Genetics Final Exam
The SRY gene encodes
-a transcription factor which binds to DNA and stimulates the transcription of testes-development genes -primary determinant
Variant Histones
-alternative histone proteins with somewhat different amino acid sequences, incorporated into chromatin in place of one of the major histone types -alter chromatin structure and influences its function
How do sex-influenced and sex-limited characteristics differ from sex-linked characteristics?
-both sex-influenced and sex-limited characteristics are encoded by autosomal genes whose expression is affected by the sex of the individual organism possessing the genes -sex-linked characteristics are encoded by genes on the sex chromosome
How are the processes of RNA polymerase II termination in eukaryotes and rho-dependent termination in bacteria similar and different?
-both use a protein that binds to the RNA molecule and moves down the RNA toward the RNA polymerase -differ in that rho does not degrade the RNA but Rat1 does
Androgen-Insensitivity syndrome
-caused by defective androgen receptor -XY but female external sex characteristics but no uterus/ovaries and do have testes inside
Segmental duplications
-greater than 1000 bps in length -mostly intrachromosomal (same chromosome) but sometimes interchromosomal (the two copies are found on different chromosomes)
problems with inversion heterozygotes
-homologous sequences align only if the two chromosomes form an inversion loop -demonstrate reduced recombination in a paracentric inversion, as gametes formed resulting in nonviable offspring
Male fruit fly develops is X:A is
0.5
Female fruit fly develops if X:A is
1
3 pathways of mRNA degredation
1. 5' cap removed followed by 5' to 3' removal of nucleotides 2. 3' end of mRNA and removes it in 3' to 5' direction 3. mRNA cleaved at internal sites
Two steps of splicing
1. 5' end of intron cleaved from the upstream exon and attached to the branch point to form a lariat 2. 3' end of intron is cleaved from the downstream exon and the ends of the two exons are spliced together
ways to classify gene mutations
1. based on the nature of the phenotypic effect 2. based on the causative agent of the mutation 3. based on the molecular nature of the defect
4 steps of repair mechanisms
1. detection 2. excision 3. polymerization 4. ligation
calculate LOD
1. find probability of obtaining the observed results under the assumption that the genes are linked with a specific degree of recombination 2. find probability of obtaining the observed results under the assumption of independent assortment 3. determine the ratio of these probabilities and the logarithm of the ratio is the LOD score
2 domains of histones
1. globular domain that associates with the other histones and the DNA 2. Positively-charged tail domain that interacts with the negatively charged phosphate groups on the DNA
Steps in determining gene order in a three point cross
1. identify nonrecombinant progeny (2 most numerous phenotypes) 2. identify double crossover progeny (2 least numerous phenotypes) 3. compare phenotypes of double crossover progeny with phenotypes of nonrecombinant progeny 4. the characteristic that differs between the double crossover and the nonrecombinant progeny is encoded by the middle gene
4 steps of bacterial replication
1. initiation 2. unwinding 3. elongation 4. termination
3 major steps of translation initiation in bacteria
1. mRNA binds to small ribosomal subunit 2. initiator tRNA binds to mRNA through base pairing 3. large ribosomal subunit joins the initiation complex
twofold effect of migration
1. prevents populations from becoming genetically different from one another 2. increases genetic variation within populations
4 steps of initiation phase in bacterial transcription
1. promoter recognition 2. formation of transcription bubble 3. creation of first bonds between rNTPS 4. escape of transcription apparatus from the promoter
four stages of translation
1. tRNA charging 2. Initiation 3. Elongation 4.Termination
How many copies of the H2B histone would be found in chromatin containing 50 nucleosomes?
100
How many genotypes possible at a locus with 5 alleles?
15 (5 homozygous and 10 heterozygous)
a human female usually needs ___ copies of X to be fertile
2 copies of X
antiterminator
2+3 hairpin forms this and it does not function as a terminator
Species A has 2n=16 and species B has 2n=14. How many chromosomes would be found in an allotriploid of these two species?
22 or 23
What is the number of possible combinations of chromosomes in independent assortment?
2^n where n is the number of homologous pairs
what is the expected frequency of heterozygotes in a population with allelic frequency x and y that is in HWE?
2xy
attenuation results when which regions of the 5' UTR region pair?
3 and 4 followed by string of Us
DNA polymerases require _____ to get started
3' OH group
attenuator
3+4 hairpin immediately followed by string or uracil forms a bacterial intrinsic (rho-independent) transcriptional terminator
A diploid has 2n= 36 chromosomes. How many chromosomes will be found in a trisomic member of this species?
37
100 meiocytes finished meiosis. 20 of them had crossing over. What would be the frequency of the recombinant gametes in the total gamete pool generated by theres 100 meiocytes?
40 gametes
Core enzyme
5 subunits; catalyzes elongation of RNA molecule by addition of RNA nucleotides
genomic library
A set of thousands of DNA segments from a genome, each carried by a plasmid, phage, or other cloning vector.
What is the second mechanism of genetic variation in newly formed gametes?
Anaphase 1 random distribution of chromosomes aka random assortment
Which bacterial enzyme removes primers?
DNA polymerase I
CpG islands
DNA regions with many CpDs commonly found near transcription start sites
DNA polymerase IV
DNA repair
DNA polymerase V
DNA repair and translesion DNA synthesis
DNA polymerase II
DNA repair; restarts replication after damaged DNA, halts synthesis
Promoter
DNA sequence that the transcription apparatus recognizes and binds
insulators (boundary elements)
DNA sequences that block the effects of enhancers in a position dependent manner
What happens in S phase?
DNA synthesis
Basic requirements of transcription
DNA template, raw materials, transcription apparatus
Direct repair vs mismatch and base-excision
Direct repairs return an altered base to its correct structure without removing/replacing the nucleotide while mmr and BER remove and replace nucleotides
In what stages are chromosomes uncondensed?
G1, G2, telophase
What is the order of stages in the cell cycle?
G1, S, prophase, metaphase, anaphase
In what stages are chromosomes unreplicated?
G1, anaphase, telophase
In what stages are chromosomes replicated?
G2, metaphase
in the presence of galactose, GAL3 binds to galactose first and then binds to...
GAL80 causing GAL80 to detach from GAL4 allowing GAL4 to activate its target genes
H3K4me3
Histone 3 trimethylated at Lysine 4 which frequently occurs near the promoters of transcriptionally active genes
Human ABO blood type allelic series
I^A = I^B > i
What features of a pedigree would distinguish between a Y linked trait and a trait that is rare, autosomal dominant, and sex-limited to males?
If Y linked, an affected male would pass to all his sons but is autosomal sex-limited, affected heterozygous males would pass it on to only half of their sons
In X linked recessive traits...
More males than females effected. Sons usually born to unaffected mothers thus skip generations. Half of a carrier mothers sons are affected. Never pass from father to son. All daughters of affected fathers are carriers.
Northern blotting
RNA molecules are transferred from a gel to a solid support which reveals the size, abundance, or tissue of the particular mRNA molecule
Pre-initiation complex
RNA polymerase II and the General TFs assemble at the core promoter
backtracking
RNA polymerase slides backward along DNA template strand for proofreading
what does RITS stand for?
RNA-induced transcriptional silencing
what does RISC stand for?
RND-induced silencing complex
Where do restriction enzymes come from?
Restriction enzymes exist naturally in bacteria, which use them to prevent the entry of viral DNA.
genetic conflict hypothesis
Suggests that genomic imprinting evolved because different and conflicting pressures act on maternal and paternal alleles for genes that affect fetal growth
What is the role of TFIID in transcription initiation?
TFIID binds to TATA box and helps center the RNA polymerase over the transcription start site. It includes TBP.
Chromatin remodeling complexes
TFs and regulatory proteins together that alter chromatin structure without altering the chemical structure of histones directly
DNA fingerprinting
The use of DNA sequences to identify individual persons
noncomposite transposons
Transposable elements in bacteria that lack insertion sequences, possess a gene for transposase, and have terminal inverted repeats
T or F: siRNAs silence genes from which the siRNAs were transcribed
True
A cross between two green corn plants yields 2/3 progeny that are green and 1/3 progeny that are yellow. What is the genotype of the green progeny?
Ww
What was the genotype of the few live F1 red-eyed males obtained by bridges when he crossed a white eyed female with a red eyed male?
X+Y
Fragile-X syndrome
X-linked genetic disorder that includes intellectual ability due to fragile sites
How do you distinguish between an autosomal recessive trait with higher penetrance in males and an X linked recessive trait?
X-linked recessive traits are only passed to sons from their mothers
Genic balance system in fruit flies
X:A ratio where X is the number of X chromosomes and A is the number of haploid sets of autosomes
Turner syndrome
XO sterile women with many phenotypes -many have XX and XO aka mosaicism
Klinefelter syndrome
XXY, XXXY, XXXXY, of XXYY males that are sterile with reduced testes and hair
one map unit is equal to
a 1% recombination rate
alpha-amanitin
a deadly compound produced by death cap mushrooms that is a potent inhibitor of RNA polymerase II
What is a dihybrid?
a genotype that involves two loci (genes) and is heterozygous for both
Hydroxylamine adds what to a cytosine?
a hydroxyl group
Shelterin
a multiprotein complex that binds to telomeres and protects the ends of the DNA from being inadvertently repaired as a double-stranded break in the DNA
super-enhancer
a number of enhancers clustered together that can stimulate higher levels of transcruption
why are pre-mRNAs capped but tRNAs and rRNAs are not?
a protein that adds the 5' cap is associated with RNA polymerase II which transcribes pre-mRNAs but is absent from RNA polymerase I and III which transcribe rRNAs and tRNAs
Transition
a purine to another puring or pyrimidine to another pyrimiding
negative transcriptional control
a regulatory protein is a repressor that binds to DNA (operator) and inhibits transcription
positive transcriptional control
a regulatory protein is an activator that stimulates transcription
How is a suppressor mutation different from a reverse mutation?
a reverse mutation restores the original phenotype by changing the DNA sequence back to the wild type sequence while a suppressor mutation restores the phenotype by causing an additional change in the DNA at a site different from that of the original mutation
Telomeres made of repeated units of
a series of adenine or thymine molecules followed by several guanine nucleotides with the string of Gs and Cs toward the end of the chromosome
genetic maps can be constructed by conducting
a series of testcrosses
Dominant epistatis
a single copy of an allele is required to inhibit the expression of an allele at a different locus
nonoverlapping
a single nucleotide may not be included in more than one codon
Alternative processing pathways
a single pre-mRNA can be processed in different ways to produce alternative types of mRNA resulting in the production of different proteins from the same DNA sequence
nonstop mRNA decay
a special protein binds to the codon-free A site of the stalled ribosome and recruits other proteins that degrade the abnormal mRNA from the 3' end
genetic bottleneck
a sudden reduction in the number of alleles in a population
a test cross for two linked genes will always produce ____ nonrecombinant than recombinant progeny a. more b. less
a. more
forward genetics depends on...
ability to generate lots of random mutations and identification/isolation of the mutations that affect a phenotype of interest
trans acting
able to control the expression of genes on other DNA molecules
cis acting
able to control the expression of genes only on the same piece of DNA
semi-sterility
about half of the gametes from an individual heterozygous for a reciprocal translocation are expected to be functional/viable
how often would HindIII enzyme cut a DNA molecule with equal base compositions?
about once every 4096 (4^6) base pairs
UV radiation
absorbed by pyrimidine bases which causes chemical bonds to form between adjacent pyrimidine molecules on the same strand of DNA creating pyrimidine dimers
GAL4
activator that regulates the transcription of genes for metabolizing galactose by binding to specific sites near the genes' promoters
acetyltransferase enzymes (HATs)
add acetyl groups to histone proteins which usually stimulates transcription
histone methyltransferases
add methyl groups to specific amino acids (lysine or arginine) of histones
Topoisomerases
add or remove rotations from the DNA helix by temporarily breaking the nucleotide strands, rotating the ends around each other, and then rejoining the broken ends
iPSCs
adult somatic cells that can be induced to dedifferentiate and revert to stem cells
Variable expressivity
affected individuals show different levels of severity of the mutant phenotype
3' untranslated region
affects the stability of mRNA and helps regulate the translation of the mRNA protein-coding sequence
Autopolyploidy
all chromosome sets from a single species
Uniparental inheritance
all cytoplasmically inherited traits are passed from mother to offspring
A male affected with an X linked dominant trait will have what proportion of offspring affected with the trait
all daughters and no sons
What statement describes an example of genetic drift?
allele m is lost when a virus kills all but a few individuals and just by chance, none of the survivors possess allele m
identical by descent
alleles are descended from a single allele that was present in an ancestor
Independent assortment means
alleles at different loci separate independently
base substitutions
alteration of a single nucleotide in the DNA
nonsense mutation
alters a codon that specifies an amino acid into a stop codon
RNA editing
alters nucleotide sequence of mRNA after transcription
lacO^c
alters sequence of DNA at the operator so the repressor protein can no longer bind to it
during elongation in bacteria...
amino acids are joined to create a polypeptide chain
what is a mutation?
an inherited change in the DNA sequence of genetic information
paramutation
an interaction between two alleles that leads to a heritable change in expression of one of the alleles without any alteration in DNA base sequence of the converted allele
How do siRNAs and miRNAs target specific mRNAs for degradation or for the repression of translation?
an siRNA or miRNA combines with proteins to form a RISC, which then pairs with mRNA through complementary pairing between bases on the siRNA or miRNA and bases on the mRNA
PacBio
analyzes DNA synthesis of single molecules of DNA
binomial expansion is used for
analyzing complex situations that involve multiple loci and many possible outcomes
Through wobble, a single ___ can pair with more than one ___.
anticodon; codon
Discontinuous replication is the result of which property of DNA?
antiparallel nucleotide strands
Autosomal recessive traits often appear in pedigrees in which there have been consanguine mating because these traits
appear only when both parents carry a copy of the gene for the trait, which is more likely when the parents are related
germ-line mutations
arise in cells that ultimately produce gametes and can be passed to future generations
somatic mutations
arise in somatic tissues which do not produce gametes
Primary (non-familial) down syndrome
arises from spontaneous nondisjunction during egg formation, mostly arising in meiosis 1 of the mother
What does the spliceosome do?
assembles the pre-mRNA in a step by step fashion
anticipation
association between the number of copies of nucleotide repeats, the severity of the resulting disease, and the probability of expansion, in which symptoms become more severe in each generation
where does a suppressor mutation occur?
at a site distinct from the site of the original mutation
how many initiation factors needed in eukaryotic translation initiation?
at least 12
Where are primers synthesized on the lagging strand?
at the beginning of every okazaki fragment
single strand binding proteins
attach to exposed ssDNA and protect it and prevents formation of secondary structures
Male-limited precocious puberty
autosomal dominant allele is expressed only in males and while females with this allele are normal in phenotype
Sex-limited means
autosomal genes are expressed in only one sex and have zero penetrance in the other sex
Each newly formed cell in mitosis contains ______ the cytoplasm and organelle content of the original parent cell a. all b. half c. none
b. hald
A DNA molecule 300 bp long has 20 complete rotations. This molecule is a. positively supercoiled b. negatively supercoiled c. relaxed
b. negatively supercoiled
which is true of CpG islands? a. the are methylated near promotors of active genes b. they are unmethylated near promoters of actively transcribed genes c. acetylation of CpG islands leads to repression of transcription
b. they are unmethylated near promoters of actively transcribed genes
A test cross for two genes far apart on the same chromosome tend to ______ the true physical distance between them because the cross does not reveal double crossovers a.overestimate b. underestimate
b. underestimate
How does bacterial DNA differ from eukaryotic DNA?
bacterial DNA is not complexed with histone proteins and is circular. bacterial DNA is associated with other proteins to keep it compact
Transduction
bacterial viruses (bacteriophages) take DNA from one bacterium to another
Transformation
bacterium takes up free DNA
how does each synthetase recognize a specific amino acid?
based on sizes, charges, and R groups of the amino acids
a minimal media usually includes...
basic nutrients such as a carbon source, chemicals that provide essential elements, vitamins, and ions
Forward genetics
begins with a phenotype and proceeds to a gene that encodes the phenotype
reverse genetics
begins with genotype/DNA sequence and proceeds to the phenotype by altering the sequence or inhibiting its expression
Transcription factors
bind to DNA sequences and affect levels of transcription
splicing regulator proteins and RNPs...
bind to sites within introns and exons and determine which splice and cleavage sites are used
allosteric regulation
binding of inducer alters shape of repressor (protein) preventing it from binding to DNA
eRF-2
binds GTP and stimulates the release of polypeptide from the ribosome
TBP (TATA binding protein)
binds to the minor groove of DNA, bending the DNA and partly unwinding it
What happens in G2?
biochemical preparation for cell division
Tus-Ter complex
blocks a replication fork moving in one direction but not the other
P elements encode...
both a transposase and a repressor of transposition
Uniparental disomy
both chromosomes inherited from the same parent
How are the principles of segregation and independent assortment related and how are they different?
both refer to separation of alleles in anaphase 1 of meiosis -segregation says these alleles separate -IA says they separate independently of alleles at other loci (on another chromosome)
DNA helicase
breaks hydrogen bonds between bases of two DNA strands moving in 5' to 3' direction
how are rare bases incorporated into tRNAs?
by chemical changes in one of the standard bases
how are microsatellites detected?
by using PCR with primers that flank the region containing tandem repeats
a dicentric chromosome is produced when crossing over takes place in an individual heterozygous for which type of chromosome rearrangement? a. duplication b. deletion c. paracentric inversion d. pericentric inversion
c. paracentric inversion
Facultative heterochromatin
can switch to euchromatin depending on cell's developmental needs
most mature somatic cells...
can undergo only a limited number of divisions and cannot be grown continuously
in the presence of allolactose, the lac repressor
cannot bind to the operator
Homozygous for a duplication
carries that duplication on both homologous chromosomes
compound heterozygote
carries two different defective alleles (one on each homologous chromosomes) at a locus that results in a recessive phenotype (caused by not having the gene activity)
peptidyl transferase activity
catalytic activity that creates the peptide bond
Rho-independent terminators
cause end of transcription in absence of rho factor characterized by inverted repeats followed by a string of adenine nucleotides
lethal mutations
cause premature death
Rho-dependent terminators
cause termination of transcription only in presence of an ancillary protein called rho factor
gain-of-function mutations
cause the cell to produce a protein or gene product whose function is not normally present
loss-of-function mutations
cause the complete or partial absence of normal protein function
incorporated error
caused by a mispaired base incorporated into a newly synthesized nucleotide chain
double monosomy
caused by loss of any two nonhomologous chromosomes
Lethal allele
causes death at an early stage of development so some genotypes may not appear among the progeny
Competent cells
cells that can take up DNA through their cell membranes
Cell line
cells that have been altered by viruses or derived from tumors that have lost the normal constraints on cell division will divide indefinitely and they can be cultured in a laboratory for a long time to produce a cell line
_____ is necessary for proper chromosome movement in mitosis and meiosis
centromere
What happens during diplotene?
centromeres of paired chromosomes move apart and the two homologs remain attached at each chiasma
reverse mutations
change a mutant phenotype back into the wild type
Aneuploidy
change in the number of individual chromosomes
genetic drift
changes in allelic frequencies over generations caused by sampling error
base analogs
chemicals with structures similar to those of any of the four standard nitrogenous bases of DNA
3 processes that affect gene regulation by altering chromatin structure
chromatin remodeling, modification of histone proteins, and DNA methylation
What happens during diakinesis?
chromosomal condensation continues, nuclear membrane breaks down, and spindle forms
Physical maps
chromosome maps calculated by using physical distances along the chromosome (often expressed as numbers of base pairs)
Genetic/Linkage maps
chromosome maps calculated by using the genetic phenomenon of recombination
structural variants
chromosome rearrangements and copy number variations
Allopolyploidy
chromosome sets are from two or more species
During telophase...
chromosomes arrive at spindle poles, nuclear membrane reforms, and the chromosomes relax
What happens during pachytene?
chromosomes become shorter and thicker, synaptonemal complex develops between homologous chromosomes
During prophase...
chromosomes condense, each chromosome possesses two chromatids, and mitotic spindle forms
What happens during zygotene?
chromosomes continue to condense and homologous chromosomes pair up and begin synapsis
What happens during leptotene?
chromosomes contract and become visible
What happens in telophase 2?
chromosomes decondense, spindle breaks down, and nuclear envelope re-forms
during metaphase...
chromosomes line up on the metaphas plate
What happens in prophase 2?
chromosomes re-condense, spindle re-forms, and nuclear envelope breaks down
What would be the result if an organism's telomerase were mutated and non functional?
chromosomes would shorten each generation
plasmid vectors
circular DNA molecules that can be replicated by a host cell with a cluster of unique restriction sites and selectable markers and an origin of replication
Rolling Circle Replication
circular DNA replication that produces multiple circular DNA molecules
Synapsis
close pairing of homologous chromosomes forming bivalents/tetrads
In gene mapping experiments using generalized transduction, bacterial genes that are cotransduced are
close together on the bacterial chromosome
Tetrad/bivalent
closely associated four-sister chromatids of two homologous chromosomes
synonymous codons
codons that specify the same amino acid
DNA library
collection of clones containing all the DNA fragments from one source
General TFs
combine with RNA polymerase to form basal transcription apparatus
Theta Replication
common mode of replication that takes place in circular DNA; bidirectional
cohesive ends
complementary ends that can spontaneously pair to connect DNA fragments
Chromatin
complex of DNA and its associated proteins
mediator
component of basal transcription apparatus made of a complex of proteins which interacts with RNA polymerase
Kinetochore
composed of proteins that asseble on the centromere to provide a site for the spindle microtubules to attach
Centromere is
constricted region on a chromosome where the kinetochore and spindle microtubules attach
Complete medium
contains all substances, such as amino acids, required by bacteria for growth and reproduction
Intersex fruit fly
contains both male and female characteristics
expression vector
contains sequences required for transcription and translation in bacterial cells
Sigma factor
controls binding of RNA polymerase to the promoter
SINEs
copies of transposable elements that have been shortened at the 5' end
Nucleosome is a
core of proteins attached to a shorter fragment of DNA
Mismatch repair system
corrects errors immediately after replication is complete
Monohybrid cross is a
cross between two monohybrids obtained from two pure-breeding parents that differ in a single characteristic
Crossing over
cross over of chromosome segments from the sister chromatid of one chromosome to the sister chromatid of the other synapsed chromosome
What is the first mechanism of generating genetic variation in newly formed gametes?
crossing over
hybrids can be obtained by
crossing two pure-line parents
site-directed mutagenesis
cut out a short sequence of nucleotides with restriction enzymes and replace it with a synthetic oligonucleotide
During cytokinesis...
cytoplasm divides and a cell wall forms in plants
the deamination of cytosine produces _____ which pairs with ____ in replication
cytosine, adenine
Which of the following is a characteristic of DNA sequences at the telomeres? a. one strand consists of G and A (or T) nucleotides b. they consist of repeated sequences c. one strand protrudes beyond the other, creating some ssDNA at the end d. all of the above
d. all of the above
Which type of transposable element possesses terminal inverted repeats? a. insertion sequence b. composite transposon c. non-composite transposon d. all of the above
d. all of the above
which of the following is a characteristic of paramutation? a.One allele is able to alter another allele when both are present in a heterozygote. b.Altered alleles must be passed on to future generations. c.Altered alleles must be capable of altering other alleles in future generations. d.All of the above.
d. all of the above
the total percentage of recombinant gametes is always ____ the percentage of meiosis where crossing over takes place a. less than b. more than c. equal to d. half
d. half
action of siRNAs and miRNAs
degrade mRNA, inhibit transcription, and chromatin modification
interference
degree to which one crossover interferes with additional crossovers in the same region
ChIP
determines where within the genome a specific protein interacts with DNA
Chromosome duplications often result in abnormal phenotypes because
developmental processes depend on the relative amounts of proteins encoded by different genes
sampling error
deviation from an expected ratio due to limited sample size
isoaccepting tRNAs
different tRNAs that accept the same amino acid but have different anticodons
genomic imprinting is caused by
differential degrees of methylation of the alleles inherited from the two parents
natural selection
differential reproduction of genotypes
What type of cells does meiosis occur in?
diploid cells aka meiocytes
Conjugation
direct transfer of DNA from one bacterium to another
FISH
directly determines the chromosomal location of a particular gene through molecular analysis
Griffith experiment
discovered bacterial transformation was responsible for virulence switch
Nucleoid
distinct clump found in a bacterial cell in the cytoplasm
Paracentric inversions
do not include the centromere
Native ChIP
does not use crosslinking and is often used for finding the locations of modified histone proteins
What is pseudodominance and how is it produced by a chromosome?
dominant wild-type allele in a heterozygous individual is absent due to a deletion on one chromosome. Thus, the recessive mutation is not masked and will show the mutational effect
lacI+ is
dominant; transacting
Alkylating Agents
donate alkyl groups to nucleotide bases
F+ cells can act as
donors
Reverse duplication
duplicated degment is inverted
Tandem duplication
duplicated segment is immediately adjacent to the original segment
Displaced duplication
duplicated segment is located some distance away from the original segment either on the same chromosome or a different one
Copy number variations
duplications and deletions that range in length from thousands of base pairs to several million base pairs
translocation heterozygotes
during synapsis in prophase 1, all 4 chromosomes involve to form a crosslike figure. crossovers may generate gametes that will result in nonviable offspring
For single crossovers, the frequency of recombinant gametes is half the frequency of crossing over because
each crossover takes place between only two of the four chromatids of a homologous pair
Gene interaction
effects of genes at one locus depend on the presence of genes at other loci
DNA polymerase III
elongates DNA
Jpx gene
encodes a lncRNA that stimulates transcription of Xist in the inactive X chromosome
Xite
encodes lncRNA that sustains Tsix expression on the active X chromosome
lacI^s
encodes superrepressors that prevent transcription from taking place even in the presence of lactose
What are some causes of incomplete penetrance?
environmental effects, mutations in other interacting genes, and epigenetics can cause IP
what does dicer do?
enzyme that chops up dsRNA molecules into tiny RNA molecules that are unwound to produce siRNAs and miRNAs
Deoxyribonuclease
enzyme that degrades DNA
Ribonuclease
enzyme that degrades RNA
Telomerase
enzyme that has both a protein and RNA component used to extend the G-rich 3' overhang
effective population size
equivalent number of breeding adults
founder effect
establishing a population by a small number of individuals, carrying only a small fraction of the original population's genetic variation
What type of chromatin constitutes most of the chromosomal material?
euchromatin, where most transcription occurs and it is relatively gene-dense
Ames test
evaluates the potential of chemicals to cause cancer using auxotrophic mutatant strains of S. typh
cis-acting elements for regulating splicing
exonic/intronic splicing enhancers and splicing silencers that help promote or repress the use of particular splice sites during RNA splicing which results in alternative splicing
negative inducible operon
expression is off. repressor binds to operator and blocks RNA polymerase so something must happen to prevent the binding of the repressor to the operator
Interphase
extended period between cell divisions when DNA synthesis and chromosome replication occur
Plasmids
extra-chromosomal, small circular dsDNA distinct from the chromosome
addition of the 5' cap
facilitates binding of ribosome to 5' end of mRNA increasing mRNA stability
Screening
finding a gene or sequence of interest in a DNA library
Group I introns
fold into a common secondary structure with nine hairpins which are necessary for splicing
Where is permanent, constitutive heterochromatin found on chromosomes?
found at centromeres and telomeres
Trisomy
gain of a single chromosome
Tetrasomy
gain of two homologous chromosomes
how is a gene inserted into a plasmid cloning vector?
gene and plasmid are cut with the same restriction enzyme and mixed together. DNA ligase seals nicks in sugar-phosphate backbone
inversions do not change ____ but can disrupt _____ at breakpoints and also can move genes in new environments and change their expressions (position effect)
gene dosage; gene function
Deletions can cause
gene dose imbalances, pseudodominance, and haploinsufficiency
How does gene interaction differ from dominance?
gene interaction is interaction between genes at different loci while dominance is interaction between alleles at a single locus
SRY gene is
gene on Y chromosome that determines maleness in humans
nonreciprocal translocation
genetic material moves from one chromosome to another without any reciprocal exchange
What is a consequence of meiosis due to the production of gametes with many different genotypes?
genetic variation
epialleles
genetically identical alleles that produce heritable differences in phenotypes through epigenetic processes
The cells produced by mitosis are
genetically identical to each other and to the cell that gave rise to them
Polytene Chromosomes
giant chromosomes arising when repeated rounds of DNA replication take place without accompanying cell divisions, producing thousands of copies of DNA that lie side by side forming a thick bundle
Rifamycins
group of antibiotics that kills bacterial cells by inhibiting their RNA polymerase
Polycistronic mRNA
group of genes transcribed into a single RNA molecule
Basal transcription apparatus
group of proteins that assembles near the transcription start site and is sufficient to initiate minimal levels of transcription
operon
group of structural genes that are transcribed together along with their regulatory elements
What happens in G1?
growth; proteins necessary for cell division synthesized
which of the following is a transition base substitution?
guanine is replaced by adenine
in meiosis with a single crossover, ___ gametes are recombinants and ____ are nonrecombinants
half, half
Heterozygous for a duplication
has one normal and one chromosome with the duplication
self-splicing introns
have ability to remove themselves from an RNA molecule without the aid of enzymes or other proteins
examples of DNA binding motifs
helix-turn-helix, zinc finger, leucine zipper
no-go decay
helps remove stalled ribosomes resulting from secondary structures in the mRNA, chemical damage to the mRNA, premature stop codons, and ribosomal defects
Underdominance (homozygote advantage)
heterozygote has lower fitness than either homozygote
In complementation test, if mutations are allelic (occur at same locus) then
heterozygous offspring have only mutant alleles and exhibit a mutant phenotype
in complementation test, if mutations are non-allelic (occur at different loci) then
heterozygous offspring inherit a mutant allele and a wild type allele; exhibit wild-type phenotype
suppressor mutations
hide or suppress the effect of another mutation
Nuclear Matrix
highly organized internal scaffolding that consists of a network of protein fibers
Neutralizing positive charge of histones would cause...
histones to bind less tightly to the DNA
What binds to the -10 consensus sequence found in most bacterial promoters?
holoenzyme
if an individual is pure-breeding it is ____ for the gene
homozygous
Hershey-Chase
identified DNA as the agent of bacteriophage infection
Avery, Macleod, and McCarty
identified DNA as the transforming agent
Two predictions of HW
if population is large, randomly mating, not affected by mutation/migration/NS then 1. allelic frequencies of a population do not change 2. genotypic frequencies stabilize after one generation in the proportions
How does incomplete dominance differ from incomplete penetrance?
in incomplete dominance, the heterozygote is intermediate between the homozygote, in incomplete penetrance, some individuals do not express the expected phenotype
Spindle assembly checkpoint
in metaphase, ensures each chromosome is aligned on the plate and attached to spindle microtubules from opposite poles
imprinted alleles are
in the genome but kept inactive throughout the individual's life
Where does RNA splicing take place?
in the nucleus before export to the cytoplasm
decoding center
in the small subunit that sense the fit between the codon on the mRNA and the anticodon on the incoming charged tRNA
efforts to map human genes are hampered by
inability to perform specific crosses and small number of progeny in most human families
in a negative repressible operon, the regulator protein is synthesized as an
inactive repressor (that can be activated by a corepressor)
Pericentric inversions
include the centromere
5' untranslated region
includes the shine-dalgarno sequence in bacteria
Polyploidy
increase in number of whole chromosome sets
inbreeding depression
increased frequency of lethal/deleterious traits with inbreeding
3' cleavage and addition of poly(a) tail
increases stability of mRNA and it facilitates binding of ribosome to mRNA at the 5' end
histone code
inheritable pattern of modifications that encode information that affects how genes are expressed
silencers have a ____ effect on the transcription of distant genes
inhibitory
Put the following in the order of which they are used in replication helicase ss binding protein Gyrase initiator protein
initiator protein, helicase, ss binding protein, Gyrase
Hfr cell is created by...
integration of an F factor into the chromosome
RNA crosstalk
interactions and competition among miRNAs, mRNAs, and other RNA molecules
lacP-
interfere with binding of RNA polymerase to promoter so they don't produce lac proteins in the presence or absence of lactose; cis-acting
in Ecoli, the concentration of cAMP is (directly/inversely) proportional to the level of available glucose
inversely proportional
catabolite repression
involves a positive control mechanism in response to low glucose
three point test cross
involves a single testcross for three genes all together at once to establish the order of the genes in a single set of progeny
Primary structure of DNA
is the nucleotide sequence
Replica plating
isolating mutant bacteria strains based on nutritional requirements
When might you seen an autosomal dominant trait skip generations?
it might skip generations when a new mutation arises or the trait has incomplete dominance
What happens to a chromosome that loses its centromere?
it will not segregate into the nucleus in mitosis and is usually lost
If a splice site were mutated so that splicing did not take place, what would the effect be on the protein encoded by the mRNA?
it would be shorter than normal
For any cell to reproduce successfully...
its genetic info must be copied, the copies must separate, and the cell must divide
Checkpoints
key transition points that regulate cell-cycle progression
efficient transcription of the lac operon occurs if
lactose is present and glucose is absent
Bacterial RNA polymerase
large, multimeric enzyme consisting of several polypeptide chains
TADs
large, spatially interacting regions of chromatin that are separated physically from other TADs
5 phases of Prophase 1
leptotene, zygotene, pachytene, diplotene, diakinesis
LINEs
like SINEs, are shortened at 5' end
RNAi
limits invasion of foreign genes (siRNA) and censors/down-regulates the expression of own genes (miRNA)
what is the effect of high levels of glucose on the lac operon?
little transcription takes place due to low concentration of cAMP
Chromosome puffs
localized swellings of the chromosome that occur under certain conditions; regions of active transcription; chromatin relaxes
core promoter
located immediately upstream of the gene, bound by basal transcription apparatus; typically includes one or more consensus sequences
Deletion mapping
looking for absence of staied bands
GWAS
looks for nonrandom associations between the presence of a trait and alleles at many different loci scattered across the genome
Monosomy
loss of a single chromosome
deamination
loss of an amino group from a base either spontaneously or induced by mutagenic chemicals
Nullisomy
loss of both members of a homologous pair of chromosomes
Deletion
loss of chromosome segment
lacZ-
lost ability to synthesize beta-galactosidase
lacI-
lost ability to synthesize lac repressor protein
lacY-
lost ability to synthesize permease
Metamale fruit fly
low viability fly with a male phenotype (X:A< 0.5)
Metafemale fruit fly
low viability fly with female phenotype (X:A> 1)
polyribosomes
mRNA with several ribosomes attached
AU-rich element
mRNAs with this element are degraded by a mechanism in which microRNAs take part
cDNA library
made of only transcribed DNA sequences
transposase enzyme
makes staggered breaks in DNA to allow transposable element to integrate into a new site
Linkage analysis
mapping that involves quantification of the extent of linkage between a phenotype (or disease) and marker loci
Why did genomic imprinting evolve?
maximum fitness can be achieved in different ways for fathers and mothers
inbreeding coefficient
measures probability that two alleles are identical by descent (F=1 means identical by descent)
Sexual reproduction consists of which two processes?
meiosis and fertilization
In what stages are chromosomes condensed?
metaphase and anaphase
the presence of the _____ in the major groove inhibits the binding of ____ and other proteins required for transcription
methyl group; TFs
Mismatch repair in bacteria distinguishes between old and new strands of DNA on the basis of
methyl groups on the old strand
what types of changes take place in prokaryotic rRNA processing?
methylation of bases, cleavage of bases, and nucleotides trimmed from the ends of rRNAs
What mechanism requires the ability to distinguish between new and template strand?
mismatch repair
neutral mutations
missense mutations that alter an amino acid but not the protein function
Base-excision repair
modified base is excised then the entire nucleotide is replaced
In analyzing a three point testcross, a student determines the interference is -.23. What does negative interference indicate?
more double crossovers than expected based on the single crossover frequency
Sex-influenced characteristics means autosomal genes are...
more readily expressed in one sex than the other (higher penetrance in one sex)
Histones
most abundant proteins in chromatin; positively charged
Translocation
movement of genetic material between nonhomologous chromosomes or within the same chromosome
Two main mechanisms of chromosome rearrangements
multiple dsDNA breaks and wrong repairs AND misalignment of repeated sequences and crossing overs (unequal crossing over)
alternative 3'cleavage sites result in
multiple mRNAs of different lengths
Requirements for any DNA molecules to stay and propagate stably in bacterial cells
must be circular and have replication origin
in order for a bacterial cell's genotype to be altered by linear DNA introduced by transformation, conjugation, or transduction, the linear DNA
must be integrated into the recipient cell's genome by recombination/crossing over
Auxotrophs
mutant strains that lack one or more enzymes necessary for synthesizing essential compounds because they have mutations that disrupt the genes that encode the enzymes
gal-
mutant that can't utilize galactose and can't grow in minimal media if galactose is only carbon source
arg-
mutant that cannot make arginine and cannot grow in minimal media unless argine provided
lac-
mutant, can't use lactose, can't grow in minimal media if lactose is only carbon source
bio-
mutant, cannot make biotin, cannot grow in minimal media unless biotin provided
what causes a ribosome to stall on mRNA?
mutation in stop codon or prematuraly terminated transcription
forward mutation
mutation that alters the wild-type phenotype
conditional mutations
mutational effects are manifested only under certain conditions
spontaneous mutations
mutations that occur under normal conditions
induced mutations
mutations that result from changes caused by environmental chemicals or radiation
Replicative transposition
new copy of transposable element is introduced at new site while the old copy remains behind at original site
CPR
newly discovered group detected largely through culture independent methods of DNA isolation
What would be the effect of introducing siRNAs that degrade Xist RNA into a female cell?
no Xist RNA would be present to coat the X so both X chromosomes will remain active
Why are sex-chromosome aneuploids more common than autosomal aneuploids in humans and mammals?
no mechanism of dosage compensation for autosomal chromatids. autosomes carry more genes. most autosomal aneuploids are spontaneously aborted
Genetic mosaicism
nondisjunction in a mitotic division may generate patches of cells in which every cell has a chromosome abnormality and other patches of cells with normal karyotype
autopolyploidy can arise through...
nondisjunction in mitosis OR meiosis
Linkage disequilibrium
nonrandom association between alleles in a haplotype
in meiosis with no crossing over, only ___ gametes are produced
nonrecombinant
crossovers within the inversion produce two non recombinant and two recombinant gametes, but only _____ gametes will be viable
nonrecombinant gametes will be viable
knockout mice
normal gene has been fully disabled
H1 Histone Protein
not part of nucleosome core particle; locks DNA in place by acting as a clamp around the nucleosome
What is the fundamental repeating unit of chromatin?
nucleosome
intergenic suppressor mutations
occur in a gene other than the one bearing the original mutation
Hfr x F-
one Hfr and one F-
directional selection
one allele or trait is favored over another
What is the outcome of a robertsonian translocation?
one metacentric chromosome and one chromosome with two very short arms
Specialized transduction
only genes near particular sites on the bacterial chromosome are transferred
G2/M checkpoint
only passed if DNA is completely replicated and undamaged
Transgenic animal
organism that has been permanently altered by the addition of a DNA sequence to its genome
(p+q)^n
p is probability of one event q is probability of alternative event n is number of times event occurs
penetrance
percent of individuals with the mutant allele that actually show the affected phenotype
Overdominance (heterozygote advantage)
phenomenon in which a heterozygote has greater reproductive success compared with either of the corresponding homozygotes
Genetic maternal effect
phenotype of offspring determined by genotype of the mother -genes are in nucleus -traits are encoded by autosomal genes that can be passed through males
in cytoplasmic inheritance, the ______ of the mother is copied to all her children as their _____
phenotype, phenotype
Pseudodominance
phenotypic effects of a recessive mutation can be manifested if the homologous chromosome has a deletion that spans the gene and is no longer able to mask the recessive mutation
Photoreactivation of UV induced pyrimidine dimers
photolyase uses energy captured from light to break the covalent bonds that link the pyrimidines in a dimer
Chiasm
physical location where two non sister chromatids cross
G-rich 3' overhang
place where special proteins bind to protect the telomere from degradation and to protect the ends of chromosome from sticking together
Fertility Factor (F)
plasmid in ecoli cell tjat is present in donor cell but absent in recipient cell; episome that contains origin of replication and some genes required for conjugation
Cosmids
plasmids that are packaged into empty viral protein coats and transferred to bacteria by viral infection
FLC
plays important role in suppressing flowering until after an extended period of cold (vernalization)
how does the poly(A) tail affect mRNA stability?
poly(A)-binding proteins and mRNA bending allows the poly(A) tail to stabilize the 5' cap which must be removed before the mRNA can be degraded from the 5' end
_______ and ______ are visible evidence of the dynamic nature of chromatin structure
polytene chromosomes and DNase 1 sensitivity
enhancers and silencers are both
position and orientation independent and contain binding sites for transcription factors that decrease transcription
Somatic Cell Hybridization can be used for...
positioning genes on chromosomes
SNPs
positions in the genome where individuals vary in a single nucleotide base useful in GWAS
CAP is used for the _______ control of many operons
positive
the ____ charged amino acids in histones attract the ____ charges on the phosphates of DNA
positive; negative
double mutant
possesses the original mutation and the suppressor mutation but exhibiting the phenotype of the nonmutated wild type
dsRNA triggers
potent gene silencing when injected into Celegans nematodes
Recessive epistasis
presence of two recessive alleles (homozygous genotype) inhibits expression of an allele at a different locus
pre-mRNA is called the
primary transcript
Addition/Sum rule
probability that either of two events will occur is the SUM of the probability of each
intercalating agents
produce mutations by sandwiching themselves between adjacent bases in DNA, distorting the 3D structure of the helix and causing single-nucleotide insertions and deletions in replication
germ-line mutations may affect the _____ not the ____
progeny, carrier
Telomeres
protective tips of linear chromosome
If Avery, Macleod, and McCarty had found that samples of heat-killed bacteria treated with RNase and DNase transformed bacteria, but samples treated with protease did not, what conclusion would they have made?
protein is the genetic material
GAL80
protein that negatively regulates the activity of GAL4 when galactose is absent
Western blotting
protein transferred from gel to membrane and an antibody that specifically binds to a particular protein is used as a probe to determine the size and the pattern of the protein's expression
DNA bound CAP facilitates the binding of RNA polymerase at the promoter through what interaction?
protein-protein interaction
cofactors
proteins recruited by TFs that either stimulate or repress transcription; they are coactivators and corepressors that do not directly bind DNA and work with TFs through protein-protein interaction
Transversion
purine to pyrimidine or pyrimidine to purine
in elongation, the creating of peptide bonds between amino acids is catalyzed by
rRNA (in the large subunit)
What happens during metaphase 1?
random alignment of homologous pairs along metaphase plate
coefficient of coincidence
ratio of observed double crossovers to expected double crossovers
Oxidative radicals
reactive forms of oxygen that damage DNA and induce mutations by bringing about these chemical changes
the start codon sets the correct ____
reading frame
eRF-1
recognizes all 3 termination codons
seed region
region of close complementarity between the miRNA and target mRNA
attenuation
regulates the continuation of transcription
What is the difference between the core promoter and the regulatory promoter?
regulatory promoter is father upstream from gene AND basal transcription factors bind to core promoter while regulatory transcription factors (like activator proteins) bind to the regulatory promoters
selection coefficient
relative intensity of selection against a genotype
fitness
relative reproductive success of a genotype
Heterochromatin
remains in a highly condensed state throughout the cell cycle, even during interphase
histone demthylases
remove methyl groups from histones
DNA polymerase I
removes and replaces primers
nucleotide excision repair
removes bulky DNA lesions (such as pyrimidine dimers) that distort the double helix
RNA splicing
removes noncoding introns from pre-mRNA, facilitating binding of ribosome at 5' end
Homology directed repair
repairs broken DNA molecule by using a sister chromatid
Nonhomologous end joining
repairs double strand breaks without using a homologous template
short flanking direct repeats
repeated sequences on both sides of most transposable elements that are generated in the process of transposition
What happens in metaphase 2?
replicated chromosomes line up on the metaphase plate
Recombinant plasmids are created using...
restriction enzymes and DNA ligase
nonsense-mediated mRNA decay
results in rapid elimination of mRNA containing premature termination codons to prevent production of aberrant proteins
rNTPS
ribose sugar and base (nucleoside) attached to three phosphate groups
Which type of replication does not include a replication bubble?
rolling circle
What type of replication requires a break in the nucleotide strand to get started?
rolling circle replication
Logarithm of Odds
scores that are used to determine the probability that genes are actually linked
DNA ligase
seals breaks/nicks in the sugar phosphate backbone of new DNA strand by catalyzing formation of phosphodiester bonds
composite transposons
segment of DNA flanked by two copies of an insertion sequence
Replicon
segment of DNA that undergoes replication and has an origin of replication
Which event takes place in meiosis 2 but not meiosis 1?
separation of chromatids
Cytokinesis
separation of cytoplasm
What happens in anaphase 1?
separation of homologous chromosome pairs and random distribution of chromosomes into newly divided cells
What happens in meiosis 1?
separation of homologous pairs, reduction of the chromosome number by half
Mitosis
separation of sister chromatids
What happens in meiosis 2?
separation of sister chromatids (equational division)
RNA coding region
sequence of DNA nucleotides that is copied into an RNA molecule
Terminator
sequence of nucleotides that signals where transcription should end
SMRT sequencing
sequence of single molecules of longer DNA/RNA fragments is determined
terminal inverted repeats
sequences on either side of a transposable element that are inverted complements of each other
DNA glycosylases
set of enzymes that catalyze the excision of modified bases
recombinant DNA technology
set of molecular techniques for locating, isolating, altering, and studying DNA degments
codon
set of nucleotides that encode a single amino acid
deletion of SRY causes
sex reversal making an XY individual develop as a complete female
response elements
short regulatory sequences in promoters or enhancers that allow genes in eukaryotes to be coordinatel expressed
Linker DNA
short segments of DNA that separate nucleosomes
fingerprinting uses what?
short tandem repeats (microsatellites) and PCR
Phased genotypes are useful for
showing linkage
What is not a function of the promoter?
signals where transcription ends
miRNAs usually _____ genes that are _____ from those which the miRNAs were transcribed from
silence; distinct
insertion sequences
simple transposable elements that carry only the information required for movement
oriC
single origin of replication in the circular chromosome of ecoli
Probe
single stranded DNA or RNA molecule with a base sequence complementary to a sequence of interest
Which type of cells have telomerase?
single-celled eukaryotes, germ cells, early embryonic cells, and certain proliferative somatic cells (such as bone marrow and cells lining the intestines)
During anaphase...
sister chromatids separate and move toward opposite poles
Fragile sites
sites that develop constrictions or gaps when the cells are grown in culture and that are prone to breakage under certain conditions
corepressor
small molecule that binds to repressor making it capable of binding to the operator
inducer
small molecule that turns on transcription by antagonizing repressor
linkers
small, synthetic DNA fragments that contain one or more restriction sites
trans-acting elements for regulating splicing
snRNPs bind to cis-acting elements and promote or repress splice-site selection
Extranuclear inheritance
some characteristics are encoded by genes located in cytoplasm
recursive splicing
some long introns are removed in multiple steps in some species
Molecular motors
special proteins that disassemble tubulin molecules and generate forces that pull chromosome toward spindle pole
Haplotype
specific set of linked alleles
What would be the result if a chromosome did not have a kinetochore?
spindle microtubules would not attach to the chromosome, chromosome would not be drawn into a newly formed nucleus, the resulting daughter cells would be missing a chromosome
Group II introns
splice by mechanism similar to the spliceosome mediated splicing of nuclear pre-mRNA and splicing generates a lariat structure
Elongation
ssDNA template used to synthesize ssDNA
cloning vector
stable, replicating DNA molecule to which a foreign DNA fragment can be attached for introduction into a cell
epigenetic trait
stably inherited phenotype resulting from changes in chromatin without alterations in the DNA sequence
the protein coding region begins with _____ and ends with ______
start codon; stop codon
variance
statistical measure that describes the variability of a trait
FLD
stimulates flowering by repressing the action of FLC
Transcription unit
stretch of DNA that encodes an RNA molecule and the sequences necessary for itstranscription
deacetylases (HDACs)
strip acetyl groups from histones and restore chromatin structure which represses transcription
what is the difference between a structural gene and a regulator gene?
structural genes encode proteins while regulator genes control the transcription of structural genes
Epigenetics
study of heritable phenotype changes that do not involve alteration of the DNA sequence
Hybrid dysgenesis
sudden appearance of numerous mutations, chromosome aberrations, and sterility in the offspring of a P= male with a P- female
imprinting
suppression of expression
What is transcription?
synthesis of an RNA molecule from a DNA template
Primase
synthesizes RNA primers
copolymers
synthetic RNAs containing two or three different bases
translesion DNA polymerases
take care of emergencies during DNA replication
Dideoxy (Sanger) sequencing
takes advantage of the chain-termination reacting caused by incorporation of ddNTP
intragenic suppressor mutation
takes place in the same gene that contains the mutation being suppressed
Examples of spontaneous replication errors
tautomeric shifts, mispairing due to other structures, incorporated errors, and replication errors, causes of deletions/insertions
Requirements of replication
template strand, raw materials, enzymes and other proteins
positive assortative mating
tendency for like individuals to mate
negative assortative mating
tendency for unlike individuals to mate
two point testcross
testcross between two genes
In RNA silencing, siRNAs and miRNAs usually bind to which part of the mRNA molecules that they control?
the 3' UTR
amino acids bind to which part of the tRNA?
the 3' end
how does the binding of transcription factors to enhancers affect transcription at genes that are thousands of base pairs away?
the DNA between the enhancer and the promoter loops out so the transcription factors bound to the enhancer can directly interact with the basal transcription apparatus
F' cells occur when...
the F factor is excised from the bacterial chromosome and carries bacterial genes with it
in dideoxy-sequencing reaction, what terminates DNA synthesis at a particular base?
the absence of a 3' OH group on the ddNTP prevents the addition of another nucleotide
what is tRNA charging?
the attachment of a tRNA to its appropriate amino acid which requires ATP energy
most transcriptional activator proteins affect transcription by interacting with
the basal transcription apparatus
what happens in RNA editing
the coding sequence of an mRNA molecule is altered after transcription so that the translated protein has an amino acid sequence that differs from that encoded by the gene
Holoenzyme
the core enzyme + sigma factor
Expressivity measures
the degree to which a given mutant allele shows the mutant phenotype
Secondary structure of DNA is
the double stranded helix
how are candidate genes that are identified by positional cloning evaluated to determine whether they encode the phenotype of interest?
the expression pattern of the gene can be examined, and the coding region of copies of the gene from individuals with the mutant phenotype can be compared with the coding region of wild-type individuals
Genomic imprinting
the expression/non-expression status of each allele is determined by parental origin
tertiary structure of DNA is
the higher order folding that allows DNA to be packed into the confined space of a cell
do initiation and termination codons specify amino acids?
the initiation codon in bacteria encodes N-formylmethionin and in eukaryotes it encodes methionine but termination codons do not specify amino acids
Positional cloning
the isolation of genes on the basis of their position on a gene map, not relying on gene products
depurination
the loss of a purine base from a nucleotide
what is the advantage of using the neo gene to disrupt the function of a gene in knockout mice?
the neo gene provides a selectable marker for finding cells that contain the disabled gene
During prometaphase...
the nuclear membrane disintegrates and spindle microtubules attach to cchromatids
During Interphase...
the nuclear membrane is present and chromosomes are relaxed
expanding nucleotide repeats
the number of copies of a set of nucleotides increases
when a population is in mutational equilibrium, what is true?
the number of forward mutations is equal to the number of reverse mutations
Product/Multiplication rule
the probability that two independent events with BOTH occur is the PRODUCT of the probability of each occurring
What is true of genomic imprinting?
the sex of the parent that transmits an allele affects the expression of the allele in the offspring
During the initiation of translation in bacteria, the small ribosomal subunit binds to which consensus sequence?
the shine-delgarno sequence
What are some advantages of using allelic frequencies to describe a population's gene pool as opposed to genotypic frequencies?
there are fewer alleles than genotypes and alleles are passed from generation to generation in sexually reproducing organisms
what is the effect of outcrossing on a population?
there will be more heterozygotes than predicted by the HW law
base analogs are mutagenic because of which characteristic?
they are similar in structure to the normal bases
Which statement is true of plasmids?
they replicate independently of the bacterial chromosome
in a polyribosome, the polypeptides associated with which ribosomes will be the longest?
those at the 3' end of mRNA
reading frame
three ways in which the sequence can be read in groups of three
deaminated 5mC because what base?
thymine
RNA polymerase V
transcribes RNA molecules taking part in heterochromatin formation in plants
Tsix
transcribes a lncRNA antisense to the Xist lncRNA
RNA polymerase I
transcribes large rRNAs
RNA polymerase II
transcribes pre-mRNA, some snRNAs, snoRNAs, and some niRNAs
RNA polymerase IV
transcribes some siRNAs in plants
RNA polymerase III
transcribes tRNA, small rRNAs, some snRNAs, and some miRNAs
inducible operon
transcription is normally off so something must happen to induce transcription (caused by an inducer)
repressible operons
transcription is normally on and something must happen to repress transcription (caused by corepressor)
negative repressible operon
transcription takes place and something must happen to make the repressor active
nonreplicative/conservative transposition
transposable element is excised from the old site and inserted at a new site without any increase in the number of its copies
DNA transposons (class II)
transpose as DNA
Retrotransposons (class I)
transpose through an RNA intermediate
Poly-X females
triple X is most common
negative repressible control by the ________ protein regulates the initiation of transcription
trpR repressor protein
T or F: autopolyploids are usually sterile
true
T or F: nitrous acid causes deamination
true
F' x F-
two F' cells
F+ x F- Conjugation
two F= cells
identical by state
two alleles are alike in structure and function but do not have a common origin
Principle of segregation
two alleles of a characteristic segregate when gametes are formed and one allele goes to each gamete
How many bands of DNA would be expected in Meselson and Stahl's experiment after two rounds of conservative replication?
two bands (one thin heavy and one thick lighter band)
a dihybrid cross is a cross between
two dihybrids (involving the same two genes)
Complete linkage
two genes are located very close together on the same chromosome and do not exhibit crossing over within the interval between two loci
Morgan's idea
two genes far apart are more likely to undergo a crossover
Duplicate recessive epistasis
two recessive alleles at either of two different loci are capable of suppressing a phenotype
a two strand double crossover arises when
two separate crossover events take place between two loci and between the same two of the four chromatids of a homologous pair
Diploid cells have
two sets of chromosomes
independent assortment produces four types of progeny in 1:1:1:1 ratio with two ____ and two ___
two types of recombinant progeny and two types of nonrecombinant/parental progeny
reciprocal translocation
two-way exchange of chromosomal segments between the chromosomes
Gyrase
type II topoisomerase that eases tension
Positive supercoiling
type of DNA tertiary structure where molecules are overrotated
Negative supercoiling
type of DNA tertiary structure where molecules are underrotated
Euchromatin
undergoes normal process of condensation and decondensation in the cell cycle
stem cells
undifferentiated cells that can form every type of cell in an organism (pluripotent)
Transformation requires...
uptake of DNA from surrounding medium AND its incorporation into a bacterial chromosome or plasmid
when treated with sodium bisulfite, unmethylated cytosine is converted into what?
uracil
Specialized transduction requires a phage to
use specific integration sites
LOD score of 3 or higher is
usually considered convincing evidence for linkage
Traditional (morphological) markers
variable genes with easily observable phenotypes and known chromosomal location information
Microsatellites
variable numbers of short DNA sequences repeated in tandem
CENP-A
variant histone in centromeres that takes place of usual H3 histone; needed for assembly of proteins associated with kinetochore
RFLPs
variations in DNA sequence that can be detected by cutting the DNA with restriction enzymes
BACs
vectors originally constructed from the F plasmid
DNase 1 Sensitivity
when DNA is tightly bound to histone proteins, it is less sensitive to DNase 1 whereas unbound DNA is more sensitive to DNase 1
Haploinsufficiency
when a single copy of a gene is not enough to produce a wild-type phenotype
30 nm Fibers
when chromatin is in a condensed form, nucleosomes fold on themselves to form a dense, tightly packed structure that makes up a fiber
When does LD persist longer?
when loci are close together making crossover less common (low recombination rate)
maternal imprinting
when maternal allele is not expressed
paternal imprinting
when paternal allele is not expressed
concept of dominance
when two different alleles are present in a genotype, only the trait encoded by the dominant allele is observed in the phenotype
Origin of replication
where DNA synthesis begins
IRES
where ribosomes can bind directly without first attaching to the 5' cap
complementation test determines...
whether mutations are at the same locus (in same gene) or not by crossing parents homozygous for different recessive mutations (with same phenotype)
In genomic imprinting, what determines how much methylation of a certain area takes place?
whether the gene passes through the egg or the sperm
Prototrophs
wild-type bacteria that can use simple ingredients to synthesize all the compounds necessary for growth and reproduction (grow in minimal medium)
lac+
wild-type that can use lactose as carbon source
gal+
wild-type that can utilize galactose
arg+
wild-type, can make amino acid called arginine
bio+
wild-type, can make vitamin called biotin
