Exam 1 Flashcards
____________ are the natural determinant of inheritance
chromosomes
Define pro-nuclear fusion
sperm and egg fuse
define exons
retained in mRNA
define introns
spliced out of mRNA
define CDS
coding sequences
what does UTR do?
regulate transcription
___________________ are proteins that bind to regulatory DNA
transcription factors
what are the 5 conclusions of Mendelian genetics?
- offspring resemble their parents
- genes come in pairs
- genes don’t blend
- some genes are dominant
- genetic inheritance follows rules
transcribed regions serve as ______________ for RNA
template
What are the differences between mRNA, tRNA, and rRNA?
mRNA: template
tRNA: recognize codons
rRNA: build proteins
What is the purpose of non-transcribed regions?
regulatory DNA
what are 4 examples of non-transcribed DNA?
- transcription factors
- promoter
- enhancer/activator
- silencer/repressor
What are the goals of the human genome project?
sequence the entire human genome
provide the data free to the world
____________ sequencing is chain termination using dideoxynucleotides
Sanger Sequencing
_________ sequencing requires higher sequencing coverage
shotgun
Define mosaic in genome terms
first genome sequences were stitched together
Define sequencing
determine the order of nucleotides
Define capillary electrophoresis
uses fluorescent dyes
DNA separated by color
define sequence coverage
number of times each nucleotide is read
why is sequence coverage important?
assembly and minimize errors
define BACs
bacterial artificial chromsomes
draft genome, telomere to telomeree, dideoxynucleotides; what are these 3 things from?
human genome project
Sanger is an example of 1st or 2nd generation sequencing?
1st
In Sanger sequencing, addition of ddNTP causes what?
chain termination at site of insertion
what were the first nucleotides labels?
radioactive P32
How was fluorescent dye an advantgae to use?
increased ability to obtain large amounts of sequencing data
In primer walking; what do you start with?
known sequence
designed primer
how does shotgun sequencing work?
fragment DNA into smaller pieces
clone into vectors
what is the down side to shotgun sequencing?
overlaps
Why kind of labels does NGS use?
fluorescent dyes
_______________ is the output of capillary electrophoresis
chromattogram
in a chromatogram, what is on the x and y axis?
x: time
y: fluorescence
define adaptor sequence
short piece of DNA we know the sequence of that will be used on flow cell and hybridized
define hybridized
binding between two fragments of DNA
define overlap
regions of similarity between regions
define overhang
unaligned ends of the sequence
define contigs
set of DNA segments that overlap and provide a better representation of genome region
define scaffolds
combined contigs
define sequence coverage
how many times a strand has been sequenced
what is an example of 2nd generation sequencing
illumina
NGS is sequencing by __________
synthesis
define bridge amplification
generates copies of identical DNA sequences in clusters on flow cell
does Sanger sequencing or NGS add adaptors
NGS
does Sanger sequencing or NGS generate polony arrays
NGS
does Sanger sequencing or NGS generate electrophoreisis
Sanger
if the assemble is made of more long connected is it more or less contiguous?
more
what does SMRT mean
single molecule real time sequencing
why is SMRT useful?
very long reads
how are errors corrected in SMRT
circular DNA
define gene predication
identifying the locations of genes
define functional annotation
adding biological context
define empirical stratagies
use transcriptomic data to define genes
define Ab inito stratagies
predict the genes computationally
what is the first strategy of empirical?
expressed sequence tag (ETS) analysis
what is an example of 3rd generation sequencing?
PacBio
SMRTbell template, ZMW wells, and labeled nucleotides; which 3rd gen is this?
PacBio
what is the second strategy of empirical?
high-throughput transcriptomics
what does high-throughput transcriptomics start with as a template?
RNA
what is the 1st prediction of Ab inito?
pattern matching
what are signal sensors
short motif such as poly-A or start/stop
what are content sensors?
pattern of codon usage
what is the 2nd prediction of Ab inito?
sequence similarity
how does sequence similarity work?
a known set of genes form species A is used to identify the genes from a freshly assembled sequence B genome
what does BUSCO hypothesize
some genes evolve under single copy control
define reverse transcription
RNA to DNA
what is mRNA enrichment
adding a bunch of Ts to mRNA and using a magnent to attract them
what are HMMs used for
create protein domain images
_________ is a website for protein domains
SMART
what do transcription factors do?
regulate transcription
longer transcripts produce more reads which means read count are normalized to the __________ length
transcript length
what is gene ontology?
set of classes with relations that operate between them
what are the 3 classes of gene function
- molecular function
- cellular function
- biological process
what is molecular function
activities that occur at the molecular level
what is cellular function
location in which gene preforms its function
what is biological process
larger programs accomplished by multiple activities
GO terms are _______ in a chart
nodes
what is differential expression
why do some people die from the flu then some dont
what are the 2 domains of transcription factors
DNA binding domain
regulatory domain
see graphs
a
