Developmental Genetics & Epigenetics Lecture Notes

A series of flashcards covering key vocabulary and concepts from the lecture notes on developmental genetics, epigenetics, mutations, DNA repair, cancer genetics, and biotechnology.

Reporter Genes

Inserting a visible gene (like GFP for fluorescence or LacZ/Lactase for color) under a specific promoter to see where that gene is "turned on".

Morphogens

Molecules that establish a concentration gradient to influence cell fate.

Myostatin

A repressor that inhibits muscle growth. A "knockout" results in double muscle phenotypes.

Histone Acetylation (HATs)

Adds acetyl groups to lysine tails. This neutralizes the positive charge, loosening DNA for more expression.

Histone Methylation

PRC2 adds methyl groups to H3K27, tightening chromatin for less expression.

DNA Methylation (DNMTs)

Adds methyl groups to CpG islands. This is "remembered" across cell divisions and silences genes.

Genomic Imprinting

Process where one allele is silenced by methylation based on the parent of origin.

• Paternal IGF2: Promotes fetal growth.

• Maternal IGF2R: Limits growth to save resources.

RISC

• (RNA-Induced Silencing Complex):Works on mRNA in the cytoplasm to inhibit translation (miRNA) or degrade mRNA (siRNA).

RITS

RNA-Induced Transcriptional Silencing complex : Works on DNA in the nucleus to recruit methyltransferases and stop transcription.

lncRNA

Long noncoding RNA that can act as a scaffold for gene regulation.

 XIST for X-inactivation).

Silent Mutation

Mutation that does not change the amino acid sequence.

Missense Mutation

Mutation that results in a single amino acid change.

Nonsense Mutation

Mutation that introduces a premature stop codon.

Frameshift Mutation

Mutation caused by insertion or deletion of nucleotides, altering the reading frame.

Mismatch Repair (MMR)

• During S-phase. Uses methylation on the old strand to know which side to fix.

Nucleotide Excision Repair (NER)

•  Fixes bulky lesions like thymine dimers.

Base-Excision Repair (BER)

Mechanism to repair genetic damage by removing and replacing single nucleotides.

Aneuploidy

Abnormal number of individual chromosomes, e.g., Trisomy 21.

Polyploidy

Extra sets of chromosomes (Common in plants).

Oncogenes

Mutated proto-oncogenes that lead to uncontrolled cell division. Dominant gain-of-function (like a stuck gas pedal). Example: Ras (GTP-bound always "on").

Tumor Suppressor Genes

 Normally inhibit division Normally inhibit division. Recessive loss-of-function (like broken brakes). Example: p53 (triggers apoptosis/repair).

BRCA1/2: Repair double-stranded breaks; mutations lead to inherited cancer risk.

BRCA1/2

Genes involved in the repair of DNA double-strand breaks, mutations increase cancer risk.

PCR

Polymerase Chain Reaction, a method used to amplify DNA.

Gel Electrophoresis

Technique that separates DNA fragments based on size. Moves DNA toward the positive end; smaller fragments move faster.

Induced Pluripotent Stem Cells (iPSCs)

Adult cells reprogrammed to a pluripotent state using specific master genes.

Epigenetic Memory

The persistence of DNA methylation patterns across cell divisions.

Haploinsufficiency

Condition where a single functional copy of a gene is insufficient to generate a normal phenotype.

Fragile X Syndrome

Genetic disorder caused by an expanding nucleotide repeat (specifically the triplet CGG) in the FMR1gene on the X chromosome.-Polyglutamine,

The Mechanism:

• Normal individuals have a few repeats.

• Affected individuals have hundreds of repeats.

• Excessive repeats lead to DNA methylation of the promoter, which silences the gene.

• The "Fragile" Site: Under a microscope, the X chromosome appears to have a "break" or a thin thread at the end of the long arm because the DNA is not properly condensed.

• Phenotype: It is the leading cause of inherited intellectual disability and is more severe in males (who only have one X)..

Prader-Willi Syndrome

• Cause: Deletion of a specific region on Chromosome 15 inherited from the Father.

Phenotype: Chronic overeating (obesity), small hands/feet, intellectual disability.

Angelman Syndrome

• Cause: Deletion of the same region on Chromosome 15, but inherited from the Mother.

• Phenotype: "Happy puppet" syndrome—frequent laughter, jerky movements, and severe speech impairment.

totipotent

can form an entire organism (including the placenta);p

• Pluripotent (like iPSCs)

• can form any body tissue but not the whole organism.

 four master regulator genes used to create iPSCs (Induced Pluripotent Stem Cells):

1. Oct4

2. Sox2

3. Klf4

4. c-Myc

Reverse Transcriptase

Hox Genes

Hox Genes

Master regulators that give segments their identity (e.g., legs vs. antennae).

Epigenetic Memory

DNA methylation patterns are passed to daughter cells during mitosis.

BT Toxin

A bioinsecticide gene from bacteria that causes paralysis and death in pests.

c-Met Signaling

• is involved in cell proliferation, migration, and embryogenesis, but it does not typically induce apoptosis (programmed cell death).

Beckwith-Wiedemann Syndrome:

• Cause: Imbalance in the IGF2/IGF2R imprinting (growth factors).

• Phenotype: Overgrowth syndrome; infants are much larger than normal and have an increased risk of tumors.

• Down Syndrome (Trisomy 21)

Three copies of chromosome 21. Often caused by nondisjunction during meiosis.

Cri-du-chat Syndrome:

• Caused by a deletion on the short arm of Chromosome 5.Haploinsufficiency—one copy of the gene isn't enough to produce a normal phenotype (e.g., the abnormal larynx that causes the "cat-cry" sound).

Human Chromosome 2 (Evolutionary Note):

• Our chromosome 2 is the result of a Robertsonian Translocation(fusion) of two smaller chromosomes found in great apes.

Xeroderma Pigmentosum (XP):

• Cause: Mutation in the Nucleotide Excision Repair (NER) pathway.

• Result: The body cannot fix thymine dimers caused by UV light. Patients have a 1000x higher risk of skin cancer.

• Lynch Syndrome (HNPCC):

• Cause: Mutation in the Mismatch Repair (MMR) genes.

• Result: High risk of colon and ovarian cancers because replication errors aren't caught.Li-Fraumeni Syndrom

Li-Fraumeni Syndrom

• Cause: Inherited mutation in p53 (the "guardian of the genome").

• Result: Extremely high risk of developing many different types of cancer at a young age.

•  What is the molecular cause of Fragile X Syndrome?

An expansion of CGG nucleotide repeats in the FMR1 gene, leading to DNA methylation and gene silencing.

• Why do Prader-Willi and Angelman syndromes differ if they have the same deletion?

• Genomic Imprinting. Prader-Willi is a paternal deletion; Angelman is a maternal deletion of the same region on Chromosome 15.

A patient cannot repair thymine dimers caused by sunlight. What disorder do they have, and what pathway is broken?

 Xeroderma Pigmentosum (XP); the Nucleotide Excision Repair (NER) pathway is defective

Define Haploinsufficiency in the context of Cri-du-chat.

• When a single functional copy of a gene (due to a deletion of the other copy) is not enough to produce a normal phenotype.

 What is the "Guardian of the Genome" and what happens if it is mutated?

•  If mutated, it leads to Li-Fraumeni Syndrome, where cells cannot arrest the cell cycle or undergo apoptosis in response to DNA damage.

• Determination

• Determination: Signals (growth factors) turn on the myoD gene. The cell becomes a myoblast. It is now "determined" but doesn't look like muscle yet.

• Differentiation

• Differentiation: The MyoD protein turns on other genes like Myosin and p21 (to stop the cell cycle). The cells fuse to become muscle fibers.

gene gun process.

 involves accelerating DNA-coated particles (usually gold or tungsten) into cells using high-pressure ga

• Somatic:

• Occur in body cells; passed to clones via mitosis.

Germ-line:

Germ-line: Occur in reproductive cells; passed to future generations via meiosis

• Nature of Cancer:

• A family of diseases caused by unique combinations of genetic errors.

• Drivers vs. Passengers:

• Driver mutations contribute to cancer; passenger mutations have no effect.

• HER2:

• A growth factor receptor that fuels 10% of breast cancers; targeted by Herceptin.

Transitions:

(Purine to Purine, A↔G).

Transversions:

: Purine to Pyrimidine (A↔C/T).

Conservative mutation

if the mutated amino acid has similar biochemical properties (-acid to acid).

Radical mutation

if the mutated amino acid has different biochemical properties (-acid to base).

Neutral mutation

• there is no change in function-but any effects present are detrimental. 

Translocations

• Reciprocal ( or Robertsonian

• Reciprocal

• Reciprocal (exchange between chromosomes)

• Robertsonian

• (two chromosomes fuse, like Human Chromosome 2).

Repair Mechanism

Accuracy

When it Acts

What it Fixes

Mismatch Repair

Highly Accurate

S-phase

Replication errors (A-G, C-T)

Repair Mechanism

Accuracy

When it Acts

What it Fixes

Homologous Recombination

Error-Free

After replication

Double-strand breaks (uses template)

Repair Mechanism

Accuracy

When it Acts

What it Fixes

Non-Homologous End Joining

Error-Prone

Anytime

Double-strand breaks (no template)

Repair Mechanism

Accuracy

When it Acts

What it Fixes

Nucleotide Excision (NER)

Accurate

Anytime

Bulky lesions like thymine dimers

• Cloning Vector:

• For making copies of DNA.

Expression Vector

Expression Vector: For making the protein product.

• Transformation

• Transformation: Taking up DNA from the environment. <15kb

Transduction

Transduction: DNA delivered by a virus.25kb

Prairie Voles

(Monogamous): Possess a longer microsatellite repeat, leading to higher receptor expression and increased social bonding. High density of Vasopressin receptors in the brain.

Meadow Voles (Polygamous):

Possess a shorter micro satellite, leading to lower receptor expression and a lack of pair-bonding.-more sexually promiscuous behavior. Low density of Vasopressin receptors in the brain.

Huntington Disease:

Caused by an expanding nucleotide repeat (CAG). Unlike Fragile X (which is silenced), Huntington's involves a "toxic gain of function" where the mutant protein kills brain cells.

Achondroplasia (Dwarfism):

A constitutively active mutation in the FGFR3 gene (a growth factor receptor). This is a dominant gain-of-function mutation where the receptor is "stuck on," inhibiting bone growth.

Familial Adenomatous Polyposis (FAP):

Caused by a mutation in the APC gene (a tumor suppressor). Patients develop thousands of polyps in the colon, leading to a near 100% risk of colon cancer if left untreated.

What are the two essential components of the CRISPR system?

Cas9 protein (the scissors) and sgRNA (the guide that finds the target DNA).

Cas9 Protein

An enzyme that acts as "scissors" to cut DNA at a specific location.

Single Guide RNA (sgRNA):

Single Guide RNA (sgRNA): A custom-designed RNA sequence that "guides" the Cas9 protein to the exact matching DNA sequence in the genome

Oxytocin Functions:

• Childbirth: Stimulates uterine smooth muscle contractions.

• Milk Letdown: Stimulates the contraction of breast smooth muscle so milk can be released.

• Behavior: Facilitates maternal bonding, trust, and social recognition.

Vasopressin Functions:

• Water Conservation: Regulates kidney function and electrolyte balance.

• Blood Pressure: Causes blood vessel constriction

The Signaling Pathway for oxytocin:

These neuropeptides bind to receptors on the cell surface, triggering a phosphorylation cascade that leads to a specific cellular response (like muscle contraction or gene expression)

Cloning by Embryo Splitting

Cloning by Embryo Splitting: Dividing a developed embryo into multiple parts and implanting them in surrogate mothers to create genetically identical individuals

Ectogenesis

Ectogenesis: The growth of a fetus outside of the human body using artificial wombs.

iPSCs in Reproduction

iPSCs in Reproduction: The ability to potentially create "embryoids" (artificial embryos) from stem cells without needing sperm or eggs.

pseudogenes

These are "fossil" genes that have accumulated so many mutations that they are no longer functional. We still have the DNA for them, but they are "turned off" permanently.exhuman egg-laying genes).

Robertsonian Translocation (fusion) History

Human Chromosome 2 was formed by the fusion of two separate chromosomes that remain separate in chimpanzees and gorillas. This explains why humans have 46 chromosomes while other great apes have 48.

why you use Reverse Transcriptase to make a human protein in a bacteria.

Bacterial cells do not have Spliceosomes. If you give them a human gene with introns, they cannot cut them out, and the resulting protein will be gibberish. Take human mRNA (which has already had the introns removed), use Reverse Transcriptase to turn it back into DNA (called cDNA), and give that to the bacteria.

"Two-Hit Hypothesis"—

you are born with one "hit" (mutation), so it only takes one more mutation in any cell to start a tumor.

How does the Two-Hit Hypothesis relate to inherited cancer (like Li-Fraumeni)?

Individuals inherit one mutated copy of a tumor suppressor gene (Hit 1). They only need one spontaneous mutation in the second copy (Hit 2) in any cell to develop cancer.

Constitutively Active mutation using an example.

• : A mutation where a protein is "always on." Example: Achondroplasia (FGFR3 is always signaling to stop bone growth) or Ras in cancer.

multipotent

Restricted to a specific tissue lineage (e.g., blood cells). Vital for maintaining and repairing the tissue they are found in, such as blood, bone, or skin.

Induced pluripotent stem cells are ____________ cells

that are reprogrammed by introducing _____________

genes.

somatic (body), master regulator

Uses bacteria to introduce foreign DNA into genome of plant cells to

make genetically modified crops: ____________

Agrobacterium

Transformation in bacterial cells allow for

horizontal gene transfer

Cells that have permeable membranes and can readily take up DNA:

competent cells

Cloning Vector

● Small piece of DNA in which

foreign DNA can be inserted

and then transferred into host

● Used to obtain multiple copies

of inserted DNA segment