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Genomic Biology > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

____________ are the natural determinant of inheritance

A

chromosomes

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2
Q

Define pro-nuclear fusion

A

sperm and egg fuse

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3
Q

define exons

A

retained in mRNA

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4
Q

define introns

A

spliced out of mRNA

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5
Q

define CDS

A

coding sequences

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6
Q

what does UTR do?

A

regulate transcription

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7
Q

___________________ are proteins that bind to regulatory DNA

A

transcription factors

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8
Q

what are the 5 conclusions of Mendelian genetics?

A
  1. offspring resemble their parents
  2. genes come in pairs
  3. genes don’t blend
  4. some genes are dominant
  5. genetic inheritance follows rules
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9
Q

transcribed regions serve as ______________ for RNA

A

template

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10
Q

What are the differences between mRNA, tRNA, and rRNA?

A

mRNA: template
tRNA: recognize codons
rRNA: build proteins

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11
Q

What is the purpose of non-transcribed regions?

A

regulatory DNA

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12
Q

what are 4 examples of non-transcribed DNA?

A
  1. transcription factors
  2. promoter
  3. enhancer/activator
  4. silencer/repressor
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13
Q

What are the goals of the human genome project?

A

sequence the entire human genome
provide the data free to the world

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14
Q

____________ sequencing is chain termination using dideoxynucleotides

A

Sanger Sequencing

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15
Q

_________ sequencing requires higher sequencing coverage

A

shotgun

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16
Q

Define mosaic in genome terms

A

first genome sequences were stitched together

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17
Q

Define sequencing

A

determine the order of nucleotides

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18
Q

Define capillary electrophoresis

A

uses fluorescent dyes
DNA separated by color

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19
Q

define sequence coverage

A

number of times each nucleotide is read

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20
Q

why is sequence coverage important?

A

assembly and minimize errors

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21
Q

define BACs

A

bacterial artificial chromsomes

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22
Q

draft genome, telomere to telomeree, dideoxynucleotides; what are these 3 things from?

A

human genome project

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23
Q

Sanger is an example of 1st or 2nd generation sequencing?

A

1st

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24
Q

In Sanger sequencing, addition of ddNTP causes what?

A

chain termination at site of insertion

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25
what were the first nucleotides labels?
radioactive P32
26
How was fluorescent dye an advantgae to use?
increased ability to obtain large amounts of sequencing data
27
In primer walking; what do you start with?
known sequence designed primer
28
how does shotgun sequencing work?
fragment DNA into smaller pieces clone into vectors
29
what is the down side to shotgun sequencing?
overlaps
30
Why kind of labels does NGS use?
fluorescent dyes
31
_______________ is the output of capillary electrophoresis
chromattogram
32
in a chromatogram, what is on the x and y axis?
x: time y: fluorescence
33
define adaptor sequence
short piece of DNA we know the sequence of that will be used on flow cell and hybridized
34
define hybridized
binding between two fragments of DNA
35
define overlap
regions of similarity between regions
36
define overhang
unaligned ends of the sequence
37
define contigs
set of DNA segments that overlap and provide a better representation of genome region
38
define scaffolds
combined contigs
39
define sequence coverage
how many times a strand has been sequenced
40
what is an example of 2nd generation sequencing
illumina
41
NGS is sequencing by __________
synthesis
42
define bridge amplification
generates copies of identical DNA sequences in clusters on flow cell
43
does Sanger sequencing or NGS add adaptors
NGS
44
does Sanger sequencing or NGS generate polony arrays
NGS
45
does Sanger sequencing or NGS generate electrophoreisis
Sanger
46
if the assemble is made of more long connected is it more or less contiguous?
more
47
what does SMRT mean
single molecule real time sequencing
48
why is SMRT useful?
very long reads
49
how are errors corrected in SMRT
circular DNA
50
define gene predication
identifying the locations of genes
51
define functional annotation
adding biological context
52
define empirical stratagies
use transcriptomic data to define genes
53
define Ab inito stratagies
predict the genes computationally
54
what is the first strategy of empirical?
expressed sequence tag (ETS) analysis
55
what is an example of 3rd generation sequencing?
PacBio
56
SMRTbell template, ZMW wells, and labeled nucleotides; which 3rd gen is this?
PacBio
57
what is the second strategy of empirical?
high-throughput transcriptomics
58
what does high-throughput transcriptomics start with as a template?
RNA
59
what is the 1st prediction of Ab inito?
pattern matching
60
what are signal sensors
short motif such as poly-A or start/stop
61
what are content sensors?
pattern of codon usage
62
what is the 2nd prediction of Ab inito?
sequence similarity
63
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
64
what does BUSCO hypothesize
some genes evolve under single copy control
65
define reverse transcription
RNA to DNA
66
what is mRNA enrichment
adding a bunch of Ts to mRNA and using a magnent to attract them
67
what are HMMs used for
create protein domain images
68
_________ is a website for protein domains
SMART
69
what do transcription factors do?
regulate transcription
70
longer transcripts produce more reads which means read count are normalized to the __________ length
transcript length
71
what is gene ontology?
set of classes with relations that operate between them
72
what are the 3 classes of gene function
1. molecular function 2. cellular function 3. biological process
73
what is molecular function
activities that occur at the molecular level
74
what is cellular function
location in which gene preforms its function
75
what is biological process
larger programs accomplished by multiple activities
76
GO terms are _______ in a chart
nodes
77
what is differential expression
why do some people die from the flu then some dont
78
what are the 2 domains of transcription factors
DNA binding domain regulatory domain
79
see graphs
a

Genomic Biology (6 decks)

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