Term
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Definition
| Molecule or region of DNA that replicates as a single unit |
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Term
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Definition
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Term
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Definition
dNTP monomers added to 3'end of an RNA primer
Goes in 5' > 3' direction |
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Term
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Definition
Messelson Stahl
Each parental strand remains intact and serves as a template for a daughter strand |
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Term
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Definition
marks human chromosomes
takes the place of Thymidine
After 2 rounds of replication, one chrom is fully labled while the other is half labled |
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Term
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Definition
In circular DNA
Bi-directional
2 forks that move outward from origin of replication |
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Term
Bi directional
(eukaryotes) |
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Definition
linear-replication bubble moves out from origin in both directions
fuses with incoming bubbles |
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Term
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Definition
topoisomerase
breaks the DNA
swivels the end in opposite directions to relieve tension |
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Term
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Definition
| Unwinds DNA at replication fork |
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Term
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Definition
| Initiates new strand synthesis |
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Term
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Definition
| bind and stabilizes single stranded DNA at fork |
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Term
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Definition
| joins fragments on lagging strang |
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Term
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Definition
free 3'-oh group
-12 RNA nucleotides and 20 DNA nucleotides
Made via DNA polymerase delta |
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Term
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Definition
-E.Coli
-elongates 5' > 3'
-creates phosphodiester bonds between nucleus and new strand
-creates -OH bonds between new strand and template |
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Term
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Definition
-Eukaryotes
-elongates 5' > 3'
-creates phosphodiester bonds between nucleus and new strand
-creates -OH bonds between new strand and template |
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Term
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Definition
-Done via DNA polymerase
-exonuclease activity breaks phosphodiester bonds when a new base is unable to pair with parent strand
-able to look back one strand
-errors occur 1/10,000-improved x1000 |
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Term
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Definition
-primer has a triphosphate but ligase can only join a monophosphate
-pol 1 removes ribonucleic acids from 5' end and replaces with deoxynucleic
-ligases joins the 3'-oh with 5'-P |
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Term
| Eukaryotic Lagging strand |
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Definition
-Protein RPA joins and unwinds RNA and DNA and stabilizes by binding to it
-recruits endonucleases that cleave the unwound RNA/DNA via phosphodiesterbond
-Pol delta adds correct bases to single strand
-DNA ligase forms final bond to fragment
-exonucleases break down the released primer |
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Term
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Definition
A way to sequence DNA
DNA is sequenced with nucleotides with no 3'-OH (which halts elongation)
As replication continues, small fragments of varying sizes are produced
Seperate by size and read the final base
smallest > largest = 5' > 3' |
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Term
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Definition
Happen in cell lineage-meiosis
evolution |
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Term
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Definition
Happen in body cells
mitosis
cancer |
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Term
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Definition
Base is replaced by something else
The next round of replication its pair is "fixed"
A-T>G-T>G-C |
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Term
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Definition
Pyrimidine>pyrimidine
Purine>Purine |
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Term
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Definition
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Term
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Definition
| If a nuc in the 3rd position of a codon undergoes a transition mutation, the same amino acid is still coded for |
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Term
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Definition
| Changes the codon to a stop codon |
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Term
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Definition
| Changes the Amino acid it encodes for |
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Term
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Definition
A-T>T-A in 2nd codon for 6th amino acid in the Bchain of hemoglobin
Glu>Val
Crescent shaped blood cells which are hard to carry O2
*nonsynonymous |
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Term
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Definition
Insertion/deletion = frame shift
-if a multiple of 3, it will eliminate amino acids
If it is not a multiple of 3, it will push the reading frame down/up |
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Term
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Definition
strands of trinucleotide repeats
the growing strand briefly dissociates and reanneals upstream
Replication continues and the loose piece stretches out, breaking parent strand
-requires mismatch repair on parent |
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Term
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Definition
mu=# mutations per bp per generation
U=# mutations per genome per generation |
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Term
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Definition
| replication errors, indel/base substitutions |
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Term
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Definition
structures can exist in different forms
Keto Thymine pairs with A
Enol Thymine pairs with G |
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Term
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Definition
damaging to DNA
Guanine which normally pairs with C can pair with H2O2 (ROS)=8-oxoguanine which pairs with A |
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Term
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Definition
ds elements transpose from place to place
Ac allows them to function
human genome: 44.7% |
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Term
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Definition
Double strand is cut leaving an overhang
Over hang of the 3' end binds with the 5' end of the ds element leaving a gap where the overhang is on the other strand
Gap is repaired= duplication of target sequence |
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Term
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Definition
| determines the distance between cuts that were made on DNA strand |
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Term
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Definition
transcribed into RNA
reverse transcriptase uses RNa as a template to make a complimentary DNA daughter strand using tRNA as a primer
Endonucleases cleave the RNA which is the primer for the 2nd DNA strand
This DNA is inserted similar to cut and paste |
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Term
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Definition
no terminal repeats
transcribed as RNA using normal polymerase
RNA inserts into nicks in host molecule
Reverse transcription occurs at the site of insertion
*LINES encode their own reverse transciptase, SINES relies on other elements |
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Term
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Definition
| extrinsic source of mutation |
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Term
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Definition
base looks similar to Thymine and can be incorperated into a DNA strand pairing with A
(rare) |
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Term
Mismatch repair
(effectiveness) |
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Definition
happens 10^-5 per replication
most are corrected via proofreading=10^-7
99.9 corrected via mismatch repair=10^-10 |
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Term
Mismatch Repair
(Process) |
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Definition
A wrong base is detected
one of the strands is cut and the region around the base is removed
exonucleases break down to just beyond the mismatch
The leftover single stranded gap is filled by DNA polymerase and sealed via ligase |
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Term
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Definition
Sequence of bp in a DNA strand determines the sequence of amino acids in a protein in a colinear manner
Mutants in the DNA will cause mutants in the same place on a dNA chain |
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Term
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Definition
RNA polymerase recognizes a promoter on the DNA
Single stranded RNA is produced by adding NTPs on the 3' end
Doesn't require a primer |
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Term
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Definition
DNa template for RNA
One piece of DNA is used, doesn't matter which one
Termination sites are located so that they don't overlap with transcribed regions |
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Term
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Definition
1 RNA polymerase with 6 polypeptide units
promoters are recognized by upstream sequences at -35 and -10 called a TATA box |
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Term
RNA synthesis (Eukaryotes)
RNA polymerase 1 |
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Definition
| only synthesizes 2 large rRNA molecules: 18S and 28S |
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Term
RNA synthesis (eukaryotes)
RNA pol 2 |
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Definition
| Synthesizes all mRNAs and other small RNAs |
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Term
RNA synthesis (eukaryotes)
RNA pol 3 |
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Definition
| synthesizes tRNA and 5SrRNA |
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Term
RNA synthesis (eukaryotes)
RNA pol 3 |
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Definition
| synthesizes tRNA and 5SrRNA |
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Term
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Definition
only in eukaryotes
converts primary transcript into mRNA |
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Term
| Initiation (RNA processing) |
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Definition
| modified Guanine is added to 5' end (capping) |
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Term
| Elongation (RNA processing) |
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Definition
| 3' ends are trimmed and a poly-A tail is added for stability (longer tail = more stable) |
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Term
| Termination (RNA processing) |
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Definition
RNA splicing
excision of introns and joining of exons
mRNA is released and the introns are removed
exon junctions are marked with EJCs |
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Term
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Definition
nucleotide at branch attacks the end of the 5' exon breaking up the exon/intron
this creates a loop connecting to branch site
*unusual 2'>5'
Donor exon (the one that was just cut) attacks the acceptor exon, cutting the intron and joining the two exons
The loop with a tail is degrades
EJCs are left behind at junctions
mRNa can be spliced at different points=different protein |
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Term
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Definition
where intron splicing takes place
has proteins and SnRNPS which contain sequences complimentary to the RNA |
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Term
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Definition
mutations that occur near the ends can fuck up the mRNA
a) mutated splice is not removed=in mRNA=mutant protein
b) splices at the wrong point (cryptic site which is only used when the preferred site is unavailable) = mutant protein |
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Term
| Trancriptional regulation in Galactose metabolism when Galactose is present |
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Definition
requires 3 enzymes (GAL1,7,10)
GAL3p binds with galactose and ATP which holds GAL 80p in the cytoplasm
In the nucleus GAL4p attatches with an upstream activator sequence (UAS) near each of the GAL genes
it also recruits transcription machinery
necessary genes are transcribed |
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Term
| Trancriptional regulation in Galactose metabolism when Galactose is absent |
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Definition
GAL3p cannot bind GAL 80p and it can enter the nucleus
GAL80p binds the transcriptional activator site in GAL4p and prevents recruitment of transcriptional machinery
*cis transcriptional regulation |
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Term
Premature Termination codon
(PTC) |
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Definition
in mRNA
=shorter peptide=very bad loss/gain of function |
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Term
| Nonsence mediated mRNA decay |
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Definition
degredation of mRNAs that have PTCs
NMD machinery scans transcripts 3'>5' beginning at EJCs looking for PTCs and recruit endonucleases to degrade bad mRNA |
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Term
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Definition
RNA helicase
triggered by protein phosphorylation |
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Term
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Definition
contains M1F4G which is involved in mRNA processing/splicing
brings together hUPF1 and hUPF3 |
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Term
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Definition
| has RNA recognition abilities but does not bind to it |
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Term
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Definition
| segments of DNA are twisted around each other to be more compact |
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Term
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Definition
opposite twists
also can compact
common in bacteria |
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Term
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Definition
wraps around a DNA duplex
nicks one strand and the ends are swiveled around the intact strand and the ends are put back together |
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Term
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Definition
grabs 2 duplexes
breaks one
passes the other through it then repairs the break |
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Term
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Definition
| total genomic structure of bacterial cells |
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Term
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Definition
| DNA of all chromosomes and proteins in eukaryotes |
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Term
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Definition
beads on a thread
the whole structure is a chromatin
beads are nucleosomes |
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Term
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Definition
H1,H2A,H2B,H3,H4
make up core particles with 2 of each (except H1)
DNA strand is wound around the particle (bead)
H1 binds the particle and linker DNA (DNA extending from the strand wrapped around) |
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Term
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Definition
coiled strings of nucleosomes
loops>domains>territory>an entire arm of chromosome |
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Term
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Definition
region of chromosome that is narrow at the joining of arms
central component of kinetochore
where spindle fibers attach for movement during the cell cycle |
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Term
| Different attachment to centromere |
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Definition
localized: microtubules attach at a single region
halocentric: centromeres throughout the length of chromosome |
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Term
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Definition
End of a linear chromosome
repeated sequence
Telomerase adds telomeres to the 3' ends so they are not degraded |
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Term
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Definition
has sequences similar to telomere
it is a template for synthesis/elongation
base pairs with the telomere and more bases are added
*repeats often include Guanine because it can hydrogen bond with itself |
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Term
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Definition
genomic sizes differ between species but no correlation
can have same number of genes but different sized genomes
*repetitive sequences account for a lot of larger genomes, high concentration near centromere |
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Term
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Definition
colors are added to chromosomes by mixing with a set of flourescently labeled DNA strands
Each one is specific to a different Chromosome |
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Term
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Definition
| autosomes arranged in pairs and arranged from longest to shortest (sex is last) |
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Term
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Definition
old way of organizing chromosomes
stained them and each one had a unique stain pattern and organized the same way |
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Term
| organization of an individual chromosome |
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Definition
short arm: p
long arm: q
the arm regions are numbered from centromere to telomere, (these regions are also additionally numbered
1p34.2=chromosome 1, short arm, band 36, second bank |
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Term
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Definition
have no centromere
unstable because they get lost during cell division |
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Term
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Definition
have two centromeres
unstable because of unpredictability |
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Term
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Definition
chimps have 2 acrocentric chromosomes instead of our chromosome 2
telomeres of the short arms used to be a dicentric chromosome with 2 very close centromeres, one of which eventually became inactive
Chimps have 48 chromosomes
humans have 46 |
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Term
| x chromosome dosage compensation |
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Definition
| increased activity of genes on x chromosome in males who only have one or decreased activity in females |
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Term
x chromosome dosage compensation
(fruit flies) |
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Definition
| a protein is put on the X chromosome in males which opens up the chromatin so that all the genes are hyperregulated |
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Term
x chromosome dosage compensation
(worms) |
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Definition
| A protein is put on the X chromosome in females that decreases transcription to the level of males |
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Term
x chromosome dosage compensation
(mammals) |
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Definition
one chromosome at random in females is inactive
The inactive chromosome is preserved in subsequent generations |
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Term
x chromosome dosage compensation
(calico cats) |
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Definition
orange fur and black fur is on different x chromosomes
Some fur somatic cells, the black xchrom will be inactive and others the orange= pathces of fur
*males cannot have this because they only have one X chrom |
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Term
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Definition
about the same time mammals seperated from birds, SRY (testicles) evolved
once this happened, recombination became less frequent = divergent of X and Y |
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Term
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Definition
| diploid with an extra copy of individual chromosomes |
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Term
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Definition
| unbalance of chromosomes (polysomy) |
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Term
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Definition
multiple of chromosome pairs (polyploidy)
*better tolerated because there is a better chance of survival of the chromosomes |
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Term
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Definition
during meiosis parts of chroms are paired with eachother = 2 centromeres at one pole and 1 at the other
This creates 2 pairs of gametes, one pair having 2 copies of the trisomic chrom and the other 1 |
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Term
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Definition
one unpaired chrom and two paired
same final result |
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Term
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Definition
chromosome with a segment mission
larger the deletion= larger damage |
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Term
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Definition
linear order of a group of genes is reverse the normal order
ectopic exchange btw inverse repeats=linear order reverse of the normal order
paracentric: occur outside of centromere (all on one arm)
pedicentric: span the centromere |
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Term
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Definition
| the region is present twice |
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Term
| Copy number polymorphism (CNP) |
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Definition
variation in the presence/absence of certain genes
happen from large deletions |
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Term
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Definition
recombination between repeated DNA at different sites along the SAME chromosome
*males Y chromosome can delete a section of its gene out = infertility |
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Term
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Definition
tandem (duplication is adjacent to its copy)
unequal crossing over = a single copy of the region, a triplicon and 2 strands with the duplication
*better then deletion |
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Term
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Definition
x-linked
unequal crossing over in the section of the gene containing red/green pigment
red and green get combined and you lose the ability to distinguish |
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Term
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Definition
a genome with multiple complete sets of chromosomes
plants, fungi, amphibians
change in ploidy = immediate speciation
higher ploidy = higher probability of error |
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Term
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Definition
18 chroms in one species, 36 in another (2 complete sets of 18)
monoploid is the single set of chroms (9)
during meiosis, chroms synaps to form bivalents (9 for 18 species)
gamete receives 1 chrom from each bivalent |
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Term
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Definition
| set of chromosomes that are the basic that is multiplied in a polyploid |
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Term
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Definition
| set of chromosomes that is present in the gamete (half the total... 9 in an 18 species, 18 in a 36 species) |
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Term
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Definition
increase happens at meiosis
formation of unreduced gametes with double normal compliment of chromosomes
these fuse= polyploid zygote |
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Term
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Definition
mitosis
doubling of compliment chromosomes = polyploidy |
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Term
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Definition
| all chromosomes derive from a single diploid ancestor |
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Term
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Definition
| chromosomes comes from 2 different diploid species (diploid from each parent) |
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Term
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Definition
autonomously replicate
nonessential
prokaryotic |
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Term
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Definition
| encodes the gene that allows plasmids to transfer via a pilus that extends from a F+ to an F- cell |
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Term
| rolling circle replication |
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Definition
how plasmids transfer DNA
initiated at 3' end of nicked strand
nucleotides added to 3' end forcing the 5' end away and into the F- cell
Lagging strand replication completes new strand
When a circle is complete the pilus breaks and the cells seperate |
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Term
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Definition
can move from bacterial genome to/from plasmids
allows for antibacterial resistance |
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Term
High Frequency of Recombination
(HFR) |
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Definition
Happens when F plasmid integrates into host cell chromosome through recombination
there is a matching insertion sequence on the chromosome and plasmid which attacks and is where the gene is inserted |
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Term
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Definition
A way of mapping the genome
HfrxF- matings
number of recombinants of an allele increase with time while the cells are in contact
E.Coli requires 100 minutes |
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Term
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Definition
created by breakage/reunion between homologous sections of and F donor chromosome
=Fragment of chromosome DNA = recipient cells are diploid |
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Term
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Definition
| bacterial DNA fragment transferred from one cell to another via a phage particle containing bacterial DNA |
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Term
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Definition
phage attached to a host and injects nucleic acid which is transcribed/translated into many phage proteins
new nucleic acid molecules are fragmented then packaged into protein shells which are released from cell
some phages carry fragmented DNA some carry their own which is inserted into a new bacteria
Recombination incorporates the new DNA
*phage kills a cell with its own DNA but bacterial DNA does not kill it |
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Term
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Definition
recipient cells acquire genes from free DNA
Cell uptakes DNA fragment and recombines with a strand of donor DNA replacing the homologous segment in recipient
*allows for genetic mapping, cells that are near each other are commonly co-transformed |
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Term
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Definition
| G1(pre DNA synthesis)>S(DNA synthesis)>G2(post DNA synthesis)>G2(post DNA synthesis)>Mitosis |
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Term
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Definition
| where spindle pole is organized |
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Term
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Definition
| microtubule rind structures in the centrosome that organizes microtubules |
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Term
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Definition
budding yeast DNA that can reproduce at 23 deg but not 36deg
at 36 deg the cell stopped at their place in the cell cycle continuing on with that stage |
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Term
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Definition
helps with eukaryotic regulation of cell cycle
budding yeast: once cdk interacts with
other cyclins and plays multiple roles
mammals: different cdks at different stages
*function has been preserved because human cdks can be interchanged with yeast |
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Term
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Definition
add a phosphate to -OH on Ser, Thr, Tyr
cyclin binds the target and the cdk phosphorylates=structure/function change
*appear in cycles in a cell depending on when it is needed |
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Term
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Definition
cells accumulate at the G1 restriction point
RB protein holds transcription factor E2F in an inactive form
growth factor combines with receptor making cyclin D
RB phosphorylates cyclin D
RB is phosphorylated, inactivating it which frees E2F which stimulates transcription |
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Term
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Definition
cyclinB-cdc2 remains inactive in cytoplasm after DNA synthesis
Cyclin B is phosphorylated which hides the nuclear export signal = accumulation of cyclin B-cdc2 in nucleus
This is dephosphorylated which in turn phosphorylates |
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Term
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Definition
| looks at how large groups of genes are effected as a group by external change |
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Term
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Definition
transcriptional profiling
extract RNA, run on a gel
transfer RNa to membrane
hybridize membranes with labeled gene specific probe and expose |
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Term
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Definition
trancriptional profiling
flat surface with 10,000 spots with immobilized DNA that is hybridized fluorescent labeled DNA
The amount of color is how much a gene is expressed |
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Term
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Definition
| p53 is elevated which elevates p21 which blocks cyclin cdk |
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Term
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Definition
| elevated p53 results in p21 and GAADD45 which inhibits DNA polymerase |
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Term
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Definition
| elevated p53 elevates 12-3-3sigma which stops activation of cyclinB-cdc2 |
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Term
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Definition
alleles of genes that contain gain of function mutations derived from proto-oncogenes
ex: RAS stimulates cell growth, mutant RAS cannot return to inactive state so it remains active |
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Term
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Definition
normally activate cell death, mutation results in loss of function
ex: p53 monitors damage in checkpoints, without it the cell will continue to go through cycle despite damage |
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