Genetics Final

Facultative Heterochromation

-sometimes repressed

• depends on is it is methylated or acetlated

Facultative Heterochromation

• Always repressed

• Is methylated

What happens during G1 of cell cycle

Cell is doing cell things

What is the function of insulators in euk gene regulation

They are boundaries that block specific transcription factors from

activating transcription of the incorrect gene.

What is the promotor in prok gene regulation

The site where RNA pol attaches to start transcription

What does an inducer do

An inducer attaches to a repressor which turns tc on

What does an inhibitor do

Attaches to an activator to turn tc OFF

What does an effector do

Attaches to an activator to turn tc ON

Neg Inducible Operon

Regulated by a repressor

Inducer turns repressor off

Pos inducible operon

Regulated by activator

Effector turns it on

Neg repressed operon

• regulated by repressor

• compressor turns it off

Pos repressed operon

• regulated by activator

• inhibitor turns it off

How does the lac operon work

When lactose is present it binds to repressor so it can’t stop tc

When lactose is not present repressor binds to operator to stop tc

Where/ how can a euk gene be regulated

During transcription

Post transcription (pre mrna)

translation

post translation

What are transcription factors

Transcription factors are specialized proteins that bind to specific DNA sequences to control the transfer of genetic information from DNA to RNA. By acting as cellular switches, they turn genes on or off by helping or blocking the attachment of the enzyme RNA polymerase.

How do miRNAs reduce the amount of mRNA in cells

MicroRNAs (miRNAs) reduce target mRNA amounts by guiding the RNA-Induced Silencing Complex (RISC) to complementary sequences on messenger RNAs. This binding triggers two primary processes: mRNA destabilization (shortening the poly-A tail to speed up decay) and direct enzymatic cleavage of the transcript.

What is alternative splicing/when does it happen?

Alternative splicing is a normal cellular process where coding pieces of RNA (exons) are joined in different ways. This lets a single gene make many different proteins. It happens inside the cell nucleus during gene expression, right after a gene is copied into pre-mRNA and before it turns into mature mRNA.

What is the E,P,A site in translation?

• A: Accepts and binds the incoming, charged tRNA carrying the next single amino acid

• P: Holds the tRNA attached to the growing polypeptide chain where peptide bonds form

• E: Holds the empty (uncharged) tRNA just before it leaves the ribosome to pick up a new amino acid

What is the difference between HATS and HADS

• HATs add acetyl (tc on)

• HDACS remove acetyl (tc OFF)

missense mutation

single base pair changes the amino acid

synonymous mutation

base pair change does the change the amino acid

nonsense mutation

changes amino acid to a stop codon (UAA, UAG, UGA)

frameshift mutation

the gain or loss of 1 or 2 (or multiples of 1 or 2) (not

3 or multiples of 3) nucleotides resulting in a change in the reading frame

during translation

transversion mutation

purine to pyrm or vice versa (A—>T)

transition mutation

purine to purine or pyrm to pyrm (A—> G)

Nucleotide exicision repair

Nucleotide excision repair is a vital cellular pathway that fixes bulky, helix-distorting DNA damage caused by UV radiation and environmental chemicals.

What is the difference btwn mismatch repair and base exicision repair?

Mismatch repair (MMR) and base excision repair (BER) are both single-strand DNA repair pathways, but they fix different types of errors: MMR corrects normal, mispaired nucleotides left behind after replication, while BER repairs chemically altered or damaged individual bases.

What is the difference between DNA pol 3 and 1

DNA Polymerase I and III are prokaryotic enzymes with distinct roles. DNA Polymerase III is the primary replicative engine that rapidly elongates the DNA strands, whereas DNA Polymerase I primarily acts as a cleanup and repair tool that removes RNA primers and fills the resulting gaps. [1, 2, 3, 4, 5]

Phosphodiester bonds

Between 5 prime OH and 3 prime H of adajacent nucleotide

What are the levels of compaction of DNA?

• DNA Double Helix: The base level of uncompacted genetic material, measuring about 2 nm wide. [1, 2]

• Nucleosomes ("Beads on a String"): DNA wraps 1.65 times around a core of eight histone proteins to form a 10-nm nucleosome structure, shortening the DNA about 7-fold. [1, 2]

• 30-nm Fiber: Histone H1 helps coil nucleosomes and linker DNA into a thicker 30-nm fiber, making the DNA about 50 times shorter. [1, 2, 3]

• Looped Domains: The 30-nm fiber forms loops attached to a central protein scaffold, reaching 300 nm in width. [1, 2, 3]

• Condensed Metaphase Chromosome: The loops coil and fold further during cell division, creating a fully packed 700-nm chromatid or 1400-nm metaphase chromosome. [1, 2, 3, 4, 5]

What is Rho dependent termination

Rho-dependent termination is a mechanism that stops bacterial transcription using the Rho protein, rut sites, and ATP energy. In this process, the Rho protein attaches to the growing RNA strand and moves along it to pull the strand away from the RNA polymerase enzyme. [1, 2, 3, 4, 5]

How are genes regulated in prok

Different types of regulatory proteins can change how genes are expressed by binding

to the operator or other regulatory regions

What is a cofactor?

• Molecules than can either help activator or repressors be turned on or off

• inducers, corepressors, effectors, inhibitors

What does a corepressor do

• helps turn repressors ON which turns transcrip OFF

What is transcriptional regulation in eukaryotes?

• Open/Closed chromatin.

• Alternative promoters.

• Specific transcription factors and

other regulatory proteins bind to DNA

and influence when, where and how

much transcription occurs.

What is an enhancer sequence

• a binding site for specific transcrip factors bind (activators) to turn on transcrip

What is a silencer sequence?

• a binding site for specific transcrip factors bind (repressors) to turn on transcrip

Where are binding sites found?

• Far from the core and proximal promoters

• Can be upstream, downstream, introns

what is the relationship between cdks and cancer

Cyclin-dependent kinases (CDKs) are key proteins that control how cells grow and divide. In cancer, CDKs become hyperactive or deregulated, causing cells to multiply without stopping.

What are proto oncogenes

Proto-oncogenes are normal genes that help cells grow, divide, and stay alive. If these genes mutate or become too active, they turn into cancer-causing genes called oncogenes.

What is PCR

PCR uses a repeating cycle of heating and cooling in a machine. The process uses key ingredients like a DNA template, primers (short pieces of matching DNA), building blocks called nucleotides, and a heat-safe enzyme called Taq polymerase. [1, 2, 3, 4]

• Denaturation (Heating): The sample is heated up to split the double-stranded DNA into single strands.

• Annealing (Cooling): The machine cools down so the primers can attach to the correct spots on the single DNA strands.

• Extension (Reheating): The temperature goes up slightly so Taq polymerase can build new matching DNA strands. [1, 2]

How does CRISPR work

• Guide RNA (gRNA): A tiny, lab-made piece of genetic code designed to match the exact sequence of the target DNA you want to change.

• Cas9 Enzyme: A protein that acts like a pair of molecular scissors to make a clean break in the DNA strand.

The Editing Process

• Find: Scientists program the guide RNA with the target sequence, which then leads the Cas9 scissors straight to the exact spot on the genome. [1, 2]

• Cut: The Cas9 protein arrives and cuts both strands of the DNA at that precise location. [1, 2]

• Repair: The cell senses the broken DNA and tries to fix it naturally. Scientists can trick this repair phase to turn a bad gene off, remove a bad section, or paste in a brand-new, healthy piece of DNA

What are the three levels of nucleotide sequences?

Highly repetitive: least complex

– Centromeres and Telomeres

• Moderately repetitive: intermediate

– Selfish genetic elements (like

transposons), rRNA and tRNA gene

clusters

• Unique: most complex

– Genes (coding and regulatory regions)

What is sanger sequencing

• DNA Copying: The target DNA is mixed with normal building blocks (dNTPs), a primer, and a DNA polymerase enzyme. [1, 2, 3]

• Chain Termination: Special modified nucleotides called dideoxynucleotides (ddNTPs) are added. Each type of ddNTP (A, T, C, or G) carries a unique fluorescent dye. [1, 2]

• Random Stopping: When the enzyme accidentally picks up a fluorescent ddNTP instead of a normal nucleotide, the DNA chain stops growing. [1]

• Fragment Sorting: This random stopping creates DNA pieces of many different lengths, each ending with a known colored base. [1]

• Reading the Color: A machine sorts these pieces by size using capillary electrophoresis and uses a laser to read the glowing colors in order, revealing the original DNA sequence. [1, 2]

What is Illumina sequencing?

• Library Preparation: DNA is cut into small pieces, and special short adapter sequences are attached to both ends.

• Cluster Generation: The prepared DNA binds to a glass slide (flow cell) and is copied many times over to make small clusters of identical DNA.

• Sequencing by Synthesis: Fluorescently labeled nucleotides flow over the cell. Only one matching base attaches at a time.

• Imaging: A light source causes the newly added base to glow, and a camera takes a picture to record which base was added.

• Cleavage: The fluorescent tag and block are washed away so the next base can lock in, and the cycle repeats. [1, 2, 3, 4, 5]

What is Pacific biosciences

• Long Reads: Unlike traditional short-read methods, PacBio reads continuous DNA fragments that span thousands of base pairs, making it easier to map repetitive areas of a genome. [1, 2, 3, 4, 5]

• HiFi Sequencing: Combines long read lengths with greater than 99.9% consensus accuracy by sequencing the same circular DNA molecule multiple times. [1, 2, 3]

• Real-Time Observation: Uses specialized microchips (SMRT cells) with microscopic wells to watch DNA polymerase build strands and record fluorescent signals as each base is added. [1, 2]

Genetic drift vs. Gene flow

Genetic drift and gene flow are both core mechanisms of evolution that change allele frequencies (the ratios of different gene versions) in a population over time. The main difference is that genetic drift is a random change in gene frequency due to chance (often in small groups), whereas gene flow is the transfer of genes between separate populations through migration and interbreeding.