quiz 1 Flashcards
at what levels is gene expression regulated
chromatin structure
transcription
mRNA processing
mRNA stability
translation
posttranslational modification
central dogma
dna rna protein
messenger RNA
carries genetic information from DNA to ribosome
coding RNA
transfer RNA
noncoding RNA
small RNA that contains a binding site for an amino acid
ribosomal RNA
noncoding RNA
part of ribosomal structure
transcription unit
stretch of DNA that encodes for an RNA molecule and sequences needed for transcription
template strand
nucleotide strand used for transcription
non template strand
strand which is not used for transcrition
template strand names
antisense strand
minus strand
non-coding strand
3’ to 5’
nontemplate strand names
sense strand
plus strand
coding strand
5’ to 3’
“same as RNA”
which strand is usually shown on databases
nontemplete strand
promotor
a dna sequence that the transcrition apparatus recognizes and binds
RNA coding region
sequence of DNA nucleotides that is copied to an RNA molecule
consensus sequence
sequences that show considerable similarity between genes
prokaryotic promotor elements
-35 consensus sequence
-10 consensus sequence
terminator
a DNA sequence that signals where transcription should end
upstream
towards promotor
downstram
towards terminator
what does prokaryotic RNA polymerase bind to
consensus sequences
what does prokaryotic transcription not require
a primer
kinds of promotors in eukaryotic transcritption
cis-acting
core promotor
regulatory promotor
promotor elements in eukaryotes
TATA box
GC box
CAAT box
transcription factors in eukaryotes
trans acting
are attracted to promotor elements
attracts RNA polymerase to transcription start site
TFIIA,B,D,E,F,H
enhancers and silencers
sequences that interact with transcription regulatory proteins and stimulate or repress transcription
RNA processing
5’ cap
poly A tail
splicing
5’ cap functions
ribosome binding
translation initiation
stability
splicing
poly a tail functions
stability
ribosomal attachment
passage into cytoplasm
sequences required to splice
5’ splice site
3’ splice site
branch point
two major phases of cell cycle
interphase
m phase
primary nucleotide structure
nucleotide sequence of single stranded
secondary nucleotide structure
base pairing between strands
tertiary nucleotide structure
three dimentional shape of paired strands
double helix
quaternary nucleotide structure
higher order folding facilitated via polynucleotide-polynucleotide and polynucleotide-protein interactions
nucleosome
DNA double helix bound to histone core
chromatosome
adding h1 histone to the nucleosome
beads on a string
10nm
30nm solenoid
coiled chromatosome
chromatin
solenoid is looped and attatched to non-histone scafold proteins
centromere
region of chromosome where spindle fibers attatch
telomeres
protect ends of linear chromosomes
g rich repeats
form a g loop
proteins bind to form
euchromatin
loose
dispered throughout nucleus
weak binding of h1 histones
non-uniformly compacted
may or may not be actively expressed
heterochromatin
tight
remains highly compacted
not usually expressed
telomers, centromere, barr body, y chromosome
cytogenetics
obtain non-dividing cells and induce them to divide in culture
adult white blood cells or skin bibroblasts
fetal cells
how are non dividing cells induced to divide
phytohemagglutinin
q banding
stained with quinacrine dye that binds to AT rich regions
g banding
partial digestion with trypsin
stained with Giemsa
binds heterochromatic AT rich regions
most commonly used method
r banding
heat and stain with Giemsa
staines GC rich regions
t banding
stains telomeres
c banding
stains centromeres
how is banding resolution increased
by elongating chromosomes
long arm
q for quite large
short arm
p for petite
proximal
towards centromere
distal
towards telomere
linkage mapping
crossing over events
recombination frequencies
map units or centimorgans
roughly additive
in situ hybridization
labeled probe with flourecent label
what is the probe in in situ hybridization
a single stranded DNA fragment complementary to a region of interest
synthesized or isolated from genomic DNA DNA copies of RNA
longer probes are more specific
metaphase FISH
hybridize labeled probe to metaphase spread
resolution of sevral megabases
Fiber FISH
hybridize labeled insert to stretched chromatin
kilobase resolution
interphase FISH
hybridize labeled insert to interphase cells
chromosome painting
label a series of different probes from the same chromosome
molecular karyotyping
chromosomes separated by flow cytometry
single nucleotide polymorphism (SNP)
1/300 nucleotides are polymorphic
frequency of rare allele is greater than 0.01
single nucleotide varient (SNV)
not polymorphic
restriction fragment length polymorphism (RFLP)
SNP within a palindromic sequence
results in the creation or destruction of a restriction endonuclease site
short interspersed nuclear elements (SINE)
mobile element
transposon derived
100-700 bp in length
13% of human genome
long intersperced nuclear elements (LINE)
mobile DNA element
transposon derived
7kb in length
21.1% of human genome
copy number variation (CNV)
number of copies of a genetic sequence varies from one individual to another
tandem repeats
minisatellites- 10-60 nucleotides
microsatellites - short tandem repeats (STR) 1-6 nucleotides
why is copy number variation more informative than SNPs
more alleles
increased variation in genotype in different individuals
origin of tandem repeat polymorphism
meiotic recombination within repeats
polymerase stuttering during replication
large copy number variants
tandem repeats with a large copy number
1447 regions with variable repeats > 1kb
12% of genome
average size is 250 kb
fragile sites
regions where chromatin is uncoiled
are there more SNPs or CNVs in genome
SNPs
what is responsible for the greatest number of nucleotides that vary between individual genomes
copy number varients
TGAC- database of genomic varients
varients observed in healthy individuals
decipher
pathogenic varients data base
complete linkage
markers are located so close to eachother that recombination is so so so so rare
0 cM
linkage disequilibrium
a chromosomal segment exists as a block that is rarely broken by recombination
haplotypes and haplotype blocks
haplotype
a set of alleles linked together on the same chromosome segment that are transmitted as a block
HapMap
first attempt to look at human variation
2 million SNP
269 healthy individuals
11 populations
SNPs grouped into haplotypes
1000 genomes project
more through look at variation
2504 individuals
26 populations
low coverage whole genome sequancing
targeted deep exome sequencing
dense SNP data
88.3 million variants
model free linkage analysis
usually affected sib pairs
low sample size and statistical power
limited to broad regions of the genome based on linkage analysis
candidate gene association
choose genomic regions based on previous research
usually limited to protein encoding genes
poor reproducability
quantitative trait loci (QTL)
broad regions of the genome associated with quantitative traits
usually use hundreds or thousands of markers
Genome-Wide Association Study (GWAS)
uses SNP analysis to find specific nucleotides and haplotypes associated with traits
most multifactorial traits are influenced by a large number of genomic regions
