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