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Genomic Biology > Exam 1 > Flashcards

Exam 1 Flashcards

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
Q

what were the first nucleotides labels?

A

radioactive P32

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26
Q

How was fluorescent dye an advantgae to use?

A

increased ability to obtain large amounts of sequencing data

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27
Q

In primer walking; what do you start with?

A

known sequence
designed primer

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28
Q

how does shotgun sequencing work?

A

fragment DNA into smaller pieces
clone into vectors

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29
Q

what is the down side to shotgun sequencing?

A

overlaps

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30
Q

Why kind of labels does NGS use?

A

fluorescent dyes

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31
Q

_______________ is the output of capillary electrophoresis

A

chromattogram

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32
Q

in a chromatogram, what is on the x and y axis?

A

x: time
y: fluorescence

33
Q

define adaptor sequence

A

short piece of DNA we know the sequence of that will be used on flow cell and hybridized

34
Q

define hybridized

A

binding between two fragments of DNA

35
Q

define overlap

A

regions of similarity between regions

36
Q

define overhang

A

unaligned ends of the sequence

37
Q

define contigs

A

set of DNA segments that overlap and provide a better representation of genome region

38
Q

define scaffolds

A

combined contigs

39
Q

define sequence coverage

A

how many times a strand has been sequenced

40
Q

what is an example of 2nd generation sequencing

A

illumina

41
Q

NGS is sequencing by __________

A

synthesis

42
Q

define bridge amplification

A

generates copies of identical DNA sequences in clusters on flow cell

43
Q

does Sanger sequencing or NGS add adaptors

A

NGS

44
Q

does Sanger sequencing or NGS generate polony arrays

A

NGS

45
Q

does Sanger sequencing or NGS generate electrophoreisis

A

Sanger

46
Q

if the assemble is made of more long connected is it more or less contiguous?

A

more

47
Q

what does SMRT mean

A

single molecule real time sequencing

48
Q

why is SMRT useful?

A

very long reads

49
Q

how are errors corrected in SMRT

A

circular DNA

50
Q

define gene predication

A

identifying the locations of genes

51
Q

define functional annotation

A

adding biological context

52
Q

define empirical stratagies

A

use transcriptomic data to define genes

53
Q

define Ab inito stratagies

A

predict the genes computationally

54
Q

what is the first strategy of empirical?

A

expressed sequence tag (ETS) analysis

55
Q

what is an example of 3rd generation sequencing?

A

PacBio

56
Q

SMRTbell template, ZMW wells, and labeled nucleotides; which 3rd gen is this?

A

PacBio

57
Q

what is the second strategy of empirical?

A

high-throughput transcriptomics

58
Q

what does high-throughput transcriptomics start with as a template?

A

RNA

59
Q

what is the 1st prediction of Ab inito?

A

pattern matching

60
Q

what are signal sensors

A

short motif such as poly-A or start/stop

61
Q

what are content sensors?

A

pattern of codon usage

62
Q

what is the 2nd prediction of Ab inito?

A

sequence similarity

63
Q

how does sequence similarity work?

A

a known set of genes form species A is used to identify the genes from a freshly assembled sequence B genome

64
Q

what does BUSCO hypothesize

A

some genes evolve under single copy control

65
Q

define reverse transcription

A

RNA to DNA

66
Q

what is mRNA enrichment

A

adding a bunch of Ts to mRNA and using a magnent to attract them

67
Q

what are HMMs used for

A

create protein domain images

68
Q

_________ is a website for protein domains

A

SMART

69
Q

what do transcription factors do?

A

regulate transcription

70
Q

longer transcripts produce more reads which means read count are normalized to the __________ length

A

transcript length

71
Q

what is gene ontology?

A

set of classes with relations that operate between them

72
Q

what are the 3 classes of gene function

A
  1. molecular function
  2. cellular function
  3. biological process
73
Q

what is molecular function

A

activities that occur at the molecular level

74
Q

what is cellular function

A

location in which gene preforms its function

75
Q

what is biological process

A

larger programs accomplished by multiple activities

76
Q

GO terms are _______ in a chart

A

nodes

77
Q

what is differential expression

A

why do some people die from the flu then some dont

78
Q

what are the 2 domains of transcription factors

A

DNA binding domain
regulatory domain

79
Q

see graphs

A

a

Genomic Biology (6 decks)

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