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Exam 4 Flashcards

1
Q

What is negative control?

A

Gene transcription is actively repressed so the gene would be “on” all the time in the absence of a repressor protein

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2
Q

What is positive control?

A

Gene transcription is induced so the gene is only turned “on” in the presence of an activator protein

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3
Q

What does an effector molecule do in negative control?

A

Changes the shape of the repressor in order for the repressor to not bind

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4
Q

What does an effector molecule do in positive control?

A

Changes the shape in order to allow the activator to bind

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5
Q

What is an allosteric site?

A

Where allosteric effectors bind in the regulatory protein to change activity

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6
Q

What does permease do?

A

Transports lactose into the cell

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7
Q

What does beta-galactosidase do?

A

Cleaves lactose to produce galactose and glucose

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8
Q

What is the I gene?

A

Encodes for the repressor protein outside of the lac operon

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9
Q

What does lactose do to the repressor?

A

Serves as an allosteric effector by binding to the repressor protein at the allosteric site when it is present so the repressor cannot bind

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10
Q

What does an I- mutant do?

A

Produces a defective repressor protein that prevents binding of the protein to DNA, resulting in constitutive gene expression (always on)

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11
Q

What does an I^s mutant do?

A

Prevents lactose from binding to the still functional protein so the repressor is always bound, resulting in constitutive suppression of gene expression

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12
Q

What is the operator?

A

The DNA sequence to which the repressor binds

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13
Q

What does an O^c mutant do?

A

Results in inability of repressor protein to bind to DNA so there is constitutive gene expression

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14
Q

Where does RNA polymerase bind?

A

The promoter at the -35 region (TTGACA) and the Pribnow box (TATAAT)

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15
Q

What happens if there is a mutation that changes the conserved -35 and/or Pribnow box sequences?

A

The RNA polymerase cannot bind and there is no transcription at all

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16
Q

Why does glucose block induction of lactose metabolism?

A

It is preferable so the glucose blocks induction of lactose metabolism so the bacteria can be efficient and process glucose first

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17
Q

How does glucose block induction of lactose metabolism?

A

It blocks the activity of adenylate cyclase so ATP isn’t converted to cAMP which cannot bind to CAP and form a complex and bind to the promoter to facilitate RNA polymerase binding so there isn’t active expression of the lac operon

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18
Q

What are cis regulatory elements?

A

Regulatory elements that are in the same segment of DNA as the gene of interest (within a few kb) like the operator and promoter

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19
Q

What are trans regulatory elements?

A

Factors produced by other genes that act on the gene of interest like the I gene and repressor producing the protein that binds to the operator

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20
Q

What is the trp repressor mechanism of transcription regulation?

A

Trp repressor binds tryptophan and turns off the operon when tryptophan levels are adequate

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21
Q

What is the attenuation mechanism of transcription regulation?

A

When there are low levels of tryptophan there is a much longer stall in transcription that creates the formation of a stem and loop between 2 and 3 that is much less stable than the normal so the ribosome breaks through and transcription continues

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22
Q

Mutations in the operator sequence result in _____ of the lac operon.

A

Constitutive expression

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23
Q

What effector molecule directly interacts with the Lac repressor protein?

A

Lactose

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24
Q

The primary control point at which gene expression is regulates in prokaryotes is initiation of _____?

A

Transcription

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25
True or False? Structural gene order in prokaryotic operons often corresponds to the reaction order in the biosynthetic pathway these genes participate in.
True
26
A mutation that makes adenylate cyclase insensitive to glucose metabolites would cause ______ of the lacZ and lacY genes under what conditions?
Transcription in the presence of glucose and lactose
27
What is the trp operon controlled by?
Trp repressor and attenuation
28
How do effector molecules repress transcription of negatively regulated genes?
By stimulating activity of repressor proteins
29
How is DNA kept inactive in eukaryotic cells?
Chromatin
30
What are three consensus sequences required for efficient formation of the pre-initiation complex and RNA polymerase binding in eukaryotic promoters?
GC-rich box (GGGCGG ~200 bp away), CAAT box (GGNCAATCT ~75 bp away), and TATA box (TATA ~25 bp away)
31
What happens when there is a mutation at any of the three consensus sequences?
Dramatic reduction in transcription at these three sites
32
What are general transcription factors and which ones are they?
Proteins required for transcription of ALL genes by binding to DNA to form the pre-initiation complex like TBP, TFIID, TFIIF, TFIIH, and TFIII
33
What are specific transcription factors?
Transcription factors that directly bind to DNA to influence transcription of target genes
34
What do transcription factors do?
Stimulate or inhibit transcription by helping or hindering formation of the pre-initiation complex; stabilizes binding of RNA polymerase to the core promoter
35
What are some cis elements?
Core promoter (TATA box), proximal promoter elements (CAAT box and GC-rich box), enhancers, and silencers
36
What are some trans elements?
RNA polymerases, transcription factors, co-activators, and co-repressors
37
What is the difference between co-activators/repressors and transcription factors?
Co-activators/repressors do not directly bind to DNA
38
What are enhancers and silencers?
Gene regulatory proteins that are several thousand base pairs away from the gene
39
What allows specific transcription factors to interact with proteins?
Looping
40
What is the function of the DNA-binding domain?
Needed for specific transcription factor to bind to enhancer/silencer DNA sequence
41
What is the function of the activation domain?
Needed to interact with proteins bound to promoter to speed up or slow down transcription; assist to attract, position, and modify general transcription factors and RNA polymerase II at the promoter
42
What is Gal4?
A yeast transcription factor involved in galactose metabolism
43
What is synergism?
Interaction between two factors such that their combined effect is greater than the sum of their individual effects
44
What is an example of synergism?
When macrophages are exposed to pathogens they produce nitric oxide by converting arginine to citruline via the gamma interferon and LPS creating a greater activity of nitric oxide synthase
45
What are heterochromatin?
A type of chromatin that are darkly stained because they are more tightly packed where most transcription takes place
46
What are the divisions between heterochromatin?
Constitutive (no gene expression) and facultative (some gene expression)
47
What are euchromatin?
A type of chromatin where it is lightly stained because it is less tightly packed where most gene expression occurs
48
What are nucleosomes?
The base unit of chromatin that is 8 protein subunits (2 of H2A, H2B, H3, and H4) attached to about 145 bp of DNA that are held together by H1 histone
49
What is the process of chromatin remodeling?
The enhanceosome comes to a region NEAR the promoter that helps recruit the HAT protein. The co-activator protein is then recruited and further adds acetylation and recruits RNA polymerase. Finally, the SWI-SNF nudges the nucleosome off the TATA box so RNA polymerase can bind
50
What is an enhanceosome?
A collection of transcription factors that assembles in response to infection
51
What does histone acetyltransferase do?
Adds acetyl groups to histone tails
52
What does histone deacetyltransferase do?
Removes acetyl groups from histones and leads to decreased transcription
53
What is epigenetics?
The study of inherited changes in gene expression without a change in the underlying DNA sequence
54
What chromosomal region does most transcription take place in?
Euchromatin
55
What allows us to have different cells like skin and liver?
Epigenetic tags
56
What is genomic imprinting?
Involves direct methylation of DNA
57
What type of imprinting is when the allele from the mother is silent and the allele from the father is expressed?
Maternal imprinting
58
What is Barr Body?
One of the X chromosomes is randomly inactivated via methylation early in development
59
Why is gene regulation more complicated in eukaryotes?
Each gene is controlled by a separate promoter, there are many DNA switches for each gene, there are many DNA binding proteins for each gene, and chromatin organization affects the expression of genes
60
What is epigenetic inheritance?
The inheritance of chromatin states from one cell generation to the next
61
Why are more sophisticated gene regulatory mechanisms needed in eukaryotes compared to prokaryotes?
Eukaryotes undergo complex development that may extend over long periods, prokaryotic cells have simpler organization and lack organelles, eukaryotes are multi-cellular, and eukaryotes have tissues and organs with distinct functions
62
What is totipotency?
Cells in a zygote are initially able to develop into any cell type
63
Why can stem cells become any cell they need to?
Because they remain in a totipotent state
64
How is it determined what type of cell it becomes?
Epigenetic and which genes are turned on or off
65
What is cell fate?
Cells go through a step by step process in which they irreversibly differentiate into certain cell types
66
What can be said of a multipotent or pleuripotent cell?
It can form any kind of cell within its system but is no longer totipotent and cannot become any cell in general
67
What is a development field?
A set of cells that interact with each other to form a particular structure like tissue, organ, or limb
68
What are morphogens?
Molecules (i.e. mRNA, proteins, hormones) from specific cells tell other cells to follow a specific fate
69
What are organizers?
Clusters of cells that have the ability to organize the development of surrounding tissues
70
How do limbs develop?
Fibroblast growth factor (a morphogen) induces formation of an organizer called the apical ectodermal ridge, which organizes cells to become the limb and another organizer called zone of polarizing activity that determines anterior vs. posterior orientation by producing a morphogen called sonic hedgehog
71
What is ectoderm?
Outer layer of embryo
72
What is mesoderm?
Middle layer of embryo
73
What happens in AER is removed from the limb bud?
Further development ceases
74
What happens if an extra AER is grafted on a limb bud?
Additional limbs are formed
75
What happens in leg mesoderm tissue is added to the wing AER?
Morphogens produced by AER tell cells to become wings and signals from leg mesoderm tell cells to become leg so toes are formed at the end of the limb
76
What happens if the limb mesoderm is replaced with non-limb mesoderm?
Limb development ceases
77
What are some major development decisions?
Separation of germ line from somatic cells, establishment of position information early in development (A-P axis and D-V axis), differentiation of germ layers, differentiation of tissues, and segmentation
78
How does differentiation of tissues occur?
Specific tissues only develop certain germ layers like nervous tissue develops from the ectoderm
79
What are homeotic mutations?
One part of the body is transformed to resemble another
80
Where do loss of function mutations occurr in drosophila?
Ultrabithorax gene transforms hindwing to forewing so 2 sets of wings form
81
Where do gain of function mutations occur in drosophila?
Antennapedia gene transform antennae to legs
82
What do hox genes do?
Control the identity of segments and appendages
83
What can be said of chromosome order in drosophila?
Chromosome order of genes in each complex matches the order of body regions that are influenced by each hox gene
84
What can be said of gene order in drosophila?
Gene order parallels the pattern of expression in the embryo
85
Why can a single gene mutation create drastic changes in development?
Because Hox genes are transcription factors so the genes contain a highly conserved 60 amino acid homeobox domain required for binding DNA and they bind to DNA regulatory elements to activate or repress expression of hundreds of other genes critical in embryo development
86
How is A-P axis set up?
There is a positive and negative end of the tubulin monomers and the negative end is the anterior end where bicoid mRNA is attached and the positive end is the posterior where nanos mRNA is attached
87
How can the A-P axis be visualized?
In situ hybridization reveals a dark blue staining for bicoid (anterior) and light blue staining for nanos (posterior)
88
How is bicoid protein and nanos protein distributed along the A-P axis?
Asymmetrically
89
How is the hunchback mRNA distributed along the A-P axis?
Evenly
90
Why is the hunchback protein asymmetrically distributed?
The bicoid protein at the anterior end positively regulates hunchback and nanos protein acts to inhibit hunchback mRNA translation so translation is blocked at the posterior end. The combination produces a gradient of the hunchback protein
91
What do gap genes do?
Control formation of contiguous blocks of segments in drosophila embryo along the A-P axis and are regulated by bicoid and hunchback protein levels
92
What are pair-rule genes?
Transcription factors expressed in the zygote following fertilization that govern the formation of segments and expression of segment polarity genes
93
How is expression of eve gene determined?
Protein gradients of the combination of bicoid and hunchback (positive activator) as well as giant and kruppel genes (negative repressor)
94
What is the process of determination of ventral side?
High spaetzle levels promote binding to the toll receptor in the extracellular space that allows the toll receptor to go through a conformational change leading to phosphorylation of toll receptor on cytoplasmic side that sets up signal cascade by activating TUB, which activates PLL which phosphorylates cactus leading to ubiquitination (degradation) of cactus so dorsal can migrate to nucleus and can now stimulate transcription of genes needed to differentiate cells on that side of the embryo to become the ventral side
95
When is genetic sex determined?
At fertilization
96
When is gonadal sex determined?
Between 6-8 weeks along
97
How is a male sex determined?
Y chromosome is activated so SRY gene is expressed in cells of the bipotential gonad which initiates testes differentiation by activating male-specific transcription factors at the sox9 gene, which is necessary for biopotential cells to differentiate into male sertoli cells
98
What is the default of the biopotential gonad?
Ovaries
99
What happens once the gonads differentiate into ovaries or testes?
We get the production of certain hormones
100
What do leydig cells produce?
Testosterone that promote formation of male internal structures, male genetalia, and the male brain
101
What do sertoli cells produce?
Anti-mullerian hormone that leads to regression of female internal structures
102
How is sexual determination in drosophila different from humans?
Determined by ratio of X chromosomes to autosomes
103
How does sex differ in drosophila?
X chromosomes express numerator proteins and Y chromosomes express denominator proteins; SXL protein is produced only when a homodimer is formed from numerator proteins; SXL splices Tra properly in females and in males a critical stop codon isn't removed in the Tra mRNA so nonfunctional Tra is produced; In females Tra protein leads to alternative splicing of the doublesex (dsx) gene producing dsx^f protein and in males Tra isn't present so there is a different alternative splicing of the dsx gene to produce dsx^m protein
104
Genes with products provided by the female to the egg that establish the anteroposterior are called...
Maternal-effect genes
105
True or False? mRNA transcripts for Hox genes are expressed at uniform levels throughout the fruit fly embryo but differ in the segments they regulate
False
106
The maternal-effect bicoid gene codes for...
A DNA-binding transcription factor

Genetics (5 decks)

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