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BIO109 - Developmental Biology > Lecture 4 - Genes and Development > Flashcards

Lecture 4 - Genes and Development Flashcards

1
Q

principles in gene development

A
  1. genomic equivalence
  2. selective gene expression
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2
Q

all cells contain identical set of genes

A

genomic equivalence

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3
Q

expts in genomic equivalence

A
  1. Spemann
  2. Briggs & King
  3. Wolffian regeneration
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4
Q

different cells activate different genes at different times

A

selective gene expression

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5
Q

“__ __ __ from the same __ __”

A
  • differential gene expression
  • nuclear repertoire
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6
Q

from DNA to chromosome

A
  1. DNA
  2. Nucleosome
  3. Solenoid
  4. Looped Chromosome
  5. Condensed Chromosome
  6. Mitotic Chromosome
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7
Q

dna size

A

2nm

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8
Q

nucleosome size

A

11nm

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9
Q

solenoid size

A

30nm

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10
Q

looped chromosome size

A

300nm

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11
Q

condensed chromosome size

A

700nm

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12
Q

mitotic chromosome size

A

1,400 nm

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13
Q
  • 10 year project
  • physically map the human genome
A

the human genome project

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14
Q

duration of the human genome project

A

1988-2003

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15
Q

human genome

A

3x10^9 bp)

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16
Q

results of the human genome project:
total no. of genes

A

~30K

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17
Q

results of the human genome project:
shortest gene

A

histone - 500 NT

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18
Q

results of the human genome project:
largest gene

A

DMD (dystrophin gene) - 2,200kb

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19
Q

results of the human genome project:
Chrom I

A

2,968 genes

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20
Q

results of the human genome project:
Chrom Y

A

231 genes

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21
Q

results of the human genome project:
Chrom 17

A

associated with diseases

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22
Q

eukaryotic gene structure

A
  1. promoter region
  2. cap sequence or ACATTG
  3. ATG codon
  4. exons
  5. introns
  6. translation termination codon
  7. 3’ untranslated region
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23
Q

binding site of RNA polymerase and subseqent initiation of transcription

A

promoter region

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24
Q
  • transcription initiation stie
  • represents the 5’ end of RNA, which will receive a “cap” of modified nucleotide soon after it is transcribed
  • vary among genes; necessary for the binding of mRNA to ribosomes and its translation
A

cap sequence or ACATTG

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25
Q

cap sequence or

A

ACATTG

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26
Q

why is cap sequence necessary

A

for the binding of mRNA to ribosomes and its translation

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27
Q

for initation of translation

A

ATG codon

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28
Q
  • intervening sequence between initiation points of transcription & translation
  • determines the rate of translation initiation
A

leader sequence

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29
Q

base pairs coding for a protein

A

exons

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30
Q
  • non-coding sequences interspersed among the exons
  • may be longer and more numerous than exons
A

introns

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31
Q

TAA

A

translation termination codon

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32
Q

translation termination codon

A

TAA

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33
Q
  • transcribed but not translated into protein
  • AATAA sequence where a “tail” of adenylate resudes are added
  • poly(A)tail confers stability and translatability on the mRNA
A

3’ untranslated region

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34
Q

sequence in the 3’ untranslated region

A

AATAA

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35
Q

how many adenylate residues are added in AATAA sequence

A

200-300

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36
Q

confers stability and translatability on the mRNA

A

poly (A) tail

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37
Q

Levels of control

A
  1. differential gene transcription
  2. selective RNA processing
  3. selective mRNA translation
  4. differential protein modification
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38
Q

levels of gene control

A
  1. transcription
  2. posttranscriptional
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39
Q

to become an active protein the RNA must be?

A
  1. processes into mRNA (removal of introns)
  2. translocated from nucleus to cytoplasm
  3. translated by the protein-synthesizing apparatus
  4. posttranslationally moified to become active
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40
Q

two types of regulatory elements

A
  1. cis-regulators
  2. trans-regulators
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41
Q

represent specific DNA seqence on a given chromosome which act only on adjacent genes

A

cis-regulators

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42
Q

dfiferent types of cis-regulators

A
  1. promoters
  2. enhancers
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43
Q
  • required for the binding of RNA polymerase and accurate initiation of transcription
  • specify the times and places of transcription
A

promoters

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44
Q
  • DNA sequence
  • activate the utilization of the promoter
  • control the efficiency and rate of transcript
  • functions by binding to transcription factors
  • activate only promoters on the same chromosomes
A

enhancers

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45
Q

promoter structure

A
  • TATA box or Goldberg-Hogness box
  • about 30 bp
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46
Q

where is TATA box found

A

~30bp upstream from site where transcription begins

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47
Q

can be analyzed by determining which of its bases are necessary for efficient transcription

A

functional anatomy

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48
Q

promoter function

A
  1. bind RNA polymerase
  2. specify the places and times the transcription can occur from the gene
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49
Q

will not bind to naked DNA sequence

A

eukaryotic RNA polymerases

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50
Q

what do eukaryotic RNA polymerases require to bind efficiently to the promoter

A

protein factors

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51
Q

transcribes protein-coding genes

A

RNA pol II

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52
Q

how many protein have been shown necessary for the proper initation of transction by RNA pol II

A

6

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53
Q

proteins that have been shown necessary for the proper initation of transction by RNA pol II

A

basal transcription factors

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54
Q

recognizes the TATA box through one of its subunits

A

TFIID

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55
Q

subunit of TFIID

A

TATA-binding protein (TBP)

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56
Q

TFIID serves as the what?

A
  • foundation of transcription initiation complex
  • serves to keep nucleosome from forming in this region
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57
Q

stabilizes TFIID

A

TFIIA

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58
Q

TFIID can bind to what after stabilizied by TFIIA

A

TFIIB

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59
Q

other transcription factors used to release RNA pol from complex

A

TFIIE, F, G

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60
Q

requirement for enhancers

A
  1. DNA sequence that can activate the utilization of a promoter, controlling the efficiency and rate of transcription from that particular promoter
  2. primary elements responsible for tissue-sepcific transcription
  3. function by binding specific regulatory proteins called transcription factors
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61
Q

function of enhancers

A

regulate the temporal and tissue-specific expression of all differentially regulated genes

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62
Q

importance of enhancers

A
  1. required by genes for their transcription
  2. major determinant of differential transcription in space and time
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63
Q

the combination of transcription factors that causes particular genes to be transcribed

64
Q

the same transcription factors that activate the transcription of one gene can be used to what?

A

repress the transcription of other genes

65
Q

repress tha transcription of other genes

A

negative enhancers = silencers

66
Q
  • soluble molecules from one gene and interact with genes on the same or different chromosomes
  • with sequence specific DNA-binding domain
A

trans-regulators

67
Q

trans-regulators have sequence specific __ __ __

A

DNA-binding domain

68
Q

enables that transcription factor to interact with proteins involved in binding RNA polymerase

A

trans-activating domain

69
Q
  • proteins that bind to enhancer or promoter reigons and interact to activate or repress the transcription of a particular gene
  • can bind to specific DNA sequences
  • can be grouped together in families based on similarities in structure
A

transcription factors

70
Q

share a common framework structure in their DNA-binding sites, and slight differences in the amino acids at the binding site can alter the sequence of the DNA to whcih the factor binds

A

transcription factors

71
Q

Three major domains of transcription factors

A
  1. DNA-binding domain
  2. trans-activating domain
  3. protein-protein interaction domain
72
Q

recognizes a particular DNA sequence

A

DNA-bingind domain

73
Q
  • activates or suppresses the transcription of the gene whose promoter or enhancer it has bound
  • enables the transcription factor to interact with proteins involved in binding RNA polymerase
A

trans-activating domain

74
Q

allows the transcription factor’s activity to be modulated by TAFs or other transcription factors

A

protein-protein interaction domain

75
Q
  • are sequences tat act specifically to block transcription
  • useful in restricting the transcription of a particular gene to a particular geoup of cells or regulating the timing of the gene’s expression
76
Q

ex of silencer

A

when the endodermal tube contacts with the cardiac mesoderm, the heart precursors are able to instruct the endodermal tube to begin forming the liver and to start transcribing liver-specific genes

77
Q

Trans-regulatory factors

A
  1. homeodomain proteins
  2. zing finger standard
  3. basic helix-loop helix TF
  4. basic leucine zipper
  5. nuclear hormone receptors
  6. Sox-2 TF
78
Q
  • critical for specifying the anterior-posterior body axes
  • 60aa arranged in a helix-turn-helix, such that the third helix extends into the major groove of the DNA it recognizes
A

homeodomain proteins

79
Q

major groove of Hox tf

80
Q

minor groove of Hox TF

81
Q

mutation transform body segment to another

82
Q

region that comprises the homeodomain and then 2nd DNA-binding region

A

POU domain

83
Q
  • has two or more “DNA-binding fingers” helical domains
  • coordinatied by 2 cysteins and 2 histidines
A

zinc finger standard

84
Q

ex. of zinc finger

85
Q

critical for kidney and gonads development

86
Q

for hindbrain development

87
Q
  • binds to DNA via a region of basic AA (10-13 res)
  • may form a dimer with positive or negative regulators
A

basic helix-loop helix TF (bHLH)

88
Q

ex. of basic helix-loop helix TF

89
Q

alpha helix with several luecine reside that bind with other bZip proteins

A

basic leuzine zipper (bZip)

90
Q

mediate the effect of hormones on genes

A

nuclear hormone receptors

91
Q

bends DNA from “I” to “L”

92
Q

important in mammalian primary sex determination

93
Q

types of RNA polymerase

A
  1. RNA Pol I
  2. RNA Pol II
  3. RNA Pol III
94
Q

transcribes large ribosomal RNAs

95
Q

crucial to cell differentiation - determine which genes transcribed and produced

A

transcription of a gene

96
Q

post-transcriptional processes

A
  1. capping
  2. polyadenylation
  3. splicing
97
Q

addition of 7-methyl-guanylate to the 5’ end of pre-mRNA

98
Q

what is added during capping

A

7-methyl-guanylate

99
Q
  • a chain of 150-200 adenylate nucleotide is attached to the 3’ end of the pre-mRNA after transcription
  • stabilize the mRNA and alloows its exit and translation
A

polyadenylation

100
Q

how many adenylate nucleotide is added during polyadenylation

A

150-200 adenylate

101
Q

removal of non-coding sequences from pre-mRNA to produce the mature mRNA

102
Q

acts on the gene

A

epigenetic mechanism

103
Q

chemical modifications

A
  1. methylation
  2. acetylation
104
Q

can inactivate genes

A

methylation of DNA

105
Q

allows DNA unpacking and transcription

A

acetylation of histones

106
Q
  • might change the structure of the gene thus regulation its activity
  • stabilizies nucleosomes and prevents transcription factors from binding
A

DNA methylation

107
Q

three areas in which DNA methylation can contribute to differential gene activity

A
  1. methylation of promoter
  2. responsible for distinguishing certain egg-derived and sperm-derived genes in mammals
  3. continued repression of the genes on one of the two X chromosomes in each female mammalian cell
108
Q

temporal and spatial regulation on genes encoding tissue-specific proteins

A

methylation of promoter

109
Q

only one will be expressed during early development

A

distinguishing between certain egg/sperm-derived genes

110
Q

where does methylation occur exclusively

A

lysine 9 of histone 3
(H3-K9)

111
Q

what does methylation promote binding of

A

HP1 proteins (heterochromatin proteins)

112
Q

condensed and replicates after most of the chromatin

A

heterochromatin

113
Q

genes are active only if derived from paternal

A

gene imprinting

114
Q
  • removal of acetyl group
  • H4 lysine 16
A

deacetylation

115
Q

deacetylation

A

H4 lysine 16

116
Q

removes the positive charge from histone reducing the force of attraction with DNA leading to wider opening of the chromatin

A

acetylation of lysine

117
Q
  • restores the positive charges and promotes close attraction between histone and DNA
  • condensed chromosome
A

deacetylation

118
Q

200 or so adenyl groups added to the 3’ end

A

polyadenylation

119
Q

initiates transcription producing 20-25 NT

A

CTD (carboxyl terminal domain)

120
Q

% of genes repressed in a cell

121
Q

% of genes expressed in a cell

122
Q

control of gene expression before transcription

A
  1. selective gene amplification
  2. gene rearrangement
  3. chemical modifications
123
Q

posttranscriptional-selective RNA processing

A
  1. censorship
  2. hnRNA splicing
124
Q

which nuclear transcripts are processed into cytoplasmic messages “chosen few”

A

censorship

125
Q

the same nuclear RNA is spliced into different mRNAs

A

hnRNA splicing

126
Q

% of human genes that are alternatively spliced

127
Q
  • process results in down regulation of a gene at the RNA level (after transcription)
  • there is also gene silencing at the transcriptional level
A

post-transcriptional gene silencing (PTGS)

128
Q

other term for post-transcriptional gene silencing (PTGS)

A

RNA interference / RNAi

129
Q

gene silencing at transcriptional level

A
  1. transposons
  2. retroviral genes
  3. heterochromatin
130
Q

splicesosome complex

A

splicing regular protein+ snRNPS & SF joined

131
Q

joins exons

132
Q

important source of protein diversity

A

alternative gene splicing

133
Q

different types of alternative RNA splicing

A
  1. alternative 5’ splicing
  2. alternative 3’ splicing
  3. intron retention
  4. mutually exclusive exons
  5. exon skipping
134
Q

part of an exon may be included in the splicing at 5’ end

A

alternative 5’ splicing

135
Q

part of an exon may be included in the splicing at 3’ end

A

alternative 3’ splicing

136
Q

an intron is included in the final mRNA

A

intron retention

137
Q

% of human genes with intron retention

138
Q

different exons found in 2 diferent mRNAs

A

mutually exclusive exons

139
Q

2x bigger than ordinary baby zebra

A

zebroid foal

140
Q
  • the longer an mRNA persists, the more protein can be translated from it
  • stability of a message - length of its poly(A) tail depends upon sequences in the 3’ untranslated region
A

differential mRNA longevity

141
Q

polyadenylation confers stability

A

increase rate of translation

142
Q

affects longevity of casein during lactation

143
Q
  • stored oocyte mRNA - informations are dormant until translated at/near fertilization
  • activated by ionic signals at fertilization/ovulation
  • other stored messages encode proteins that determine the fate of cells
A

selective inhibition of mRNA translation

144
Q

provide positional information in the Drosophila embryo

A

bicoid and nanos

145
Q
  • time of mRNA translation regulated, but so is the place of RNA expression
  • after fertilization, it is found only in vegetal blastomeres
A

control of RNA expression by cytoplasmic localization

146
Q

post-translational modifications

A
  1. phosphorylation
  2. lipidation
  3. ubiquitination
  4. disulfide bond
  5. acetylation
  6. glycosylation
147
Q

adds a phosphate to serine, threonine or tyrosine

A

phosphorylation

148
Q

attaches a lipid, such as a fatty acid, to a protein chain

A

lipidation

149
Q

adds ubitquitin to a lysine reside of a target protein marking it for destruction

A

ubiquitination

150
Q

covalently links the 5’ atoms of two different cysteine residues

A

disulfide bond

151
Q

adds an acetyl group to the N-terminus of a protein to increase stability

A

acetylation

152
Q

attaches a sugar, usually to an “N” or “O” atom in an amino acid side chain

A

glycosylation

153
Q

how do cells become different

A

selective gene expression

154
Q

when does contrl of gene expression occur

A

at different levels from transcription to translation

155
Q

initates and maintain specific gene expression

A

particular combination of gene regulatory proteins (TF)

156
Q

gene control is a __, not a linear diagram

157
Q

gene is not an indepent entity controlling the synthesis of protein:

A

it both directs and is directed by protein synthesis

BIO109 - Developmental Biology (8 decks)

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