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Fall 2014 > LSBDA Midterm > Flashcards

LSBDA Midterm Flashcards

1
Q

DNA

A
  • The genetic material, consisting of nucleic acids (4 types)
  • Adenine, Thymine, Guanine, Cytosine
  • Cannot be sequenced directly; they must be subject to many biochemical steps for library preparation
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2
Q

base pair

A
  • A unit of DNA made up of a nucleic acid

- Either ATGC

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3
Q

RNA

A

-Transcription generates RNA from DNA template

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4
Q

mRNA

A
  • Stands for messenger RNA
  • Type of RNA that codes for protein
  • Consists of AUGC
  • Uracil instead of Thymine
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5
Q

protein

A
  • Made of amino-acids (20 of them)
  • Protein information cannot flow back to nucleic acids
  • Translation generates protein from RNA template
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6
Q

amino acid

A
  • There are 20 of them
  • Building blocks of protein
  • Each has physical, chemical, and biological characteristics.
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7
Q

central dogma of molecular biology

A

-“deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.”

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8
Q

DNA replication

A

-The copying of DNA

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9
Q

transcription

A

-Generation of RNA from DNA template

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10
Q

translation

A

-Generation of protein from RNA template

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11
Q

chromosome

A
  • bundled DNA, wrapped in histones

- DNA, chromatin, nucleosomes

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12
Q

splicing

A

-The adjoining of different exons in different combinations

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13
Q

alternative splicing

A
  • A regulated process during gene expression that results in a single gene coding for multiple proteins
  • particular exons of a gene may be included within or excluded from the final processed mRNA produced from that gene.
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14
Q

poly adenylation (poly-A tail)

A
  • the addition of multiple adenosine to the 3’ end of pre-mRNA
  • Important in mRNA nuclear export, stability, resistance to degradation
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15
Q

cellular differentiation

A

-The ability of a cell to produce different cells with very different physical characteristics despite having the same genome.

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16
Q

promoter

A

-a region of DNA that initiates transcription of a particular gene, located near the transcription star site of genes upstream of the DNA (toward the 5’)

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17
Q

exon

A

-nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing

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18
Q

intron

A

-nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated

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19
Q

5’UTR

A

-5’ untranscribed region of DNA

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20
Q

3’UTR

A

-3’ untranscribed region of DNA

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21
Q

TSS

A
  • transcription start site
  • labeled 3’ if it starts at the end of the 3’ end of the mRNA
  • labeled 5’ if it starts at the end of the 5’ end of the mRNA
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22
Q

TES

A

-transcription end site

-

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23
Q

technical replicates

A
  • replicates that share the same sample (i.e. the measurements are repeated)
  • usually not necessary, unless the goal is to study the technology
24
Q

biological replicates

A

-the same type of organism is grown/treated under the same conditions

25
Q

chgrp

A
  • change group

- chgrp [OPTION] GROUP FILE

26
Q

chown

A
  • change owner

- chown [OPTION] [OWNER][:[GROUP]] FILE

27
Q

chmod

A
  • change file modes or Access Control Lists

- chmod [OPTION] MODE [,MODE] FILE

28
Q

cp

A
  • copy file

- cp [OPTION] SOURCE DIRECTORY

29
Q

dd

A
  • convert and copy a file

- dd [OPERAND]

30
Q

df

A
  • display free disk space

- df [OPTION] [FILE]

31
Q

ln

A
  • make links

- ln [OPTION] TARGET DIRECTORY

32
Q

ls

A
  • list directory contents

- ls [OPTION] [FILE]

33
Q

mkdir

A
  • make directories

- mkdir [OPTION] DIRECTORY

34
Q

mktemp

A
  • make temporary file name (unique)

- mktemp [OPTION] [TEMPLATE]

35
Q

mv

A
  • move (rename) files

- mv [OPTION] SOURCE DIRECTORY

36
Q

realpath

A
  • print the resolved path

- realpath [OPTION] FILE

37
Q

rm

A
  • remove files or directories

- rm [OPTION] FILE

38
Q

touch

A
  • change file timestamps

- touch [OPTION] FILE

39
Q

cat

A
  • concatenate files and print on the standard output

- cat [OPTION] [FILE]

40
Q

comm

A
  • compare two sorted files line by line

- comm [OPTION] FILE1 FILE2

41
Q

cut

A
  • remove sections from each line of files

- cut OPTION [FILE]

42
Q

head

A
  • output the first part of files

- head [OPTION] [FILE]

43
Q

nl

A
  • number lines of files

- nl [OPTION] [FILE]

44
Q

paste

A
  • merge lines of files

- paste [OPTION] [FILE]

45
Q

sort

A
  • sort lines of text files

- sort [option] [FILE]

46
Q

split

A
  • split a file into pieces

- split [option] [input [prefix]]

47
Q

tail

A
  • output the last 10 (default) part of the files

- tail [option] [file]

48
Q

uniq

A
  • report or omit repeated lines

- uniq [option] [input [output]]

49
Q

wc

A
  • print newline, word, and byte counts for each file

- wc [option] [file]

50
Q

basename

A

-strip directory and suffix from filenames

51
Q

date

A

-print or set the system date and time

52
Q

dirname

A

-strip last component from file name

53
Q

du

A

-estimate file space usage

54
Q

echo

A

-display a line of text

55
Q

id

A

-print real and effective user and group IDs

56
Q

metacharacter

A
  • special characters that are not literal

- literal characters must be represented with a “/” before the character

Fall 2014 (5 decks)

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