32P was associated with the bacterial cells and 35S was associated with the phage particles. D) The 32P was associated with the culture medium and 35S was associated with the bacterial cells. E) Both 32P and 35S were associated with the phage particles.
Rest (arrest), continue to divide, differentiate, apoptosis
"Fates" of cells after each round of mitosis during development
transposable genetic elements
"Jumping genes" DNA sequences thatcan move within the genome by enzyme driven process, transposition
mutations
"biochemical changes in the gene makeup; may change nature and/or the amount of product made by the gene; not all bad- ultimate source of genetic variation
replicative transposition
"copy and paste" of the tranposon
nonreplicative transposition
"cut and paste" of the transposon
Translesion DNA polymerases
"error-prone" polymerases have no proofreading ability, and can replicate acorss lesion that would stall DNA polymerase II
embryonic stem cells
"pluripotent," can produce all the cells of the body
conordance
% of twin pairs that both have the same phenotype for a trait
discordance
% of twin pairs that have a dissimilar phenotype
large inflammatory immune response
(...seen in CD) may be caused by other immune system proteins later recognizing the invader
termination stem loop
(3-4 stem loop) halts RNA polymerase progress along the DNA within the leader reigon
cas
(CRISPR associated protein) DNA endonuclease cuts creating a double-strand
Retrotransposons
(Class I transposable elements) are composed of DNA by transpose through an RNA intermediate; RNA copied into DNA by reverse transcriptase; reverse-transcribed DNA inserts into a new location where flanking direct repeats are formed
DNA transposons
(Class II transposable elements) transpose as DNA sequences and may be replicative and nonreplicative
DNA profiling
(DNA fingerprinting, forensic genetic analysis) utilizes the genetic variation present in individuals to make identifications Used for: 1. Paternity testing: 2. Forensic applications: analyzing biological evidence from crime scenes; identifying human remains
square root method
(assumes HW equilibrium) A gene has two alleles, dominant and recessive; the trait is recessive q term calculated as the square root of the frequency of the homozygous recessive class, and p is calculated and 1.0-q
allele, genotype
(inbreeding self fertilizing plants) ____ frequencies remain the same but, ____ frequencies change each generation
lod score
(logarithm of the odds ratio) based on analysis of transmission in pedigrees; determined the likelihood of linkage for many recombinant frequencies called theta value
Allelic differences
(polymorphisms) are the ultimate cause of phenotypic differences between individuals of a species
variance
(s^2) a measure of the spread of distribution around the mean- interprets how much variation within the sample sum of square of the difference between each individual value and mean divided by the degrees of freedom, number of independent variables
depurination
(spontaneous error) loss of a purine from a nucleotide by breaking the covalent bond linking the nucleotide base to a sugar
synthetic lethality
(synthetic enhancement) where two single mutations are viable but a double mutant is inviable
hereditary disease may be due to
- A single gene mutation that causes the hereditary disease - A mutation in one (or more) of multiple genes that cause the hereditary disease - Multi-factorial: A combination of genes plus the influence of outside factors (environment) causes the onset of the disease
Genetic Variations include
- Single nucleotide polymorphisms - structural variations, such as insertions and deletions (indels) and inversions - copy-number variant (CNV) repeated section of genome
the wild type phenotype restored
- an organisms tat recieves the wild type version of the mutated gene will have?
3 principal ways that chromatin remodelers move nuecleosomes
- cause nucleosomes to slide along DNA or remove them from DNA, usually uncovering enhancers or promoters - cause nucleosome repositioning, silencing transcription - can change the composition of histones, activating gens
Golden rice
- edible part lacks several important micronutrients - endosperm synthesizes a precursor in carotenoids synthesis
gene therapy human sickle cell
- expression of the yamanaka factors to reprogram the cells into iPS cells - homologous recombination gene replacement and CRISPR-Cas genome editing - use "disarmed" viral vectors to target cells
genome architecture
- genomes vary enormously in size and gene number - gene number generally increases with organismal complexity - genomes also vary in proportions of coding vs noncoding sequences
constructing DNA libraries
- genomic DNA is isolated and fragmented into smaller pieces - ligated into cloning vectors and transformed into bacteria - collectively contain clones representing all sequences from the genome - mRNA sequences cannot be cloned directly for cDNA libraries
main genetic consequences of inbreeding in a population
- increase in frequency of homozygous genotypes - decrease in frequency of heterozygous genotypes
genetic consequences of inbreeding for populations
- increase in homozygous genotype frequency - decrease in heterozygous genotype frequency
four primary modes of organellar gene inheritance
- maternal inheritance of organelles - paternal inheritance of organelles in gymnosperms - selective degradation or silencing of organellar DNA from on parent (chlamydomonas) - biparentla inheritance (saccharomyces)
maternal inheritance in mammals
- mothers and all their children share identical MT DNA - MT DNA can trace maternal lineages
L1 elements
- particularly common LINES (long interspersed nuclear elements) that are associated with spontaneous human mutations - encode a protein with nuclease and reverse transcriptase function and may also encode a second RNA binding protein ~600,000/genome that vary in length from 6.5-8 kb; full length
molecular cloning
- plasmid cloning vectors replicate independently of bacterial chromosome and always remain separate - equipped with an origin of replication -contains genes for a trait that permits bacteria with the plasmid to be selectively grown - recombinant DNA amplified by repeated cycles of DNA replication
Human genome project
- started in 1990 using "clone by clone" - applied WGS in 1998 - "draft" of human genome in 2000
sources of error that lead to inaccurately high heritability values
- stronger shared maternal effects in MZ than dz twins - differences in treatment between MZ and DZ twins - greater similarity of G x E interactions in MZ than DZ twins
rna polymerase binds to
-10 and -35 sequences
Procedure of Ames test
-bacteria are exposed to experimental compounds in the presence of purified mammalian liver enzymes and plated on a medium lacking histidine - number of reversion mutations from his- to his+ are assayed - most commonly strains of Salmonella typhimurium are used
basic mechanism of organellar genome inheritance
-based on uniparental or biparental transmission - genetically determined and independent of the type of parent
Holliday Model (1964)
-first model of meiotic recombination important features: - now known that meiotic recombination is initiated by double strand breaks in DNA and ds breaks that initiate recombination are not spontaneous. they are generated by enzymatic activity
four technologies of reverse genetics
-genome editing -homologous recombination and insertion mutations - RNA interference -TILLIN
transmission depends on
-growth, division and segregation of the organelles themselves - division and segregation of nucleoids in the organelle - replication of the individual organellar genomes
two guiding principles of speciation by Charles Darwin
-hereditary variation exists in all species and control phenotypic variability - natural selection allows for increased survival and reproduction in individuals with favored phenotypic attributes
cloning genes by complementation
-identify genes by complementation of a recessive mutant phenotype by introduction of a wild-type gene -transformation efficiency is important
3 basic classifications of hereditary disease
-mendelian conditions (single genes, basic inheritance patterns) - chromosomal conditions - multifactorial conditions
RNA interference
-method for silencing a gene of interest -dsRNA complementary to the target gene can be introduced into cells or organisms by injection, by infection with a dsRNA virus or via a transgene carrying DNA that will produce dsRNA -mRNA from the target gene will be degraded through the action of DIver and argonaute enzymes
evolution and application of RNAi in eukaryotes
-protects genomes against mutational effects of transposable genetic elements
chloroplast genome
-structure similar to bacteria and mitochondria - generally circular but some linear ones are kown - less diverse than MT genomes ~120-200 kb in size, encodes 100-250 genes - always encodes rRNA - tRNAs encoded in the CP
biparental inheritance in yeast
-yeast that can grow with aerobically or anaerobically - mitochondrial mutations do not prevent growth of yeast cells but cause them to grow more slowly than wild type (petite vs grande)
mistmatch repair by MutS and MutH in ecoli
1) MutH binds to hemimethylated DNA 2) MutS binds to a base-pair mistmatch and attracts MutL, and the complex contacts MutH 3) MutH cleaves the unmethylated (new) DNA strand, generating a single strand gap 4) the gap is filled by DNA polymerase activity to repair the mismatch
SDSA (synthesis dependent strand annealing) process
1) double stranded break 2) digestion at the ends of broken strands, binding of Rad51 3) formation of D loop for new replication 4) new strand synthesis using intact strands as template 5) duplex reformed, strands are ligated
movement of transposable genetic elements
1) excision of the new elements from its original location and insertion in a new locations 2) Duplication of the element and insertion of the copy in a new location
evolutionary genomics steps
1) gene duplication 2) gene duplication by unequal crossover 3_) exon shuffling 4) reverse transcription 5) derivation of exons from transposable elements (TE) 6) lateral gene transfer 7) gene fission/ fussion 8) de novo derivation from noncoding sequence
(steps) forward genetics
1) genetic screen mutagenesis 2) mutant phenotype 3) identify function of gene sequence
two modes of allosteric actions
1) some repressor proteins undergo inactivation of their DNA-binding domains through allosteric changes after binding an inducer at the allosteric site 2) other repressors undergo activation of the DNA-binding domain upon allosteric binding to a corepressor
characteristics of transposition events
1) staggered cuts are made in both strands of DNA at the new target site for transposable element insertion (leaves short single stranded overhangs) 2) ds-transposable element inserted into new site 3) DNA replicated at new site of insertion (to fill ss gaps) producing flanking direct repeats
insertion of a DNA transposon
1) staggered cuts cleave the DNA strands of the target sequence 2) single stranded ends result from staggered cuts of the target sequence 3) the transposable element is inserted into the target sequence 4) the gaps are filled by dna polymerase
mechanisms of positive control of Transcription
1) the DNA-binding domain is inactive until an allosteric effector compound binds and induces a conformational change 2) certain activator proteins have a DNA-binding domain that is converted to inactive state by binding on an inhibitor
HW predictions
1. Allele frequencies remain stable over time 2. Alleles distribution into genotypes is predictable 3. Stable equilibrium frequencies of alleles and genotypes are maintained 4. Evolutionary and non random mating effects are predictable
CODIS STR markers (criteria)
1. Have known chromosome locations; assort independently of other CODIS markers (most are in non-coding regions, some are in introns of genes) 2. Have multiple alleles in all populations examined 3. Carry alleles that can consistently, reliably, and accurately amplified by PCR 4. Produce PCR products that allow for distinguishing of alleles from one another clearly enough for automated PCR amplification 5. Gel electrophoresis is used to reliably identify and distinguish each allele variant (even in a multiplex)
Production of transgenic vertebrates lead to variable transgene expression
1. Integration of the transgenes as multicopy concatemers 2. chromosome environment of the gene's location
consequences of maternal inheritance of the MT genome
1. MT mutation inheritance is based on mother's genotype 2. maternal lineage of organisms can be examined 3. maternal history of species can be interpreted 4. Human genetic diseases caused by mitochondrial mutations are maternally inherited
Steps for forensic analysis of DNA:
1. Obtain biological material and reference specimens 2. Use PCR to make copies of allele variants present at each STR locus (multiplex) an analyze using gel electrophoresis 3. determine if there is a "match" in DNA patterns
steps of generalized transduction
1. P1 pahge attached to donor bacterium and inject its dna into the cell 2. replication of phage chromosome; transcription and translation to produce phage proteins 3. progeny phages are assembled normally, but some phages receive a host DNA fragment instead of a phage DNS 4. host cell lysis releases all the progeny phages
HW assumptions
1. Population size is infinite 2. Random mating occurs in the population, allowing genotype frequencies to be predicted by alleles frequencies 3. Natural selection does not operate 4. Migration (gene flow) does not introduce new alleles 5. Mutation does not introduce new alleles 6. Genetic drift does not occur
5' cap functions
1. Protection of mRNA from rapid degradation 2. Facilitating transport of mRNA out of the nucleus 3. Facilitating subsequent intron splicing 4. Enhancing translation efficiency by orienting the ribosome on the mRNA
base nucleotide excision repair
1. UVR AB complex binds opposite a thymine dimer 2. UVR B denatures the DNA around the lesion 3. UVR A departs; UVR C binds and catalyzes 3' and 5' cuts 4. DNA helicase UVR D helps release the damaged single strand; DNA polymerase and DNA ligase fill and seal the single stranded gap. the lesion has been removed and the DNA duplex has been restored
The concept of storing DNA profiles is based on
1. Use of a defined set of loci (DNA sequences) usually the CODIS loci (STRs) 2. A standard set of conditions (primers, etc.) used to produce each set of PCR products
NGS methods
1. are being widely used in many studies, and are becoming more affordable and routine 2. Can dramatically increase the #s of alleles detected for CODIS loci based on DNA sequence differences vs size or length differences 3. Used for genome level studies can also reveal entirely new classes of DNA sequence variants for identification purposes
steps of lysogenic cycle
1. attachment 2. Injection of phage dna 3. integration of phage chromosome 4. excision of prophage 5. resumption of lytic cycle
lytic cycle (6 steps)
1. attachment (of phage to host cell) 2. injection (of phage chromosome into the host, followed by circularization of the phage chromosome 3. replication of phage DNA (using host enzymes and other proteins) 4. transcription and translation of phage genes 5. packing of phage chromosome into phage heads 6. lysis of the host cell (and release of progeny phage particles
five features of mendel's breeding experiments
1. controlled crosses 2. used pure-breeding strains to begin experimental controlled crosses 3. selection of dichotomous traits 4. quantification of results 5. used replicate, reciprocal and test crosses
five classes of mutations identified
1. coordinate genes 2. gap genes 3. pair-rule genes 4. segment polarity genes 5. homeotic genes expressed in sequence during embryogenesis; mRNA and protein expression patterns of each gene reflect (in time and space) its mutant phenotype
conclusion consistent with models of continuous phenotypic variation in quantitative traits
1. corolla length in the plant is based on segregation of alleles of multiple genes 2. phenotypic expression of each genotype is influenced by environmental factors; partially explains the variation observed even in the pure-breeding lines
five important feature of epigenetic modification
1. epigenetic modification patterns alter chromatin structure 2. they are transmissible during cell division 3. they are reversible 4. they are directly associated with gene transcription 5. they do not alter dna sequence
Functions of Polyadenylation
1. facilitating transport of mature mRNA across the nuclear membrane to the cytoplasm 2. protecting the mRNA from degradation 3. Enhancing translation by enabling the ribosomal recognition of mRNA
2 characteristics of genomic islands
1. group of genes in the island are much more similar to genes of distantly related species than a more closely related species 2. island region has a ratio of G-C base pairs to A-T base pairs that is substantially higher or lower than the average in the rest of the genome
autosomal dominant inheritance characteristics
1. males and females have the trait in ~ equal frequency (no sex bias) 2. each individual who has the trait has at least one parent with the trait 3. either gender can transmit the trait to a child 4. if neither parent has the trait, none of their kids will
autosomal recessive inheritance
1. males and females have the trait in ~ equal frequency (no sex bias) 2. individuals who have the trait are often born to parents who do not (parents are heterozygous) 3. if both parents have the trait, all children will have it 4. the trait is not usually seen in each generation, rather it is typically seen among siblings
bacterial tRNA processing
1. many tRNAs are cleaved from a large precursor tRNA 2. nucleotides are trimmed from the ends 3. individual nucleotides in different tRNAs are chemically modified 4. tRNAs fold into 3D structure that include 4 double stranded stems 5. Post transcriptional addition of bases
Repair of UV induced DNA damage
1. photoreactivation repair by photolase 2. photolase binds to UV induced product (damage) 3. light energy used to break chemical bonds (thymine dimers) 4. damage repaired
Base excision repair steps
1. recognition of damage 2. removal of damage 3. single strand "nick" (break) in DNA 4. New DNA synthesis to repair strand
downstream
3' end of coding segment of the gene
double holliday junctions (DHJs)
3' end of invading strand joins to the 5' end of a strand segment that was initally part of the invading strand, non sister chromatids are now connected by ____ _____ _____ which can be resolved in two ways (one of which results in recombination)
loops in attenuation
3-4 and 2-3 stem of the trpL attenuator region mRNA region
branch stie
3rd consensus region- 20 to 40 nucelotides upstream of the 3' splice site
nonhomologous end joining (NHEJ)
4 step process that repairs double-strand breaks occurring before DNA replication; error-prone and may lead to mutations
2 activities of pol I to complete replication
5'-3' exonuclease activity and 5'-3' polymerase activity
polyadenylation signal sequence
5'-AAUAAA-3'
-35 consensus sequence
5'-TTGACA-3'
A) inversion(s)
A balancer chromosome includes a recessive lethal allele, a marker dominant allele, and _______. A) inversion(s) B) must have multiple copies C) a GFP signal D) can only be used in Drosophila
transposable genetic element
A class of DNA sequences that can move from one chromosome location to another, either by excision and reinsertion or by replication and reinsertion of the replicated copy
lagging strand
A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.
two-hybrid system
A method for discovering whether two proteins interact using the GAL4 protein of yeast, which is separated into a DNA-binding domain and a transcriptional activation domain. The two GAL4 domains are fused with the two proteins of interest respectively, and the resultant fusion proteins are assayed for their ability to activate transcription, which indicates interaction of the two proteins of interest.
alpha proteobacterial endosymbiont
A model for eukaryote evolution suggests an archaeal ancestral cell acquired the
Hardy-Weinberg Equilibrium
A model to calculate the frequencies of alleles and genotypes in a theoretical population that is infinitely large, practices random mating, and does not experience evolutionary change - under these conditions, allele and genotype frequencies should remain constant
E) these mutants can be used to identify the function of the gene
A mutagenesis screen provides 24 alleles shown by complementation analysis to be in the same gene, which of the following is true A) the gene being studied must be present in more than one copy per haploid genome B) the gene must be highly conserved in evolution C) the gene, in whole or in part, must be involved in transformation D) the gene must be involved in regulating a signal pathway E) these mutants can be used to identify the function of the gene
triplet-repeat expansion
A mutant DNA polymerase that increases the frequency of strand slippage would increase the frequency of which type of mutation? A) missense B) transposition C) splice site D) transition E) triplet-repeat expansion
A B and E
A mutation in the Oca2 gene (a gene involved in pigmentation) results in an albino phenotype. What type of mutation could have occurred? A) frameshift B) deletion C) insertion D) synonymous mutation E) missense mutation
A reversion or reverse mutation returns mutant line to a wild type state
A mutation that returns a mutant line to a wild type state is called A) forward mutation B) neomorphic mutation c) reversion/reverse mutation D) a novel mutation E) impossible mutation
recombination hotspots/ coldspots
A region with a recombination rate that is higher.lower than average for the number of nucleotide base pairs present
C) Use several ~1000bp portions of the DNA sequence to search for the closest matches from among the entire available database.
A researcher is annotating a newly-sequenced chromosome that they constructed from contigs sequenced from a sample of Antarctic ice. The cell/organism that the chromosome came from is not known, however it yielded a single circular chromosome. You are asked to run a BLAST search to help this researcher identify the most related organism in GenBank. What would be the best strategy? A) Compare the most unusual portion of this newly-discovered chromosome to al known animal genomes. B) Look for an exact match to the whole chromosome. C) Use several ~1000bp portions of the DNA sequence to search for the closest matches from among the entire available database. D) Look for a nearly identical match to a very small part (20-40 bp) of the chromosome from all known ice bacteria. E) Perform many careful one-by-one comparisons between the newly-discovered DNA sequence and species selected from GenBank, one at a time.
Irisplex
A sensitive DNA tool for accurate prediction of blue and brown eye color in the absence of ancestry info
single nucleotide polymorphisms (SNPs)
A single base pair difference in a specific genome location detected by comparing individual DNA sequences; more commonly used markers than other markers ; involves variants where one bp is subbed by another bp, typically in a noncoding region ~3.3 million in human genome
A) CRISPR-cas
A single nucleotide in a genome can be targeted for mutagenesis using the technique, adapted from a bacterial defense system A)CRISPR-cas B) RNAi silencing C) PCR and DNA sequencing D) Transposon insertion
Australia, Tasmania, and New guinea
About 47k to 55k years ago, a single migration of ancient humans from the Indonesian Archipelago colonized the continent consisting of currentday
the C terminus
Active RecA targets the lambda repressor monomer and cleaves off what?
C) somatic mutations accumulate with age
Age is the greatest risk factor for cancer because____ A) germline mutations accumulate with age B) cell division is rare in older people C) somatic mutations accumulate with age D) tumor suppressors do not work as well in older people E) older people have weaker immune systems
A) apoptosis
All of the following are hallmarks of cancer except ____ A) apoptosis B) angiogenesis C) evasion of growth suppressors D) metastasis E) sustained cell production
NGS
Alleles defined on the basis of DNA sequence differences within repeats
Gel method
Alleles defined on the basis of size or length of repeat region
pribnow box
Also known as the -10 sequence, consists of a sequence TATAAT that is used as a promoter for DNA transcription.
independent evolution of multicellularity in the two kingdoms
Although the mechanism of developmental patterning in plants and animals is similar, the genes involved in development are not related, consistent with the
changing allele frequencies in the population over time
As a result of natural selection certain alleles will be passed to the next generation more often than others which leads to?
reproductive isolation
As populations diverge over time, new species can arise due to
Infinite population, random mating, no evolutionary change
Assumptions of hardy-Weinberg equilibrium
Combined paternity index (CPI)
Individual PI values are multiplied and their product is
3 forms of DNA
B-form, A-form, Z form
constitutive transcription
Bacterial genes expressed continuously (performing routine tasks undergo continuous transcription aka?
manipulation in vivo
Bacteriophage site-specific recombination systems cre-lox recombination system
Denisovans
Based on nuclear DNA_____ are more closely related to Neanderthals than either was to humans
E) all of these are possible treatment strategies
Cancer therapy includes which of the following? A) drug treatments targeting dividing cells B) radiation targeting cancerous cells C) modified immune cells D) drugs targeting specific enzymes/ proteins E) all of these are possible treatment strategies
∆q=µp-vq
Change in frequency generation of A₂ (=∆q) is calcualted as
McClintock's resutls
Chromosome breakage often occurred at the Ds gene ("dissociation") when another gene Ac ("activator") was present Ds= control element (controlled expression of other genes); but Ac elements contain a transposase gene (not Ds)
E) fertilization of the cell egg with a sperm cell followed by implantation in a surrogate mother
Cloning animals by nuclear implantation involves all of the following except? A) induction of cell division and implantation of blastocyst in the surrogate mother B) removal of somatic cells and extraction of a diploid donor nucleus from the animal to be cloned C) removal of an egg cell, extraction of the nucleus, and injection of the diploid donor nucleus D) a low frequency of success likely due to variations in the completeness of epigenetic programming of the somatic cell nucleus E) fertilization of the cell egg with a sperm cell followed by implantation in a surrogate mother
Gene pool
Collection of genes and alleles found in the members of a population
E) none of the above
Common mutational targets affecting susceptibility to cancer include all of the following except ______. A) the cell cycle B) DNA repair genes such as BRCA1 C) mitochondrial function D) growth-limiting genes such as APC E) none of the above
GC rich box
Consensus sequence of 5'-GGGCGG-3' located -90 or further upstream
DOGMA
DNA --(Transcription)--> RNA --(Translation)--> protein
process is ongoing
DNA continues to move between organelles and the nucleus; rate of transfer is surprisingly high
CODIS (combined DNA information system) loci
DNA from STRs or "short tandem repeat" loci used today for paternity testing and criminal investigations are the ___ (markers)
transcriptomics
DNA microarrays and high-throughput sequencing of cDNA ("RNA-seq") are used in
DNA proofreading
DNA polymerases correct occasional errors due to 3' to 5' exonuclease activity
UV exposure and skin cancer
DNA repair systems of most organisms can identify and correct most pyrimidine dimers but those that are not repaired can cause disruption of replication; disruptions lead to mutations and are the primary cause of the strong association between these excessive consequences of photoproducts
S phase
DNA replication and chromosome duplication
Whole genome shotgun (WGS) sequencing
DNA representing entire genome is fragmented and sequences - paired-end sequencing to bridge gaps - contigs physically linked are assembled into scaffolds - issues with repetitive DNA
activator binding site
DNA sequence to which an activator protein binds to regulate gene expression. Term refers to regulatory sites in bacteria; in eukaryotes, the equivalent sequence would be called an enhancer element.
Template strand
DNA strand from which RNA is synthesized
PCR requires
DNA template DNA Polymerase - (Taq) dntps (A,G,T,C) buffer solution two different ssDNA primers
A-form
DNA that is occasionally detected in cells and is common in bacteriophage
categories of transposable elements
DNA transposons and retrotransposons
Matting patterns and effect ion of evolutionary processes on alleles
Determine how alleles are dispersed into genotypes, and their frequencies in successive generations
Paternity index (PI)
Determined as x/y X is the probability that the non maternal allele comes from the putative father Y is the probability the allele comes from another male in the population
(dominant) increase, (recessive) decrease
Directional NS against recessive phenotype causes the frequency of the dominant allele to ____ and the recessive to ____
WGS
Drosophila was the first eukayotic genome with significant elements sequences using?? - 170 Mb genome (120 Mb euchromatin an d50 Mb heterochromatin)
DYS gene
Duchenne muscular dystrophy
A portion of the gene pool in its genome
Each member of a population carries _____
splicing mutation
Efficient splicing of introns from mRNA requires specific sequences at either end of the intron; mutations that alters these nucleotides are
lacZ gene
Encodes Beta galactosidase
lacY gene
Encodes the enzyme permease
Paternity testing
Every non maternal marker carried by a child must also be carried by the father
Illegitimate recombination
Exchange of genetic information between non-homologous DNA molecules
homozyogus IBD
F also used to estimate proportion of loci that are ___
Hfr chromosome
F factor in Hfr strains integrated into the bacterial chromosome; formations occurs rarely
Parents and progeny produced by controlled crossed are used as sources of DNA
F1 progeny may be used in a backcross to one of the parental lines
Radiation mutagens
Fast neutron, x ray and gamma ray
mtDNA studies
First evidence for an african origin of modern humans came from ?
5, 7
For an F2 generation resulting from a dihybrid cross 2 genes--> ? phenotypic classes 3 genes --> ? phenotypic classes
Fst= 0.05-0.25
Fst= ? between major geographic human populations
major cell cycle checkpoints
G1, S, G2, Metaphase
cases vs controls
GWAS compares " ____" (organisms with a certain phenotype) to "____" (those without the certain phenotype) to assess association
9 genome regions
GWAS identified how many genome regions significantly associated with CD?
marker variants associated with phenotypic variation
GWAS scans the entire genome by statistically testing for ____?
size and gene number
Genomes vary enormously in ____ and ____ ____
Population
Group of interbreeding organisms
D) gene families
Groups of genes that are evolutionarily related are called ________. A) gene domains B) SNPs C) metagenomes D) gene families E) gene duplications
writers
HMTs, HATs
ABO blood type alleles
HW equilibrium values can be determined for more than two alleles ex?
Random mating and absence of evolutionary change
Hardy and Weinberg showed that with ___ ___ and the ______, allele frequencies result in a stable equilibrium frequency
raw material of evolution
Heritable variation that provides the _____ begins at the molecular level, with changes in DNA sequence and proteins
riboswitch active
High TPP concentration initiates the riboswitch that terminates transcription by intrinsic termination
major gene
Human OCA2 gene has several alleles that strongly influence eye color and skin tone called a
over 50%
Human genome contains how much repetitive DNA
trinucleotide repeat expansion
Huntington's disease is caused by what kind of mutation? A) base substitution mutation B) frameshift mutation C) pericentric inversion D) trinucleotide repeat expansion E) not due to a mutation
translational and transcriptional control
LGT between bacteria/archaea and eukaryotes is relatively rare due to the different?
rare
LGT between eukaryotes is also
negative interference
I<0 more double crossovers are produced than predicted
it depends on what the changed nucleotide is
If the 1st nucleotide in a codon is mutated to a different nucleotide, what would be the effect on the encoded protein?
Lighter (reddish) colored hair
If you have variants that produce less eumelanin that pheomelanine you will have ___ colored hair d
Darker hair
If you have variants that produce more eumelanin than pheomelanine you will have (what color hair)
fully redundant genes
In evolutionary genomic what kinds of genes are not maintained for long periods?
if an entire gene including regulatory sequences is duplicated
In evolutionary genomics when does this occur? - both copies can produce a functional protein; the genes are redundant and free to evolve new functions
point mutations
Localized mutations that occur at a specific location, rather than over a larger span on a gene are better known as what? A) copy number variants B) monosomies C) point mutations D) transposable elements E) none of the above
Riboswitch not active
Low TPP concentration generates antitermination and thi operon transcription
screening test
MSS is a ______ test; indicated increased likelihood of a condition rather than presence of a condition
monophyletic
MT are ____, all descended from a single ancestor, suggesting a single endosymbiotic event CP also ___, descended from a single endosymbiotic event at least 1.2 billion years ago
Natural selection, mutation, gene flow, and genetic drift
Major evolutionary influence that cause populations to deviation from HW-equilibrium include
reduced fertility of hybrid offspring
Mating between a polyploid species and a nonpolyploid one can result in
interference (I)
Measured on a zero to 1.0 scale, the measurement of the independence of crossovers. Expressed as 1.0 minus the coefficient of coincidence.
transcriptional and Postranscriptional regulation
Mechanisms for regulating gene expression?
law of segregation
Mendel's first law describes the units of heredity, their separation into gametes, and the random union of the gametes into progeny in predictable proportions
law of independent assortment
Mendel's second law states that during gamete formation the segregation of alleles at one gene is independent of the segregation of alleles at another gene - 9:3:3:1 ratios generated in mendel's dihybrid crosses
somatic, germline (D)
Most cancers are caused by ____ mutations whereas a minority of cancers is caused by ____ mutations. A) germline; inherited B) germline; somatic C) inherited; somatic D) somatic; germline E) somatic; random
VNTRs or STRs
Most common sequences used today for DNA profiling
Helix turn helix (HTH) motif
Most common structural feture kf proteins in bacteria where two alpha helical regions interact with the onverted repeats
transcriptional
Most of the regulation of gene expression in bacteria occurs at the ________ level.
E) transcriptional repression and epigenetic modification
Multicellular organisms generally utilize more complex gene regulation than unicellular organisms via mechanisms that include? A) transcriptional repression B) polycistronic RNAs C) epigenetic modification D) polycistronic RNAs and transcriptional repression E) transcriptional repression and epigenetic modification
Product rule
Multiply genotype frequencies for several loci
heterozygous genotype
NS can produce and maintain genetic diversity within a population when the _____ genotype is favored
nuclear mitochondrial sequences
NUMTS
coding strand
Nontemplate strand of DNA, which has the same sequence as the mRNA except it has thymine (T) instead of uracil (U); complementary to template strand
How many different genes have been identified?
Number of genes controlling a phenotype of interest, use complementation test experiments
hybrid dysgenesis
P elements were discovered because they produced _____ in which sterility occurs in F1 progeny of certain crosses - only when lab strain females called M cytotype are mated to P strain males is this observed in the offspring
nonsignificant deviation
P values >5% between observed and expected results (ie deviations are due to chance events) hypothesis rejected
Ancestry testing
Partial matching to a related person is also the basis for ___?
S checkpoint
Pass if DNA replication is complete and has been screen to remove base pair mismatch or error
coding region
Portion of gene that contains the information needed to synthesize the protein product
A) metagenomics
Previously unidentifiable microorganisms have now been identified through ________. A) metagenomics B) transcriptomics C) reverse transcription D) evolutionary genomics E) proteomics
Lactose in lac Operon of E Coli
Produces three polypeptides needed for metabolism of lactose
blunt ends
RE cleaves 5' or 3' ends of double-stranded DNA lacking any single -stranded overhangs ( ex Hind1)
Argonaute
RISC contains what protein family; degree of complementary base pairing determines gene silencing
antisense RNA
RNA molecule that is complementary to part of a certain mRNA
RNA interference (RNAi)
RNA-mediated gene expression discovered that Double stranded RNA (dsRNA) was taking part in a regualtory mechanism now called?
RNAi in eukaryotes serves as an) experimental tool in research
RNAi can be used to reduce expression of selected genes to determine the effect of the phenotype and discover effects of the gene
RNAi silences gene expression transcriptionally
RNAi can bind to mRNA targets by complementary base pairing, leading to destruction of the target mRNA or can block its transcription
RNAi silences gene expression post- transcriptionally
RNAi can enter the nucleus and bind DNA to block transcription of the target gene
how any different mutant alleles of each gene have been identified?
Range of phenotypic variation, multiple independent mutation in each gene
mitochondrial transmission
Relatively small number of initial mitochondria allows heteroplasmic mothers to produce homoplasmic wild type offspring
LTR gag pol env LTR
Retroviral genome structure
b) a genetic map
Shotgun sequencing requires all of the following except? A) software capable of comparing DNA sequence B) a genetic map C) a DNA sequencing technology D) many overlapping DNA sequences E) a computer
immune system functions
Some Denisovan sequences in modern humans are involved in ____
cryptic splice sites
Some base-pair substitution mutations produce new splice sites that replace or compete with authentic splice sites during mRNA processing
preinitiation complex (PIC)
TFIIA, TFIIB, TFIIF, and RNA pol II join the complex, followed by TFIIE and TFIIH to form the ____ which directs RNA pol II to the +1 position where it begins to assemble mRNA
general transcription factors
TFs of the PIC
reversion mutations
The Ames test is designed to identify the rate of ________ that restore the ability of bacteria to synthesize their own histidine, thus eliminating the need for histidine supplementation of the growth medium. A) forward mutations B) reversion mutations C) chromosome rearrangements D) transduction events E) none of the above
reference genome sequence
The DNA sequence of the individual or individuals used to construct the initial complete genome sequence
genetic and environmental variance
The F2 phenotypic variance results from ____ and _____ variance
sugar phosphate backbone
The alternating chain of sugar and phosphate to which the DNA and RNA nitrogenous bases are attached
chromosome 3 of drosophila
The five genes of the Antennapedia complex and the three genes of the bithorax complex are both found on? but are usually organized into a single cluster in other organisms
Phenomena in and eumelanin
The two pigments involved in hair color are?
bioinformatics
The use of computational approaches to decipher DNA-sequence information
Familial or kinship identification
To identify a person or remains, alleles of DNA from the unidentified person or remains are matched to either a reference DNA sample (from a known source) or partial DNA matches of a close relative
DNA-protein interaction
Transcriptional control of gene expression requires?
altered gene expression
Transposons can integrate into the promoters of genes, what is the most likely outcome of such an event? A) frame shift B) altered gene expression C) amino acid substitution D) point mutation E) deamination
3 genes of the bithorax complex
Ultrabithorax (Ubx), abdominal-A (abd-A), and Abdominal-B (Abd-B)
Evolution of ABC Genes
Unlike the Hox genes, the B and C class genes are not found in earlier lineages of plants, such as ferns, lycophytes, and bryophytes
Hypervariable DNA sequences
Used to develop a pattern of DNA fragments that is essentially unique for each person
Next generation sequencing (NGS) methods
Used to produced large amounts of DNA sequence data relatively cheaply and quickly; goal is to obtain large numbers of very short reads, each covering ~90 (or less) bases of DNA
DNA phenotyping
Using DNA to make prediction of the phenotype
Va, Vd, Vi
Vg can be partitioned into different kinds of allelic effects such as
genetic variation
Vp of a high heritability traits is largely due to _____ _____
partitioning phenotypic variance (equation)
Vp= Ve + Vg
F1 are genetically uniform
Vp=Ve
both parental lines are genetically uniform
Vp=Ve; Vg=0
Metagenomics
WGS sequencing of DNA isolated from natural communities composed of a range of organisms (metagenome) - provides information on species diversity of gene sequences of organisms living in particular environments
DNA binding domain and allosteric domain
What are the two active sites that repressor proteins usually have to perform their functions?
RNA has a ribose sugar and uracil nitrogenous base
What are two distinguishing features of RNA?
to describe genetic color or kernel corn in wheat
What did Nilsson- ehle use the multiple gene hypothesis for?
D and E
What is true concerning transitions/transversions? Circle all correct answers. A) transversions occur more frequently B) transitions and tranversions occur at roughly equal rates C) C substituted for G and A substituted for T is considered a transition D) C substituted for T and G substituted for A is considered a transition E) C substituted for G and A substituted for T is considered a transversion
hotspots of mutation
What term describes a gene or region of a genome where mutations occur much more often than average? A) hotspots of mutation B) mutation central C) mutation sink D) mutation vacuum E) universe of mutations
B
What type of bond is formed between the hydroxyl group of one nucleotide and the phosphate group of an adjacent nucleotide, forming the sugar-phosphate backbone of DNA? A) glycosidic bond B) phosphodiester bond C) ester linkage D) hydrogen bond E) ionic bond
D
What types of bonds are formed between complementary DNA bases? A) glycosidic bonds B) phosphodiester bonds C) covalent bonds D) hydrogen bonds E) ionic bonds
Ac removal of Ds from a C gene
What would restore purple color in an otherwise colorless kernel?
translocated to the host nucleus
When one eukaryote envelops another, nuclear genes of the eukaryotic endosymbiont are
transposase
Which enzyme is required to mobilize transposons of any type? A) RNA helicase B) telomerase C) terminal inverted repeats D) reverse transcriptase E) transposase
A) gene A controls the expression of many genes
Which is more likely to be the case for gene A found at the hub of a genetic network, compared to gene B, in the same network but not in a hub? A) gene A controls the expression of many genes B) gene B encodes a protein that interacts with many different proteins C) gene A encodes a transcription factor that controls the expression of one gene D) gene A is highly expressed E) gene A is a nuclear gene, while gene B is mitochondrial
E
Which methods did Seymour Benzer use to study 20,000 mutants of the rII region of the T4 bacteriophage? A) genetic complementation analysis only B) intragenic recombination analysis only C) deletion-mapping analysis only D) intragenic recombination analysis and deletion-mapping analysis only E) genetic complementation analysis, intragenic recombination analysis, and deletion-mapping analysis
C) homologous recombination occurs much more frequently than illegitimate recombination
Which of the following is FALSE regarding the formation of transgenic animals? A) For a transgenic animal line to be produced from a chimera, the transgene must be carried by germ line or germ cells. B) Either integration of multiple copies of the transgene or position effect can lead to variability in the expression of the transgene. C) Homologous recombination occurs much more frequently than illegitimate recombination. D) DNA is usually inserted into eggs or embryos since totipotency is not characteristic of most animal cells. E) If some cells of the embryo do not receive the introduced DNA, the result is an organism with cells of different genotypes; the organism is known as a chimera.
C
Which of the following is NOT a step in transformation? A) Donor cell DNA binds to a receptor site on the recipient cell. B) The donor cell lyses, releasing pieces of its chromosome into the environment. C) Both strands of the donor cell DNA are degraded. D) DNA fragments pair with homologous regions of the recipient cell chromosome. E) DNA recombines with the recipient cell chromosome.
C
Which of the following is incorrect about genetic analysis and mapping in bacteria and bacteriophages? A) Conjugation requires cell-to-cell contact. B) Generalized transduction uses lytic phage and specialized transduction uses a lysogenic phage. C) Transformation requires a vector to carry donor DNA fragments to the recipient cell. D) Conjugation, transformation, and transduction all require recombination. E) Conjugation, transformation, and transduction can all be used to map the order of genes on a bacterial chromosome.
B
Which of the following is true of a bacterial strain that is his+ lac+ gal- ampR. A) It is auxotrophic for histidine. B) It will grow on ampicillin. C) It is unable to synthesize histidine. D) It can use galactose as an energy source. E) It is unable to break down lactose.
D) II, V, I, III, IV
Which of the following lists the steps for cDNA library preparation in the correct order? I. Partially degrade the mRNA with RNase H II. Isolate mRNA from a specific cell/ tissue with an oligo-dT primer that hybridizes to poly-A tail III. Synthesize a strand of cDNA using DNA polymerase with mRNA fragments as primers IV. Ligate cDNAs into a cloning vector V. Create a single-stranded DNA molecule complementary to the mRNA using reverse transcriptase A) II, V, IV, III, I B) II, III, V, I, IV C) I, II, III, IV, V D) II, V, III, IV
E
Which of the following regarding lateral gene transfer is false? A) It may occur by conjugation, transformation, or transduction. B) It facilitates rapid genome evolution. C) It can convert benign bacteria into pathogens that cause disease. D) It allows an organism to rapidly acquire whole segments of chromosomes containing multiple genes. E) It increases the efficiency of antibiotics against normally sensitive strains.
it is error-prone
Which of the following statements is true of non-homologous end joining (NHEJ)? A) it is a single-strand repair pathway B) it does not occur C) it is error-free D) it does not involve DNA repair E) it is error-prone
Barbara McClintock
Who discovered transposition using crosses involving three linked genes, C, Sh, and Wx in maize C= purple kernels c1= yellow (colorless) Sh= plump kernels sh= shrunken Wx= shiny kernels wx= wavy
frequencies
With HW equilibrium _____ will remain constant from one generation to the next
Bacteria, archaea, and eukarya
Woese et alshowed (late 1970s) that all forms of lif fell into three domains:
XIST
X inactivation specific transcript, can only act on the chromosomes from which it is being transcribed and not the homolog
Xist gene located on XIC
X-inactivation specific transcript _____ ____ is the in what location on the X chromosome
inactive
Xist on the euchromatic X
active
Xist on the heterochromatic X
his - strain grows on an his - plate.
You have conducted an Ames test on a given compound. Which of the following would be classified as a positive result on the Ames test? A) his - strain grows on an his - plate. B) his - strain grows on an his+ plate. C) his+ strain grows on an his - plate. D) his+ strain grows on an his+ plate. E) his+ strain grows on either an his - or an his+ plate.
enhancer sequence
You have identified a mutation in a gene that seems to decrease transcription of another gene 2000 bp away from the mutation site in a eukaryote. What is the regulatory sequence, which can be found within another gene, has likely been mutation in this instance?
parental genotypes
___ __ unite to reproduce at proportions predicted by their frequency
polymorphic alleles
___ in human genomes have resulted from serial founder effects and locally restricted new mutations
introgression
___ of Neanderthal DNA into the modern human genome (~4%) is found in all non-africans but not subsaharan africans - indicates interbreeding was after migration out of Africa
chromatin
___ plays an important role in gene regulation of eukaryotes
gene number
____ ____ generally increases with organismal complexity
sequence variants
____ ____ in candidate genes are assessed to see if they correlate with the phenotype variation
spatial and temporal
____ and ____ control of gene expression results in subdivision of drosophila embryo into its characteristic segments
low p53 levels
____ in healthy cells, but levels of the ATM protein increase in response to cell damage
Phenotypes
____ produced by backcross progeny are assessed and results compared to genetic markers in individual organisms
biochemical mechanisms
_____ _____ recognize the presence of DNA damage and initiate a repair response consists of tightly regulated genetic process; this process is in action throughout the cell cycle
M cytotype, P strain
_____ females lack P elements while ______ males contain several dozen
single celled, multicellular
______ _____ eukaryotes contain fewer genes than ________ eukaryotes
homeodomain
a 60 amino acid protein domain encoded by the homeobox that contains a motif (helix turn helix) previously recognized in transcription factors in bacteria and phage
CAP binding site
a bacterial regulatory sequence to which the CAP-cAMP complex binds to positively regulate gene expression
origin of eukaryotes model 2
a bacterium acquired the endosymbiont and as a result eukaryotic features sucha as a nuclear membrane developed, shouble be no "intermediate" eukaryotes, lacking MT
nonsense mutation
a base-pair change that creates a stop codon in place of a codon specifying an amino acid
missense mutation
a base-pair change that results in an amino acid change in the protein
CARD15
a candidate gene involved in production of a protein involved in recognizing bacterial proteins and stimulating an immune response
nucleotide base analog
a chemical compound with a structure similar to a DNA nucleotide base; these can pair with normal nucleotides-DNA polymerases cannot distinguish from normal nucleotides
no gene-environment interaction
a discrete phenotype for each genotype
DNA clones
a fragment of DNA that is inserted into a vector, such as a plasmid, cosmid, or artificial chromosome
stop codon
a gene has acquired a mutation in which the protein product has 50 additional amino acids at the end. What region of the gene was likely mutated?
transgenes
a gene that has been modified in vitro by recombinant DNA technology and introduced into the genome via transformation
delayed early genes
a group of genes in lambda bacteriophage that are exrpressed following expression of early genes that initiate lytic cycle
no QTL linked to the marker
a lod score below the threshold suggests?
in vitro fertilization (IVF)
a long standing method of assisted reproduction for individuals and couple unable to conceive on their own
restriction map
a map showing the numbers and relative positions of target sites for restriction enzymes of a DNA molecule
Coefficient inbreeding (F)
a measure of the probability of homozygosity for an allele obtained in identical copies from an ancestor
allele counting method
a method of gene counting in which allele frequencies calculated as twice each homozygote class plus the heterozygotes, divided by twice the total population p=[2(A₁A₁)+(A₁A₂)]/ twice the total population
genotype proportion method
a method of gene counting in which each homozygote frequency is added to half the heterozygote frequency to determine p and q p=f(A₁A₁)+½f(A₁A₂)
(C) thymine dimer
a mutation commonly seen upon exposure to UV light: A) a chromosome rearrangement B) due to strand slippage C) a thymine dimer D) due to transposable element E) A SNP
syncytium
a mutlinucleated cell in which the nuclei are not separated by cell membranes
TILLING (targeted induced local lesions in genomes)
a population of individuals is randomly mutagenized, to near saturation, and the DNA from the resulting lines is screened by PCR to identify mutation in the desired gene
ethyl methanesulfonate (EMS)
a powerful alkylating agent that induces transition mutations through its action on guanine
Transition mutations
a purine is replaced by another purine (A-G) (or one pyrimidine replaces another T-C)
transversion mutations
a pyrimidine is replaced by a purine (or vice versa)
inverted repeats
a recognition and a stabilizing helix are separated by a "turn" in each polypeptide
genetic bottleneck
a relatively large population is reduced to a small number by significant event unrelated to natural selection
open chromatin
a relaxed association between DNA and nucleosomes, and allows for access by regulatory proteins
trpR protein
a repressor protein coded by the sixth gene outside the trp operon that is activated when bound to tryptophan
Guthrie test
a simple, inexpensive procedure that accurately identified newborn infants with PKU using just a few drops of their blood obtained from a "heel stick"
two protein segments contact DNA
a single polypeptide may fold to form two domains that bind the target DNA sequences
apurinic site
a site in DNA that is missing a purine base, most repaired before replication but if unrepaired, DNA polymerase will usually compensate by putting an adenine into the site during replicaiton
low heritability
a small proportion of Vp of a trait with ____ ____ can be attributed to genetic variation
affected
a small proportion of the population in threshold traits will be over the threshold and will have an _____ phenotype
chrorionic villus sampling (CVS)
a small tube is passed into the uterus to obtain tissue from the chorion on the outside of the placenta; fetal cells can be cultured and used for genetic testing or chromosome analysis cells are obtained as early as the 10th week of pregnancy but their is a risk of fetal loss
copy number variants (CNVs)
a specific type of structural variant due to insertions or deletions (indels) greater than 1 kb in length - form of structural variations that cause alteration of the DNA in a genome - either delete or duplicate a bp - cause a cell to have an abnormal number of copies of one or more places in a chromsomes
lambda phage
a temperate phage that can undergo the lytic cycle or lysogenic cycle
philadelphia chromsome
a translocation between chrom 9 and 22; associated with a form of leukemia
phosphodiester bond
a type of bond that links nucleotides in one strand of dna between the 5' phosphate group of one nucleotide and the 3' hydroxyl of another
multiple cloning site (MCS)
a vector DNA sequence containing several unique restriction enzyme target sequences facilitating cloning of inserted DNA fragments
Radiation (UV) induced photoproducts
aberrant structures with additional bonds involving nucleotides (EG adjacent thymines)
Yamanaka factors
act as pioneer factors to activate embryonic gene expression and reprogram epigenetic marks on the chromatin
silencer sequences
act in a similar manner like enhancer to repress transcription of their target genes
HAT "writers"
activator proteins recruit?
G1
active gene expression and cell activity; preparation for DNA synthesis
micro RNA (miRNA) small interfering RNA (siRNA)
active in plant and animal cells and are involved in posttranscriptional regulation of mRNA
alkylating agents
add bulky side groups such as methyl (CH3) and ethyl (CH2-CH3) groups to bases; addition of bulky side groups interferes with DNA base pairing by distorting the DNA double helix
hydroxylating agents
add hydroxyl groups to a recipient compound; can mispair with adenine, creating a C-G to T-A transition mutation
histone methyltransferases (HMTs)
add methyl groups to the N terminal histone tails; these act as writers
Additive variance (Va)
added effects of all alleles contributing to the trait
methyl groups
added to specific nucleotides, not AA in histone tails
photoreactive repair
addresses UV induced damage; takes place in bacteria, single-celled eukaryotes, plants and some animals (NOT in humans)
5'-3'- polymerase activity
adds DNA nucleotides to the 3' end of the DNA segment preceding the primer
hydroxylamine
adds a hydroxyl group to cytosine, creating hydrolaminocytosine
coordinate genes
affect an entire pole of larva
average or mean value
after constructing the frequency distribution you should calculate the ?
pN
after gene flow ___ calculated as the weighted average of p in island (pi) and mainland (pc) pops
mutagens
agents that cause DNA damage leading to mutations
transcription factor (TF) proteins
aids RNA pol II to recognize and bind to promoter sequences in eukaryotes
second-site reversion
aka suppressor mutations; occurs by mutation in a different gene that compensates for the original mutation, restoring the organism to wild-type
carcinogens
all _____ are mutagens, but not all mutagens are also ______
mutagens
all carcinogens are _____ but not all ______ are also carcinogens
homoplasmy
all copies of an organelle gene are the same; cells have organelles with same genotype
balanced polymorphism
allele frequencies are maintained by selection favoring the heterozygote
Fixation index (Fst)
allele frequencies are the same between two population when Fst= 0; all allele frequencies differ when Fst =1
evolution occurs
allele frequencies change when ___?
sampling error
allele frequencies of the new populations may differ from the original populations as a result of ____
population evolution
allele frequency change over time is evidence of ____ ____
additive traits
alleles of each gene can be assigned a value that indicates its contribution to the polygenic trait
genetic markers
alleles of either expressed genes or noncoding chromosomal regions identifying a specific region of a chromsomes. can be used to trace or identify another gene, the chromosome, or a cell, organ or individual (include, VTRs, SNPs, RFLPs)
epistasis
alleles of one gene block (mask) expression of another gene
recombinant chromsomes
alleles of syntenic (linked) genes can be reshuffled when crossing over occurs between homologs to produce __
positive eugenics
allow only people with "good" traits to reproduce
transgenic mice (mus musculus)
allows scientists to dissect many aspects of human development and physiology, as well as mouse development and physiology
Promoter mutations
alter consensus DNAs of promoters; some cause mild to moderate reductions in transcription levels, whereas other may abolish transcription
lysogenic cycle
alternate, temporary life cycle of temperate phages involving integration of the phage chromosome into the bacterial chromosome
alleles
alternative forms of a gene
constitutive heterochromatin
always heterochromatic
low (plants), severe (animals)
among plants that reproduce by self-fertilization, inbreeding depression is ___, whereas among animals it is ___
corepressor
an accessory molecule required for a repressor protein to exert its function
inducer
an accessory molecule that binds to a protein that leads to activation of gene expression. can bind to a repressor protein and prevent its function or bind to an activator protien and stimulate its function
inhibitor
an accessory molecule that converts activator proteins to an inactive conformation by binding to an allosteric binding domain of the activator protein
Vertebrate steroid receptors (SRs)
an ancestral receptor with a single original function duplicated and diversified to produce new genes and proteins
on maternal chromosome
an enhancer drives expression of H19 and an insulator proteins blocks IGF2 expression
synthesis dependent strand annealing (SDSA)
an error free process called that repairs double-strand breaks that occur after replication; begins with trimming of one of the broken strands, followed by attachment of the protein Rad51
NHEJ
an error prone mechanism of double-stranded DNA break repair in eukaryotic genomes in which damaged nucleotides are removed and blunt ends of strands are joined
SDSA (synthesis dependent strand annealing)
an error-free mechanism for repair of DNA double strand breaks occurring after the completion of DNA replication and utilizing strand invasion to provide wile0type sequences for repair
lac operon
an inducible operon under negative and positive control
holoenzyme
an intact complex of multiple subunits, with full enzymatic capacity
endosymbiont
an organism that lives within the body or cell of another organisms
autosomal genetic diversity
analysis has shown that _____ is greater in african populations than in non-African pops
phenotypic variance (Vp)
analyzing quantitative trait variation aims to examine the factors that contribute to ____ ___ whihc can be divided into genetic variance (Vg) and environmental variance (Ve)
bicoid mRNA
anchored to the anterior region of the egg during oogenesis; is translated after fertilization to an anterior-to-posterior protein gradient
Mitochondria and chloroplasts
ancient origins and product of endosymbiosis
propagate clonally
animals do not readily _______ _____ in nature (some exceptions)
body-plan axes
anterior-posterior, dorsal-ventral, and left-right
lambda Phage infection
antiterminatiors and repressors control ___ ____ _____ of e.coli
dosage compensation
any mechanism that compensates for the difference in number of copies of genes between males and females
imprinted
any patten of _____ genes that differs from the normal pattern has profound consequences
heritability values
are accurate for the environment and population in which they are measured
multicellular eukaryotic cis elements
are complex with multiple binding sites and can be located at a distance form one gene, either upstream, intronic, or occasionally exonic
"adult" vs "embryonic" stem cells
are defined in terms of "potency" (potential)
polygenic traits
are influenced by multiple genes
mitochondrial genome
are maternally inherited in mammals, mutate at a faster rate than the nuclear genome and show many differences even in closely related populations
nuclear encoded MT proteins
are transported into the MT
assumptions of HW
are unattainable in real populations
loss of function mutations
are usually more recessive, therefore further breeding is required to make mutations homozygous
spontaneous mutations
arise in cells without exposure to agents capable of inducing mutation; primarily through errors in DNA replication or spontaneous changes in the chemical structure of a nucleotide base
differentiated
as development process, cells become ______ taking on different morphologies and different physiological activites
serial founder effect
as humans migrated from africa, subsequent splittings of migrant groups became less and less genetically diverse
increases
as the number of additive genes contribution to a trait increases, the number of possible phenotypic categories also _____
initial committed complex
assembled TFIID bound to the TATA box form the ____
guide RNA (gRNA)
assists the additions of uracil in RNA editing ;contains a sequence complementary to the mRNA that it edits
heterozygous frequency by 1/2
assuming initial parent is heterozygous, self-fertilization leads to a decrease in ____ by ___ in each generation
5' splice site
at the 5' intron end and contains a consensus sequence with a nearly invariant GU dinucleotide at the 5'-most end of the intron
3' splice site
at the opposite end of the intron has an 11 nucleotide consensus with a pyrimidine-rich region and a nearly invariant AG at the 3'-most end
Huntington's disease
autosomal dominant disorder; affected individuals undergo progressive degeneration of the nervous system and mental deterioration; late age of onset (symptons 1st begin btwn ages 30-50)
sickle cell
autosomal recessive disorder, due to a mutation in the Beta globin gene
endosymbiosis theory
bacteria established endosymbiotic relationships with their hosts and evolved along with the hosts to produce the organelles (MT and CP)
lac-
bacteria that are unable to utilize lactose
lac+ phenotype
bacteria with this phenotype can grown on media containing lactose as the only sugar
late genes
bacteriophage gens are expressed late in the lytic cycle. encode protein products required for packaging of phage particles and lysis of the host cell (late promoters and late operators are the regulatory sequences responsible for this type of activation)
synonymous mutation
base pair change that does not alter the resulting amino acid (redundancy of the genetic code)
Phylogenetic trees
based on shared features of DNA, protein sequences or morphological characters, most closely related species have the smallest number of differences between their molecular sequences
lod score
based on the probability of the data if a QTL is linked to the marker, divided by the probability of the data if there is no QTL linked to the marker - calculated for several genetic markers along the chromosome to be analyzed
exons
become part of mature mRNA and encode protein segments
maternal genes (mother)
before (and at) fertilization, all gene expression comes from ?
Reverse genetics
begins with a gene sequence and then identifies an associated mutant phenotype
glucose
between glucose and lactose, which is the preferred substrate for the lac operon?
activator proteins
bind at regulatory DNA sequences called activator binding sites; binding facilitates RNA polymerase binding at promoters and helps initiate transcription; have a DNA binding domain
repressor proteins
bind other sequences to hinder transcription
activator proteins
bind regulatory sequences to stimulate transcription
DnaA
bind the 9-mer sequences, bends the DNA, and breaks hydrogen bond in the A-T rich 13-mer region
RNA-induced silencing complex (RISC)
bind to and denatures the small fragments of dsRNA created by dicer
TBP binding proteins (TBP) and associated factors (TAF)
bind to the the tata box
double stranded region
binding between the mRNA and its antisense RNA creates ____ ____ region of the message
Negative control
binding of a repressor protein to a regulatory DNA sequence and preventing transcription of a gene or gene cluster
positive control
binding of an activator protein to regulatory DNA and initiating gene transcription
histone modification
binding of epigenetic factors to histone "tails" alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated
promoter
binds RNA polymerase
RISC protein complex
binds to separate the strands to create miRNAs
cro protein
binds to the exposed operators and ultimately triggers the resumption of the lytic cycle
drosophila mutations
bithorax- four wings antennapedia- leg in place of an antenna
0.0-1.0
both broad sense and narrow sense heritability are expressed as proportion ranging from ?
beckwith- weidemann syndrome
both chromosomes in geneomic expression paternally expressed
russell silver syndrome
both chromosomes in genomic imprinting maternally expressed
double strand breaks (DSBs)
both strands of DNA are damaged, so neither strand can act as a template for repair
terminal inverted repeat (IR) sequenes
bracket insertion sequences (IS) that contain a tranposase gene
lysis
breakage of a donor cell and fragmentation of the donor DNA
repressor proteins
broad category of regulatory proteins that exert negative control of transcription; can be activated or inactivated via interaction with other compounds
domains of gap gene expression
broad gradients of maternally provided coordinated gene products are transformed into what with discrete boundaries occurring through cooperative binding of tf's and cross regulatory interactions among the gap genes themselves
joint probability
calculated by multiplying the prior probability by the conditional probability
conditional probability
calculated using info such as traits of other offspring of the same parent as the individual of interest
pioneer transcription facotors
can access their binding sites in heterochromatin
SOS repair system
can be activated in response to heavily damaged DNA in E.coli cells; accomplished by activation of translesion DNA polymerases in a process known as translesion DNA syntehsis
therapeutic transgenes
can be passed onto the progeny
induced mutations
can be produced by mutagens in an experimental setting to study types of damage caused, the mutation process itself, or repair responses to damage
random mutants
can be produced by transposon insertions and screen for insertion mutations in the desired gene
evolutionary impacts
can be quantified by determining the change in allele frequencies
genetic linkage
can be quantified to map the positions of genes on chromosomes
maternal lineages
can be traced back in time and allow identification of a common ancestor
maternal lineages
can be traced by following mutational changes back in time
double recombinant or double crossover progeny
can be used to determine the gene order (the occurrence of 2 crossovers between homologous chromosomes in a particular region. May involve two, three or all four chromatids)
H^2 (broad sense heritability)
can be used to measure the magnitude of genetic influence over phenotypic variation of a trait when Vg cannot be partitioned
gene counting
can be used whether or not a population is in HW equilibrium (genotypes of all members are identifiable)
trans-acting regulatory proteins
can bind to their target sequences on any chromosome
DSBs
can cause chromosome instability and incomplete replication, possibly leading to cell death; they also increase risk of cancer and chromosome structural mutations
MT DNA sequences
can decipher genealogical history and evolutionary relationship
chromatin modifiers
can enzymatically modify histones by adding or removing acetyl or methyl groups to particular amino acid residues
(Pioneer factors)
can initiate transition from heterochromatin to euchromatin; can be a single protein or different proteins can associate together forming a pioneer complex; bind to dna and open heterochromatin by recruiting chromatin modifier and remodeling complexes; prep chromatin for when other transcription factors become available
methylation
can play a role in converting open chromatin to closed chromatin
pharmacogenetic screening
can predict individual responsiveness or reaction to certain medications; used for several drugs such as the blood thinner warfarin
Founder effects and genetic drift
can result in high frequencies of autosomal recessive disorders in the new population that are rare in the original population
mitochondrial mutation
can result in human genetic diseases
T-DNA
can undergo illegitimate recombination to integrate into the plant genome randomly - genes can be replaced by a transgene of interest
Li-Fraumeni syndrome
cancer development strongly associated with mutation of the p53 gene
Ve=0
carefully controlled lab experiments can sometimes control all envrionmental variable
Transfer RNA (tRNA)
carries amino acids to ribosomes where they are assembled into proteins
R (resistance) plasmid
carries antibiotic resistance genes that can be transferred to recipient cells
histone demethylases (HDMTs)
carries out demethylation
composite transposons
carry a transposon gene, flanking IS elements, and one or more additional genes between IS elements that confer a growth advantage in certain environments (eg antibiotic resistance gene); ~10,000 bp in length
RNA polymerase
catalyzes the addition of each ribonucleotide to the 3' end of the nascent strand and forms phosphodiester bonds between nucleotides
open promoters
cause genes to be constitutively expressed
mutation in Card15 (3020insC)
causes a frameshift that results in a premature stop codon
Leber's hereditary optic neuropathy (LHON)
causes blindness in late adolescence/ early adulthood; pleiotropic defects include heart abnormalities
loss of entire bithorax complex
causes most abdominal segment to develop as T2
(features of) hybrid dysgenesis
causes sterility, a high mutation rate, chromosomal aberration, and nondisjunction - cytoplasm of M type females lack a repressor of transposition that would otherwise protect the egg from these effects
spatial
cell and tissue based for example: expression in fetal liver vs bone marrow
M phase
cell division Mitosis(somatic cells) meiosis (germ cells)
meiosis
cell division process that produces reproductive cells or gametes
mitosis
cell division that produces two identical daughter cells each of which should contain the same genetic info as the parental cell
terminally differentiate
cells exiting from the cell division cycle may take on a specialized function aka - most cells that undergo this also lose the ability to divide (exception stem cells)
"knowing"
cells have a way of _____ their locations with regard to these axes; a combination of internal and external signals provides cells with this information
germ cells
cells involved in reproduction, may contain one of each chromosomes pair, or the haploid number n
stem cells
cells that retain the ability to divide for self renewal and to give rise to other cells; may be able to provide cells for replacement tissues/organs
informational genes
cellular processes (resemble archaea)
constitutive mutants
certain mutations of the lac operon lead to genes that are transcribed continuously whether or not lactose is available aka
attenutation
certain repressible operons have a second regulatory capability which can fine-tune transcription to match the immediate needs of the cell
adaptation
certain variant forms give individuals that posses them a higher rate of survival and reproduction
Interrupted mating
cessation of conjugation by breaking the conjugation pilus; stops mating before the Hfr chormosme can be completely transferred to the recipient cells
genetic drift
chance fluctuations of allele frequencies that result due to "sampling error"
restriction fragment length polymorphisms (RFLPs)
changes in DNA sequences that are detected using DNA cutting enzymes called restriction endonucleases (Restriction enzymes) ; can be combined with pedigrees to study inheritance patterns
temporal or spatial
changes in gene expression can be?
covered promoters
characterize genes whose transcription is regulated; transcription is blocked until nucleosomes are displaced or removed from the promoter
differentiation
characterized by changes in patterns of gene expression in different cell types; these progressively limit which genes can still be expressed in the cell
EMS (ethyl methanesulfonate)
chemical mutagens used for mutagenesis
chromatin modifier proteins
chemically alter histone proteins in the nucleosomes by adding or removing chemical groups (e.g. acetyl and methyl groups)
chromatin structure relaxed (forms open promoters) vs condense chromatin (closed structures)
chromatin modifiers change the strength of the nucleosome DNA associations What change in the chromatin forms open promoters? and what leads to closed structures?
eukaryotic transcription
chromatin remodeling and modification regulates what?
endoreduplication
chromosome replication without cell division
homologous pairs (homologs)
chromosomes which carry genes for the same traits at a particular locus
insulator sequences
cis-acting sequences located between enhancers and promoters of genes that need to be protected from the action of the enhancers
3 class of recessive floral homeotic mutants
class, a, b, and c
chemical mutagens
classified by their modes of action on DNA as follows: 1. nucleotide base analogs 2. deaminating agents 3. alkylating agents 4. oxidizing agents 5. hydroxylating agents 6. intercalating agents
UVR C
cleaves the damaged DNA strand 4 or 5 nucleotides flanking the damage
cyanobacteria
closest relatives of chloroplasts
alpha proteobacteria
closest relatives of mitochondria are free living ?
CRISPR
clustered regularly short palindromic repeats; are transcribed into a noncoding RNA and processed into crRNAs
operons
clusters of genes undergoing coordinated transcriptional regulation by a shared regulatory region; common in bacterial genes
operons
clusters of genes undergoing coordinated transcriptional regulation shared by a regulatory region, common in bacteria genomes
Variable Tandem Repeats (VNTR)
clusters of varying numbers of repetitive DNA sequences of more than 10 bps each that are variable among individuals, can be used as genetic markers
frameshift
coding sequence mutation that cause wrong sequence of amino acids
synonymous
coding sequence mutation that causes no amino acid sequence change
missense
coding sequence mutation that changes one amino acid
nonsense mutation
coding sequence mutation that creates stop codon and terminates translation
two categories of point mutations
coding sequence mutations and regulatory mutations
DNA library
collection of cloned fragments of DNA from a single source
microbiome
collection of microbial community
genomic libraries
collections of cloned DNA fragments that represent the entire genome of an organism; includes repetitive and noncoding sequences
complementary DNA libraries (cDNA) libraries
collections of only a portion of the genome, representing mRNA produced by an organism or cell type
knockout libraries
collections of where most or all of the genes have been mutated (usually insertion of exogenous DNA)
Ribosomal RNA (rRNA)
combines with numerous proteins to form ribosomes
positional information, induction, inhibition, asymmetric cell divisions
common mechanisms for directing cell differentiation and pattern formation
chemical, radiation, insertional
common mutagens used for mutagenesis
evolutionary genomics
comparison of genomes, both within and between species. it illuminates the genetic basis of similarities and differences between individuals or species
relationships and diversification of populations
comparisons of allele frequencies between populations can identify ___?
small interfering RNAs (siRNAs)
complementary RNAs that come from exogenous sources or other endogenous transcription
coding strand
complementary partner of the template strand
genome
complete set of genetic information (genes and/or DNA) carried by a species
MutS/MutL
complex that binds to MutH
dna nucleotides
composed of a deoxyribose (5-carbon) sugar, a phosphate group, 1 of 4 nitrogenous bases: adenine, guanine, thymine, cytosine
transposable DNA
composes nearly half of the human genome ~45%
carcinogens
compounds that induce cancer; ability to produce tumors in animal model
mutagens
compounds that induce mutations
synteny
conserved order of consecutive genes along the length of a chromosome or chromosomal segment
lod score of 3.0 or higher
considered significant evidence in favor of linkage at the theta value
cis elements
consist of single binding site and are located close to and generally 5' of the gene
genetic networks
consist of small numbers of essential genes participating in many interactions; many nonessential genes participating in fewer interactions
newborn testing
consists of a set of mandated genetic tests that usually require only a few drops of blood from a "heel stick"; required in every state in US and many foreign countries; icludes 3 dozen + genetic diseases that are preventable or greatly affected by early and ongoing treatment
lac operon structure
consists of multipart regulatory region and 3 structural genes
RNA
consists of ribose, a phosphate group, 1 of 4 nucleotide bases A,C, G and U (Uracil)
quantifying phenotypic variation
construct a frequency distribution of values for that trait
eukaryotic expression vectors
contain eukaryotic features for regulation of transcription, polyadenylation and termination signals
pathogenicity islands
contain genes for proteins that promote host invasion and genes that produce toxic compounds (ex. ecoli has this that can cause diarrhea and meningitis)
insertion sequences (ISs)
contain terminal inverted repeats surrounding (flanking) a gene (or genes) encoding tranposase
core promote region
containing TATA box and other sequences, is immediately adjacent to the start of transcription
F' donor bacterium
contains a functional but altered F factor derived from imperfect excision of the F factor from and Hfr chromsoem
F' factor
contains all its own DNA plus a segment of the bacterial chromosme
selective growth medium
contains compounds that permit growth of exconjugant cells of specific genotypes and prevent donor and recipient growth
F (fertility) plasmid
contains genes that promote their own transfer from donors to recipients
regulatory region of lac operons
contains the promoter, operator, and CAP binding site
early genes and early promoters
control transcription of genes to determine whether the phage enters the lytic or lysogenic cycle
p53 repair pathway
controls cell responses to mutation by deciding to: 1) pause the cell cycle at the G1-to-S transition to allow time for repair; or 2) direct the cell to undergo programmed cell death
PL
controls leftward transcription beginning with the N gene. Leftward transcription results in expression of the cl gene ( lambda repressor protein)
PR
controls rightward transcription of immediate early genes beginning with cro (produces cro repressor)
promoter
controls the access of RNA polymerase to the gene; found immediately upstream (5') to the start of transcription (+1 nucleotide)
Forward mutation
converts a wild-type allele to a mutant allele
Reverse mutation (reversion)
converts mutant allele to wild-type or near wild-type allele
Translation
converts the genetic message carried by mRNA into a sequence of amino acids joined together by covalent peptide bonds
reverse transcriptase
copies RNA into DNA
Zmax value
corresponds to the recombination frequency that is most likely to be correct
bacterial chromosome
covalently closed circular molecule of double stranded DNA, relatively small
cas-encoded Rnases
crRNAs
AP endonucleases
creates a single stranded "nick" near the ap site
semiconservative replication
creates two new duplexes
transgenic vertebrates
creation involves injection of DNA directly into the nucleusm of a fertilized egg cell - randomly integrates into genome by illegitimate recombination
introgression line
crossover locations identified by analysis of genetic markers and each ______ is characterized for a trait phenotype
hypoxanthine
deamination of adenine by nitrous acid produces _____, whihc can mispair and lead to A-T to G-C base-pair substitutions
segment polarity genes
defects affect patterning within each of the 14 segments; expressed in a portion of each parasegment
homeotic genes
defects alter the identity of one or more segments; affect broad domains with boundaries set by pair rule genes
Phylogenetic species concept
defines a species as the smallest recognizable group with unique evolutionary history
Morphospecies concept
defines species based on morphology
chromatin
defining feature of eukaryotic DNA is packing into?
heterochromatin
densely packed chromatin
choose a mtuagen
depends on both the research organism and the type of mutant alleles desired; in all cases, mutants of interest must be crossed to wild-type to ensure that the collected mutant have only the mutation of interest
Response to selection (R)
depends on the difference between the population mean and the mean of the mating individuals can be passed on to progeny: R= S(h²) h²=R/S
cotransduction frequency
depends on the distance between two genes; can be used to determine the relative order of 3 or more genes
complementary DNA (cDNA) libraries
derived by mRNA
chloroplasts
derived from a precursor organelle, a plastid enclosed by a double membrane, and possess a third membrane (thylakoid membranes)
Near isogenic lines (NILs)/ introgression lines (ILs)
derived from different backcross progeny that are self-fertilized over many generation to form highly inbred lines - genetically identical at nearly all genes except for different crossover products near the site of a QTL
MT and CP
descendants of free living bacteria that took part in ancient infections of eukaryotic cells
island model of migration
describes one way gene flow from pop 1 into pop 2 - gene flow from a a mainland pop to an island pop
pattern formation
describes the interacting events that organize the differentiating cells of embryo to establish the body-plan aces
Molecular evolution
describes the process by which genetic changes (genes and genomes) can influence phenotypic variation
(the) Ames test
designed to first detect if a chemical (or compound) is a mutagen (mutagenic)
genetic screens
designed to identify genes involved in particular processes
genome wide association studies (GWAS)
detects and locates genes that influence traits as a group of multiple genes; looks for associations between traits and groups of alleles in populations; typically uses SNPs as genetic markers due to frequent distribution in most genomes
TA 100 strain
detects base substitutions (his- to his+)
TA 1538 strain
detects frameshift mutations (his to his+)
mutation selection balance
determine equilibrium frequency of the mutation allele (q_E) -rate of elimination of deleterious alleles by natural selection (s) - rate at which new mutant alleles are generated (µ) q_E=√µ/s
genetic markers
determined for the original parental lines and the backcross progeny
hershey chase experiment
determined in 1952 that bacteriophage T2 uses DNA (32P), not protein (35S), to reproduce within host E. coli cells
X/ austomsome ratio
determines gender based on the number of X chromosomes to set of autosomes males: ratio fo 0.5 and females 1.0
carrier genetic testing
determines if a person is a heterozygous carrier for a recessive disease
Bayesian analysis
determines the probability of a certain genotype occurring in a certain family member
Chi-sqaure test
determines whether observed genotype frequencies in populations are significantly different from those predicted by HW equilibrium
presymptomatic genetic testing
determines whether or not a person carries a mutation that will cause future disease
Lethal alleles
detrimental single gene mutations that cause death in the organism, recessively inherited (only homozygotes die), low frequency in populations
eukaryotes
differ in gene number and gene density - differ in proportion of repetitive DNA in their genomes
differential loss
difference in MT gene content reflect ___ ____ in different species
epigenetic
differences resulting from different chromatin states affecting gene transcription; heritable patterns or changes in gene expression that are not associated with any change in DNA sequence; heritable through mitosis or meiosis
allele
different (alternative) version of the same gene that arise from mutations
amino terminal sequences
different sequences that target the protein to different location within the organelle; target organellar proteins to their final locations
Z/W system
different system for sex determination when females have 2 different sex chromosomes (ZW) and males have the same (ZZ)
plastids
differentiate into chloroplasts in response to light
exonucleases
digest nucleotides from the "nick" through the mismatched nucleotide
chromosome theory of heredity
discovery of genes on the X chromosome supported that certain processes equalize the expression of genes carried on the sex chromosomes: x-linked and Y linked
highly pleiotropic
diseases phenotypes are ____ _____ due to dependence of cell on mitochondrial function
repair enzyems
distinguish between the original, correct nucleotide and the new, mismatched nucleotide using the presence of methylation on the original strand
sympatric species
diverge while occupying the same geographic area (clear examples occur occur in plant species that diverge through polyploidy)
cytokinesis
divides the cytoplasmisc fluid and organelles between the daughter cells at the end of mitosis
southern blotting
dna transfer
some functional RNA's
do not encode proteins but instead perform other roles in the cell
mutant CFTR channel
does not move chloride ions, causing sticky mucus to build up on the outside of the cell
high heritability
does not preclude environmental factors
Dominance variance (Vd)
dominance relationships where heterozygous individuals are not intermediate between two homozygous states
delayed age of onset
dominant mutation can sidestep or delay natural selection if they have this; abnormalities are not evident until after the affected individual has reached reproductive age (ex: Huntington disease)
neomorphs
dominant mutation that result in gains of novel gene function
genome editing
done by precisely changing a nucleotide sequences at a specific locus to desired sequence
F' cells
donor cells carrying F' factor
F+ cells
donor cells that possess F factor
heteroduplex
double strand DNA formed from DNA DNA of different homologs; may contain nucleotide mismatches
differ among segments
downstream targets of hox genes
maternal effect
drosophila egg has clear anterior-posterior and dorsal-ventral polarities due to ?
injection, infection (with a dsRNA virus), via a transgene (carrying DNA that will produce dsRNA)
dsRNA complementary to the target gene can be introduced into cells or organisms by?
Xeroderma pigmentosum
due to a deficiency in DNA repair cells from patients with this rare autosomal recessive disease can excise thymine dimers only at reduced rates of 0-90% of normal, as a result even normal levels of exposure to UV Light causes skin cancer; occurs at a frequency of about 1:250,000 in the US
acestral hox gene cluster
duplicated during the evolution of the vertebrate genome which now contain four copies
lysogenic cycle
during the transcription of the lambda phage what occurs when lambda repressor (dimer) bidns to OR1 and OR2
lytic cycle
duringthe transcription of the lambda phage what occurs when Cro binds to OR3
stripe
each "_____" is established by its own enhancer modules of cis-acting regulatory sequences
combinatorial control
each enhancer module responds to specific combinations of gap genes
chromosomes
each organelle contains multiple copies of its _____
multinucleated syncytium
early embryogenesis begins with a series of nuclear divisions without any cytoplasm division, producing a _____ ______
Pr and Pl
early gene transcription begins at two promoters; transcription on one or the other dpends on which operator sites are occupied
"switch"
early genes compete for control of a genetic _____
MutH
ecoli protein that binds to (hemi)methylated DNA region' breaks a phosphodiester bond on the 5' side of the guanine of a GATC sequence on the unmethylated daughter strand
stripes of gene expression
emerge from the domains of gap gene expression and are narrower
most chloroplast proteins
encoded by nuclear genes but are produced and regulated through interactions between the two genomes
Transfer RNAs (tRNAs)
encoded in dozens of forms and are responsible for binding an amino acid and depositing it for inclusion into a growing protein chain
lacY
encodes enzyme permease; facilitates lactose transport across the cell membrane
pol
encodes reverse transcriptase
env
encodes the outer envelope
lacA gene
encodes transacetylase
lacA
encodes transacetylase; protects against harmful by-products of latose metabolism
lacZ
encodes β-galactosidase; cleaves lactose into two monosaccharides (glucose and galactose)
produce dsRNA
endogenous genes, endogenous non-gene sequences, exogenous sources
E(var) mutations
enhance mutant phenotypes by encouraging spread of heterochromatin; mutations enhance heterochrmatin formation and restrict w+ expression to small patches (mostly no eye color)
insulators
ensure that only the target gene is regulated by the enhancer and allow formation of DNA loops containing enhancers and their target promoters while excluding non-target genes
Drosha
enzyme complex that cuts the pri-mRNA
Dicer
enzyme in gene silencing that cuts the dsRNA into small fragments that are then bounds by RISC
Rna polymerase
enzyme that synthesizes RNA transcripts
photolyase
enzyme that uses energy from visible light to break the bonds producing the photoproduct; is encoded by the E.coli phr (photreactive repair) gene
writer
enzymes add chemical groups to chromatin
eraser
enzymes removes groups from chromatin
heritable through mitosis
epigenetics from one generation of cells to the next
heritable through meiosis
epigenetics from one generation of organism to the next
Interactive variance (Vi)
epistatic interactions between alleles of genes contributing to a quantitative trait
founder effect
establishment of a new population by a small number of founding organisms can produce a difference in allele frequencies
narrow sense heritability (h²)
estimates the proportion of phenotypic variation that is due to additive gene variation h²=Va/Vp
Narrow sense heritability (h^2)
estimates the proportion of phenotypic variation that is due to additive genetic variation (h²=Va/Vp)
Broad sense heritability (H²)
estimates the proportion of phenotypic variation that is due to total genetic variation H²=Vg/Vp
Broad sense heritability (H^2)
estimates the proportion of phenotypic variation that is due to total genetic variation H²=Vg/Vp (where Vg= Va+Vd+Vi)
selection differential (S)
estimating the potential response to selection for a traits begins with calculation of the difference between the means of the whole population and the breeding population
(origin of eukaryotes) model 1
eukaryotic cell that had a nucleus but no MT subsequently acquired an alpha proteobacterium as an endosymbiont - suggests possibility that some eukaryotes that lack MT still exist
recessive
eventually the ____ allele may be completely eliminated, though this can be a slow process
reproductive isolation
evolutionary change at the species level is driven by _____ that can result from any conditions that prevents one population form mating with others
Xist
ex of lncRNA that is involved in X chromosome inactivation in eutherian mammals (balance gene dosage)
informational genes and operational genes
examination of genes from yeast compared with bacteria and archaeal species show that the yeast nuclear genes can be divided into two sets
development of c. elegans vulva
example of how inductive and inhibitory signal direct specific fates in a group of pluripotent cells
example Translation blockage
example: antisense RNA and riboswitches
example of inducible transcription
example: lac operon
example of mRNA destruction
example: riboswitches
example of repressible transcription
example: trp operon
example of attenutation
example: trp operon and riboswitches
Y linked inheritance
exclusively patrilineal (farther to son)
partial diploids (merozygotes)
exconjugants that contain a complete F' factor (contain two copies of genes- one of the bacterial chromosome and the other of the F' factor)
hox genes in vertebraes
exhibit similar patterns of spatial organization and expression during development
large-sclae gene loss
existing cyanobacteria have much larger genomes than chloroplasts, thus what took place during the evolution of chloroplast
variation
exists among members of populations, can be inherited in genes
homologous recombination
exogenously supplied DNA sequences can contain the desired nucleotides; required a significant length of DNA sequence in common between the recombining molecules
time-of-entry mapping
experiments that test for gene transfer at timed intervals used to determine the distance between genes
two models
explain where the additional genes in the nuclear genome of eukaryotes came from
maternal/ paternal
expressed gene copy in genomic imprinting is always ____ in some imprinted genes and always ____ in others
genes of bithroax complex
expressed in overlapping sets of thoracic and abdominal parasegments with sharp anterior boundaries and diffuse posterior boundaries\ act in combo to specify the identify of these parasegments; their expression levels vary among the parasegments in which they are expressed
immediate early genes
expressed shortly after circularization; genes expressing immediately upon infection of a host bacterial cell by bacteriophage lambda
standard deviation (s)
expresses deviation from the mean in the same units as the scale of measurement of the sample
realizator genes
expression contributes to the characteristic features of each segment
Rad52 and Rad59
extension of the invading strand of DNA synthesis within the broken strand are guided by the intact template strands assisted by these which proteins?
episomes
extrachromosomal elements found in bacteria
modifier genes
eye color is influenced by genes to a lesser degree(a gene that modified the effect of a major gene )
B
f1) Which of the following is false regarding plasmids? A) They are small double stranded circular DNA molecules. B) They contain essential genes for metabolism. C) They can have genes that promote their own transfer from one bacterium to another. D) They can carry genes for antibiotic resistance. E) They generally replicate autonomously.
Rad51
facilitates the invasion of the intact sister chromatid by the resected end of the broken strand
nondisjunction
failed chromosome separation
lacP⁻
fails to bind RNA polymerase or does so weakly
lacO^c
fails to bind repressor protein, resulting in continuous (constitutive) transcription
molecular basis of duplication
fat of duplicated genes depends on???
genetic hitchiking
favored allele and alleles linked to it will rise in frequency
stabilizing selection
favors an intermediate phenotype over extremes, and phenotypic variance is reduced (same mean but reduced variance)
natural selection (NS)
favors the reproductive success of some members of a population over others
X linked dominant
females heterozygous and males hemizygous for the dominant allele express the dominant phenotype
X linked recessive inheritance
females homozygous for the recessive allele and males hemizygous for it display the recessive phenotype
mosaics
females that are heterozygous for X linked genes; one expresses the maternal X and the other the paternal X; alleles for both chromosomes are expressed approx. equally over the whole organism
tRNA genes (than) codons
fewer unique ____ genes than ___ in MT genomes
induced pluripotent stem (iPS) cells
fibroblasts can be reprogrammed in vitro to behave like stem cell
dna polymerase
fills in gaps in dna nucleotides
Dolly the sheep
first cloned mammal - diploid nucleus isolated - injected into an egg (w/ nuclues removed) - embryo is genetically identical to the donor - the only one of 270 injected eggs that resulted in birth of a sheep
recessive phenotype
first cousin matings produce a child with a ____ at a higher frequency compared to random matings
genetic liability
first degree relatives of an affected person are more likely to be affected than an average person in the population, due to ___ ____
Haemophilus influenzae
first genome sequences by paired end WGS sequencing with the complete genome assemble into single contig
comaparative sequences analyses
first step to predicting regulatory sequences (usually enhancer modules in eukaryotes)
pioneer factors
first to bind regulatory molecules, facilitating binding of additional transcription factors
beta carotene
five plant derived enzymes are needed to produce what?
change by mutation and migration, not NS
fixed allele frequencies can only be change by ____ and ____ not ____
genomics
focuses on sequencing, interpretation, and comparison of genomes of different organisms
proteomics
focuses on the study of the complete set of proteins encoded in a genome
Recombinant DNA technology
for amplifying, maintaining, and manipulating DNA sequences in vitro and in vivo - fragment and purify DNA into easily managed pieces - create copies of DNA fragments of identical sequence - determine the exact sequence of specific DNA - introduce specific DNA into organisms and assay the phenotypic effects
genotype (mother,) phenotype (zygote)
for maternal effect genes, the _____ of the mother determines ____ of the zygote
inducer-repressor complex
formation alters the DNA-binding domain of the repressor and prevents it from binding the operator (O) site
active transcription
formation of euchromatin
transcriptionally inactive
formation of heterochromatin
6-4 photoproduct
formed by a covalent bond between the 6 carbon on one thymine and the 4 carbon on the other adjacent thymine
transductant
formed by the integration of donor DNA into a recipient cell's chromosome by homologous recombination
lariat intron structure
formed when the 5' intron end binds to the branch point adenine
conjugation pilus
forms between donor and recipient cells during conjugation
Ribosomal RNA (rRNA)
forms part of the ribosomes
types of reversion mutations
forward mutation reverse mutation true... intragenic... second-site (surppressor mutaitons)...
insertion sequences
found in bacterial, archaeal and viral genomes, plasmids too; contains ~800-2000bp of DNA and inserts by replicative or nonreplicative transposition
small nuclear RNA (snRNA)
found in eukaryotic nuclei, where multiple join with numerous proteins to form spliceosomes that remove introns from precursor mRNA
adult stem cells
found in many tissues (blood, hair, skin, etc.) but are less "potent" (one or a few types of cells)
CAAT box
found near -80 position
Shine-Dalgarno sequences
found upstream of protein coding genes in MT of some organism, but most do not have these
insertion sequence (IS) elements
four large components of F factor; when shared by an F plasmid and a bacterial chromosome recombination can occur
1-m
fraction contributed by island residents
m
fraction of individuals (alleles) from mainland population is __?
cotransduction mapping
frequency of contransduction is higher for genes close together due to the likelihood of 2 genes being packaged together into a single phage head, followed by the chances of separation be a crossover event in the recipient
P element structure
full length p elements ~2900 bp long and contain a gene for transposase flanked by 31 bp inverted repeats
conserved noncoding sequences (CNSs)
functional regulatory sequences and genes that produce functional RNAs
chimeric genes
fusions, where regulatory and coding sequence from multiple genes are recombined resulting in a gain of function allele due to ectopic expression; can cause any gene to be driven by any regulatory sequences that will function in the host organism
functional or comparative approaches
gene annotation is characterized using ____ or ______
"sampling error"
gene drift refers to chance fluctuations of allele frequencies that result due to "____"?
short term
gene flow can change allele frequencies in the admixed population
long term
gene flow equalizes allele frequencies between populations that remain in genetic contact
"bacterial" genes
gene flow from bacterial endosymbionts has resulted in what kind of genes in the nuclear genomes of eukaryotes
negative and positive control
gene regulation in bacteria is transcriptional regulation involving
regulatory proteins and individual transcription factors
gene regulation in eukaryotes is unlike bacteria due to:
"disarmed" viruses
gene therapy uses " " to deliver/ remove genes and gene products
nuclear genome
genes "lost" from organelles have been relocated to where? (ancient and recent DNA transfers)
long terminal repeat (LTRs)
genes carried on retrotransposons are flanked by
microRNAs (miRNAs)
genes encode precursonrs of dsRNA that are cleaved into?
examining DNA sequences
genes in QTL regions are located by ?
metabolic or biosynthetic
genes in a particular operon nearly always participate in the same _____ or _____ pathway
orthologs (orthologous genes)
genes in different species that are derived from a single ancestral gene in the species' last common ancestor
NUMTS and NUPTS
genes in the nucleus recently derived from organelles
syntenic genes
genes located on the same chromosome - linked together and do not assort independently
regulated transcription
genes responding to changing environmental conditions require?
maternal effect genes
genes that act in the mother to impart gene products (RNA or protein) into the egg and subsequently the embryo. for these genes, the embryonic phenotype is determine by the genotype of the mother rather than that of the embryo
quantitative trait loci (QTLs)
genes that contribute to phenotypic variation in quantitative traits
homologs (homologous genes)
genes that descended from a common ancestral gene and constitute a gene family
paralogs (paralogous genes)
genes that originated by a duplication event
mutation hotspots
genes with elevated mutation rates, sometimes due to large gene size
genotype
genetic constitution (makeup) of an organism
frequency of an allele every generation
genetic drift can raise or lower the ____?
small populations
genetic drift occurs in all population but is especially prominent in ?
translation, lipid metabolism, or DNA repair
genetic networks identify groups of genes w/ similar molecular function such as
three point test cross analysis
geneticists can efficiently map three linked genes simultaneously
mt- CP
genome is degraded
mt+ CP
genome is selectively maintained
protein domains
genome segments coding for conserved ____ _____
coding vs noncoding
genomes also vary in their proportions of _____ vs _______ sequences
sister taxa
genomic difference between ____ _____ define the differences between two species
rs or rsid number (Reference SNP ID)
genomic sequence location adress that are used to identify SNP variants
(p+q)^2
genotype frequencies can be computed using the binomial expansion
linkage equilibrium
genotype of a chromosome at one gene is expected to be independent of its genotypes for other genes
Kruppel
gradient of hunchback protein is critical for regulation of other gap genes such as ____ which is repressed by high levels of hunchback but is activated in the central region of the embryo where the bicoid levels are moderate
gene families
groups of genes that are evolutionarily related via successive gene duplication events that are followed by diversification
lambda phage genome
has about 48 kb of linear double-stranded DNA encoding nearly 60 genes
RNA-seq
has the potential to be more quantitative , easily distinguish between similar sequences such as splice variants of the same gene, or SNPs
Oc mutants
have altered operator sequences to which the repressor protein cannot bind and the structural genes are continuously expressed
DNA-binding proteins
have amino acids with side chains that associate with nucleotides of particular DNA sequences; simultaneously contacts multiple nucleotides; specificity is dictated by the chemical makeup of nucleotides
bacterial artificial chromosomes (BACs)
have an insert capacity of 100- 200 kb (plasmids only up to 20kb)
Eukaryotic transcripts
have caps, tails, exons (coding information) and introns (removed from transcript prior to translation)
Copia elements of Drosophilia
have central elements 5-8.5 kb long that contain gag and pol genes, flanked by 250-600 bp LTRs; >5% of total genome is composed of various types
bacteria and archaea
have fewer genes and higher gene density due to lack of introns, compact gene regulatory sequences and overall lower complexity
Secondary and tertiary endosymbiotic events
have occurred between different lineages of eukaryotes
class B mutants
have transformations in the middle two whorls, with sepals replacing petals and carpels in place of stamens
class A mutants
have transformations in the two outer whorls, with carpels in place of sepals and stamen in place of petals
train in a population
heritability for a given ____ in a ____ can change
potential response of a trait to selection
heritability is an important measure of ?
genetic differences
heritability measure of the degree to which ____ ___ contribute to phenotypic variation of a trait
C elegans
hermaphrodite nematode worm, in which the vulva forms a portal through which eggs are laid
greater degree of response to selection
high narrow sense heritability values correlate with ____?
disadvantages of MSS
higher likelihood of false positive (suggests a problem when there is none)
Vg=0
highly inbred populations where all individuals are homozygous alleles controlling a trait
thritorax (TrxG)
histone acetylation maintain active gene expression
polycomb (PcG)
histone deacetylation repress target gene expression
in eukaryotes
homologous recombination takes place in prophase I of meiosis and is initiated by controlled double-strand DNA breaks
parental chromosomes or nonrecombinant chromosomes
homologs that don't reshuffles alleles under study
how closely they are linked to the causative mutation
how do mutations segregate?
complementary Hydrogen bonding between the anticodon of the tRNA and the codon of the mRNA
how is a tRNA able to recognize its proper mRNA codon?
3 mechanisms (chromatin remodelers, chromatin modifiers, loosely bound histones)
how many mechanisms are there by which trans acting proteins access target DNA sequences
choose a model organism and choose a mutagen
how to design forward genetic screens?
derived
human alleles are ___ if they differ from the alleles shared by chimps and ancestral
Beta globin LCR
human beta globin gene encodes beta globin polypeptide, 2 copies of which join two copies of alpha-globin to form hemoglobin
ancestral
human genes are ___ if they are shared by humans and gorillas but differ in chimps
recent population expanison
humans have reduced individual genetic diversity compared to all other primates; consequence of
what are bacteriophages composed of?
icosahedral head, hollow protein sheath, and sometimes a set of tail fibers
homodimers
identical polypeptides
flanking direct repeats
identical repetitive sequences flanking the sites of insertion of transposable genetic elements
terminal inverted repeats
identical sequences found at both ends of a transposable genetic element. The sequences are inverted relative to one another.
large scale genetic screens
identified directing pattern formation in drosophila embryos, focused on embryonic and larval genes, mutations identified were assigned to five gene classes
quantitative measurement
identify influences on phenotypes in terms of _____ ______
double mutant
identify interacting genes (e.g. synthetic lethality)
intraspecific comparisions
identify sequence polymorphisms responsible for genetic differences among individuals of a single species
interspecific comparisons
identify sequences conserved over evolutionary time, based on comparisions between species
redundant pathways
identifying gene interactions provides clues to gene function if two genes are found in same or _____ _____
candidate genes
identifying genes responsible for QTL variation requires identifying ______? genes potentially responsible for the observed variation
Product rule
if 2 or more events are independent of one another the likelihood of the simultaneous or consecutive occurrence is the _______ of their individual probabilities
(favored allele) fixed at 1.0, (unfavorable allele) eliminated
if NS progresses for enough generations, the frequency of the favored allele will become ___ and the unfavorable allele will become ____
a possible role for the gene
if a gene of unknown functions is found to participate in a particular network, this suggests ?
recessive homozygote
if a recessive allele is more frequent in a population, chances of a _____ in a first cousin mating is only a few times more likely than in a random mating
the lod is greater than 1.0
if frequency is greater in the case group than the control group ___?
concordance would be 100% in MZ twins
if phenotype is 100% genetically determined...
Vp= Ve+Vg
if the F1 are crossed, now there will be both genetic and environmental variability among the F2 so:
apoptotic pathway
if the p53 induced pause of the cell cycle persists too long, the ____ ____ is induced
genotype corresponds to a distinct phenotype
if there is no gene-environment interaction then
Vg= 0 and Vp=Ve
if two different pure-breeding parental lines are genetically uniform
translocation
illegitimate exchange between non-homologous chromosomes
expression of lambda genes
immediate early genes, delayed early genes, late genes
eugenics
improvement of qualities of species through selective breeding
wilkens
in 1988, ____ used H² analysis to describe the genetic contribution to the evolution of an eye tissue in cave fish
5' GATC 3' sequences
in E.coli methylation is common on the adenine of
Dicer and Argonaute enzymes
in RNA interference mRNA from the target gene will be degraded through the action of what?
DNA-RecA-SSB complex
in SOS repair in ecoli what complex forms?
pol V (polymerase five)
in SOS repair in ecoli what displaces pol III, synthesizes a short stretch of new DNA across the lesion, and is then replaced by pol III, which resume normal replication
RecA (activates transcription of several genes including pol V)
in SOS repair in ecoli what protein activates transcription of several genes, including pol V
RecA (proteins coats the template strand ahead of the lesion)
in SOS repair in ecoli what proteins coats the template strand ahead of the lesion when already bound by SSB protein?
DNA pol III stall at damaged DNA
in SOS repair in ecoli what stalls at damaged DNA?
LTRs (long terminal repeats)
in Ty elements of yeast the central element is flanked by _____ that contain promoters that direct transcription of different genes in the central region
contractile ring of actin
in animal cells this creates a cleavage furrow around the cell to pinch the cell into two
mt- parent
in chlamydomonas chloroplast segregation, mitochondria are preferentially transmitted by the mt- parent
balancer chromosomes
in drosophila these allow for specific chromosomes to be transmitted intact through multiple generations: 1. one or more inverted segments to prevent transmission of chromosomes that have undergone crossing over 2. a recessive allele resulting in lethality so that individuals cannot be homozygous for the balancer 3. a dominant mutation producing a visible phenotype so that segregation of the chromosomes can be followed through generations
prune killer (K-pn) and mutant prune (pn)
in drosophila what combination of alleles results in lethality but mutation alone is viable
RISC
in gene silencing what uses complementary base pairing to attach guide strand to mRNA and degrade target and/or prevent their translation
multiprotein complex
in humans and other animals a _____ _____ acts as a genomic sentry to identify DNA damage
lactose unavailable and glucose available
in lac operon transcription regulation what causes the lac repressor protein to bind to the operator sequence (lacO) and inhibit transcription
repressor dimer
in lysogeny maintenance and termination what causes activation
repressor monomer
in lysogeny maintenance and termination what causes inactivation
3 (transcripts) 3 (promoters) under mitochondrial control
in mammals how many polycistronic mRNA transcripts are produced from how many promoters and under what control
vector
in molecular cloning isolated DNA fragments are inserted into a _____; to amplify the dna
lactase
in newborns, lactose digestion is carried out by the enzyme ____ encoded by the LCT gene on chromosome 2
genes will be normally expressed
in partial diploids, if lac+ and lac-
RNAi also plays a protective role in response to viral infection
in plants, viral infection of a single leaf can generate and RNAi response; blocking viral replication an protecting the plant from infection
fixation
in small populations one allele will ultimately reach ____ (frequency 1.0) without other evolutionary influences
additive genes
in some traits, the continuous distribution of phenotype results from incremental contributions by multiple genes
biparental
in some, cytoplasmic organelles are contributed to the zygote by both parents
immediate evolutionary change in allele frequencies
in the island model of migration the admixed population has ____?
allolactose
in the lac operon what acts as the inducer?
nanos gene
in the posterior region the product of the ____ gene prevents translation of maternal hunchback mRNA
repressor
in the λ phage which protein, the produce of the cI gene, blocks the transcription required to initiate the lytic cycle?
genetic mosaics
in transgenic animals DNA can also be injected into cells that will subsequently be transplanted into an embryo and develop as?
homologous, illegitimate
in transgenic animals _____ recombination occurs less frequently than ______ recombination
promoter sequences
in transgenic bacteria what is paced upstream of the MCS
in 5' UTR of the mRNA
in transgenic bacteria where is the Shine-Dalgarno sequence located
alleles into gentoypes
inbreeding is a type of nonrandom mating that alters distribution of ___ into ____
alleles
inbreeding will share a greater proportion of ___ with one another than random members of a population
normal reproductive process
inbreeding, for self fertilizing plants and some self fertilizing animals, is a _____
enhancer sequences
increase the level of transcription of specific genes by binding portions that interact with the proteins that are bond to gene promoters to drive gene expression, may be upstream or downstream of the gene and may promote conformational changes in DNA needed for transcription
Directional NS
increases the frequency of certain alleles over others with variable intensity, based on the strength of selection
conservation of Hox gene clusters
indicates that a common ancestor possessed such a cluster, specifying the pattern along the anterior-posterior axis
Manhattan plot
indicates the locations of genes contributing to the development of traits and conditions; higher green bar on plot the stronger the association between a potential contributing gene and a chromosomal location
sum rule
individual probabilities are _____; this rule is used when more than one outcome will satisfy the condition sof the probability question
selection coefficient (s)
individuals that reproduce less successfully than the favored genotype have their relative fitness decreased by a proportion
differential reproductive fitness
individuals with a favored phenotype survive to reproductive age at higher rate and/or reproduce at higher rates as a result of the favored phenotype
consultands
individuals working with genetic counselors
saturation mutagenesis
induce mutations in every gene of a population of mutagenized individuals
transcriptional regulation
inducible transcription, repressible, transcription, attenuation
Retroviruses
infect cells and have genomes composed of ssRNA; on infection RNA is transcribed into dsDNA by reverse transcriptase allowing the DNA to parasitize the host cell
environmental and developmental
influence of ___ and ___ factors on threshold traits is important - plays a role in determining if individuals with a genetic liability near the threshold end up having the trait
Gene environment interactoin
influence of the environment on the expression of genes and the phenotypes of organisms
cis acting
influence transcription of genes only on the same chromosome ex: lac operator mutations
interactome
info on protein-interaction network in many model systems, collectively called the
high p53 level
initiates G1 arrest; allows for time to repair damaged DNA
SWR1
insert modified histone (H2A--> H2A.Z) to facilitate displacement and modify transcription
knock-in
inserting a functional gene, often creating a gain-of-function allele is called a?
Frameshift mutations
insertion or deletion of one or more base pairs in the coding region, may alter the triplet reading frame of the message; wrong amino acid sequence is produced starting at the point of mutation; may result in a completely altered protein being constructed
transposable elements in bacterial genomes (as well as plasmids and viruses)
insertion sequences (ISs), composite transposons, noncomposite transposons
mutagenic effects of transposition
insertional inactivation causes certain mutations in humans for example: hemophilia A and coffin-lowry syndrome; in plants, insertional activation causes the round versus wrinkled pea phenotype seen by Mendel
transfer DNA and transposons
insertional mutagens used for mutagenesis
whole-genome duplication
instantly provides duplicate sets of genes referred to as homeologs that can subsequently undergo sub and neofunctionalization, the latter a driver of evolution
illegitimate recombination
integrated DNA into the host genome at a random, nonhomologous location
prophage
integrated phage dna in lysogenic cycle
spatial control of gene expression
interaction of the transcription factors with regulatory sequences of target gens provides ???
systems bniology
interactions in genetic networks can be combined with other information about the genes to predict biological functions known as
introns
intervening segments that are removed from pre-mRNA (common in eukaryotic genes, rare in bacterial genes, occasionally found in archaeal genes)
Crohn's disease
intestinal disorder influenced by inherited variation
transgenes
introduce to create transgenic organisms
cosuppression
introduced gene and the plant's normal pigment-producing gene were both suppressed
Transgenic organisms
introduction of a gene from one organism into the genome of another organism - must be transcribed and translated for expression -examples bacteria, plants, animals- salmon and mice
Gene knockouts
involve gene insertion that deletes the entire coding region of the gene, resulting in recessive loss-of-function null alleles
trinucleotide repeat expansion disorders
involve strand slippage mutations that cause some hereditary diseases in humans and other organisms
zygotic genes
involved in developmental processes; these are transcribed in the zygote or embryo
translation repressor proteins
involved in one of the mechanism for translation regulation in bacteria by binding to mRNA near the Shine-Dalgarno sequence to prevent translation
molecular basis of development
involves establishment and maintenance of different patterns of gene expression as cells differentiate and become specialized
Drosophila development
is a paradigm for animal development
mitochondrial genome
is a single molecule in most species; gene content and size varies considerably - all descended from a common bacterial ancestral genome
mtDNA
is not packaged in chromatin (genome is anchored to the inner membrane) transcribed by an RNA polymerase similar to that found in bacteria; regulation of mitochondrial gene expression varies among species (reminiscent of bacterial operon)
divergence
isolated populations locally adapt and can result in ____
DNA ligase
joins DNA segments; seals gap among okazaki fragments
modification enzymes
keep host DNA methylated
high concentrations of hunchback protein
kruppel is repressed by?
5 genes of the antennapedia complex
labial, Deformed, Sex combs reduced, proboscipedia, and Antennapedia act in combination to specify the head and thoracic parasegments
trans-acting
lacI+ produces a protein that is capable of diffusing and interacting with both operators in a partial diploid aka
Lac operon structural genes
lacZ, lacY, lacA
the 3 lac operon structural genes
lacZ, lacY, lacA
F- cells
lack an F factor
Neutral petites
lack most of their mitochondrial function
beta(β) galactosidase linkage
lactose is a disaccharide of glucose and galactose joined by what kind of linkage?
glucose and galactose
lactose is a disaccharide of what?
replisome
large protein complex found at each replication fork; contains 2 copies of Pol III and other proteins
genomic islands
large unique regions that help identify Lateral gene transfer
distortion
leads to DNA nicking that may not be efficiently repaired
P males X M females
leads to hybrid dysgenesis
homeotic genes in drosophil
led to the discover of vertebrae gene containing homeoboxes
advantages of MSS
less invasive, less risk
genomic libraries
libraries derived from genomic DNA of an organism
Binomial Probability
likelihood of a series of events; contains two variable p and q being the frequency of one outcome or the other (p+q)=1; expand equation by power of n= number of successive events (p+q)^n
prior probability
likelihood that the hypothesis that an individual has a certain genotype is true
genome wide association studies (GWAS)
link the presence of a sequence variant with a QTL influencing a specific phenotype
point mutations
localized mutations that occur at a specific identifiable position in a gene or a specific location anywhere else in the genome; such mutations have varied consequences depending on the type of sequence changed and the location of the affected gene pair
golberg hogness (TATA) box
located at about position -25 consensus sequence is 5'-TATAAA-3'; principal binding site during promoter recognition
MutS
locates and binds to the DNA mismatch and then forms a complex with MutL
a QTL linked to the marker
lod scores above threshold suggest?
inconclusive
lod scores between -2 --> 3.0 ; more data needed to reach a conclusion
chromosomes
long molecules of double-stranded DNA and protein that carry genes
euchromatin
loosely packed chromatin
Deamination
loss of an amino group (NH₂) from a nucleotide base (Ex: cytosine is converted into uracil)
genetic redundancy
loss of function of either gene alone is compensated by the other non-mutant gene; most obvious case two genes encode very similar proteins that can function interchangeably; may also result form the compensatory action in genes with little or no sequence similarity
polymorphic loci, heterozygous loci
loss of genetic diversity determine by percentage of _____ in the population or the percentage of _____ in average individual
mutations at DNA level
lower than phenotypic level ~10⁻⁹ per replicated base pair
posttranscriptional regulation
mRNA destruction, translation blockage
nothern blotting
mRNA transfer
induced pluripotent stem (iPS) cells
made by adding in 4 specific genes (transcription factors), may help to produce pluripotent stem cells without using embryos
(genome editing:) CRISPR-cas9
made up of DNA- cutting enzyme and a programmable RNA molecule (guide RNA) this can be used to precisely target nearly any gene
threshold of genetic liability
majority of a population is below the? in polygenetic and multifactorial inheritance, a trait with different phenotypes (affected/ unaffected) that are determined by whether individual organism are above or below a particular critical value on the phenotypic scale
Pseudoautosomal regions (PARS)
makes synapsis of X and Y chromosomes possible during prophase I in males 2 ____ on X and Y chromosome: ____ 1 and _____ 2
newborn genetic testing
mandated in all 50 US states, tests newborns for 3 dozen or more treatable rare genetic dissease
selective advantage; genetic drift
many adaptive alleles selected for in our past may no longer have ____; will likely undergo _____
modular
many eukaryotic proteins are _____, consisting of distinct domain that are joined together
back crossed
many mutant strains are ____ ____ with wild type strains to separate the one causative mutation from other mutations
asexually
many plant produce _____, producing clones that are genetically identical
genetic complementation analysis
mate two pure breeding strains with similar mutant phenotypes and observe phenotypes in the f1 generation
H19
maternally expressed on chromosome 11
inbreeding
mating between related individuals; a type of nonrandom mating that alters distribution of alleles into genotypes
CP ribosomal proteins
may be encoded by nuclear or chloroplast genomes
ribosomal proteins
may be encoded in MT or the nucleus
molecular probes
may bind (hybridize) to target proteins or nucleic acid sequences on the membranes
strand slippage
may cause alterations in number of DNA repeats when the DNA polymerase of the replisome temporarily dissociates from the template and a portion of the newly replicated DNA forms a temporary hairpin; leads to re-replication of some of the repeats and an overall increase in the number of repeats on the daughter strand
hotspots or coldspots
may lead to placement of genes farther apart or closer together, respectively on the recombination map than on the physical map
individual transcription facotrs
may regulate tens to hundreds of target genes
mutation rate
measured by (1) counting the number of mutations affecting a phenotype and (2) determining the frequency of mutations per base pair
maternal serum testing (MSS)
measures levels of 3 proteins in a pregnant woman's blood between the 15th and 20th week of gestation; levels are associated with elevated risks of two trisomy conditions; elevated level of one of the proteins indicates possible neural tube defect
heritability
measures the proportion of phenotypic variation that is due to genetic variation; differs across traits
intrinsic termination
mechanism dependent only on the presence of the repeat induces a secondary structure needed for termination
hox genes
members of the homeobox gene clusters found throughout metazoans; the genes often pattern the anterior-posterior axis and are homeotic genes
mondern synthesis of evolution
merges evolutionary theory with experimental, mathematical, and molecular population biology - gives more complete pic of the factors and mechs that produces evolutionary changes in populations
operational genes
metabolic processes (resemble bacteria)
environmental factors
methods are used to detect gene interactions; concluded that ____ _____ contribute to continuous variation
injection into eggs, embryos, or cells that give rise to gametes
methods to introduce transgenes in transgenic animals involve
DNA methylation
methyl group (an epigenetic factor found in some dietary sources) can tag DNA and activate or repress genes
Restriction modification systems
methylate the restriction site in bacteria, protecting bacteria sequences from digestion
on the paternal chromosome
methylation inactivates the icr and blocks H19 expression; the enhancer drives IGF2 expression
knockin mice
mice created with gain of function alleles
knockout mice
mice created with loss of function alleles by homologous recombination
loss of function mutations
mice embryos with ____ in hox genes exhibit defects in identity and serially repeated structures such as vertebrae
median
middle value
ames test
mimics what happens when animals are exposed to compounds, and determines if the compound or any of its breakdown products is mutagenic
moderate gene-environment interaction
minor overlaps between phenotypes in the F2
mismatch repair
mismatched nucleotides that escape DNA polymerase proofreading may be detected and repaired by
usually circular
mitochondiral chromosomes are?
mitosomes
mitochondria of Giardia are reduced to small membrane bound structures lacking a genome called ?
multiregional (MRE) hypothesis
modern humans emerged gradually and simultaneously from earlier homo erectus migrations on different continents ~2 million years ago
chromatin remodeling
modifications that reposition nucleosomes to open or close promoters and other regulatory sequences
allosteric effector compound
molecule that binds to the allosteric protein domain and subsequently induces a change in the bound protein
cell cycle checkpoints
monitored by protein interactions for readiness to progress to the next stage
not totipotent
most animal cells are ___ _______, so cloning animals from single differentiated cells is very complicated
B-form
most common form of DNA and has a right handed twist of the helix
UV radiation
most common mutagen of most organisms
Alu elements
most common of the short interspersed nuclear elements (SINEs) and actively generate mutations - vary in length 100-300 bp and are flanked by 7-20 bp direct repeats - human genome contains more than 1 million of these elements
helix-turn-helix (HTH) motif
most common structural feature of proteins in bacteria consists of Two alpha helical regions interacting with the inverted repeats of regulatory DNA sequences
mode
most common value int he distribution
uniparental
most eukaryote species observe _____ (maternal) inheritance of organelles
mosaic
most genomes contain a ______ of gene families derived from ancient or recent duplication events ~ one gene duplication per 3000 to 10000 years
transcription factors
most of the early-acting genes that establish the anterior-posterior axis encode?
nuclei
most organellar proteins are encoded where?
P element
most prominent type of transposable element in Drosophila melanogaster
psuedogenes
most redundant genes degenerate into ______; accumulate mutations, making them nonfunctional
transcriptional regulation
most regulation of gene expression in bacteria; results from interactions between DNA-binding proteins and regulatory sequences of DNA
gene flow
movement of alleles into and out of populations - can introduce novel alleles -increase frequency of existing alleles - remove existing allleles
normal CFTR channel
moves chloride ions to the outside of the cell
stem-loop structure
mrna containing inverted repeats form into a short hairpin which is followed by a series of U's in the mRNA that causes the RNA polymerase to destabilize
TFIID
multisubunit protein containing the TATA-binding protein (TBP) and subnits of TBP associated factor (TAF) that binds to the tata box
choose a model organism
must be able to progress through its life cycle in a lab, have a short generation time, produce a reasonable number of progeny and be amenable to crossing- simple is often better (Ex drosophila)
gene regulatory switches
must be controlled by phage gene expression to redirect action of host genes
causative mutations
must be distinguish from wild-type polymorphisms
immune system to invading microbes
mutant allele produces a protein with a small fraction of wild type protein activity, reducing sensitivity of the __?
forward genetics
mutant phenotypes provide information on the wild-type function of a gene and insight into biological processes
gap genes
mutants are missing large contiguous sections
pair rule genes
mutants are missing parts of adjacent segment pairs in alternating patterns; expressed in striped that do not exactly correspond to segments of the adult insect
Y chromosome short tandem repeats (Y-STR) polymorphisms
mutate rapidly; useful for forensic or paternity assesments
suppressive petites
mutated mitochondrial DNA
neofunctionalization
mutation in one of the copies could provide a new function not provided by the other copy
thalassemia
mutations in alpha and beta globin genes produce a hereditary anemia known as? some with no mutation in either of the globin genes
subfunctionalization
mutations in each copy can produce two genes with complementary functions
DNA damage repair disorders
mutations in genes that participate in DNA damage repair cause an organisms to be highly sensitive to chemical mutagens and to radiation; also greatly increase the organism's susceptibility to cancers caused by exposure to mutagens
situation
mutations in potentially different genes can produce the same, or very similar, mutant phenotypes
transposons
mutations in the RNAi system can reactivate ____ by reversing transcriptional silencing
natural selection
mutations in the real world are commonly subject to ____
somatic mutations
mutations that occur in cells that are not in the germ line (somatic cells divide by mitosis) Only the direct descendant of the original mutated cell will carry the mutation
germ line mutations
mutations that occur in germ-line cells, giving rise to sperm and egg; can be passed from one generation to the next
endosymbiosis
mutual relationship in whihc one organism is housed in another
imprinting control region (icr)
name of insulator sequences that plays an important role in genomic sequencing
NF1 gene
neurofibromatosis
acetylation
neutralizes the positive charge and relaxes the histone/DNA interaction
admixed population
new population formed following migration
embryonic stem (ES) cells
new somatic gene therapy makes it possible for gene editing in ____ _____ _____ that corrects a disease causing mutation
F1 generation
newly induced mutation can be identified in which generation? produced by breeding mutagenized males with wild type females
lacI
next to but not part of the operon, encodes lac repressor protein and is constitutively expressed
lacY⁻
no functional permease
LacZ⁻
no functional β-galactosidase
lacA⁻
no transacetylase
Non Watson and Crick base pairing
non-complementary base pairing, similar to third base wobble, sometimes occurs during DNA replication
somatic cells
nonreproductive cells of the body, usually with chromosomes present in pairs diploid number (2n)
Beta-A
normal (wild type) allele (A) of this gene with site- produces two smaller fragmetns
totipotent
normal plant can be regenerated from a single isolated plant cell
myostatin gene
normally limits muscle growth; splicing error may lead to muscle overdevelopment
genes of bithorax complex
normally repress posterior expression of antennapedia
heteroplasmy
not all copies of an organelle gene are the same; cells contain a mixture of alleles
genome replication
not tightly coupled to the cell cycle
nucleomorph
nuclear genome of the endosymbiont that encodes only some gene for products targets to the plastid and some for maintenance of the ____ genome
segregational or nuclear petites
nuclear mutant
NUPTS
nuclear plastid sequences
homeobox
nucleotide sequence of 180 bp long found in homeotic genes and encodes a homeodomain (60 amino acids) forming a DNA binding domain
2n+1
number of phenotypic categories is calcualted as? (where n=number of genes)
phenotype
observable traits of an organism
coefficient of coincidence
observed double crossovers/expected double crossovers
shotgun sequencing
obtain redundant sequences of fragmented target DNA (library_ to assemble contiguous sequences (contig)
somatic mutations
occur in cells that are not part of the germ line
homologous recombination in bacteria and archaea
occurs during events such as conjugation and as a consequence of double strand break repair
polyadenylation muations
occurs in a rare mutant form of the human alpha globin gene leading to sever reduction in functional alpha globin protein produced
mitochondrial translation
occurs on ribosomes that resemble bacterial ribosomes
intragenic reversion
occurs through second mutation elsewhere in the same gene
Nick translation
occurs when DNA polymerases initiate removal and replacement of nucleotides, including the AP site; DNA ligase seals the sugar-phosphate backbone
position effect variegation (PEV)
occurs when chromatin is placed near heterochromatin, which spreads into the euchromatin, silencing genes
disruptive selection
occurs when the extreme phenotypes are favored over the intermediate phenotypes - the phenotypic variance is increased and a phenotypic split may occur within the population (same mean but increased variance)
lactose (lac) operon
of E.coli produces three polypeptides needed for metabolism of glucose
direct to consumer genetic testing
offered by for-profit companies, either for carrier testing or to provide info about inheritance of genetic markers associated with certain hereditary conditions (risk factors)
regulatory proteins
often found in large complexes in eukaryotes
cohesive (cos) ends
once inside the host cell the lambda phafe circularizes by joining two single stranded _____ of about 12 nucletoides in length
allosteric domain
one active site of repressor proteins that binds a molecule or protein and causes a change in conformation of the DNA binding domain (allostery)
DNA binding domain
one active site of repressors protein that locates and binds operator DNA sequence or other target regulatory DAN sequences
the next generation begins with the new frequencies
one allele frequencies are changed....
epigenetic heritability
one female X chromosome is almost completely inactivated; this is a random process
pleiotropy
one gene effect more than one aspect of phenotype (ex: albinism- defect in one gene (pigmentation) affects eye color, skin color, hair color, etc)
genotypes of autosomal genes
one generation of random mating produces HW equilibrium frequencies for ___?
two hybrid system
one method to identify interaction that uses the GAL4 transcription factor from yeast
random x inactivation hypothesis (lyon hypothesis)
one of the two x chromosomes in each female somatic cell is randomly inactivated and is visible near the nuclear wall as a condensed Barr Body
bithorax complex
one of two homeotic gene clusters in drosophila consisting of 3 genes that act in combination to specify the thoracic and abdominal parasegments
antennaapedia complex
one of two homeotic gene clusters in drosophila consisting of 5 genes that act in combination to specify the cephalix and thoracic parasegments
directional natural selection
one phenotype with a homozygous genotype has a higher relative fitness than other phenotypes
hunchback protein
only found in the anterior of the embryo; int he posterior region
square root
only used if a population is in HW equilibrium
SWI/SNF
open chromatin structure exposing promoters and regulatory sequences
lacO
operator that binds the lac repressor protein to block transcription of operon genes
inducible operon
operon that is not expressed under one set of environemental condition but
repressible operons
operons involved in anabolic pathways operate through activity of the end product to block transcription of the operon
mutagenesis
organisms is treated with a mutagen to create mutations randomly throughout the gene - can produce hundreds of new mutations
cases
organisms with a certain phenotype
w=1.0
organisms with the highest reproductive success are assigned a value of
ISWI
organizes and moves nucleosomes to repress transcription
oriC
origin of replication in E. coli which contains about 245 bp of A-T rich DNA and is subdivided by 3 13-bp sequences followed by 4 9bp sequences
fluctuate
over generation allele frequencies will ____
allele frequencies equilibrium established
over infinite generations, with constant mutation rates, and no other evolutionary forces
clone by clone sequencing
overlapping fragments sequences to produce a physical map
generalized transducing phages
package pieces of donor DNA (based on size) into progeny phage heads
organellar DNA
packkaged similar to bacteria, and differently than nuclear DNA
genetic potential
parents transmit a _____ ____ to offspring that may or may not be met, depending on various influences
RecA protein
part of the DNA repair cascade and its role is to activate recombination
transfer DNA (T-DNA)
part of the plasmid is transferred from the bacterium to plant cell nuclei upon infection
Metaphase checkpoint
pass if all chromosomes are attached to mitotic spindle
G2 checkpoint
pass if cell size is adequate and chromosome replication is successfully completed
G1 checkpoint
pass if cell size is adequate, nutrient availability is sufficient, and growth factors (signals from other cells) are present
IGF2
paternally expressed on chromosome 11
prenatal testing
performed during pregnancy to detect a condition in a fetus (prior to birth); most commonly uses placental tissue through chorionic villus sampling or amniotic fluid through amniocentesis
Complete dominance
phenotype of heterozygote is identical to dominant homozygote
incomplete dominance
phenotype of heterozygote is intermediate between two homozygous types (dosage effect)
codominance
phenotype of heterozygote shows expression of both alleles; shows in an individual with two dominant alleles so both alleles contribute to phenotype
developmental and environmental factors
phenotypes are also influenced by what?
Discontinuous variation
phenotypes of single-gene traits assigned to discrete, sharply distinguishable categories for instance qualitative phenotypic variation
thymine dimer
photoproduct formed by covalent bonds between the 5 and 6 carbons of adjacent thymines
common systems for direct DNA repair
photoreactive repair, nucleotide excision repair (NER), mismatch repair
genes
physical units of heredity; define DNA sequences
no migration
pi=pc
restriction fragments
pieces of DNA resulting from restriction enzyme cutting that can be polymorphic in length
long noncoding RNAs (lncRNAs)
play critical roles in gene regulation in eukaryotic cells; long RNAs that lack substantial open reading frames and act as scaffolds linking regulatory proteins to affect gene expression
ATM protein
plays a pivotal role in communicating DNA damage through signal transduction to activate transcription of the p53 gene - activates the "p53 repair pathway"
bicoid gene
plays major role in establish the anterior-posterior axis
Transposable elements in eukaryotic genomes
pleniful and highly varies with two types: 1) short sequences with inverted repeats (ex Ac/Ds elements, P elements) 2) retrotransposons (Ex: Alu sequences and TY and copia elements)
genetic linkage mapping
plots the positions of genes on chromosomes
Regualtory muations
point mutations that alter the amount (but not the amino acid sequence) of protein product produced by a gene; affect regions such as promoters, introns, and the regions coding for 5'-UTR and 3'-UTR segments
Continuous variation
polygenic and multifactorial traits with a range of values in uninterrupted continuum for instance quantitative phenotypic variation that include both genetic and environmental influences of phenotype
threshold traits
polygenic with a continuous distribution, some alleles each contributing a certain level of genetic liability
Allopatric speciation
populations are separated by a physical barrier and new species develop in separate geographic locations
sympatric speciation
populations share a single habitat but are isolated by genetic, behavioral, seasonal or ecosystem based mechanisms that prevent gene flow
Ve
portion of the phenotypic variance due to variability in environment
glucose
preferred energy source of E.coli (metabolized by glycolysis)
G2
prep for cell division
blocks attachement
presence of double stranded region in the mRNA prevents _____ _____ to the ribosome and thus blocks translation
biparental inheritance (CP)
presence of two organelle genomes allows recombination between them
low copy number plasmids
present in one or two copies per bacterial cell and usually cannot replicate independently of the bacterial chromosome
prezygotic mechanisms
prevent mating between members of different species or zygote formation from interspecies mating (behavioral isolation, gametic isolation, geographic isolation, habitat isolation, mechanical isolation, temporal isolation
negative eugenics
prevent people with "bad" traits from reproducing ex: holocaust
single stranded binding proteins (SSBs)
prevents unwound DNA from reannealing
penetrance
probability that a phenotype will appear when a specific genotype is present 100% when genotype is always expressed in the phenotype
Probability (P) value
probability that the results deviate as much or more from the expected results by chance
identical by descent (IBD)
probability that two alleles in a homozygous individual were obtained from a common ancestor of the two inbreeding organsims
inhibition
process in which a cell prevents its neighbors from adopting a certain fate
RNA editing
process of altering the sequence of RNA molecule after transcription
gene annotation
process of assigning biological functions to DNA sequences; aims to describe biochemical, cellular, and biological function of genes, in addition to location and structure within the genome - genes wit similar sequence likely encode products with similar biochemical functions
mitosis
process of cell division that produces identical daughter cells
induction
process that brings lysogeny to an end and reinitiates the lytic cycle
alternative intron splicing
processing of identical transcripts in different cells can lead to mature mRNAs with different combinations of exons and thus different polypeptides (alternatively spliced mRNAs are localized to very different tissues and parts of the body)
trithorax mutations
produce phenotypes like loss of function hox mutations
primary microRNA (pri-miRNA)
produce transcripts that fold back upon themselves to produced dsRNA
transposase
produced by the transposable element to make staggered cuts in both strands of DNA at the new target site for transposable element
allolactose
produced during the breakdown of lactose and acts as an inducer compound
messenger RNA (mRNA)
produced from protein producing genes and is an intermediary between DNA and protein; only type of protein that undergoes translation
Xist RNA
produced on the X chromosome to be inactivated; it spreas along the length of the chromosome and inactivates almost all of the genes
Permease
produces a gated channel at the cell membrane that allows lactose to enter the cells and the enzyme β-galactosidase to break the β-galactosidase linkage; faciliates lactose transport across the cell membrane
one generation of random mating
produces an equilibrium distribution of genotype frequencies, that can be predicted from alleles frequencies
gag
produces the outer capsid
Conditional probability
product and sum rules used (before a cross is made) to predict the likelihood of certain outcomes - applied when information about the outcome modifies the probability calculation
BRCA1 protein
product of the ____ gene implicated in familial breast and ovarian cancer susceptibility
mendelian priciples
progeny of matings are predicted using ___ ___
mRNA, tRNA, rRNA
prokaryotes and eukaryotes produce which of the following types of RNA
endosymbionts
prominent exception of Lgt is transfer of genes from _____ to hosts (eg. chloroplasts and mitochondrial genes)
normal function of antenna pedia
promote the differentiation of thoracic appendages into legs; its misexpression in the head transforms antennal segments into legs
types of regulatory mutations
promoter mutation, polyadenylation mutations, splicing mutation
direct repair mechanism of DNA damage
proofreading activity of DNA polymerase
Vg
proportion of phenotypic variance due to genotype differences; can be partitioned into different kinds of allelic effects: Va, Vd, Vi
transaceytlase
protects against harmful by products of lactose metabolism
nucleoid
protein dna complexes that contain multiple copies of the organelle genome
western blotting
protein transfer
histones
proteins around which DNA can wind for compaction and gene regulation
UVR A and UVR B
proteins of base nucleotide excision repair that recognize damage, form a complex, bind to DNA
nucleotide excision repair
proteins recognize and bind to the damaged region - segment of nucleotides is removed from the damaged strand - dna polymerase fills in gap, dna ligase seals the sugar phosphate backbone
chromatin remodelers
proteins that change the distribution or composition of histones in three principal ways
readers
proteins that recognize modified histones
rRNA genes
provide a universal sequence for comparison of evolutionary genomics
role of genetic couselors
provide info to support couples choosing to go ahead wtih pregnancy, or those choosing to terminate the pregnancy
enhancer and silencers
provide quantitative and qualitative control of gene; bind regulatory proteins and interact with proteins bound to other promoter regions, can be close or far upstream or downstream from the genes they regulate; or even within the genes they regulate
Telomerase RNA
provides a template for synthesis of repetitive DNA telomere sequences
P generation
pure breeding parental generation plants
Vp=Ve
pure breeding parental lines that are genetically uniform (Vg=0) can be crossed to produce genetically uniform F1 where ____=____
recombination frequency
r= number of recombinant/ total number of progeny - is likely a reflection of the physical distance between two genes
MT genes
rRNA in mitochondria are always encoded by
replicative segregation
random segregation of organelles during replication - affects the proportion of mutants in a cell -can lead to genetically mosaic organism -wild-type alleles may complement mutant alleles
variable expressivity
range of phenotypes resulting forma given genotype
theta value
ranges from 0 (complete linkage) to 0.5 (independent assortment)
Z form
rare form of dna that has a zigzag appearance due to its left handed twist of the helix
tautomeric shifts
rare, transient shifts in the chemical forms of bases - keto and amino
µ
rate at which new mutant alleles are generated
forward mutation rate (µ)
rate of a new mutation arising A₁→A₂
s
rate of elimination of deleterious alleles by natural selection
Reverse mutation rate (v) or reversion rate
rate of mutation in the opposite direction A₂→A₁
Denaturation
reaction mixture is heated to ~ 95C to denature the DNA into single strands
primer annealing
reaction temp is reduced to ~45-68C to allow primers to hybridize to their complementary sequences in the target DNA
primer extension
reaction temperature is raised to 72C to allow Taq to synthesize DNA by extending primers
the wild type allele in heterozygotes
recessive deleterious mutations are masked by ___?
homozygous recessive individuals
recessive mutations are subject to selection only in __?
restriction enzymes
recognize a specific DNA sequence and cuts both strands at the recognition site - recognize and cleave viral dna - first identified in bacteria, where they protect against viral infection
DNA glycosylases
recognize and remove modified bases, creating an AP (apyrimidiminic) site
map units (m.u) aka centiMorgan (cM)
recombination frequencies between two genes can be converted into units of physical distance 1% recombination = 1 m.u. or 1 cM
histone acetyltransferases (HATs)
recruited by activators and add acetyl (COCH3) groups to positively charge residues int eh N-terminal histone tails; these act as writers
writers and erasers
recruited to specific chromatin locations by tans-acting transcription proteins/ DNA binding proteins to modify histone tails
variegated eye
red patches are produces by cells in which w+ is transcribed, and white patches by cells in which w+ is inactivated by heterochromatin spread
inbreeding depression
reduction in fitness of inbred organisms, often due to the reduced level of heterozygosity
selective sweep
reduction or elimination of polymorphisms at a locus under selection
trpL region
region of trp operon that contains 4 repeat DNA sequences and the mRNA produced contains complementary repeats as well as start and stop codon 14 amino acid polypeptide
Promoters and enhancers
regulate the initiation of transcription
cis-acting regulatory sequences
regulate transcription of genes on the same chromosome as the sequences
termination region
regulates cessation of transcription
initiation and amount
regulation of transcription includes control of both ______ and _____ of transcription
promoter
regulator mutation that changes timing or amount of transcription
cis acting
regulator sequences that bind trans acting regulatory proteins to control eukaryotic transcription
inverted or direct repeats
regulatory DNA sequences in bacterial DNA frequently have ______ or ______ repeats
polyadenylation
regulatory mutation that alters sequence of mRNA; Mutation of this signal sequence at the 3' end of eukaryotic mRNA can block the proper 3' processing of mRNA;
splice site
regulatory mutation that improperly retains an intron or excludes an exon
DNA replication mutation (eg, triplet repeat expansion)
regulatory mutation that increases (or less often, decreases) number of short repeats of DNA
universal genetic code
regulatory sequences may differ greatly between organisms; must be combined with host regulatory sequences
closed chromatin
regulatory sites are covered by nucleosomes, restricting access by regulatory proteins
retrotransposons
related to retroviruses; all carry pol and some contain gag; non encode env, thus they can be reverse transcribed and inserted into host DNA, but are unable to produce viral particles
long and short interspersed nuclear elements (LINEs/ SINEs)
relatively abundant and can cause mutations
dominant mutations
relatively rare, are usually gain-of function mutation
DNA topoisomerase
relaxes supercoiling
deletion mapping
relies on wild type phage produced by intragenic recombination between a revertible mutant and a nonrevertible mutant of the same gene - if 2 mutation overlap, recombination cannot produce a wild type copy of the gene - if the two mutation don't overlap, recombination can produce a wild type copy of the gene
histone deacetylases (HDACs)
remove acetyl groups, which are recruited by repressors; these act as erasers
5' to 3' exonuclease activity
removes RNA primers
deaminating agent
removes amino groups from nucleotide bases
DNA polymerase I
removes and replaces RNA primer with DNA
UVR D
removes the damaged fragment
DNA mismatch repair
removes the uracil from the DNA (caused by deamination) and replaces it with cytosine, restoring the wild-type sequence
photoreactive repair
repair of UV-induced photoproducts catalyzed by photolyase activated by visible light; photoproducts of UV exposure can inhibit DNA replication and also lead to mutation
dispersed repetitive DNA
repetitive DNA not at telomeres or centromeres is called?
telomeres
repetitive sequences at the ends of linear chromosomes that ensure that a portion of a telomere can be safely lost without consequence to the organism
plasmid cloning vectors
replicate independently of bacterial chromosome and always remain separate
high copy number plasmids
replicate independently of the bacterial chromosome; number of plasmids per cells increases rapidly
two types of DNA transposition
replicative transposition and nonreplicative transposition
Are mutant alleles dominant or recessive compared to wild type?
represent loss of function or gain of function; use mendelian genetics
lod score less than 2.0
represent significant evidence against genetic linkage
tryptophan present
repressor is activated by the corepressor and bind trpO to block operon gene transcription
tryptophan absent
repressor protein cannot bind the operon is transcribed
HDAC "erasers"
repressors recruit?
prezygotic and postzygotic mechanisms
reproductive barriers include both ?
Rho-dependent termination
requires a different termination sequence and the rho protein
polycomb mutations
resemble gain of function hox gene mutations
thylakoid membranes
reside in stroma of the chloroplast, where protein complexes for photosynthesis are embedded
RNA editing
responsible for posttranscriptional substitutions of the nucleotide sequence of some mRNAs
after cell cycle, a cell may
rest (arrest), continue to divide, stop dividing and differentiate into specialized body cells, die (apoptosis)
su(var) mutations
restrict heterochromatin spread or interfere with its formation; this suppresses mutant phenotypes so more wild-type cells are seen; mutations block efficient formation of heterochromatin and leave most cells with active w+ transcription (mostly red eye)
Postzygotic mechanisms
result in failure of a fertilized zygote to survive, or survival of but sterility of the individual produced (hybrid breakdown, hybrid inviability, hybrid sterility)
mutations in homeotic genes
result in replacement of one body part with another
independent origins
resulted in horizontal transmission of chloroplasts among unrelated eukaryotic lineages
codon bias
results from differences in which codons are used when there is ore than one codon for a given amino acid - interferes with expression due to relative scarcity of some tRNAs
continuous variation of polygenic traits
results from multiple genes that may exert different amount of influence
loss of bicoid activity
results in loss of anterior segments and duplication of posterior abdominal segments
loss of Ubx activity
results in parasegments 5 and 6 having a combination of Hox gene products that are normally found in parasegment 4
UV light activates DNA repair
resumption of the lytic cycle follow lysogeny induction is like a switch, triggered by DNA damage such as? that activates what?
stem cells
retain the ability to divide (for self renewal) and give rise to other cells May be able to provide cells for replacement tissues/ organs
genetic screens
reveal that mutations at additional loci can cause homeotic mutant phenotypes that fall into two classes
rho utilization (rut) site
rho dependent termination sequences have a ____ where the rho protein attaches after transcription to catalyze the separation of the mRNA from the RNA polymerase
telomerase
ribonucleoprotein that extends telomeres in germ line cells
Homologous nucleotides
same nucleotides descended from the common ancestor
DNA ligase
seals the sugar-phosphate backbone
attenutation of (trp operon)
second mechanism of trp operon that is controlled by folding of the mRNA from the 162-bp trpL region
suppressor mutations
second mutation surppresses the first mutant phenotype caused by the first mutation
hoemotic genes
segments of the embryo acquire their unique identities through the action of ? that act in combination to specify the identity of each body segment
Okazaki fragments
segments of the lagging strand
multiple-gene hypothesis
segregation of alleles of multiple genes play a role in phenotypic variation of certain traits
directional, stabilizing, disruptive selection
selection operating over many generations has three possible modes that each affect mean and variance in populations
h^2= 1.0
selection response is expected to be greatest when
metagenome
sequence derived from whole-genome shotgun sequencing of DNA from entire natural communities consisting of a range of organisms
recent transfers to the nucleus
sequence similarity between NUMTS and NUPTS and respective organelle sequences suggests what?
nonconserved sequences
sequences conserved in genomes of two or more species are more likely to be functional than ?
CpG islands
sequences rich in CpG that have a strong selection for maintenance of cytosines; this reflects a functional role for such regions
operators
sequences that activated repressors bind to to block transcription initiation;
open reading frames
sequences that could encode polypeptides and help predict gene structure based on recognition
proteome
set of the proteins in a cell, tissue or organism
transcriptome
set of transcripts present in a cell, tissue, or organism
contemporary SR proteins
show strong gene and protein sequence similarity and belong to one of two clades (estrogen receptors (ERs) and other SR proteins)
consolidated map
shows gene order and the cumulative number of minutes, site, and orientation of each integrated F factor
frequency distribution
shows the proportion of individuals exhibiting each value (or category) of that measured trait; individuals should be a random sample, not selected for any attribute related to the trait being studied
Beta-S
sickel cell allele (a) is lacking one RE cutting site- produces one relatively larger fragment
none of the above
sickle cell anemia is: A) always due to the same mutation B) due to a single base substitution in the β globin gene C) due to a single amino acid substitution in the β globin protein D) all of the above E) none of the above
compound is mutagenic
significant increase in the reversion rate in treated strains relative to controls; this includes strains with one type of mutation (base mutation) compared to those with another (frameshift) and untreated strains
RNAi
silences gene expression transcriptionally and postranscriptionally
noncomposite transposons
similar to composite transposons in that they have additional genes but lack IS elements; transpose in the same manner as composite transposons
activator and repressor proteins
similarities of gene regulation in eukaryotes and bacteria
cotransformation
simultaneous transformation of two or more genes
CRTI
single bacterial enzyme
sickle cell anemia
single base substitution in the Beta globin gene DNA; affects only amino acid #6 (out of 140 amino acids) in the Beta globin polypeptide; causes a single amino acid change (Glu to Val) in the Beta globin polypeptide
guide strand
single strands act as (biologically active) in gene silencing
chlamydomonas
single-celled haploid green alga; mt+ or mt- mating types ffor most matings the CP genome is contributed by the mt+ parent, CP inheritance in the remaining is biparental
sticky ends
single-stranded segments produced by some restriction enzyme cuts (ex: EcoR1)
mitochondrion
sites of energy production, where electron transport is coupled to oxidative phosphorylation to generate ATP - genome contain some of the genes needed to carry out its functions
MicroRNAs (miRNA)
small RNA molecules with roles in regulation of genes expression in plants and animals
nonhomologous end joining (NHEJ)
small deletions often remain at the break site, with possible loss- or gain of function
plasmids
small double stranded circular DNA molecules that can be used in a variety of recombinant DNA applications
significant genetic drift of allele frequency
small population size provides the conditions under which sampling error can produce ___
lacI^s
so called super repressor, unable to bind the inducer (allolactose) blocking all transcriptase
conserved
some enhancer sequences that are ____ among different species indicate evolutionary constraint or enhancer diversification
DNA intercalating agents
some molecules are able to fit in between DNA base pairs and distort the DNA duplex; can result in frameshift mutations due to added or lost nucleotides
LCR
some thalassemia cases were due to deletions or chromosome rearrangements that altered the ____ region causing abnormal expression of the globin genes
distinct categories
some traits may have continuous variation of phenotype, but the phenotypes can still be divided into ____ ____
determine phenotypic variation
sort of genetic and nongenetic (environmental) factors that
CpG dinucleotides
specialized DNA methyltransferases add methyl groups primarily to cytosines located in? , most methylated at the C
locus control regions (LCR)
specialized enhancer that regulate transcription of multiple genes complexes
Genomic imprinting
specialized example of epigenetic regulation in certain mammalian and flowering plant genes; affects a small number of genes and involves the expression of only one of the inherited alleles of a genes, depending on the parent from which it is inherited
Organelles
specialized membrane-bound subunit within the cell individual eukaryotic cells may contain multiple ____ contain many more proteins than they encode in their genomes
Biological species concept (BSC)
species are groups of organisms capable of interbreeding but isolated from other species - can't be used with fossilized remains or extinct species; not applied to organisms not engaging in sexual reproduction cases of interspecies hybridization
haplotype
specific array of SNPs in a small region on a single chromosome; may differ between the members of a chromosome pair
trithorax and polycomb
specific modification through histone-3 methyltransferase activity
gametes
sperm and eggs in animals and pollen and eggs in plants
result of splicing mutations
splicing errors and the production of mutant proteins due to the retention of intron sequences in the mRNA
cellular blastoderm
stage of drosophila embryogenesis in which the nuclei are located at the periphery of the embryo and are enclosed by cell membranes
syncytial blastoderm
stage of nuclei embryogenesis in which the nuclei are located at the periphery of the embryo but are not separated by cells membranes
amino
standard chemical forms of A and C can shift to rare Imino form
keto
standard chemical forms of G and T can shift to rare enol forms
Cas9
staphylococcus has one Cas protein which is?
Totipotency
state of a cell when it can give rise to any and all cell types of an organism
QTL mapping
statistical methods used to detect and map QTLs - identifying regions of chromosomes likely to contain QTLs - identified by frequent co-occurrence of a genetic marker in organisms with a particular phenotype - leads to identification of potential chromosome location of a QTL, but does not identify the molecular basis of the QTL
Pure breeding (true breeding) strains
strains that consistently produce the same phenotype
mitochondria
strictly maternally inherited in mammals, with no recombination of alleles
molecular genetics
studies inheritance and variation of nucleic acids, proteins, genes and genomes
gain-of-function
studies may use regulatory sequences from one gene and coding sequences from another or coding sequences from two different genes for what?
mutations are rare
studies of gene mutation frequencies have shown that_______ A) mutations are rare B) mutation are common and adaptive C) mutation frequencies are consistent between organisms, and each region of DNA is equally susceptible to random mutations D) mutations occur only at certain nucleotides and not others E) mutations affect RNA, but do not change DNA sequence
transcriptomics
studies the complete set of genes that undergo transcription in a cell
evolutionary genetics
studies the origins of genetic relationships among organisms, and the evolution of genes and genomes
Proteomics
study of all the proteins- proteome- expressed in a cell, tissue or individual
transcriptomics
study of gene expression from a genomic perspective (transcriptome) - the study of all the transcripts collectively known as the transcriptome, within a cell, tissue or organism
functional genomics
study of gene function from a whole genome perspective - many genes are analyzed simultaneously to determine expression patterns, interactions and biological functions
Transmission genetics (Mendelian genetics)
study of inheritance through the transmission of genes and genetic material in successive generations
morphogens
substances whose presence in differing concentrations directs developmental fates
Primer walking
successive synthesis of primers based on progressive attainment of new sequences
mtDNA variation
suggest evolution of modern humans in Africa, followed by migration around the world
phylogenetic evidence
suggests that multiple secondary symbioses took place; some eukaryotes acquired a photosynthetic eukaryotic symbiont
p^2+2pq+q^2=1
summation of genotype frequencies equations
noninducible
super-repressor mutation lead to a ____ operon and cells that are unresponsive to the presence of lactose
facultative heterochromatin
switch between euchromatin and heterochromatin
types of coding sequence mutations
synonymous, missense, nonsense
microsynteny
synteny at the level of just a few genes, where chromosomal synteny is not conserved
pri-mRNA
synthesizes in the nucleus and processed into miRNAs by dicer activity; forms a double stranded stem with free ends and a single stranded loop end
DNA polymerase III (holoenzyme)
synthesizes new DNA only in the 5' to 3' direction
primase
synthesizes rna primers
RecBCD pathway
system of homologous recombination in bacteria -DNA double strand breaks initiate the process which attracts the RecA protein (homolog of Rad51) -RecBCD then attaches to the region where REcA is bound, leading to single-strand invasion and D loop formation -RuvAB and RuvC proteins bind and complete homologous recombination
DNA endonucleases
target the location and create a double-strand at the site which is fixed using NHEJ, homologous recombination (CRISP-cas9)
homologous recombination (CRISPR cas-9 mediated genome editing)
targeted approach of transgenic mice to insert transgene into a specific locus in genome
germinal gene therapy
targets cells of the germ line, which give rise to gametes
somatic gene therapy
targets somatic cells whose descendants will not give rise to germ cells
r looping
technique that demonstrates the presence of intron sequences
phylogenetic shadowing
technique whereby conserved sequences are identified by first eliminating sequences that are not served in closely related species
phylogenetic footprinting
technique whereby conserved sequences are identified by searching for similar sequences in species separated by large evolutionary distances
positional information
term for the cues and signals that together inform a cell about its relative position in the embryo ( good model= french flag with pattern of 3 stripes and simple concentration gradient each specifying different "fates")
G0
terminal differentiation and arrest of cell division; either cell remains specialized but does not divide or eventual death (apoptosis)
3-4 stem loop
termination stem loop
Preimplantation Genetic Diagnosis (PGD)
testing for hereditary diseases in embryos (in utero) or embryos produced by in vitro fertilization
allelic phase
the arrangement of alleles of linked genes on parental chromosomes; can be determined when a disease-causing allele is seen to segregate along with a known genetic marker
Cotransduction
the closer two genes are on a donor chromosome, the more likely they will be transduced to a recipient together
evolutionary genomics
the comparative study of genomes phylogenomics or comparative genomic
lactose to galactose + glucose
the enzyme β-galactosidase catalyzes what reaction?
homologous recombination
the exchange of genetic material between homologous molecules of DNA
basal transcription
the inducer-repressor complex alone yield ____ of only a a small number of polycistronic mRNAs. not sufficient for metabolism of lactose
att site
the integration site of temperate phages (same 15-bp sequence called attp in temperate bacteriophage and attB in e.coli host )
one generation of random mating
the island model is not in HW equilibrium initially because it requires ___?
inducible systems
the lac operon is an ___ ____ which is turned on only when an inducer compound is available
homotetramer
the lac repressor protein lacI is a _____ with a DNA- binding domain that bind to the lacO sequence
allolactase
the lacI repressor protein has an allosteric domain that binds the inducer ____
directional selection
the mean phenotypic value is shifted in one direction because one extreme of the phenotype distribution is favored; the phenotypic range is narrowed and variance is reduced (changed mean and reduced variance)
less obvious the difference between categories
the more phenotypes that occur, the?
leading strand
the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5' to 3' direction
Environmental variance (Ve)
the portion of the phenotypic variance due to variability in environment inhabited by individuals in a population
induction
the process of when a cell induces its neighbors and acquires a certain fate
allostery
the property belonging to some enzymes of changing conformation at the active site as a result of binding a substance at a different site; alters repressor function
genetic variance (Vg)
the proportion of phenotypic variance due to genotype differences
exconjugant cell
the recipient cell produced by conjugation with its genetic information modified by receiving DNA from the donor cell
2 (dimeric), 3(trimeric), or 4 (tetrameric) polypeptides
the regulatory protein can consists of how many proteins in a multimeric complex
stem loop structures
the repeat sequences of the trp operon can form what?
base pair substitution mutation
the replacement of one nucleotide base pair by another; leads to a single polymorphism (SNP)
reversible
the repressor binding (lacI) is _____ and it is occasionally released from lacO; which allows very low level of transcription from the operon even in the absence of lactose
covergent evolution
the same mutant traits evolve independently in different populations
CAP-cAMP binding region
the site where positive control of the lac operon occur composed of catabolic activator protein (CAP) and cyclic adenosine monophosphate (cAMP)
origin of replication (ori)
the specific sequence of DNA at which DNA replication begins
parasegments
the stripes of gene expression of pair-rule gens occupies the posterior of one segment and the anterior of its neighbor
low genetic diversity and very different allele frequencies
the surviving population of a genetic bottleneck is likely to have ______ and very different ______ from origional population
cro or lambda repressor
the three operator sequences each have a 17-bp target sequence for binding of either?
polycistronic mRNA
the three strucutral genes of the lac operon are transcribed as a single ___ which is translated to produce three distinct polypeptides
Experimental approach of gene annotation using cDNA
theoretically, complete set of cDNA clones representing all the genes from an organism would allow complete annotation
Ty elements of yeast
these retrotransposons are found in yeast and can cause insertional mutations; central element is about 6kb long, flanked by LTRs of about 330 bps; both LTRs contain promoters that direct transcription of different genes in the central region
tryptophan (trp) operon
this operon in E.coli contains five structural genes for synthessis and a regulatory region with a promoter, operator and leader region that contains the attenuator region
controls
those without the certain phenotype
affected or unaffected (normal)
threshold traits are often encountered in medical situations where individuals can be either _____ (having the condition) or _____ (normal)
temporal
time based for ex: β globin gene expression rises at birth
crRNA
to edit a genome, which sequences is replaced with one that will target the sequence to be edited
relative fitness (w)
to quantify natural selection intensity, compare the reproductive success of other genotypes relative to the most favored genotype
Vp
total phenotypic variance
guideRNA sequence
tracerRNA and cRNA sequences can be fused into what?
nuclear genes
traits controlled by organellar inheritance can also be influence by
histone deacetylases
trans acting regulators of gene transcription include?
RNA pol II and III
transcribe miRNA and siRNA
tracerRNA
transcribed from the tracer RNA gene; one region of this RNA binds to the cas endonuclease and the other binds to a crRNA
RNA polymerase II (RNA pol II)
transcribes protein coding genes and most small nuclear RNA genes
RNA polymerase I (RNA pol I)
transcribes several ribosomal RNA genes
RNA polymerase III (RNA pol III)
transcribes tRNA, one small nuclear RNA, and one ribosomal RNA
Transduction
transfer of dna from one bacterium to another by a viral vector
lateral gene transfer (LGT)
transfer of genetic material between individual bacteria or archaea and other organisms (Ex: endosymbiosis that led to mitochondria and chloroplasts in eukaryotes)
lateral gene transfer (LGT)
transfer of genetic material between two species - occurs with genes encoding proteins for metabolic functions - not common for information processing proteins
transduction
transfer of genetic matieral from a donor to a recipient cell by way of a bacteriophage
blotting
transfer of nucleic acids or proteins from a gel to a durable synthetic membrane material
conjugation
transfer of replicated DNA from a donor to a recipient through a conjugation pilus
class c mutants
transformations in the 3rd and 4th whorls, with petals instead of stamens and cells that should form carpels act as additional floral meristems
transformant
transformed daughter cell after DNA replication and cell division
positive-negative selection
transformed mouse cells are cultured so that only those with the positive selectable marker and no the negative selectable marker will survive
non-targeted approach
transgene randomly inserted into the genome through illegitimate recombination
ti plasmid
transgenic plants contain a large (200 kb) tumor-inducing plasmid
autosomal inheritance
transmission of genes carried on autosomes, chromosomes found in both males and females
Organellar Inheritance
transmission of genes on organelle genomes opposed to nuclear chromosomes
organizer
transplanted region groups of cells that possess the ability to influence the fates of cells in the surrounding tissues via non-autonomous signals
tRNAs
transport amino acids to ribosomes
precursor microRNA (pre-miRNA)
transported to cytoplasm, where Dicer removes terminal loop
insertional inactivation
transposable elements that are inserted into wild-type alleles create mutations; usually leads to a nonfunctional gene product
corepressor
tryptophan acts as a ____ by binding to the tryptophan repressor and activating it
antitermination
tryptophan starvation
identical or monozygotic twins
twin that share all of their alleles (Vp=Ve)
fraternal or dizygotic twins
twins that are no more closely related than any pair of siblings; share 50% alleles in common (Vp=Ve +1/2Vg)
enhancer and silencer sequences
two categories of DNA regulatory sequences that lead to differential expression of genes
complementary base pairing
two complementary sticky ends can be combined by?
enhancer at H19 and the insulator aka icr (imprinting control region)
two important regulatory sequences in genomic imprinting between genes
translation regulation in bacteria
two mechanisms -one binds protein to an mRNA to prevent its translation (translation repressor proteins bind mRNA near the Shine-Dalgarno sequence) - the other uses complementary antisense RNA to block mRNA translation
double strand break repair
two mechanisms: 1.) Non homologous end joining (NHEJ) 2.) synthesis-dependent strand annealing
phylogenetic footprinting vs phylogenetic shadowing
two methods for identifying conserved noncoding sequences and they approach the task from opposite directions
gene counting and square root
two methods that can be used to determine allele frequencies:
polygenetic inheritance
two or more genes contribute to a phenotype (ex: eye color, skin color, etc)
features of transposable elements
two sequence feature in common for most cases: 1) the transposable element contains terminal inverted repeats 2) the transposable element is bracketed by flanking direct repeats at the site of insertion
CRISPR-Cas9
type of immune system discovered in bacteria. Adapted tis components into a biotechnology tool for editing DNA; may be applied to gene therapy or agriculture, often with ethical considerations to examine
incorporated error
type of mispairing that includes G with T pairing or C with A pairing
to define the molecular function of every gene in an organism
ultimate objective of functional genomic studies
mutation
ultimate source of all new genetic variation in populations - a slow process, with small and gradual effects on allele frequencies in populations
lacI⁻
unable to bind to operator
forward genetic screens
unbiased and require no prior knowledge of the molecular function of particular gene product to be successful
alternative sigma factors
under heat stress (e.g. 45 °C) E.coli use what to activate heat stress genes to protect cells from certain types of heat induced damage
hunchback mRNA
uniformly distributed throughout the egg
helicase (DnaB)
unwinds the double helix
proximal elements
upstream of the core promoter region that also regulates genes
transformation
uptake of DNA from the environment
statistical analysis
used ____ ____ to show quantitative traits result from segregation of alleles of multiple genes with an additive effect
presympto
used for genetic conditions with a late age of onset
expression vectors
used for proper expression of trangenes
Chi squared (x²) test
used for quantifying how closely an experimental observation matches the expected outcome x²=ε(O-E)²/E where o=observed values E= expected values larger x² reflects greater deviation between O and E
DNA polymerases
used in the process as the new strands are produced in 5'- 3' direction
reporter genes
used to investigate gene regulation; a gene can act as this if its product can be detected directly or produces a detectable substance
Genetic modifier screen
used to see if mutations in a second gene can modify the phenotype of the first mutation, ex: enhancer screen and surpressor screen
multiple high-throughput technologies
used to study protein expression, modification, and interactions
Dideoxynucleotide DNA sequencing
uses DNA polymerase and DNA primers to replicate new DNA from a single-stranded template
transgenic plants
uses a natural plant transformation system from the soil bacterium agrobacterium tumefaciens ex: golden rice
aminocenteis
uses a needle to penetrate the uterus and placenta of a pregnant woman to obtain amniotic fluid, which contains fetal cells between the 14th and 18th week of pregnancy; risk of fetal loss
Transcription
uses one strand of DNA to direct synthesis of a single stranded RNA transcript
Reverse transcription
uses reverse transcriptase and an RNA template to produce complementary DNA (cDNA)
Gene therapy
using genes to cure or alleviate disease symptoms
passenger strands
usually degraded in gene silencing
asymmetric divsion
usually when a cell divides the daughter cells inherit the same set of transcription factors and chromatin states that existed in the original cell, but in some cases daughter cells inherit distinct subsets of the factors present in the original cell referred to as ?
Translesion DNA synthesis
utilizing a bypass polymerase, a mechanism for replicating DNA in the presence of damage that blocks replication by the common polymerase.
mutant alleles
variation in numbers of organelles and their genomes can influence the phenotypic effects of ____ _____
gag and env
viral genes that are encoded by integrated virus
bacteriophages
viral particles that infect bacterial host cells
bacteriophage
viruses that infect bacterial cells in order to reproduce
vulval precursor cells (VPCs)
vulva of c elegans forms during the last larval stage from six cells called ? three of which form the vuvla itself
SWI/SNF, ISWI, SWR1
well known chromatin remodelers are protein complexes
DNA methyltransferases
what adds methyl groups to cytosines located in CpG dinucleotides
transfer events
what are detected by comparative genomics of organelle, nuclear, and bacterial genomes
various sources that produce dsRNA
what are regulatory RNAs derived from?
Posttranslational modifications
what can also differ and prevent production of correctly functioning transgene protein products?
chromosome 11 (IGF2 and H19)
what chromosome does differential genomic imprinting occur on in humans?
destroying the embryo
what does harvesting embryonic stem cells mean?
they encode the same amino acid
what does it mean for two codons to be synonymous
obligate parasites
what experiences genome contraction?
his, leu, pheA, thr
what four amino acids are bacterial operons with attenuator control of transcription
they silence transcription of selected genes
what happens in gene silencing when chromatin modifying enzymes are directed to the nucleus?
transcription of the lac operon is induced
what happens to transcription of the lac operon when lactose is available to the cell and glucose is not
leads to constitutive expression
what happens when the lacI- gene produces a mutant form of repressor protein that is unable to bind the operator sequenc?
kruppel (is)
what is activated in regions where at least moderate levels of bicoid are present?
human height
what is an example of a polygenic trait with continuous variation?
allolactose
what is produced with synthesis of Beta-galactosidase that binds tot he allosteric of domain of the lac repressor
recruit transcription factors that form the initiation complex
what is the role of a promoter region of a gene
heteroplasmic and homoplasmic descendants
what kind of descendants can heteroplasmic cells produce?
endosperm
what synthesizes a precursor in carotenoids synthesis
recessive mutations
what type of mutations are easier to identify in self fertilizing organisms; fertilized F1 individuals produce an F2 generation from which ____ _____ can be identified
result: many flowers were variegated called cosuppression
what was the result of Jorgensen et al's experiment after introducing an additional gene for pigment production into petunias to deepen flower color
kernels were purple
what was the result of Mclintocks experiment when chromosomes were both intact?
Transformation
when a recipient cell takes up a fragment of donor DNA from the surrounding growth medium
protease activity
when bacterial DAN is damaged by UV light, the ____ ____ of RecA is activated
enhancer elements
when conserved throughout vertebrate evolution regulate genes controlling vertebrate body plan development
linkage disequilibrium
when frequencies of certain haplotypes in a population deviate significantly from what is expected
intervening DNA is excised
when loxP sites are direct repeats
intervening DNA is reversed in orientation
when loxP sites are inverted relative to each other
q_E=µ
when mutation is dominant and complete selection (s=1) acts against a lethal dominant mutant allele then
lac operon transcriptionally silent
when no lactose or glucose is available the lac operon is?
negative control
when no β-galactosidase is produced and no allolactose in the cell, the lac repressor binds to lacO preventing transcription this is known as?
opines
when plant cells divide uncontrollably they produce amino acids called ? that only bacterium can use as an energy source
catabolite repression
when the cap-camp complex is not bound to the lac promoter region, transcription is very inefficient
inner cell mass of embryos
where are embryonic stem cells from?
in mammalian MT
where are rules of third-base wobble more lenient than for nuclear genes
B (somatic mutations can occur during mitosis in embryonic or fetal development)
which of the following is true of mutations in somatic cells? A. they are not normally passed from one generation to the next B. they can occur during mitosis in embryonic or fetal development C. they affect only the individual carrying them D. all of the above E. none
deletion
which of the following usually causes a change in a reading frame? A) transversion B) deletion C) missense D) transition E) transversion or missense
leader region
which region contains the attenuator region in the trp operon
the cohesive (cos) site
which region of the lambda phage genome enables the linear chromosome to circularize when it enters a host cell?
promoter and termination regions
which region(s) of a gene are NOT found within the mRNA transcript?
OR1, OR2. OR3
which sequences are exprosed and end the negative regulation of cro
silent
which type of pr mutation is possible due to redundant nature of the genetic code? A) silent B) missense C) nonsense D) frameshift E) splice site
homeologs
whole genome duplication leads to duplicate sets of genes called
so that regulatory proteins can easily access the DNA sequences
why are some regulatory sequences no tightly bound by histones?
due to genetic redundancy
why do forward genetic screen miss genes?
substantial gene-environment interaction
wider phenotypic ranges and significant overlaps
more gene-environment interaction occurs
wider the potential range of phenotypic values that may occur
DNA trinucleotide repeats
wild type alleles of the genes in question normally have a variable number _________; an increase in this beyond a certain threshold causes disorders
grande
wild type of yeast
complementation
wild-type offspring are obtained; the mutations are known to affect two different genes
true reversion
wild-type sequence is restored by a second mutation within the same codon
infectious diseases
will likely continue to influence selection
chromsome regions
with GWAS ___ ___ can be identified and inspected more closely for candidate genes
Ac transposed Ds into C gene inactivating C (resulting in mutant phenotype)
with chromosome breakage what would cause mutant phenotypes: yellow/shrunken/ waxy sectors in Mclinktocks kernel experiment?
migration and admixture
with continued ____ and ____, phenotypic and genotypic differences between populations are expected to decrease
how hox genes interact
with more posteriorly expressed genes repressing expression of more anteriorly expressed genes
hunter-gatherer
within Africa ____ pops in the south and east exhibit the greatest genetic diversity
replicated error
without repair, this event converts the replication of the incorporated error into a mutation
hunchback
zygotically transcribed, under control of bicoid, but is also maternally provided as mRNA
Recent african origin (RAO) hypothesis
~120-200k years ago humans emerged from a small african pop that migrated out of africa displacing earlier homo erectus migrations
major groove, minor groove
~12A wide 6A wide regions where DNA proteins can make direct contact with nucleotides
Cystic fibrosis transmembrane (CFTR) gene
~250,000 base pairs in length (26 exons), most common mutation ~70% of cases net result loss of Phe amino acid sequence (frameshift mutation/deletion of 3 bases)
equilibrium occurs
∆pi=0
