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