genetics test 2

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236 Terms
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extranuclear inheritance / cytoplasmic inheritance
inheritance patterns involving genetic material outside the nucleus
where genetic material of mitochondria and chloroplasts are located, can contain several copies of the chromosome
oxidative phosphorylation
main function of the mitochondria, a process used to generate ATP
all the genetic material an organism possesses
variation in the number of complete sets of chromosomes
variation in the number of particular chromosomes, occurs through nondisjunction
textra copy of all the genes, can express too much of the genes on this chromosome
one less copy of all genes, can express too little of the genes on this choromosome
occurs when homologs are pulled to the same pole or the centromere does not split
familial down syndrome
trisomy 21, chromosome 21 and 14 are fused together
deletion / chromosomal deficiency
occurs when a chromosome breaks and a fragment is lost
results from a deletion of a small terminal portion of the short arm of chromosome 5
gene family
consists of two or more genes that are derived from the same ancestral gene
descent from a common ancestor
decent from a common ancestor by genome division
descent from a common acestor by duplication within a genome
globin gene
encode subunits of proteins that bind oxygen, 14 paralogs on three different chromosomes
total amount of genetic information stays the same, linear sequence is rearranged
balanced translocation
formed by breakage and reunion of chromosomes, recombination between repeate sequences
reciprocal translocations
DNA gets swapped between non-homologous chromosomes or broken DNA's reactive ends created by breaks are recognized by repair enzymes and joined together
nonreciprocal translations / unbalaned translocations
the transfer of genetic material occurs in only one directio
robertsoninan translocation
fusion of two telocentric chromosomes in the centromere region
psuedoautosomal regions, critical to segregation of x and y chromosomes during male gametogenesis
male-specific region Y
sex-determining region y
testis-determining factor, triggers testes formation, binds DNA and regulates gene expression
psuedoautosomal inheritance
the very few genes found on both X and Y chromosomes, has gotten shorter in evolutionary time
have multiple complete sets of chromosomes
monoploid set
basic chromosome set, from which all the other genomes are formed
have all chromosomes in the polyploid sepcies derive from a single diploid ancestral
comeplete sets of chromosomes from two or more different ancestral species, much more common
chemicals that kill or inhibit the growth of bacteria, used to treat bacterial infections. will target different cellular processes to restrict bacterial growth
carbon-source mutatns
cannot utilize a particular carbon source (sugar) for energy
a mutant that lost the ability to break down and use the sugar lactose as its only carbon source
unable to synthesize an essential nutrient
a bacterium that has lost the ability to synthesize the amino acid leucine
synthesizes all essential compounds
antibiotic resistance
bacterium can grow in the presence of antibiotic that it was formerly sensitive to
rich / complete media
all nutrients are supplied
minimal media
has very few nutrients
only the organism with the phenotype of interest grows -- live or die only
all phenotypes will grow, but they will be different (ie. colony shape, color, growth rate, enzyme production)
direct DNA transfer between a donor and recipient bacterium, requires interaction between bacterial cells
transfer of DNA from one bacterium to another via a bacteriophage
uptake of extracellular DNA released from dead bacterium, requires a receptor and competence factors
lederberg and tatum experiment
demonstrated genetic transfer by bacterial conjugation, bacteria were able to transfer DNA so all necessary nutrients are produced
how bacteria physically interact during conjugation
fertility factor / f factor
confers the ability to donate DNA (fertility) during conjugation
episome / plasmid
small, extrachromosomal circular piece of DNA that determines f factor, also contains genes for tranferring itself to cells that lack f factor
f+ cells
have the f factor, serve as donors (recipients become f+)
f- cells
lack f factor, act as recipients, can act as donors once converted to f+
small circular pieces of DNA, contain one or more genes, replicate independently of the bacterial chromosomr plasmidse
r plasmids
confer antibiotic resistance
col plasmids
encode colicins that can kill neighboring bacteria
virulence plasmids
carry genes that turn bacterium into pathogenic strains
conjugative plasmids
plasmids which are transmitted via conjugation, also carry the genes requires for conjugation
tra & trb
play a role in a the transfer of DNA
hfr cells
high frequency of recombination, derived from f+ strains. act as donor strains, created when an f factor integrates into the chromosome. recipients of hfr strains do not become f+ or hfr (stay f-)
interrupted mating experiments
demonstrated that specific genes in an hfr strain are transferred and recombined sooner than others, used a map gene order on the chromosome based on their time-of-entry from a donor hfr strain into a f- recipient strain
f' plasmids
f plasmids excised along with some chromosomal DNA, recipient cells become f'
merozygote / merodiploid
partially diploid, seen in f' plasmids
a virus that specifically attacks bacterial cells, composed of genetic material surrounded by a protein coat, can follow the lytic cycle, the lysogenic cycle, or both
virulent phages
only undergo a lytic cycle
temperate phages
can follow both lytic and lysogenic cycles
generalized transduction
any piece of bacterial DNA can be incorporated into the phage
transduction step 1
infection of the donor cell, gene can be inseted in phage particle (rare)
transduction step 2
infection of the recipient cell, gene combined with recipient genome
natural transformation
DNA uptake occurs without help
artificial transformation
DNA uptake occurs with the help of special techniques
competence factors
proteins that facilitate the binding, uptake, and incorporation of DNA into the bacterial chromosome
cells that can take up DNA
helicase (DnaB)
unwinds the DNA helix as replication proceeds, travels 5' to 3'
ssDNA binding protein (SSB)
binds and protects ssDNA
RNA polymerase which can synthesize a RNA primer for initiation, requires DNA template and ribonucleotide triphosphates
DNA polymerase 1,3
synthesize DNA, prooofread, involved in replication
reduce increased coiling generated during unwinding
DNA polymerase 1
remove RNA primers, active on the lagging end, proofreads, synthesizes DNA to fill in gaps from primer removal
join the gap-filling DNA to the adjacent strand, joins 3'-OH with 5'-phosphate
temperature sensitive mutants
can survive at a low/permissive temperature, and will fail to grow at the nonpermissive temperature (which is higher)
origin of replication, where replication starts
DnaA box
a DNA sequence that is bound by the protein DnaA
DnaA protein
binds DnaA boxes and to each other, causes DNA bending --> separation of strands in the AT-rich region
DNA adenine methyltransferase (Dam)
methylates the A on both strands of GATC immediately after replication -- the parental strands are methylated but it takes several minutes for the daughter strands
cut DNA from an end
cut DNA internally
DNA polymerase 2,4,5
involved in the repair of damaged DNA
DNA polymerase 3 holoenzyme
has all of it's protein subunits, processive (stays on the DNA template for a long time)
core enzyme
has just the bare essentals to do the job
the measure of the number of nucleotides added by a DNA polymerase enzyme before it falls off/disassociates from the template
B-subunit clamp
prevents the core enzyme from falling off the template during DNA synthesis
leading strand
3' end points into the replication fork
lagging strand
5' end points into the replication fork
replication bubble
bidirectional synthesis of leading and lagging strands from one origin of replication
termination sequence, on opposite side to oriC
protein tus
termination utilization substance, binds to the ter sequences, stops the movement of replication forks
intertwined circular molecules as a result of DNA replication
origin recognition complex, multi-subunit protein binds to origins
mini-chromosome maintenance, includes helicase and ATPase
load MCM tonto DNA, considered RLF
replication licensing factors, their removal allows replication to proceed, which limits replication to once per cell cycle
inhibits CDT1
pol a
associates with the primase, adds DNA to RNA primers
proliferating cell nuclear antigen, eukaryotic counterpart of the B sliding clamp in bacteria
ends of linear chromosomes, long stretches of short repeating sequences, preseve the integrity and stability of chromosomes
ribonucleoprotein (RNA and protein), inclides a reverse transcriptase domain
RNA mulecules are synthesized by an enzyme, RNA polymerase from DNA
in the nucleus of eukaryotic cells, the RNA usually undergoes chemical modification-- adds 5' cap, introns are removed by splicing, adds poly-a tail. the cleavage of a large RNA transcript into smaller pieces, 1+ becomes a functional RNA molecule
the processed RNA molecules is used to specify the order which amino acids are joined together to form a polypeptide chain
gene product
end protein made
RNA polymerase
a multi subunit enzyme that synthesizes RNA from a DNA template, consists of a RNA synthesizing core plus specifity factors, uses a DNA template to direct synthesis
specificity factors
needed to recognize and bind promoter DNA
DNA sequences that promote gene expression, direct the exact location where RNA polymerase binds to DNA to initiate transcription
coding strand
has the same sequence as the RNA
template strand
has the complement sequence as the RNA
consensus sequence
most commonly occuring bases for transcription initiation
LOGO alignment
graphical comparison of nucleotide or amino acid sequences
closed complex
promote DNA base-paired, DNA is not unwound
open complex
promoter DNA is unwound, hydrogen bonds are broken between the template and coding DNA strands, incoming NTPs can pair with the template strand
end of RNA syntesis, occurs when the short RNA-DNA hybrid f the open complex is forced to separate
rho-dependent termination
requires a protein known as rho
stop signal
transcription terminantion sites are inverted repeat sequences which can form loops in RNA
TATA box
core promoter element in eukaryottes
intervening sequences, regions of the initial RNA transcript that are not expressed in the amino acid dequence of the protein
RNA splicing
introns are removed and the exons are joined or spliced together in the mature mRNA
regions that are retained in the mRNA
RNA enzyme / catalytic RNA
small nuclear ribonucleo-protein particles, composed of RNA and protein
alternative splicing
refers to the phenomenon that pre-mRNA can be spliced in more than one way, produced two or more polypeptides
the number of proteins that a cell can make
multiprotein RNase, main activity is 3'--5' exonuclease, degrades mRNA without a polyA tail
splicing repressor
repressor prevents recognition of a splice site, spliceosome cannot use that splice site, and skips it
allows each strand to serve as a template for synthesis of the other
meselson and stahl
determined the mechanism of DNA replication using heavy 14-N
structures that contain the genetic material, complexes of DNA and proteins
comprises all genetic material that an organism possesses
bacterial chromosomes
single circular chromosomes, looped with DNA-binding proteins and then supercoiled
requires for proper segregation during mitosis and meiosis
kinetochore protein
link the centromere to the spindle apparatus
prevent chromosome shortening
repeating structural unit within eukaryotic chromatin, composed of a double stranded segment of DNA wrapped around an octamer of histone proteins
histone octamer
composed of two copies each of four different histone proteins
histone h1
attaches to the DNA at its juncture with the nucleosome
solenoid model
regular, spiral configuration containing six nucleosomes per turn
zig-zag model
less regular nucleosomes do not contact each other
nuclear matrix
composed of two parts, nuclear lamina and internal matrix proteins
nuclear lamina
fibers that line the inner nuclear membrane
internal matrix proteins
connected to the nuclear lamina and fills interior of nucleus, structural and functional role remains controversial
matrix-attachment regions (MARs)
anchored to teh nuclear matrix, creating radial loops
radial loops
play a role in compaction, organizes chromosomes within the nucleus
chromosome territory
where each chromosome in the nucleus is located, discrete and nonoverlapping
chromosome territories, where chromosomes occupy specific regions
tightly compacted regions of chromosomes, transcriptionally inactive
less condensed regions of chromosomes, transcriptionally active
constitutive heterochromatin
regions that are always heterochromatic, permanently inactive with regard to transcription, usually contain highly repetitive sequences
facultative heterochromatin
regions that can interconvert between euchromatin and heterochromain, ie. barr body formation during development in females
prokaryotic alpha subunit
5'-3' polymerization, core enzyme: elongates
prokaryotic e subunit
3'-5' exonuclease, polynucleotide chain
repetitive sequences
can cause misalignment between homologous chromosomes
deletions and duplications
can be caused by abnormal crossing over/recombination between homologous chromosomes
break point effect
inversion break point occurs in a vital gene
position effect
a gene is repositioned in a way that alters its gene expression
pericentric inversion
centromere lies within inverted region
paracentric inversion
centromere lies outside inverted region
inversion loop
must form in order for the normal and inversion chromosome to synapse properly
occurs when there is no centrosome, if centrosomes move to opposite poles, and sometimes caused by deletion and duplication
y-linked genes
non-essential or male-specific functions
causes of antibiotic resistance
prescribed when not relevant, treatment not followed to completion, overuse (especially in agriculture)
p1 phage
infects E. coli
p22 phage
infects salmonella typhimurium
conditional mutant
can survive at a permissive condition, but will fail to grow at a nonpermissive condition
ts mutants
less stable at higher temperatures and therefore lose their function
rapid stop
subset of ts mutants, encoded enzymes needed for replication of DNA after it already started
slow stop
subset of ts mutants, completed their current round of replication but could not start another, encoded genes needed for initiation of replication
rapid stop mutants
dnaE, dnaX, dnaN, dnaZ, dnaZ, dnaG, dnaB
slow stop mutants
dnaA, dnaC
alpha subunit of DNA polymerase 3, synthesizes DNA
T subunit of DNA polymerase 3, part of the clamp loader complex, promotes the dimerization of two DNA polymerase 3 proteins together at the replication fork
Y subunit of DNA polymerase 3, helps the B subunit bind to the DNA
primase, needed to make RNA primers
helicase, needed to unwind the DNA strands during replication
DnaA protein that recognizes the DnaA boxes at the origin
DnaC protein that recruits DNA helicase to the origin
methylation before replication
full methylated parental strands, replication initiated well
methylation immediately after replication
hemi-methylated, replication poorly initiated
trombone model
lagging strand must loop to invert the physical, but not biological direction of synthesis
separates catenanes (decatenation)
eukaryotic alpha polymerase
initiates DNA replication in conjunction with primase
eukaryotic epsilon polymerase
replication of the leading strand
eukaryotic delta polymerase
replication of the lagging strand
eukaryotic gamma polymerase
replication of mitochondrial DNA
eukaryotic beta polymerase
DNA repair and other functions
polymerase switching
pol a is replaced by polymerase delta and polymerase epsilon for elongation
bacterial RNA polymerase holoenzyme
recognizes promoter DNA
bacterial RNA polymerase B, B'
bacterial RNA polymerase w
bacterial RNA polymerase a
2x, DNA and transcription factor binding, CTD recognizes UP-elements
bacterial RNA polymerase sigma factor
promoter recognition, initiation only (not elongation or replication), can recognize promoter elements
core RNAP
synthesizes RNA with B, B', w, a (x2)
intrinsic termination
no protein is required to physically remove the RNA from the DNA
stabilizes the RNA pol pausing
RNA polymerase 1
transcribes most rRNA (ribosomal) genes
RNA polymerase 2
all protein-coding genes, miRNA genes, genes for non-coding RNA
RNA polymerase 3
tRNA (transfer RNA), 5S rRNA (ribosomal), small RNAs
transcription factor for RNA polymerase 2, binds to the TATA box, a complex of proteins that includes TATA-binding protein (TBP) and several TBP-associated factors
binds to TFIID, promotes the binding of RNA polymerase 2 to the core promoter
bound to RNA polymerase 2
bind to RNA polymerase 2 to form a preinitiation or closed complex
acts as a helicase to form an open complex, phosphorylates the CTD of RNA polymerase 2, which breaks the contact between RNA polymerase 2 and TFIIB
released after the open complex is formed
c-terminal domain
n-terminal domain