1
Q
bred thousands of pea plants (Pisum sativum) in his abbey garden. He discovered that traits aren’t “blended” like paint, but passed down as discrete “factors” (which we now call genes).
The Father of Genetics
A
Gregor Mendel:
2
Q
Gregor Mendel:
States that for any given trait, one allele (dominant) will mask the presence of another allele (recessive) in the phenotype, ensuring that heterozygous offspring express only the dominant trait.
A
Law of Dominance and Uniformity:
3
Q
Gregor Mendel:
Proposes that every individual possesses two alleles for any particular trait, which separate (segregate) during gamete formation (meiosis). As a result, each gamete carries only one allele, and offspring inherit one allele from each parent.
A
Law of Segregation:
4
Q
Gregor Mendel:
Dictates that alleles for different traits are distributed to sex cells independently of one another. The inheritance of one trait (e.g., color) does not affect the inheritance of another (e.g., shape).
A
Law of Independent Assortment:
5
Q
A Dutch botanist who worked with evening primroses. He is credited with introducing the concept of mutations—sudden changes in genes that lead to new traits. According to de Vries’ mutation theory, living organisms can develop changes to their genes that greatly alter the organism
A
Hugo de Vries
6
Q
A German botanist who worked with maize and peas. He was instrumental in defining “Mendelism” and later discovered incomplete dominance (where traits do sometimes blend, like red and white flowers making pink)
A
Carl Correns
7
Q
An Austrian agronomist who verified Mendel’s laws through his work with various legumes. While some historians debate the depth of his theoretical understanding compared to the others, his simultaneous publication helped cement the “Laws of Inheritance.” Rediscovered Mendel’s laws in 1900.
A
Erich von Tschermak
8
Q
In 1905, he coined the term “Genetics”
He also introduced the essential vocabulary we still use today to describe alleles:
Homozygous: Having two of the same alleles.
Heterozygous: Having two different alleles.
Allele: Originally “allelomorph,” describing the alternative forms of a gene.
A
William Bateson
9
Q
punnett square, allowed scientists and students to visually “see” how alleles from two parents could combine. It remains one of the most used tools in biology classrooms today.
A
Reginald punnett
10
Q
The Journal of Genetics was founded in 1910 by the duo
A
William Bateson and Reginald Punnett.
11
Q
took the Greek word gonos (birth/origin) and shortened it to “gene.”
A
Wilhelm Johannsen
12
Q
Selection is ineffective in a Pure Line, why?
A
Because there is no genetic variation (geno, you cannot change the average size of the offspring by picking the biggest parents
13
Q
was an American graduate student working with Brachystola magna (a large lubber grasshopper). Grasshoppers were the perfect “model organism” because their chromosomes are large and easy to see under a microscope.
He watched chromosomes pair up and then separate during meiosis (the creation of sperm and egg cells).
A
Walter Sutton
14
Q
German biologist experimenting with sea urchins. He fertilized sea urchin eggs with two sperm at once, creating embryos with the wrong number of chromosomes. He found that the embryos only developed normally if they had a full set of chromosomes. If even one was missing or extra, the embryo was deformed or died.
A
Theodore Boveri
15
Q
She noticed that female mealworms had 20 large chromosomes (a matching set). However, the males had 19 large ones and one tiny “misfit” chromosome. Led to the discovery of chromosome carrying factors.
A
Nettie Stevens
16
Q
when an organism has two identical alleles for a particular trait
A
Homozygous
17
Q
When an organism has two different alleles for a trait
A
Heterozygous
18
Q
sex chromosomes Found in mammals (including humans), many fishes, and some amphibians.
A
XX/XY System
19
Q
sex chromosomes Common in birds, all snakes, and some lizards.
A
ZW/ZZ System
20
Q
Morgan was initially skeptical of both Mendel’s laws and the chromosome theory. However, his discovery of a single white-eyed male fruit fly in 1910 changed everything.
Sex-Linkage: He proved that the gene for eye color was located specifically on the X chromosome, providing the first solid evidence that genes have physical locations.
The Model Organism: He established Drosophila melanogaster as the primary tool for genetic research because they breed quickly and have easily observable traits.
A
Thomas Hunt Morgan
21
Q
While still an undergraduate in Morgan’s lab, Sturtevant realized that the frequency of “crossing over” could be used to determine the distance between genes.
The First Map: In 1913, he stayed up all night to create the world’s first genetic map.
Linear Order: He proved that genes are arranged in a specific, linear order along the chromosome, much like the map you provided in your third image.
A
Alfred Sturtevant
22
Q
Nondisjunction: He observed rare instances where chromosomes failed to separate properly during meiosis. He showed that when chromosomes moved incorrectly, the corresponding traits moved with them, proving beyond any doubt that chromosomes carry the genetic material.
A
Calvin Bridges
23
Q
was interested in how new genetic variations (mutations) were created, a topic Hugo de Vries had wondered about years earlier. He discovered that exposing fruit flies to X-rays vastly increased the rate of genetic mutations. This work won him the Nobel Prize and was the first to prove that environmental factors like radiation could physically damage and change the hereditary code.
A
Hermann Muller
24
Q
Continuous variation is compatible with Mendelian genetics.
Selection acts on these small, additive differences, allowing for the slow, gradual evolution Darwin described.
core insight was that if many different genes each contribute a small, additive amount to a single trait, the result in a population will be a Bell Curve (Normal Distribution). This explains why we don’t just see “tall” or “short” people, but every height in between. Polygenic systems for sex determination, where multiple genes interact rather than a single switch. This same logic applies to traits like height.
A
Ronald Fisher
25
wanted to know what genes actually did for a living. In 1941, they shifted from studying the physical traits of fruit flies to the internal chemistry of bread mold (Neurospora crassa)
Normal Mold: Can grow on a "minimal medium" (just sugar, salts, and one vitamin) because it has the internal enzymes to build everything else it needs.
Mutant Mold: After being zapped by X-rays, some mold could no longer grow on the minimal medium.
George Beadle and Edward Tatum
26
Hypothesis discovered by George Beadle and Edward Tatum
By testing different mutants, they discovered that each mutation blocked a specific step in a chemical pathway.
If a gene was broken, the specific enzyme controlled by that gene was missing.
This proved that a gene's primary job is to provide the instructions for building a specific protein (specifically, an enzyme).
"One Gene, One Enzyme" Hypothesis
27
was an expert in X-ray crystallography. She produced the most precise images of DNA ever seen, including the famous "Photo 51."
Rosalind Franklin
28
used cardboard and metal models to "puzzle out" the structure of DNA based on Franklin’s data and Erwin Chargaff’s rules
The Double Helix: They realized DNA consists of two strands twisting around each other, held together by base pairs.
The Code: They famously noted that the specific pairing suggested a "copying mechanism" for genetic material.
James Watson & Francis Crick:
29
was Franklin's colleague at King's College. While their relationship was strained, he was the one who initially began the X-ray study of DNA.
Maurice Wilkins
30
transformed restriction enzymes from a biological curiosity into the foundational tools of modern biotechnology.
Restriction enzymes are specialized proteins found in bacteria that act as a defense system against invading viruses
Werner Arber, Hamilton Smith and Daniel Nathans
31
The Restriction Enzyme Flowchart process
Start → DNA molecule is present.
↓
Select Restriction Enzyme → Choose enzyme based on specific recognition sequence (usually 4–8 bp).
↓
Bind to DNA → Restriction enzyme locates its specific recognition site on the DNA.
↓
Check for Methylation → Some enzymes cannot cut methylated DNA (important in bacteria to protect their own DNA).
↓
DNA Cleavage → Enzyme cuts DNA at or near recognition site:
Sticky ends (overhangs)
Blunt ends (straight cut)
↓
Result → DNA fragments of defined lengths ready for downstream applications like:
Cloning
Gel electrophoresis
DNA mapping
End
32
independently discovered that genes were not continuous strings of information, but were instead broken into pieces. This discovery shattered the "one gene, one protein" simplicity of the earlier era and showed that eukaryotic DNA is much more complex than bacterial DNA.
Richard Roberts and Phillip Sharp
33
independently discovered that genes were not continuous strings of information, but were instead broken into pieces. This discovery shattered the "one gene, one protein" simplicity of the earlier era and showed that eukaryotic DNA is much more complex than bacterial DNA.
Richard Roberts and Phillip Sharp
34
combined their expertise to perform what is essentially the "Holy Grail" of genetic engineering: they created the first recombinant DNA organism. This
The Organism: Escherichia coli (E. coli)
The primary host organism for their experiment was the bacterium Escherichia coli
Herbert Boyer and Stanley Cohen
35
Herbert Boyer and Stanley Cohen specific "molecular scissors" they used was the restriction enzyme
EcoRI
36
created the world's first recombinant DNA molecule. While Boyer and Cohen perfected the "pasting" into living bacteria, Berg proved that you could chemically join DNA from two completely different species in a test tube.
Paul Berg
37
Berg's landmark study involved combining DNA from two very different organisms:
SV40 Virus: A monkey virus that can cause tumors.
Lambda Phage: A virus that infects the bacterium E. coli.
38
Unlike Boyer and Cohen, who used sticky ends naturally produced by enzymes like EcoRI, Berg used a more laborious chemical approach called
terminal transferase
39
The CRISPR-Cas9 Flowchart
Start → Target gene or DNA sequence identified
↓
Design guide RNA (gRNA) → Complementary to target DNA sequence
↓
Assemble CRISPR-Cas9 complex → Cas9 protein + gRNA
↓
Binding to target DNA → gRNA guides Cas9 to specific DNA sequence
↓
DNA cleavage → Cas9 creates a double-strand break (DSB) at target site
↓
DNA Repair Pathway Activated → Cell repairs the break via:
Non-homologous end joining (NHEJ) → may introduce insertions or deletions (indels) → can knock out gene
Homology-directed repair (HDR) → uses a template DNA → can insert or correct a sequence
↓
Result → Genome successfully edited (gene knockout or precise insertion)
40
He is the only person to have won the Nobel Prize in Chemistry twice—first for protein sequencing and later for DNA sequencing.
Frederick Sanger
41
mRNA that encodes a single protein from one gene, commonly found in eukaryotes and featuring specialized caps and tails
Monocistronic
42
mRNA that encodes multiple, often functionally related, proteins on a single transcript, typical in prokaryotes (bacteria/archaea) for coordinated gene expression.
polycistronic
43
are used as high-resolution genetic markers to distinguish between individuals, populations, and species.
are highly variable because the number of repeats (like CACACA) changes frequently due to mutations.
Microsatellites
44
what analysis is used when an individual is heterozygous for a specific restriction site, it means they inherited two different versions of that DNA segment from their parents.
Restriction Fragment Length Polymorphism (RFLP)
45
Restriction Fragment Length Polymorphism (RFLP)
Homozygous Presence
You see only the two small fragments (indicating both chromosomes were cut).
46
Restriction Fragment Length Polymorphism (RFLP)
Homozygous Absence
You see only one large fragment (indicating neither chromosome was cut).
47
Restriction Fragment Length Polymorphism (RFLP)
Heterozygous Presence
You see all three fragments on the same lane of the gel.
48
CRISPR is termed a ________ technology because it shifts genetic modification from a process of discovery (finding natural mutations) to a process of engineering (creating specific changes on demand).
"designer"
49
codes for Lac repressor
lacI
50
codes for β-galactosidase (breaks lactose → glucose + galactose; makes allolactose)
lacZ
51
codes for lactose permease (imports lactose)
lacY
52
codes for thiogalactoside transacetylase
lacA
53
Scenario A: Lactose is ABSENT (The Default "OFF" State)
Step 1: lacI gene produces Repressor Protein.
Step 2: Repressor Protein binds tightly to the Operator.
Step 3: Physical "roadblock" is created; RNA Polymerase cannot move past the Promoter.
Result: Genes are OFF; no enzymes are made.
54
Scenario B: Lactose is PRESENT + Glucose is ABSENT (The "ON" State)
Step 1: Lactose enters the cell and is converted to Allolactose (the inducer).
Step 2: Allolactose binds to the Repressor Protein, changing its shape.
Step 3: The Repressor releases the Operator.
Step 4 (The Glucose Check): Since glucose is absent, cAMP levels are high.
Step 5: cAMP binds to CAP (Catabolite Activator Protein); This active cAMP-CAP complex binds to a specific site on the DNA right next to the Promoter. This step ensures that the operon doesn't just run at a slow "idle," but instead works at maximum capacity to produce enzymes.
Increasing Affinity: When the cAMP-CAP complex binds to the DNA, it physically "grabs" the RNA Polymerase and helps it lock onto the Promoter with much higher strength.
High Expression: Because the RNA Polymerase is now stuck firmly to the DNA, it transcribes the genes (lacZ, lacY, lacA) at a very high rate.
Result: Genes are ON (High Expression); enzymes are produced to digest lactose.
55
Scenario C: Both Lactose AND Glucose are PRESENT (The "IDLE" State)
Step 1: Because Lactose is present, it is converted to allolactose, so the Repressor is removed from the Operator.
Step 2: However, high glucose levels cause cAMP levels to drop. High levels of glucose inhibit the enzyme adenylyl cyclase, which is responsible for making cAMP.
Step 3: CAP cannot bind to the DNA without cAMP.
Step 4: RNA Polymerase binds poorly to the promoter without the "Turbo Boost" from CAP. The genes (lacZ, lacY, lacA) are transcribed at a very low, "leaky" level. The cell effectively ignores the lactose until the glucose supply is completely exhausted. Once glucose runs out, cAMP levels will rise, and the system will automatically switch to Scenario B (High Expression).
Result: Genes are OFF/LOW (Basal Expression); the cell prefers to eat glucose first.
56
describes messenger RNA (mRNA) that carries the code for only one specific protein
allowing for precise control over individual protein production, with post-transcriptional processing like splicing further tailoring the final protein.
Monocistronic
57
codes for multiple proteins, making it a fundamental feature of eukaryotic gene expression
polycistronic
58
Variation in histones
This is the process of adding an acetyl group to the "tails" of the histone proteins.
To turn a gene off, the acetyl groups are removed.
Acetylation and Deacetylation
59
This is the most common epigenetic modification. It involves adding a methyl group directly to a cytosine base, specifically where a cytosine is followed by a guanine (CpG sites) using DNA Methyltransferases (DNMTs)
DNA Methylation (Eukaryotic)
60
These are stretches of DNA (typically 500 to 2,000 base pairs long) that have an unusually high frequency of the "C-G" sequence.
While much of the eukaryotic genome is cluttered with "junk" DNA and highly methylated (silenced) regions, these islands are usually kept "clean" and accessible to allow for high levels of gene activity.
CpG Island
61
explain how deactylation and acetylation affects breast cancer
Acetylation: The "Open" sign. DNA is loose, and BRCA can do its job repairing the cell.
Deacetylation: The "Closed" sign. DNA is tightly packed, BRCA is locked away, and the cancer grows because repairs stop.
The Treatment (HDAC Inhibitors): These drugs "jam" the lock open, forcing the cell to read the BRCA manual again so it can either fix itself or realize it's too damaged and self-destruct.
62
explain DNA methylation affects colon cancer
The Simplified View
Normal Colon: Methylation is in the "background," and protective genes stay "clean" and active.
Colon Cancer: Methylation moves to the "foreground," painting the protective genes shut.
The Consequence: The cell can't fix its own DNA mistakes because the repair manual (MLH1) is glued shut.
The Medical Benefit: Doctors can detect these "misplaced" methyl groups in stool or blood samples to catch cancer much earlier than standard tests might.
63
refers to reversible, sometimes heritable modifications that regulate gene activity without altering the nucleotide sequence.
Epigenetics
64
isoform mechanism
a crucial, regulated post-transcriptional process in eukaryotes where a single gene's pre-mRNA is spliced in multiple ways to produce different mRNA transcripts, allowing one gene to encode multiple protein isoforms.
Think of a gene as a sentence with several words (exons). The cell can choose to skip some words or rearrange them.
Alternative Splicing
65
isoform mechanism
The cell doesn't always have to start reading from the very beginning of a gene.
The cell can choose different "start" sites on the DNA, altering the beginning of the protein chain.
Variable Promoter Use
66
isoform mechanism
This is the most subtle level of "editing".
The Process: After the RNA is made but before it becomes a protein, the cell can manually swap out individual "letters" (nucleotides).
Post-Transcription Modification (RNA Editing)
67
what organ do cells recognizes a calcitonin-specific splice acceptor. It includes exons 1, 2, 3, and 4 to produce Calcitonin mRNA, which ultimately creates the Calcitonin peptide used for bone health.
Thyroid Cells
68
what organ do cells processes the same primary transcript differently, skipping exon 4 and instead joining exons 1, 2, 3, 5, and 6. This produces CGRP mRNA, which creates a peptide used in nerve signaling and pain.
Neuronal (Brain) Cells
69
Isoforms (Secreted vs. Membrane-Bound)
Through alternative splicing, the mRNA includes a specific section (exon) at the end that codes for a "hydrophobic tail." This tail acts like an anchor, pinning the antibody to the B-cell membrane so it can act as a sensor to detect invaders.
The Membrane-Bound Isoform:
70
Isoforms (Secreted vs. Membrane-Bound)
Through alternative splicing, the cell "edits" the mRNA to exclude that anchor exon. Instead, it finishes the protein with a "secretory tail." This turns the antibody into a soluble projectile that can be spit out (secreted) by the millions into the bloodstream.
The Secreted Isoform:
71
Immune system
Germ-line coded genes: You are born with these exact instructions.
Always on and is the first line of defense
Nucleated cells: Generalists (like macrophages) that produce anti-invader proteins
Uses vitamins and nutrients to generate attack proteins (like cytokines)
Generate proteins that will attack
Innate
72
Immune system
Recombined genes: The DNA is physically cut and "remixed" during your lifetime.
Delayed: Takes days to "learn" a new invader, but creates long-term memory
Recombination occurs in gametes during meiosis, Mix and match DNA: Breaks and rejoins DNA to create unique receptors/antibodies.
B cells and T cells: Specialists that hunt specific targets.
Adaptive
73
number of unique TCRs
10^15
74
number of T cells in human body
10^11
75
Stability: It is the inherited sequence that stays the same in almost every cell in your body throughout your life.
Inheritance: It can only be changed or "shuffled" through recombination in the reproductive cells (meiosis). This ensures that while your children are unique, the fundamental blueprint of the human species remains intact.
Germline DNA
76
is the exception to the germline DNA rule. This is where B cells and T cells physically rewrite their own DNA to create antibodies and receptors.
Instead of just reading a gene, these cells physically cut and move sections of DNA. They "mix and match" segments (called V, D, and J segments) to create a totally new sequence that didn't exist in the germline.
Somatic recombination
77
SOMATIC RECOMBINATION's Rearrangement of gene
This process is highly regulated because DNA transcribes from what direction
5' to 3'
78
what enzyme facilitates somatic recombination at Ig loci?
it is a physical rearrangement of the gene. The "unused" DNA between the segments is actually looped out and deleted from the cell entirely.
Enzyme RAG
79
SOMATIC RECOMBINATION flow
1. Recognition of the "Landing Pads"
The process begins when the RAG (Recombination-Activating Gene) enzyme complex—consisting of RAG1 and RAG2—scans the germline DNA.It specifically looks for RSS (Recombination Signal Sequences), which act as molecular "landing pads" located next to the V (Variable) and J (Joining) gene segments. These sequences ensure that RAG only cuts at the Ig loci and nowhere else.
2. Synapsis (Bringing Segments Together)RAG binds to two different RSS sites and pulls them together, creating a loop in the DNA.This brings distant segments (like a V and a J) into close physical proximity.This "synaptic complex" is the staging ground for the permanent change to the gene's position.
3. Cleavage (The Physical Break)RAG acts like molecular scissors to perform cleavage.It makes a double-stranded break in the DNA exactly at the border between the RSS and the coding segments.This physically disconnects the chosen segments from the rest of the chromosome.
4. Formation of Joints: Once the DNA is cut, the cell must clean up the mess and join the pieces back together:
80
joint where V and J segments are fused together to form a brand-new, functional gene. Because DNA transcribes from 5' to 3', this new physical sequence now provides a readable instruction for a unique antibody.
Coding Joint
81
The "unused" DNA that was looped out is joined into a circular piece of waste and discarded from the cell. The signal joint gets its name because it is the byproduct of joining the two Recombination Signal Sequences that originally "signaled" the RAG enzyme where to cut the germline DNA.
Signal Joint
82
Chains that work together to create the Y-shaped structure that identifies and neutralizes invaders. While they both undergo somatic recombination, their genetic complexity and the chromosomes they live on are quite different.
Heavy Chains and Light Chains
83
Heavy Chains and Light Chains
These form the long "trunk" and the inner part of the Y-arms. They determine the "class" of the antibody (like IgG or IgA). Uses V, D, and J segments. Chromosome 14. Happens first in B cell development.
Heavy Chains (The Core)
84
Heavy Chains and Light Chains
These are the smaller outer segments of the Y-arms. Chromosome 2 (kappa) or Chromosome 22 (lambda) Happens second, only after a heavy chain works.
Light Chains (The Arms)
85
The Two Ig light chain Loci:
Kappa and Lambda
86
The Two Ig light chain Loci:
This chromosome contains the (kappa) light-chain library, consisting of many V segments and a cluster of J segments followed by a constant (C) region.
Chromosome 2:
87
The Two Ig light chain Loci:
This chromosome contains the(lambda) light-chain library, which has its own set of V and J segments.
This serves as a secondary library. If the cell cannot make a functional light chain using its Kappa genes at chromosome 2
Chromosome 22
88
Ig light chain flow
B cells physically cut and discard pieces of their own DNA to create a functional antibody with Somatic Recombination
Somatic Recombination: The RAG enzyme binds to the Germline DNA at one of these loci.
Synapsis and Cleavage: As seen in your diagrams, RAG loops the DNA to bring a distant V segment and J segment together. It performs cleavage to snip out the unwanted DNA, creating a discarded signal joint and a permanent coding joint.
Rearranged DNA: This creates a new, permanent V-J rearranged DNA sequence on the chromosome.
Transcription and Splicing: The cell then transcribes this new sequence into RNA. Splicing removes the remaining "filler" to create a mature mRNA that combines the V-J unit with a Constant (C) region.
Translation: Finally, the cell translates this mRNA into a polypeptide chain that forms either a VLkappa or a VLlambda light chain for the final antibody.
89
Possible κ chains:
35 × 5 = 175
90
Possible λ chains:
30×5=150
91
Possible heavy chains:
45×23×6 = 6,210
92
κ-based antibodies
175×6,210=1,086,750
92
93
λ-based antibodies
150×6,210=931,500
93
94
Targets: Viruses, bacteria, or toxins that are outside your cells.
The Weapon: They use somatic recombination at the Ig loci to create custom-shaped antibodies. Permanent coding joint for an antibody from Germline DNA segments.
B Cells
95
Targets: Your own cells that have been hijacked by a virus, or cells that have become cancerous from the inside.
The Weapon: They use a T-Cell Receptor loci, which is also created through somatic recombination facilitated by the RAG enzyme. Permanent coding joint for a TCR from Germline DNA segments.
T Cells:
96
Heavy Chain uses what chromosome
Chromosome 14
97
TCR creation flow
1. The TCR Structure
The left side of the image shows the physical structure of the receptor:
alpha and beta Chains: The main functional part of the TCR consists of an alpha and a beta chain paired together.
Support Proteins: The(gamma) and(delta) subunits act as part of the surrounding complex that helps the receptor function on the T cell's surface.
2. Two Ways to "Pick and Join"
The right side of the image highlights how the T cell rearranges its DNA to create these chains:
V-D-J Recombination (Top): This process is used to create the beta chain. Similar to the antibody heavy chain, it uses a V (Variable), D (Diversity), and J (Joining) segment to create maximum diversity.
V-J Recombination (Bottom): This process is used to create the alpha chain. Like the antibody light chain, it only requires joining a V and a J segment.
98
TCR beta chain chain chromosome
Chromosome 7
99
are physical sequences of DNA that are located on the same molecule as the gene they regulate. DNA sequences (e.g., RSS, Promoters), on the same DNA molecule as the gene.
They serve as "landing pads" for regulatory proteins.
Cis-acting sites
100
TCR alpha chain chromosome
Chromosome 14
101
these factors are usually proteins (like transcription factors) encoded by genes elsewhere in the genome. They diffuse through the cell to find and bind to cis-acting sites. Proteins (e.g., RAG enzyme, Transcription factors), encoded by genes elsewhere; mobile within the cell.
Trans-acting factors
102
Variable Promoter use
Specify one single, exact transcription start site (often containing a TATA box).
Focused Promoters
103
Variable Promoter use
Common in vertebrate "housekeeping" genes, these allow transcription to start at multiple points over a 100-bp region, leading to multiple transcripts of varying lengths.
Dispersed Promoters
104
In eukaryotes, the ______ box is a highly conserved DNA sequence found in the core promoter region of many genes.
TATA
105
Prokaryotes do not have a "TATA box" by that exact name, but they use a functionally identical sequence known as the _______ box.
Pribnow
106
also known as the coding strand or sense strand, DNA strand whose base sequence is identical to the base sequence of the resulting RNA transcript
Coding sequence
107
box usually located around 75 base pairs upstream of the transcription start site; it helps determine the frequency of transcription.
CCAAT box
108
box These are often found in multiple copies and act as binding sites for specific trans-acting transcription factors (like Sp1) to enhance promoter activity. eukaryotic
GGGG
109
Prokaryotic Upstream Elements; upstream the pribnow box
TTGA
110
Human metallothionein IIA
Response Element)
Binds: Glucocorticoid receptor
Function:Activates MT-IIA transcription in response to stress hormones (like cortisol)
GRE (Glucocorticoid
111
Human metallothionein IIA
Binds: AP-2
Function: Turns on MT-IIA during oxidative stress. Important because metallothioneins help protect cells from damage
ARE (Antioxidant Response Elements)
112
Human metallothionein IIA
Binds: MTF-1 (Metal-responsive Transcription Factor-1)
Function:
Activates gene expression when heavy metals (Zn²⁺, Cd²⁺) are present. This is the core function of metallothioneins
MRE (Metal Response Elements)
113
Human metallothionein IIA
Binds: AP-2
Function: Helps maintain baseline (low-level) expression. Ensures the gene isn’t completely off
BLE (Basal Level Element)
114
Human metallothionein IIA
Binds: AP-2
Function: Helps maintain baseline (low-level) expression. Ensures the gene isn’t completely off
GC box
115
Human metallothionein IIA
(repressor) binds near the start site
Function: Prevents unnecessary transcription. Balances activation signals
p120
116
are the "security checkpoints" of the cell. They ensure that only the correct biological materials move in or out of the nucleus:
Nuclepore
117
is typically derived from exogenous double-stranded RNA, such as viral RNA or experimentally introduced RNA.
This leads to a strong and specific silencing effect, usually targeting one particular gene, and plays important roles in antiviral defense and research-based gene knockdown.
siRNA (small interfering RNA)
118
in contrast, is endogenously encoded by the cell and functions in normal gene regulation.
Because of this partial binding, a single one can regulate multiple mRNA targets, making it crucial for processes such as development, differentiation, and fine-tuning of gene expression.
miRNA (microRNA)
119
siRNA (small interfering RNA) flow
miRNA pathway (translation repression + deadenylation)
pri-miRNA (nucleus)
↓ Drosha
pre-miRNA (loop)
↓ Export to cytoplasm
↓ Dicer
miRNA duplex
↓
miRNA loaded into RISC
(Argonaute)
↓
Partial base-pairing with target mRNA
(usually 3′ UTR)
↓
Argonaute recruits GW182 (TNRC6)
↓
GW182 recruits deadenylases
* PAN2–PAN3
* CCR4–NOT
↓
Poly(A) tail shortening
(deadenylation)
↓
Loss of PABP + closed-loop structure
↓
↓ Translation
↓
Often followed by decapping
↓
mRNA degradation
120
miRNA (microRNA) flow
Direct chromatin silencing (more common in plants, fungi, some animals)
pri-miRNA (nucleus)
↓ Drosha
pre-miRNA (loop)
↓ Export to cytoplasm
↓ Dicer
miRNA / siRNA (or other small RNA)
↓
Loaded into Argonaute
↓
Formation of RITS complex
(Argonaute + small RNA + adaptor proteins)
↓
RITS targets nascent RNA
or chromatin at specific loci
↓
Recruitment of chromatin modifiers
* Histone methyltransferases
* DNA methyltransferases
↓
Deposition of repressive marks
* H3K9 methylation
* DNA methylation
↓
Heterochromatin formation
↓
Transcriptional gene silencing
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The final collection of functional proteins, greatly expanded by post-translational modifications like acetylation or lipidation.
Proteome
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illness where the problem isn't the amount of hemoglobin, but its quality. A single point mutation causes the hemoglobin molecules to stick together into long, rigid polymers when oxygen levels are low. Structural: Hemoglobin is misshapen
Sickle Cell Anemia
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illness that involves a massive "series of options" for mutations. It is a quantitative defect, meaning the body can't make enough of a specific part of the hemoglobin molecule. Hemoglobin is made of four protein chains: two Alpha and two Beta.
Thalassemia
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The Three Eukaryotic RNA Polymerases
nucleolus
The rRNA FactoryThis polymerase is found in the nucleolus and is dedicated to synthesizing the majority of ribosomal RNA.Target: Large ribosomal RNA (rRNA).Specifics: It transcribes the 18S, 5.8S, and 28S rRNA subunits
RNA Polymerase I
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The Three Eukaryotic RNA Polymerases
nucleoplasm
coding instructions that leave the nucleus.Target: Messenger RNA (mRNA).Other Targets: It also transcribes most small nuclear RNAs (snRNAs) and microRNAs (miRNAs).Role: It is responsible for all protein-coding genes.
RNA Polymerase II
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The Three Eukaryotic RNA Polymerases
nucleoplasm
This polymerase handles the smaller, "housekeeping" RNAs that support the translation process.Target: Transfer RNA (tRNA) and the 5S ribosomal RNA subunit.Other Targets: Small non-coding RNAs (sncRNAs) like U6 snRNA.Role: tRNAs act as the physical adapters between the mRNA code and amino acids during translation.
RNA Polymerase III
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core epigenetics mechanisms
DNA methylation
Histone modifications
RNA based regulation
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Which will give the fastest epicellular response?
RNA based modification - Since the molecule is "already done" (the mRNA has already been transcribed from the DNA), the cell doesn't have to wait for the nucleus to open up the genome. Processes like RNA interference (RNAi) or RNA editing act directly on the messengers already floating in the cytoplasm.
DNA methylation - It is the most stable and hardest to reverse. Attaching a methyl group directly to the DNA base (usually Cytosine). This effectively "locks" the gene in the "OFF" position.
Histone modification - This is faster than DNA methylation but slower than RNA-based changes. It involves adding or removing chemical groups (like acetyl or methyl groups) to the "spools" that DNA wraps around.
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DNA Methylation enzyme
DNA Methyltransferase (DNMT)
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occurs when there is a decrease in the normal levels of DNA methylation. Methylation usually acts as a silencer. This often leads to chromosomal instability. In cancer biology, genome-wide hypomethylation can activate "oncogenes"
Hypomethylation
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is an increase in the normal levels of DNA methylation.This adds extra "silencers" to the DNA. It tightly packs the chromatin, making the gene inaccessible to the machinery that would normally read it.This is most dangerous when it happens to tumor suppressor genes
Hypermethylation
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Why are cpg islands currently used for methylation?
Cgp islands are generally kept in a euchromatic (relaxed) state. Because they lack the bulky methyl groups, the DNA doesn't fold into tight, inaccessible knots. This openness allows RNA polymerase and transcription factors to physically land on the DNA. If CGIs were methylated and "closed," your cells couldn't read the instructions to build essential proteins.Does not resist methylation
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Demethylation can occur passively (if DNMT1 stops working) or actively through
TET enzymes
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converts unmethylated cytosines into uracil, but leaves methylated cytosines unchanged.
Sodium bisulfite
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Acetylation eznyme
Histone acetyltransferases (HATs)
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deacetylation enzyme
Histone deacetylases (HDACs)
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Histone methylation and demethylation enzymes
Enzyme: Histone methyltransferases (HMTs)
Removal: Histone demethylases
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hey are a family of enzymes that play a critical role in epigenetic regulation by adding an acetyl group from acetyl-CoA to specific lysine residues on histone tails.This modification neutralizes the positive charge on histones, loosening their grip on negatively charged DNA, which transforms condensed, inactive chromatin (heterochromatin) into a relaxed, active state (euchromatin) that is accessible for gene transcription.
Histone Acetyltransferases
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A-HATs and B-HATs
Location: Nucleus
Function: Acetylate histones already in chromatin
Role: Gene activation (transcription regulation)
Type A HATs
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A-HATs and B-HATs
Location: Cytoplasm
Function: Acetylate newly synthesized histones
Role: Chromatin assembly (NOT direct transcription control)
Type B HATs
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is a post-translational modification where methyl (–CH₃) groups are added to lysine (K) or arginine (R) residues on histone tails.
(S-adenosylmethionine) SAM is the universal methyl donor in the cell.
KMT (Lysine Methyltransferase) are enzymes that add methyl groups to lysine residues on histones.
Histone methylation
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(Methyltransferases): These enzymes (like METTL3) add the methyl group to the Adenosine on the RNA strand while it is being transcribed.
Writers
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(Demethylases): These enzymes (like FTO) can remove the methyl group. This makes the modification reversible, allowing the cell to change its mind about an RNA's fate.
Erasers
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(Binding Proteins): These are the most important part of the process. They "recognize" the m6A tag and decide what happens to the RNA. Depending on the reader, the RNA might be fast-tracked for translation or sent straight to the "trash can" (degradation).
Readers
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is a master regulator of stability. In DNA, methylation usually silences a gene. In RNA, this often acts as a timer. By tagging an mRNA with this, the cell can ensure that the transcript is degraded quickly after its job is done. Without this tag, the RNA might stick around too long, producing too much protein and throwing the cell out of balance.
m6A
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are larger and more complex. Instead of just blocking mRNA, they act as "scaffolds" or "guides" that physically recruit chromatin modifiers (like the DNMTs) to specific spots on the DNA.
Long Non-Coding RNAs (lncRNAs)
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Two major categories of Techniques to Study Epigenetics
1) Histone modification analysis
2) DNA methylation profiling
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Examples of Histone Codes for gene expression
H3K4me3
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Examples of Histone Codes for gene repression
H3K27me3
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Enzymes (e.g., Histone Methyltransferases -
HMTs, Histone Acetyltransferases - HATs) that add
modifications
Writers
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Proteins with specific domains that recognize
and bind to these marks to turn genes on or off
Readers
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Enzymes (e.g., Histone Deacetylases - HDACs,
Histone Demethylases - KDMs) that remove modifications.
Erasers
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is a core technique to study protein–DNA
interactions in vivo
Used to map binding of:
* transcription factors
* histone modifications
* chromatin remodelers
Key steps: crosslink → fragment →
immunoprecipitate → purify DNA → analyze
(PCR/seq)
Chromatin Immunoprecipitation (ChIP)
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ChIP-Seq = ChIP followed by next-generation
sequencing (NGS)
provides genome-wide binding sites for transcription
factors / histone marks
ChIP-Seq: Genome-Wide Mapping
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Combines ChIP enrichment with DNA microarray
hybridization
Used to discover binding sites (cistrome) across
the genome
Bound DNA and input DNA are fluorescently
labeled with different dyes
Hybridization signal ratio identifies enriched
regions
Useful for mapping chromatin topography and
histone distribution
ChIP-on-Chip (ChIP + Microarray)
