Lecture 3: Genes and Development - Mechanism of Cell Differentiation Flashcards
(197 cards)
1
Q
- What principle states that all cells in an organism contain the same set of genes?
A
Genomic Equivalence
2
Q
How can different cells develop into specialized types despite having identical DNA?
A
Cell Differentiation
3
Q
Give examples of experiments in genomic equivalence: (3)
A
- Spemann’s Experiment
- Briggs & King’s Experiment
- Wolffian Regeneration
4
Q
Which experiment demonstrated nuclear potential in early embryonic development?
A
Spemann’s Experiment
5
Q
Which experiment showed that differentiated cells still retain genetic information?
A
Briggs & King’s Experiment
6
Q
What provides evidence for cellular regeneration and genetic consistency?
A
Wolffian Regeneration
7
Q
What principle states that not all genes are active in every cell at all times?
A
Selective Gene Expression
8
Q
What is the concept that different cells express different genes based on their function and developmental stage?
A
Differential Gene Expression
9
Q
Give the four (4) levels of control that a eukaryotic cell has:
A
- Differential Gene Transcription
- Selective RNA Processing
- Selective mRNA Translation
- Differential Protein Modification
10
Q
Enumerate the levels of DNA packing from least to most condensed. (6)
A
- DNA Double Helix
- Nucleosome (“Beads on a String”)
- Solenoid (30 nm chromatin fiber)
- Looped Chromosome
- Condensed Chromosome
- Mitotic Chromosome
11
Q
What is the first level of DNA packing?
A
DNA Double Helix
12
Q
What structure in chromatin is described as “beads on a string”?
A
Nucleosome
13
Q
What is the 30 nm chromatin fiber of packed nucleosomes called?
A
Solenoid
14
Q
What structure represents a section of the chromosome in an extended form?
A
Looped Chromosome
15
Q
What is a more compacted section of the chromosome called?
A
Condensed Chromosome
16
Q
What is the fully condensed chromosome seen in mitosis?
A
Mitotic Chromosome
17
Q
What was the main objective of the Human Genome Project?
A
Physically map the entire human genome (~3 billion base pairs)
18
Q
When was the Human Genome Project launched? (month/year)
A
October 1990
19
Q
When was the Human Genome Project completed? (month/year)
A
April 2003
20
Q
- How long was the Human Genome Project originally planned to take?
- How long did it actually take to complete the Human Genome Project?
A
- 15 years
- 13 years
21
Q
Who led the initial phase of the Human Genome Project?
A
Dr. James Watson
22
Q
Who led the Human Genome Project from 1993?
A
Dr. Francis S. Collins
23
Q
Which organizations led the Human Genome Project?
A
International Human Genome Sequencing Consortium, NHGRI, U.S. Department of Energy
24
Q
Approximately how many genes are in the human genome?
A
~30,000
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What is the shortest human gene?
Histone (500 nucleotides)
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What is the largest human gene?
Dystrophin (DMD) – 2,200 kb
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Which chromosome has the highest number of genes?
Chromosome 1 (~2,968 genes)
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Which chromosome has the fewest genes?
Chromosome Y (~231 genes)
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Which chromosome is linked to various diseases?
Chromosome 17
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Name one major impact of the Human Genome Project. (3)
- Blueprint of human DNA
- Personalized medicine
- Advances in genetics
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Eukaryotic gene structure:
Binding site for RNA polymerase to initiate transcription
promoter region
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Eukaryotic gene structure:
What sequence marks the 5’ end of mRNA?
Cap sequence (e.g., ACATTG)
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Eukaryotic gene structure:
- Modified nucleotide __ is added after transcription.
- The sequences of this vary among genes but are necessary for mRNA binding to ribosomes and translation.
- cap
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Eukaryotic gene structure:
What is the start codon for translation?
ATG
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Eukaryotic gene structure:
The region between transcription and translation start sites.
Leader sequence
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Eukaryotic gene structure:
What is the function of the Leader Sequence?
Determines the rate of translation initiation.
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Eukaryotic gene structure:
What are the coding sequences that form the final protein?
Exons
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Eukaryotic gene structure:
What are the non-coding sequences between exons?
Introns
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Eukaryotic gene structure:
What happens to introns during RNA processing?
Removed during RNA splicing
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Eukaryotic gene structure:
What sequence signals the end of translation?
TAA (in DNA)
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Eukaryotic gene structure:
What is the 3’ Untranslated Region (3’ UTR)?
Transcribed but not translated.
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Eukaryotic gene structure:
What sequence in the 3’ UTR signals poly(A) tail addition?
AATAA
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Eukaryotic gene structure:
What is the function of the Poly(A) tail?
Enhances mRNA stability and translation efficiency.
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Eukaryotic gene structure:
How long is the Poly(A) tail?
200–300 adenine residues
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Expression of the Human β-Globin Gene:
On which chromosome is the β-globin (HBB) gene located?
Chromosome 11
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Expression of the Human β-Globin Gene:
What enzyme synthesizes pre-mRNA from DNA?
RNA polymerase II
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Expression of the Human β-Globin Gene:
What are the two modifications that enhance mRNA stability and translation? (2)
- 5’ Capping
- 3’ Polyadenylation
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Expression of the Human β-Globin Gene:
Where does translation of β-globin occur?
Ribosome
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Expression of the Human β-Globin Gene:
What does the β-globin chain combine with to form hemoglobin?
α-globin
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Expression of the Human β-Globin Gene:
What is the function of hemoglobin (HbA)?
Oxygen transport
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Levels of Gene Control:
Regulates which genes are transcribed.
Transcriptional Control
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Levels of Gene Control:
Selective RNA processing before translation.
Post-Transcriptional Control
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Levels of Gene Control:
What are the two key processes in Post-Transcriptional Control? (2)
1. mRNA processing (intron removal)
2. mRNA transport (nucleus to cytoplasm)
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Levels of Gene Control:
What happens during Translational Control?
mRNA is translated into a protein.
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Levels of Gene Control:
What is Post-Translational Modification?
Protein undergoes modifications (e.g., folding, phosphorylation) to become active.
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Types of Regulatory Elements:
What are the two main types of regulatory elements? (2)
1. Cis-Regulators
2. Trans-Regulators
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Types of Regulatory Elements:
- Specific DNA sequences that regulate genes on the same chromosome.
- Control which genes are transcribed in specific cells.
Cis-Regulators
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Types of Cis-Regulators:
- Required for RNA polymerase binding and transcription initiation.
- Upstream (~30 bp) from the transcription start site.
- Specifies the time and place of transcription initiation.
Promoters
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Types of Cis-Regulators:
- Increase transcription efficiency and rate by binding transcription factors.
- At the 5’ or 3’ ends of genes and in introns.
- Activate promoters on the same chromosome.
Enhancers
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Promoter Structure & Function:
What is the key sequence found in the promoter?
TATA sequence (TATA box or Goldberg-Hogness box)
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Promoter Structure & Function:
Where is the TATA box located?
~30 base pairs upstream of the transcription start site.
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Promoter Structure & Function:
Helps RNA polymerase bind and initiate transcription.
TATA sequence (TATA box or Goldberg-Hogness box)
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Promoter Structure & Function:
How can the functional anatomy of promoters be analyzed?
By determining which bases are essential for efficient transcription.
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Eukaryotic Transcription Initiation:
Why can’t RNA polymerase II bind directly to DNA?
It requires protein factors for proper transcription.
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Eukaryotic Transcription Initiation:
What helps RNA polymerase II bind to the promoter?
Basal transcription factors
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Eukaryotic Transcription Initiation:
Binds to the TATA box and prevents nucleosome formation.
TFIID
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Eukaryotic Transcription Initiation:
Recognizes and binds to the TATA box.
TBP (TATA-binding protein)
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Eukaryotic Transcription Initiation:
Which transcription factor stabilizes TFIID?
TFIIA
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Eukaryotic Transcription Initiation:
Helps RNA polymerase II attach to the complex.
TFIIB
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Eukaryotic Transcription Initiation:
What additional factors help RNA polymerase II function? (3)
- TFIIE
- TFIIF
- TFIIH
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Eukaryotic Transcription Initiation:
Unwinds DNA and releases RNA polymerase for transcription.
TFIIH
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Transcription:
- Proteins that stabilize TBP and support transcription.
- Prevent TBP from detaching from the TATA box.
TBP-associated factors (TAFs)
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Types of Cis-Regulators:
A DNA sequence that activates promoter usage, controlling transcription efficiency and rate.
Enhancer
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Types of Cis-Regulators:
What activates promoter usage?
Enhancer
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Enhancer Structure & Function:
What do enhancers control?
Transcription efficiency and rate
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Enhancer Structure & Function:
How do enhancers function?
Bind transcription factors
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Enhancer Structure & Function:
What do enhancers regulate? (2)
- Tissue-specific
- temporal gene expression
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Enhancer Structure & Function:
Where are enhancers located?
Far from promoters
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Enhancer Structure & Function:
What kind of genes do enhancers activate?
Cell-type specific genes
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Enhancer Structure & Function:
1. What study examined pancreatic gene enhancers?
2. What gene was used as a reporter in that study?
1. Walker et al. (1983)
2. CAT gene (chloramphenicol acetyltransferase)
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Enhancers - Walker et al. (1983):
Which cells activated the insulin enhancer?
Insulin-producing cells
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Enhancers - Walker et al. (1983):
Which cells activated the chymotrypsin enhancer?
Exocrine cells
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Enhancers - Walker et al. (1983):
What is the role of enhancers in cell specificity?
Turn on genes in specific cells
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Enhancers - Walker et al. (1983):
What type of enhancer inhibits transcription?
Silencer
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What are the three (3) major domains of transcription factors?
- DNA-binding domain
- Trans-activation domain
- Protein-protein interaction domain
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What binds to enhancers or promoters?
Transcription factors
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What are transcription factors classified by?
Structure
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Major domains of transcription factors:
What domain recognizes DNA sequences?
DNA-binding domain
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Major domains of transcription factors:
What domain regulates transcription?
Trans-activating domain
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Major domains of transcription factors:
What domain interacts with other proteins?
Protein-protein interaction domain
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DNA sequences that block transcription, restricting gene expression to specific cells or controlling timing.
Silencers
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Silencers:
1. What gene is transcribed only after gut development in fetal mouse liver?
2. What cells initially do not transcribe the albumin gene?
3. What tissue signals liver formation?
4. What happens when the endodermal tube contacts heart-forming cells?
1. Serum albumin
2. Endodermal cells
3. Cardiac mesoderm
4. Silencer is released
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List the six (6) trans-regulatory factors (transcription factors that regulate gene expression by binding to DNA regulatory sequences (such as enhancers or promoters) to control transcription).
1. Homeodomain Proteins
2. Zinc Finger Standard
3. Basic Helix-Loop Helix TF (bHLH)
4. Basic Leucine Zipper (bZip)
5. Nuclear Hormone Receptors
6. Sox-2 TF
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Trans-Regulatory Factors:
- Function: Specify anterior-posterior body axes.
- Structure: 60 amino acids in a helix-turn-helix; the third helix binds the major groove, amino-terminal contacts the minor groove.
- Small amino acid changes alter DNA sequence recognition.
Homeodomain proteins
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What do homeodomain proteins specify?
Anterior-posterior body axes
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What structure do homeodomain proteins have?
Helix-turn-helix
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What binds the major groove in homeodomain proteins?
Helix 3
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What are the two (2) homeodomain proteins/homeodomain transcription factors?
- Hox Transcription Factor
- Pou (Pit-Oct-Unc) Transcription Factor
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Homeodomain proteins:
What do Hox TF mutations cause?
Homeosis - the transformation of one structure of the body into the homologous structure of another body segment.
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Homeodomain proteins: POU Transcription Factor:
What two (2) regions form the POU domain?
Homeodomain + second DNA-binding region
101
Homeodomain proteins: POU Transcription Factor:
What pituitary-specific TF activates GH and prolactin?
Pit-1 (GHF1)
102
Homeodomain proteins: POU Transcription Factor:
What ubiquitous TF binds an 8-bp octa-box sequence?
Oct1
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Homeodomain proteins: POU Transcription Factor:
What B-cell-specific TF activates Ig genes?
Oct2
104
Homeodomain proteins: POU Transcription Factor:
What POU TF determines neuron fate in nematodes?
UNC-86
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Trans-Regulatory Factors:
Transcription factors that use zinc finger domains to bind DNA. The zinc ion stabilizes the structure.
Zinc Finger Standard
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Trans-Regulatory Factors: Zinc Finger Standard:
What stabilizes zinc fingers?
2 cysteines + 2 histidines
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Trans-Regulatory Factors: Zinc Finger Standard:
1. What TF is critical for kidney and gonad development?
2. What TF regulates hindbrain development?
1. WT
2. Krox 20
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Trans-Regulatory Factors:
- Binds DNA via a basic amino acid region (10-13 residues).
- Forms dimers with positive/negative regulators.
Basic Helix-Loop-Helix (bHLH) TFs
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Trans-Regulatory Factors: Basic Helix-Loop Helix (bHLH) TFs:
1. What muscle-specific TF forms a complex with E12/E47?
2. What differentiation inhibitor forms a complex with E12/E47?
1. MyoD
2. Id
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Trans-regulatory Factors:
- Structure: α-helix with leucine residues, forms Leucine Zipper dimers.
- These TFs contain a leucine zipper motif, which facilitates dimerization and DNA binding.
Basic Leucine Zipper (bZip) TFs
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Trans-regulatory Factors: Basic Leucine Zipper (bZip) TFs:
What bZip TF is involved in liver differentiation?
C/EBP
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Trans-Regulatory Factors:
- Mediate hormone effects on genes.
- Functions: Secondary sex determination & craniofacial development.
Nuclear Hormone Receptors
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Trans-Regulatory Factors: Nuclear Hormone Receptors
What do nuclear hormone receptors mediate?
Hormone effects on genes
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Trans-Regulatory Factors: Nuclear Hormone Receptors
What two (2) processes are controlled by nuclear hormone receptors?
- Secondary sex determination
- craniofacial development
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Trans-regulatory Factors:
- Sry-Sox bends DNA from “I” to “L”.
- Important in mammalian sex determination.
Sox-2 TFs
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Trans-regulatory Factors: Sox-2 TFs
What does Sry-Sox do to DNA?
Bends from "I" to "L"
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Trans-regulatory Factors: Sox-2 TFs
Give an example of a Sox TF. (3)
- Sry
- SoxD
- Sox2
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What are the three (3) types of RNA Polymerase?
- RNA Polymerase I
- RNA Polymerase II
- RNA Polymerase III
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What does RNA Polymerase I transcribe?
Large rRNAs
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What does RNA Polymerase II transcribe?
mRNA precursors
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What does RNA Polymerase III transcribe?
tRNA, small RNAs
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Transcription of a Gene:
What determines which genes are transcribed and expressed?
Cell differentiation
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Transcription of a Gene:
What is added to the 5′ end of pre-mRNA?
7-methyl-guanylate (Capping)
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Transcription of a Gene:
What is added to the 3′ end of pre-mRNA?
Poly-A tail (Polyadenylation)
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Transcription of a Gene:
Function of polyadenylation? (3)
- mRNA stability
- exit
- translation
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Transcription of a Gene:
What removes introns from pre-mRNA?
Splicing
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Transcription of a Gene:
Transcriptional Control
What allows one gene to produce different proteins?
Alternative splicing
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Transcriptional Control:
What regulates gene activity through chemical modifications?
Epigenetic mechanism
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Transcriptional Control:
What inactivates genes through chemical modification?
DNA methylation
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Transcriptional Control:
What modification allows transcription by unpacking DNA?
Histone acetylation
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DNA Methylation:
Where does DNA methylation occur to regulate genes?
Promoters (Cytosine residues)
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DNA Methylation:
Effect of promoter methylation?
Gene inactivation
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DNA Methylation:
What is the role of genomic imprinting?
Differentiates maternal/paternal genes
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DNA Methylation:
What ensures dosage compensation in females?
X-chromosome inactivation
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Histone Methylation:
What histone is methylated for gene silencing?
H3-K9
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Histone Methylation (H3-K9 Methylation):
What does histone methylation promote?
Chromatin repression
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Histone Methylation (H3-K9 Methylation):
Binds methylated H3-K9, silences genes
HP1 proteins
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Histone Methylation (H3-K9 Methylation):
What structure results from histone methylation?
Closed chromatin
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Mammalian X-Chromosome Dosage Compensation:
Why is X-chromosome dosage compensation needed?
Equal X-linked gene expression
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Mammalian X-Chromosome Dosage Compensation:
How do Drosophila achieve dosage compensation?
Increase male X transcription
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Mammalian X-Chromosome Dosage Compensation:
How do mammals achieve dosage compensation?
X-chromosome inactivation
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X-Chromosome Inactivation:
What type of chromatin does an inactivated X form?
Heterochromatin
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X-Chromosome Inactivation:
When does X-chromosome inactivation occur?
Implantation
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X-Chromosome Inactivation:
Is X-chromosome inactivation reversible?
No
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Effects of Mutant X Chromosome in Mice:
1. What happens to ectodermal cells?
2. What layer fails to form?
3. When does embryonic death occur?
1. Cell death
2. Mesoderm
3. By day 10
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Histone Acetylation & Deacetylation:
What happens when histones are acetylated?
Chromatin opens
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Histone Acetylation & Deacetylation:
What removes the positive charge of histones?
Acetylation
148
Histone Acetylation & Deacetylation:
What condenses chromatin and silences genes?
Deacetylation
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Polyadenylation:
1. What enzyme adds the poly-A tail?
2. Approximate number of adenylate nucleotides added?
1. Poly(A) polymerase
2. 150-200
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1. What domain initiates transcription?
2. What is produced during transcription initiation?
1. CTD (Carboxyl Terminal Domain)
2. 5'-triphosphorylated transcript
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Key Transcription Proteins (3)
1. TFs + TFs → TIC (Transcription Initiation Complex)
2. TBP-AF – Coactivators
3. Mediator Complex
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Key Transcription Proteins:
Formation of the transcription initiation complex with RNA Polymerase II.
TFs + TFs → TIC (Transcription Initiation Complex)
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Key Transcription Proteins:
TBP (TATA-binding protein) and its associated factors (TAFs) help recruit TFs and RNA Pol II.
TBP-AF – Coactivators
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Key Transcription Proteins:
Bridges activators with the transcription machinery for efficient transcription.
Mediator Complex
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Transcription Complex & Enhanceosome Complex:
What does HMG-1 (High Mobility Group 1) do?
DNA Bending
156
Transcription Complex & Enhanceosome Complex:
What is the function of the enhanceosome complex?
Facilitates transcription regulation
157
Transcriptional Control of Genes:
1. What percentage of genes are typically repressed?
2. What percentage of genes are expressed in a cell?
1. 90%
2. 10%
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Control Before Transcription:
What process amplifies genes for increased mRNA and ribosome production?
Selective gene amplification
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Control Before Transcription:
Where are lampbrush chromosomes found?
Amphibian oocytes
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Control Before Transcription:
What immune cells undergo gene rearrangement?
B- and T-lymphocytes
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Control Before Transcription:
What does gene rearrangement produce?
10 million immunoglobulins (Igs)
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Control After Transcription:
What chemical modification is involved in gene imprinting?
Methylation
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Control After Transcription:
What process leads to mosaic tissue effects (e.g., calico cats)?
X-chromosome inactivation
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Control After Transcription:
What effect does deacetylation have on chromatin?
Tightens chromatin, represses transcription
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Control After Transcription:
What stabilizes mRNA by adding ~200 adenyl groups?
Polyadenylation
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Levels of Gene Control:
What determines which transcripts are processed into mRNAs?
Censorship
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Levels of Gene Control:
What percentage of human genes undergo alternative splicing?
75%
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Levels of Gene Control:
What is the example of alternative splicing in different tissues?
Tropomyosin (muscle vs. neuronal cells)
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Post-Transcriptional Gene Silencing (PTGS):
Another name for PTGS?
RNA interference (RNAi)
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Post-Transcriptional Gene Silencing (PTGS):
What happens to genes in PTGS?
Down-regulation at the RNA level
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Post-Transcriptional Gene Silencing (PTGS)
What is an example of transcriptional gene silencing (TGS)? (2)
- Retroviral genes
- transposons
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Alternative mRNA Splicing:
What complex removes introns during splicing?
Spliceosome
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Alternative mRNA Splicing:
What joins exons after intron removal? (2)
Splicing factors (SF) & snRNPs
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Alternative mRNA Splicing:
Why is alternative splicing important?
Increases protein diversity
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Alternative mRNA Splicing:
What human health issue is linked to splicing defects?
Diseases
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Types of Alternative mRNA Splicing (5)
1. Alternative 5’ Splicing
2. Alternative 3’ Splicing
3. Intron Retention
4. Mutually Exclusive Exons
5. Exon Skipping
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Types of Alternative Splicing:
What type of splicing includes/excludes a 5’ exon portion?
Alternative 5’ splicing
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Types of Alternative Splicing:
What gene’s splicing determines apoptosis regulation?
Bc1 X
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Types of Alternative Splicing:
What type of splicing affects the 3’ exon?
Alternative 3’ splicing
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Types of Alternative Splicing:
What type of splicing keeps an intron in mRNA?
Intron retention
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Types of Alternative Splicing:
What type of splicing selects different exons for different mRNAs?
Mutually exclusive exons
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Types of Alternative Splicing:
What is an example of exon skipping?
FGFR2 gene
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1. What is a hybrid between a zebra and a donkey?
2. How does this hybrid foal compare to a zebra foal (size)?
1. Zebroid
2. Twice as large
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What determines mRNA stability?
Poly(A) tail length
185
How does polyadenylation affect translation?
Increases stability & translation rates
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Which milk protein's mRNA half-life increases due to prolactin? How much does this mRNA stability increase in lactation?
- Casein
- 28-fold
187
What happens to stored oocyte mRNAs before fertilization?
Dormant
188
What activates stored mRNAs?
Ionic signals (fertilization/ovulation)
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What proteins control cell fate in Drosophila embryos? (2)
Bicoid & nanos
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What regulates mRNA translation through spatial control?
Cytoplasmic localization
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Which mRNA is transported to the vegetal pole in frog oocytes?
Vg1
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Where does Vg1 mRNA remain after fertilization?
Vegetal blastomeres
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How does cell differentiation occur?
Selective gene expression
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At what levels is gene expression regulated?
Multiple levels (transcription to translation)
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What controls specific gene expression?
Transcription factors (TFs)
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How does gene regulation function?
As a network
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How do genes interact with protein synthesis?
Dynamic feedback system
