BIS2A

Genome

• The set of instructions needed to create an organism. They’e stored in the cell as DNA. Ex. a genome is a coded cook book to build and grow an organism, the human genome has about 23,000 recipes. Each recipe, or function unit of DNA is a gene.

  Q: What is a genome?
  A: The complete set of genetic instructions (DNA) needed to build, grow, and maintain an organism.

  Q: How can you visualize a genome?
  A: Like a cookbook containing thousands of recipes. Each recipe (gene) provides instructions for making specific proteins or functional RNAs.

  Q: Roughly how many protein-coding genes are in the human genome?
  A: About 20,000–23,000 genes.

Gene

• 2% of genes code for protein, the rest are non-coding DNA 98% with regulatory or unknown functions.

  Q: What is a gene?
  A: A segment of DNA that contains the instructions to make a functional product — usually a protein or functional RNA.

  Q: What percent of the human genome is protein-coding?
  A: About 1–2% of the human genome codes for proteins; the remaining ~98% is non-coding DNA, which includes regulatory elements, non-coding RNAs, and repetitive sequences.

  Q: Is non-coding DNA useless?
  A: No — much of it has important regulatory or structural functions, while some still has unknown roles

Genetics

• The study of how DNA works is Genetics, this allows us to see the bigger picture of DNA landscape, how DNA works and how the whole genome interacts with its environment.

  Q: What is genetics?
  A: The study of how traits are inherited and how genes function, including how DNA is passed from one generation to the next and how it controls traits and biological functions.

  Q: How is genetics different from genomics?
  A:

  • Genetics focuses on individual genes and inheritance.

  • Genomics studies the entire genome, gene interactions, and large-scale patterns.

Genomics

• The study of the genome and its environment.

  Q: What is genomics?
  A: The study of the genome — an organism’s complete set of DNA — including its structure, function, evolution, mapping, and interactions.

  Q: What does genomics include?
  A:

  • Sequencing entire genomes

  • Identifying genes (coding and non-coding)

  • Understanding gene regulation

  • Comparing genomes across species (comparative genomics)

C-value paradox

• Organismal complexity does not scale with genome size. Scientists may have predicted that larger genomes would correlate with more complex ogranims.

  Q: What is the C-value paradox?
  A: The observation that genome size (C-value) does not correlate with organismal complexity. Some simple organisms have much larger genomes than more complex ones.

  Q: What did scientists originally predict?
  A: That larger genomes would belong to more complex organisms — but this is often not true.

  Q: Why does genome size vary?
  A: Differences in non-coding DNA, including repeats and transposable elements, contribute to genome size without necessarily adding organismal complexity.

Junk DNA (non-coding DNA)

• Recognized that only around 3% of DNA actually codes to the human body, so we have around 97% of DNA that’s kind of useless.

• It’s been copied for a billion years and been left in the system as junk DNA

• 3% of our DNA does code for our human body, however 5-8% of our DNA codes for viral genes, called exosomes.

• So now we still have 90% of our DNA not being used, what does that code for? Epigenetic, is the mechanism by which environmental signals controls the developments and expression of our genetic activity, well how does it do that?

• Junk DNA is like a modifier that changes the read out of the DNA being used

• So junk DNA is not actually junk, it plays a large role in adjusting genes so the organism fits into the environment.

• Mutations or variations in non-coding DNA can affect how genes are expressed.

Exosomes: Endogenous Retroviruses

• 3% of our DNA does code for our human body, however 5-8% of our DNA codes for viral genes, called exosomes

  Q: What are endogenous retroviruses (ERVs)?
  A: Viral sequences that became permanently inserted into our genome during ancient infections. They are a type of retrotransposon.

  Q: How much of our genome comes from ERVs?
  A: Approximately 5–8% of human DNA comes from these viral-origin sequences.

  Q: Are ERVs still active?
  A: Most are inactive and no longer functional, but some can still influence gene regulation.

Epigenetics

• So now we still have 90% of our DNA not being used, what does that code for? Epigenetic, is the mechanism by which environmental signals controls the developments and expression of our genetic activity, well how does it do that?

• Can it just turn a gene on and off, but then we’d have the same genes and proteins on and off, how do we modify the genes?

Protein Modules

• Junk DNA is like a modifier that changes the read out of the DNA being used

• Protein modules are like dials on a T.V and are scattered along the length of the junk DNA

• A module can turn the gene on or off, some even change the expression of the gene. They can cut the gene, show parts of it, glue segments back together, the modulate the expression.

• As the signals from the environment come in they adjust the module of the the protein, which in turn adjusts the readout of the DNA.

• Ex. DNA of a human and gene are almost exactly the same, it’s not the gene program it’s the readout of the gene program that determines the difference.——-Ex. the same carotene that makes our finger nails and skin can make horns and claws of an animal. It’s about how we adjusted the readout. But the gene is NOT changing

• about 3,000 versions of proteins can be created from one gene based on the readout.

• So junk DNA is not actually junk, it plays a large role in adjusting genes so the organism fits into the environment.

Coding DNA

• The parts of DNA that code for proteins.

• Ribosomes make proteins from the info from coding DNA

• Gene expression is the process by which specific gene are made to produce a specific protein

  Q: What is coding DNA?
  A: Coding DNA refers to the portions of DNA that contain instructions to make proteins (protein-coding genes).

  Q: How is coding DNA used to make proteins?
  A: Through gene expression:

  • First, the gene is transcribed into mRNA.

  • Then, ribosomes translate the mRNA into a protein.

  Q: What is gene expression?
  A: The process by which information from a gene is used to produce a functional product (usually a protein)

Transposons

• Dna sequences that can move from one location on the genome to another

• Known as “jumping genes”

• Can work in two modes, first jump from one genome to another, in this case, they don’t leave anything behind, this is known as non-replicative mode of transposition. In the second mode, they make a copy that jumps from one place to another, this is know as replicative mode of transposition.

• Movement without duplication, and movement with duplication.

  Q: What are transposons?
  A: DNA sequences that can move from one location in the genome to another; also called "jumping genes."

  Q: What are the two modes of transposition?
  A:
  1⃣ Non-replicative transposition ("cut-and-paste")

  • The transposon is excised and inserted into a new location, leaving nothing behind.

  • Involves transposase enzyme.

  • Common for many DNA transposons.

  2⃣ Replicative transposition ("copy-and-paste")

  • The transposon makes a new copy which inserts elsewhere, while the original stays in place.

  • More common in retrotransposons (though some DNA transposons can also replicate).

  Q: What's the difference between movement with or without duplication?
  A:

  • Non-replicative: moves without duplication (one copy moves).

  • Replicative: makes a copy and both locations now contain the transposon.

Relevance of Transposons

• transposable elements: involved in several diseases and immune modulatory functions

• They’re very important

  Q: Why are transposable elements important?
  A:

  • They can disrupt genes or regulatory regions, contributing to some genetic diseases (e.g., insertional mutations).

  • They play roles in genome evolution by generating diversity and rearrangements.

  • Some are involved in immune system functions (e.g., antibody gene rearrangement mechanisms share similarities with transposon activity).

  • Many transposable elements are inactive but make up large portions of the genome (e.g., ~50% of human genome).

  Q: Are transposons always harmful?
  A:
  No — while some cause mutations, many transposons contribute to genetic innovation and regulatory diversity over evolutionary time

Transposons: What’s the big deal about it

• If a transposon jumps and lands in the coding sequence of a strucutral gene, then it would disrupt that particular gene, so the functional product of that gene may not be obtained

• Transposon has activity on gene expression

• Can act as an enhancer or repressor

Types of transposons (not very relevant)

• DNA transposons: DNA transposons move via a "cut-and-paste" mechanism. The transposase enzyme recognizes inverted terminal repeats (ITRs), cuts both strands of DNA to excise the element, creating a double-stranded break. The transposon is then inserted into a new genomic location, allowing it to "jump" from one site to another.

• Virus like retrotransposon: Virus-like retrotransposons (LTR retrotransposons) contain genes encoding reverse transcriptase and integrase. They are first transcribed into RNA. Reverse transcriptase converts this RNA into complementary DNA (cDNA), which integrase then inserts into a new genomic location. This is similar to how retroviruses replicate.

• Poly A retrotransposon which look exactly like a gene: Poly-A retrotransposons (non-LTR retrotransposons like LINEs and SINEs) lack inverted terminal repeats. They resemble mRNA with a 5' UTR, 3' UTR, and a poly-A tail. LINEs contain two ORFs that encode an endonuclease and reverse transcriptase. After transcription into RNA, reverse transcriptase uses target-primed reverse transcription (TPRT) to convert the RNA into DNA directly at a new site, expanding the genome and generating repeats.

Central Dogma

• The idea that DNA undergoes transcription to become RNA which gets turned into protein via translation

  Q: What is the Central Dogma of molecular biology?
  A: Information flows from DNA → RNA → Protein.

  Q: What processes are involved?
  A:

  • Transcription: DNA → RNA

  • Translation: RNA → Protein

  Q: What is an exception to the Central Dogma?
  A:

  • Reverse transcription: RNA → DNA (e.g. retroviruses, retrotransposons)

  • RNA viruses: Some use RNA-dependent RNA polymerase.

  • Telomerase: Uses an RNA template to extend DNA.

  Q: Which enzymes are involved in exceptions?
  A:

  • Reverse transcriptase (retroviruses, retrotransposons)

  • Telomerase (eukaryotic chromosome ends)

Retroviruses

• Some viruses use RNA to store genetic info, unlike most other organisms.

• Consist of genetic info and a few proteins inside a capsule, the viruses need to be inside the cell of another host organism to replicate.

• How can the RNA be copied in these viruses?

• Special kind of enzyme that turns RNA template into a DNA product. This was the same as central dogma but reverse.

• Reverse transcriptase, the enzyme that does transcription backwards.

  Q: How do retroviruses store and replicate their genetic information?
  A: Retroviruses store genetic information as RNA, unlike most organisms that store DNA.

  Q: How do retroviruses replicate inside a host cell?
  A: They use an enzyme called reverse transcriptase to copy their RNA into DNA (this is the reverse of the central dogma).

  Q: What happens to the viral DNA after it's made?
  A: The viral DNA is integrated into the host genome using another enzyme called integrase. Once inserted, the host machinery can transcribe and translate viral genes.

  Q: Why do retroviruses need host cells?
  A: Retroviruses cannot replicate on their own — they need host cell machinery for transcription, translation, and assembly of new virus particles.

  Q: What is an example of a retrovirus?
  A: HIV is a well-known retrovirus

Genome Annotation (ORFs, Gene Structure)

Q: What is genome annotation?
A: The process of identifying functional elements in DNA: protein-coding genes (ORFs), non-coding RNAs, regulatory regions, repeats, etc.

Q: What is an ORF?
A: Open Reading Frame — a stretch of DNA starting with AUG (start codon) and ending with a stop codon; likely to code for a protein.

Q: How are protein-coding genes identified?
A: Look for:

• Start codon (AUG)

• Long ORFs

• Splice junctions (in eukaryotes)

• Evolutionary conservation (similar genes across species)

• Promoter/consensus sequences

• Functional domains in proteins

Q: Why is annotation harder in eukaryotes?
A: Introns interrupt exons; genes are longer, more dispersed; more non-coding DNA.

Q: What non-coding elements are annotated?
A: rRNA genes, tRNA genes, enhancers, promoters, UTRs, repeats (retrotransposons, etc.)

Q: Why is evolutionary conservation helpful?
A: Conserved protein domains suggest important, functional genes.

Haploid v.s Diploid cells

• Haploid and diploid describes the number of sets of chromosomes. Diploid=2 and Haploid

• Sex cells, or gametes have a haploid number of chromosomes, all humans have 23 single set of chromosome.

• In fertilization we get a diploid zygote with a total of 46 chromoeoms. Each has a pair of homologous chromosomes, one form each parent.

• A diplod zygote goes through cell division many times to make all the cells needed to have a baby.

• All cells except sex cells are somatic cells and are always diploid, they have two sets of 23 chromosomes.

• The gametes are always haploid though.

• How does cell division effect the number of chromosomes in daughter cells? Somatic cells only reproduce by mitosis which results in two genetically identical diploid daughter cells.

• In contrast meiosis only produces gametes, in meiosis a diploid cell undergoes two cell divisions to produces 4 genetically different haploid daughter cells.

• Diploid=2 sets of chromosome, 1 set from each parents. Contains pairs of homologous chromosomes, chromosome number=2n, all somatic cells, reproduce by mitosis, are never gametes

• Haploid=1 set of chromosomes, ½ diploid number, no homologous chromosomes, n chromosome number, gametes only, formed by meiosis

  Q: What is the difference between haploid and diploid cells?
  A:

  • Haploid (n): 1 set of chromosomes (gametes only).

  • Diploid (2n): 2 sets of chromosomes (one from each parent; somatic cells).

  Q: Which cells are haploid?
  A: Gametes (sperm and egg). In humans, haploid cells have 23 chromosomes.

  Q: Which cells are diploid?
  A: Somatic (body) cells. In humans, diploid cells have 46 chromosomes (23 pairs of homologous chromosomes).

  Q: How does cell division affect chromosome number?
  A:

  • Mitosis: Produces 2 identical diploid daughter cells (2n → 2n).

  • Meiosis: Produces 4 genetically unique haploid daughter cells (2n → n).

Promoters and Enhancers

• During transpiration, DNA—-RNA, RNA polymerase wants to transcribe regions of DNA called genes, because these have info on making DNA. However only a small percent of the human genome is made of genes.

• How does RNA polymerase know where to transcribe? At the beginning of genes we have promoters that act as a landing pad for the promoter. It marks the start of the gene and helps bring it in for activation.

• Most promotes have the TATA box, made of adenine and thymines.

• Enhancers help RNA polymerase work much more efficiently.

• Enhancers are often many bases away, so the DNA must loop around to get close to the promoter.

  Q: What is a promoter?
  A: A DNA sequence at the start of a gene where RNA polymerase binds to begin transcription. Many promoters contain a TATA box (rich in A and T bases).

  Q: What is an enhancer?
  A: A regulatory DNA sequence that increases the efficiency of transcription. Enhancers can be located far from the gene and interact with promoters by looping the DNA.

  Q: How do promoters and enhancers work together?
  A: The promoter marks where transcription starts, while enhancers help recruit transcription factors and stabilize RNA polymerase for higher gene expression.

Lecture 18 Review

Please select one correct answer:

A. Yeast is a single-cell eukaryote but does not have sex.

B. Tetrahymena is a single-cell eukaryote but does not have meiosis.

C. Not all non-coding DNA is junk, and non-coding DNA is often essential for genome functions,

such as regulating gene expression.

D. Prokaryotes can occasionally undergo meiosis to acquire genetic diversity.

C. Not all non-coding DNA is junk, and non-coding DNA is often essential for genome functions, such as regulating gene expression.

The central dogma states that information flows from DNA to RNA to protein. Which of the following is an exception to this rule?

Please select one answer:

A. Retrotransposons use reverse transcriptase to copy-paste their copies into the genome.

B. Scientists can use a peptide sequence to determine the DNA sequence.

C. Alternative splicing of mRNA leads to a change in the flow of information from protein to RNA

Lecture 18 BIS2A Post-lecture study guide University of California, Davis: Namekawa ©2025

D. mRNA processing changes the genomic DNA sequencing.

E. RNA polymerase is required for DNA synthesis.

A. Retrotransposons use reverse transcriptase to copy-paste their copies into the genome.

Mutations

• mutation is a change of genetic material, more specifically a change of a nucleic acid

• RNA and DNA are both nucleic acids, therefore both of these can have mutations.

• Many mutations can be neutral in effect. Sometimes one base mutations can have no effect.

• Mutations can be helpful or harmful but remember they’re random.

• External factors or excessive radiation, or problems with replication during interphase can increase the probability of a mutation.

• Mutations originate at the DNA level but show their effect on the protein level.

Gene mutations

• DNA makes up genes and genes can code for proteins that influence different traits, so when a mutation happens, different proteins can be produced effecting a trait.

• If a mutation is going to happen, there are espcially vulnerable times, like during DNA replication or meiosis

• Mutations can be passed down to offspring. If the mutation is found in the sperm or egg cell, it can be inherited via sexual reproduction.

Types of mutations

• Substitution: wrong base is matched

• Insertion: an extra base or bases are added in (can be especially dangerous)

• Deletion: a base is removed (can be especially dangerous)

  • remember we read bases in three, so when we have a insertion or deletion we have a frameshift mutations

• chromosomal mutations: chromosomes are made of DNA and protein, the have lots of genes on them.

Chromosomal mutations

• Duplications: where extra copies of genes are generated

• Deletion: some of the genetic material breaks off

• Inversion: a broken chromosome section gets inversed

• translocation: fragment from one chromosome breaks off and attaches to another

Heredity

• the passing on of genetic traits from parents to offspring

Classical Genetics

• we’ve all got chromosomes, the form our DNA takes to get passed on from parent to child

• A gene is a specific section of DNA on a chromosome that contains information that determines a trait

• A vast majority of the time, a physical trait is a reflection of a bunch of genes: polygenic trait

• sometimes a single gene can influence how multiple traits are going to be expressed: pleiotropic genes

• Sometimes single traits are decided by a single gene: mendelian trait

  • ex. one gene determines the constancy of our earwax, there’s one allele that says the wax will be wet and one that says the wax will be dry. If the amino acid is Glycine you’ll have wet earwax, if it’s arginine, it’s dry.

Somatic cells versus Gametes

• Somatic cells are basically everything but sex cells and they are diploid. They’re two sets of chromosomes, one inherited from each parents.

• Gametes, sex cells, which are haploid, only one set of chromosome.

• Some plants have more than two sets of chromosomes: polyploid (not better, they just do it like that)

Heterozygous versus homozygote

• Heterozygous: two different versions of the same gene from each parent

  • ex. bB or aA

• homozygote: two of the allele inherited from both parents

  • ex: ww or TT

Phenotype

• the trait that is expressed

  • ex: blue eyes or brown eyes, blond hair or black hair.

Autosomes versus sex chromosome

• 22 pairs of chromosomes are non sex chromosomes or autosomes

• 1 pair is sex chromosomes, bio females have the XX chromosome and men have the Xy chromosome

Centra dogma and mutations

• DNA is transcribed into RNA which codes for specific proteins

• Nucleotides from DNA are transcribed into complimentary forms on RNA which are read as codons or groups of 3 to code for specific amino acids on a larger protein.

• We read DNA 3 to 5

• We read RNA 5 to 3

• If we mutate one nucleotide on DNA then that will effect the RNA sequence and the protein that follows

Point mutations

• When one of our DNA bases is replace by another

Frame shift mutation

• Instead of changing one base to another we add one to the sequence

• This changes the reading frame of RNA, remember we read RNA in codons, or pairs of 3, so if we add a base all of the codons will look different, which creates a whole new protein.

Non-sense mutations

• Any genetic mutation that leads to the RNA sequence becoming a stop codon

Missense mutation

• any genetic mutation that changes one amino acid to another

• Types of missense mutation:

  • Silent mutations: when the mutation doesn’t actually effect the protein at all, since many different RNA codons can code for the same amino acid

  • Conservative mutations: where the new amino acid is of the same type as the original.

  • Non-conservative mutation: the new amino acid is of a different type from the original.

DNA

• deoxyribonucleic acid

• DNA nucleotide is composed of a sugar and a phosphate group and one of four nitrogenous bases

  • adenine, thymine, guanine, cytosine

  • The sugar and phosphate form the backbone of DNA, while the bases determine DNA sequence.

  • Hydrogen bonds form between twi bases forming the double helical shape of DNA

  • A hydrogen bonds with T and C pairs with G

• DNA from one cell can stretch to be 2 feet long, however it needs to fit into an itty bitty cell and it does that like this:

  • First DNA is coiled into it’s double helical shape, then wrapped around histone proteins to form a nucelsome. The the nucleosomes are further wound and coiled together to form a compact structure that fits into the nucleus.

  • During cell division the DNA is organized into tightly wound chromosomes. Outside of cell division the DNA is de-condensed in the nucleus.

1. You notice that one of your yeast cultures is very fast-growing. You found DNA polymerase became

more error-prone compared to other yeast cultures, and the genome sequence changed over time.

What type of mutation might have possibly occurred? Select the most likely one.

A. A null mutation

B. A nonsense mutation

C. A frame-shift mutation

D. A missense mutation

E. A silent mutation

D. A missense mutation

• The yeast is growing faster → suggesting some change that likely altered protein function rather than completely eliminating it.

• The DNA polymerase became more error-prone, meaning the protein is still functional (polymerase is still replicating DNA), but not as accurately.

• A missense mutation changes a single amino acid, which can modify enzyme function (e.g. making polymerase more error-prone).

• Null mutations (A) would likely make the polymerase completely nonfunctional (lethal).

• Nonsense mutations (B) typically lead to truncated, nonfunctional proteins.

• Frameshift mutations (C) often destroy protein function entirely.

• Silent mutations (E) wouldn’t change the amino acid or affect function.

2. You notice that one of your yeast strains has a mutation in a coding gene in which one nucleotide

was changed to another nucleotide. However, you did not find any change in the amino acid sequence

of this protein. What type of mutation might have possibly occurred? Select the most likely one.

A. A null mutation

B. A nonsense mutation

C. A frame-shift mutation

D. A missense mutation

E. A silent mutation

E. A silent mutation

• A silent mutation is a type of point mutation where one nucleotide changes, but the amino acid sequence stays the same.

• This happens because of the redundancy of the genetic code (multiple codons code for the same amino acid).

• Since the protein sequence isn’t changed, this fits exactly with the observation in the question.

3. Scientists studying the genetic code and the influence of mutations on the translation of the code

discovered that some mutations could create a stop codon (UAG, UAA, UGA) in the middle of protein-

coding regions called nonsense mutations. This would lead to premature termination of translation and a

truncated gene product. They soon discovered other mutations elsewhere in the genome that restored

the ability of the ribosome to read through the nonsense mutations and make a full-length protein. When

they sequence the protein, they discovered a serine at this position. What could explain these observations?

A. There was a mutation in the ribosome. The ribosome cannot recognize stop codons.

B. There were mutations in a tRNA gene. The organism acquired a tRNA gene that recognizes

UAG, UAA, or UGA and brings serine.

C. There were mutations in the stop codons. The organism now uses other stop codons.

D. There was a mutation in an amino-acyl synthase gene to charge serine. The organism does not

use serine anymore.

E. None of the Above.

B. There were mutations in a tRNA gene. The organism acquired a tRNA gene that recognizes UAG, UAA, or UGA and brings serine.

• Originally, a nonsense mutation introduced a premature stop codon → truncated protein.

• Then, something allowed the ribosome to read through the stop codon and insert serine.

• The most likely explanation: a suppressor tRNA mutation occurred — a tRNA was altered so that its anticodon now recognizes the stop codon (UAG, UAA, or UGA) and inserts serine instead.

• This allows translation to continue past the stop codon, producing a full-length protein with serine in place of the stop.

4. The first figure (labeled C) below shows us the interactions between a TA base pair in DNA and an

arginine amino acid of a transcription factor (shown mostly as a yellow strand here). The codon in the

gene encoding the transcription factor

for Arg65 is CGT. A

mutation occurs that

changes this codon to

GGT. What is the

possible outcome of the

mutation?

A. Arg65 was

changed to

serine.

B. Arg65 was changed to Proline.

C. Arg65 was changed to Glycine.

D. Arg65 did not change.

E. The mutation caused premature termination.

C. Arg65 was changed to Glycine.

You are trying to decode GGT.

• The first letter = G → go to the G row on the left side of the chart.

• The second letter = G → move to the column under G across the top.

• The third letter = T → BUT!

  • The codon chart is written for mRNA, which uses U instead of T.

  • So GGT (DNA) → becomes GGU (RNA).

Gene regulation

• Different cells need to express different genes, although all of our somatic cells contain all of our genetic information, they’re specialized throughout the body, how do they know which genes to express and which to leave dormant?

  • This is done through regulatory mechanisms: (single celled organisms) If you only express genes that code for proteins that are needed by the cell in the given moment you have an advantage. If a particular resource is plentiful nearby, it should stop self producing that substance to save energy. If it is sparse in the environment it needs to kick start production. This kind of metabolic control is self regulating.

  • The products of certain enzymatic pathways act as inhibitors for that pathway, it slows down production of something that is in excess. This is feedback inhibition.

• Cells are very different from one another, even though they posses the same genetic material, this is due to struct regulation of gene expression.

• An easy way to turn genes on and off has to do with the way DNA wraps around histones to form nucleosomes.

  • when bond to histones genes cannot be expressed, in order to express a gene, the gene must become accessible.

  • This can happen if an enzyme modifies a histone through: acetylation/methylation/phosphorylation. Thus decreasing its affinity for DNA, one the gene is no longer coordinated to the histone it is available for transcription.

  • In order for transcription to proceed, proteins called transcription factors are necessary

Feedback inhibition.

• The products of certain enzymatic pathways act as inhibitors for that pathway, it slows down production of something that is in excess. This is feedback inhibition.

• The products of certain enzymatic pathways act as inhibitors for enzymes earlier in the same pathway. When enough product has been made, it binds to an enzyme in the pathway (often the first or an early enzyme), slowing or stopping further production. This prevents the cell from wasting resources by making excess product.

How to repress a gene: Operator and Operon (negative gene regulation)

• An operon is a transcription unit of genes whose products are required under identical circumstances. It facilitates the coordinated expression of multiple genes.

• The operon is a cluster of genes controlled together. It includes:
  promoter + operator + genes (which code for a protein) = operon.

• The operator is like an on/off switch. It controls whether RNA polymerase can bind to the promoter and transcribe the genes.

• Normally, the operon is on (genes are transcribed). But if a repressor binds to the operator, it blocks RNA polymerase from binding to the promoter, stopping transcription.

• If transcription is blocked, no mRNA is made, so no enzymes are produced.

• Repressors are often controlled by the amount of product:

  • If too much product is present, repressors are activated to turn the operon off.

  • If less product is present, fewer repressors are active, so the operon stays on.

How to turn a gene on (negative gene regulation)

• Normally, a repressor is bound to the operator, blocking RNA polymerase and preventing transcription.

• An inducer (isomer) can bind to the repressor and deactivate it (change its shape).

• Once the repressor is deactivated, it detaches from the operator.

• RNA polymerase can now bind to the promoter and transcribe the gene.

• Transcription leads to mRNA production → proteins/enzymes are made.

• In short: we deactivate the repressor to turn the gene on.

Positive gene regulation

• A signaling molecule binds to a protein called an activator.

• The activator then binds to DNA near the promoter.

• This increases RNA polymerase's affinity (attraction) for the promoter, making it easier for RNA polymerase to bind and start transcription.

• As a result, gene expression increases and more proteins are produced.

Transcription factors

• In order for transcription to proceed, proteins called transcription factors are necessary

• Some of these bind to a section of the promoter, usually in the TATA box because thymine and adenine are easier to break apart due to there being one less hydrogen bond.

• Binding to DNA occurs due to a binding domain that has an affinity for a specific sequence of nucleotides in the promoter. The transcription factor also has an activation domain that binds to other regulatory proteins that enhance transcription.

• In addition there are other control elements called Enhancers that interact with activators, when they bind, another protein can bend DNA to bring the activator closer to the promoter where the transcription factor can be found.

• To start transcription, special proteins called transcription factors are needed.

• Some transcription factors bind to the promoter region, often at the TATA box (a DNA sequence rich in thymine (T) and adenine (A)).

  • T and A are easier to separate because they only have 2 hydrogen bonds, unlike G-C pairs (which have 3).

• Transcription factors have two important domains:

  • DNA-binding domain: binds to a specific DNA sequence in the promoter.

  • Activation domain: interacts with other regulatory proteins to help assemble the transcription machinery and boost transcription.

• Enhancers are control elements located farther away from the promoter.

  • When activator proteins bind to enhancers, other proteins bend the DNA to bring the activator close to the promoter.

  • This helps transcription factors and RNA polymerase work together more efficiently, increasing transcription

Allosteric regulation

• enzymes usually have an active site where a substrate can bind but they can also have an allosteric site. It’s a spot where any enzyme regulator can bind.

• allosteric site is a binding site for several modules, we determine as allosteric modulators.

• If the allosteric modulator is bound then the substrate could potentially no longer bind to the active site. It can change the active site to be easier or harder for the substrate to bind.

• We have inhibitors or activators:

• There are two types of regulators:

  • Allosteric activators which increase enzymatic activity

  • Allosteric inhibitors that decrease enzymatic activity

2. Which statement about the allosteric regulation of enzymes is true?

a. it is an example of reversible direct inhibition of the active site of an allosteric enzyme

b. it is directed at the enzyme that catalyzes the allosteric step in a metabolic pathway

c. it affects the concentration of an allosteric enzyme

d. it acts by permanently modifying the active site of an allosteric enzyme

e. it is regulated by binding a compound at a site other than the enzyme's active site.

e. it is regulated by binding a compound at a site other than the enzyme's active site.

3. Which of the following conditions is crucial to prevent high activation of the lac operon but allows the

lac operon to maintain a basal level of activities?

a. Large concentrations of lactose

b. Low concentrations of lactose

c. Large concentrations of glucose

d. Low concentrations of glucose

e. Large concentrations of cAMP

c. Large concentrations of glucose

Gene regulation in Eukaryotes

• Eukaryotic cells are so much more complex then prokaryotic cells.

• Basic eukaryotic gene: exons, introns, transcription start site, promoters and enhancers

• Exons and introns: in any eukaryotic genes we have those segments of DNA that actually do code for polypeptide.

  • Exons: do code for polypeptide

  • Introns: do not code for anything useful, and get removed during splicing.

• Transcription start site: transcription begins here, a special protein complex know as RNA polymerase 2 binds to the transcription start site and this is where transcription takes place.

• Promoter: like operons in prokaryotes, but the promoters of eukaryotes are much more complex, the promoter can be broken down into core promoters, other promoters are upstream promoters. The promoters are found to the left of the start site. The TATA box is the most common core promoter.

  • The core promoter is where are the transcription factor and regulatory factors bind to. This is necessary for transcription to actually take place.

  • Transcription factor 2D: a complex of many proteins, TATA binding protein, that binds to the TATA on the core promoter

  • Transcription factor 2B: the protein needed for the interaction to take place between the RNA polymerase 2 proteins and the TATA binding protein.

• Enhancer: found much further, it’s usually found thousands of bases up or downstream our gene. The enhancer also binds special transcription factors, when a transcription factor binds, the enhancer loops around and binds to the protein complex found on the promoter, stimulating transcription, increasing the rate of transcription of then gene.

DNA and chromatin regulation

• Regulating gene expression at different steps gives cells the versatility and adaptability they need to respond to changing conditions.

• In the nucleus, DNA is tightly packed into chromatin, which is made of DNA, histone proteins, and non-histone proteins. This supercoiling helps organize DNA but also controls access to genes.

• Chromatin is organized into repeating units called nucleosomes. Each nucleosome consists of ~146 base pairs of DNA wrapped around a core of 8 histone proteins:

  • 2 copies each of H2A, H2B, H3, and H4.

• Histone acetylation:

  • Enzymes called histone acetyltransferases (HATs) add acetyl groups to the amino-terminal tails of histones.

  • This reduces the positive charge on histones, loosening their grip on DNA.

  • As a result, chromatin becomes more open (euchromatin), allowing transcription machinery to access genes and promote gene expression.

• Histone deacetylation:

  • The removal of acetyl groups by enzymes called histone deacetylases (HDACs).

  • This leads to a more condensed (heterochromatin) structure, reducing gene expression because the DNA is less accessible.

• DNA methylation

  • DNA methylation involves adding a methyl group (–CH₃) to cytosine bases, usually at CpG sites (cytosine followed by guanine).

  • This is done by enzymes called DNA methyltransferases (DNMTs).

  • Methylation generally silences genes by:

    • Blocking transcription factors from binding.

    • Recruiting proteins that further compact chromatin.

  • DNA methylation is important for:

    • Long-term gene silencing.

    • X-chromosome inactivation.

    • Genomic imprinting.

    • Suppressing transposable elements.

1. A gene has three enhancers that have distinct transcription factor binding sites. These transcription

factors are expressed in specific tissues shown with colors, and they are required for the expression of

the gene. A mutation takes place on the binding site of the green transcription factor, and it cannot bind

to the site anymore. How will this mutation affect gene expression?

A. It will affect gene expression in all 3 tissues

B. It will not affect gene expression in any tissues

C. It will lead to overexpression of the gene in tissue Z but no effect in tissues X and Y

D. It will lead to suppression of the gene in tissue Z but no effect in tissues X and Y

E. It will lead to overexpression of the gene in tissues X and Y but no effect in tissue Z

D. It will lead to suppression of the gene in tissue Z but no effect in tissues X and Y

Gene regulation: Operon

• Operon is way of regulating genes for prokaryotes (some eukaryote exceptions).

• operons are made up of a few genes that can involve enzymes, enzymes are proteins with the ability to break down or build up the substances the act on.

• Key players in an operon

  • RNA polymerase: a builder enzyme, it’s needed in order to start transcription. RNA polymerase needs a promoter, so it can find where to bind.

  • Promoter

  • Operator: a repressor can bind to an operator and block RNA polymerase to prevent the creation of mRNA

• Ex. A Lac operon: There’s a promoter, an operator and 3 genes that codes for enzymes that break down lactose. There’s a repressor and a gene that codes for the repressor and it has its own promoter. This way if there’s no lactose we don’t keep creating the enzyme to break down lactose. If lactose isn’t present the repressor binds to the operator, then the enzymes cannot be made.

  • When lactose is around, the sugar lactose, binds to the repressor, changing the repressors shape and it can no longer bind to the operator

Promoters and enhancers

• The human genome is huge and only a small percent are genes, that’s why we have promoters, which help RNA polymerase find the start of the gene.

• A promoter marks the start of the gene and marks the end of activation. Most promoters are the TATA box.

• Enhancers are short sequences that recruit activator proteins that help RNA polymerase work much more efficiently. Enhancers are often thousands of base pairs away, so the DNA must loop around to allow the enhancers get clears to the promoter.

Post translational modifications

• human proteome is vastly more complex than human genome. Post translational modifications increase the diversity of the human proteome.

• single genes can code for many proteins. Modification can occur anytime during the lifecycle of the protein, many are modified right have translation is completely. Modifications help:

  • folding into proper confirmation

  • increase stability

  • help localize protein in specific compartments.

• Modification help modify the biological activity of the protein

  • either by activating or inactivating catalytic activity

• Some modifications mark proteins for degradation.

• 1. Methylation

  • Adds a methyl group (–CH₃) to specific amino acid side chains or DNA bases.

    In proteins, methylation can regulate activity or interactions.

    In DNA, cytosine methylation at CpG sites silences gene expression.

    Enzyme: DNA methyltransferase (DNMT)

    Methyl donor: S-adenosyl methionine (SAM)

    Product: 5-methylcytosine

• 2. Acetylation

  • Adds an acetyl group to nitrogen atoms on proteins (N-acetylation).

    Commonly modifies histones (histone acetylation), reducing DNA-histone interaction and promoting transcription.

    Enzyme: Histone acetyltransferase (HAT)

    (Reversed by HDAC: histone deacetylase)

• 3. Glycosylation

  • Attachment of sugar molecules to proteins.

    Affects protein folding, structure, localization, stability, and signaling.

    Critical for cell surface proteins and immune recognition.

• 4. Lipidation

  • Addition of lipid groups to proteins.

    Helps anchor proteins to cell membranes, influencing localization and function.

• 5. Ubiquitination

  • Attaches a small protein called ubiquitin to a target protein.

    Commonly marks proteins for degradation by the proteasome.

    Also involved in DNA repair, cell cycle, and immune response.

• 6. Phosphorylation

  • Adds a phosphate group (usually to serine, threonine, or tyrosine).

    Key for regulating enzyme activity, signal transduction, and cell communication.

    Enzymes: Kinases (add phosphate), Phosphatases (remove phosphate)

epigenetic

• the study of how DNA interacts with the smaller molecules within the cell that can activate and deactivate genes.

• DNA is like a recipe book those molecules are largely what determine gets cooked and when.

• Genes and DNA are expressed when they’re read and transcribed into RNA and then into proteins by ribosomes. Epigenetic changes can boost or interfere with transcription of specific genes. The most common way interference happens is via chemical tags that wraps around DNA or the proteins its wrapped around. The set of all the chemical tags attached to the genome of a given cell is called the epigenome.

  • Ex. A methyl group inhibits gene expression by de-railing the cellular transcription machinery or causing the DNA to coil more tightly making it inaccessible. Boosting transcription is the opposite, sometimes the chemical tags loosen the DNA around the protein making it easier to transcribe.

• All of the cells in our body essentially have the same genome but its own distinct epigenome.

• The epigenome mediates a life long dialouge between genes and the environment. The chemical tag that turn genes on and off are influenced by diet, chemical exposure and medication. This can eventually lead to disease, say if a gene that makes a tumor suppressing protein is turned off.

Post-translational modifications (again)

• Types of modification:

  • Phosphorylation: most common type. The addition of a phosphate group to a protein. Used for reaction coupling (may be some reaction we want to happen but energetically unfavorable, but we can couple unfavorable to a favorable one so that the combine process is spontaneous and will occur) , other is for regulating enzyme activity (a lot of enzymes that are inactive without a phosphate group, or active when not phosphorylated so the addition will inactive them).

  • Acetylation: the addition of an acetyl group. Histone acetylation is a very important example, DNA has a negative charge and wrapped around histone proteins that are positively charged. If you were to acetyl histones and basic amino acids, it would remove the positive charge and cause the binding to loosen, making DNA more avaibale for transcription.

  • Glycosylation: the addition of a carbohydrate to a protein. This helps it fold into its proper form, another example is with viruses, viruses have a protein code and recognized as foreign by the immune system and will be destroyed, but viruses are capable of coating their proteins with carbohydrates which allows them to be shielded from the immune system

  • Hydroxylation: addition of a hydroxyl group and OH group, this is important for detoxification, many toxins that organisms encounter are hydrophobic, they don’t dissolve in water, so the hydroxyl group will oxidize the compound when you oxidize the compounds you introduce the polar OH groups so now it can be dissolved in water and excreted.

  • Methylation: addition of a methyl group. Alters gene expression, DNA when methylated could increase gene expression and in other cases decrease it. Most of the times it decreases. Ex. in females where one of the two x chromosomes is inactivated in each cell, this is for dosage compensation, so females aren’t expressing too many proteins from the x chromosome, this is due to DNA methylation.

  • ubiquitnation: involves the addition of a ubiquitin molecule to a protein. Ubiquitin is a tag that marks the protein for degradation by the proteasome.

  • Cleavge: involves the hydrolysis of a peptide bond. Whatever peptide was synthesized is going to be cleaved into two.

  • Disulfide bond formation: important for stabilizing protein structure.

Histone modification

• histone proteins are the most widely recognized proteins of chromatin, they can be modified, that constitute epigenetic information.

• What are histone proteins: There are 5

  • H1

  • H2A

  • H2B

  • H3

  • H4

  • only four of the five go on to form the nuceloeome, or the basic unit of chromatin, its built in a controlled and highly regulated manner. Nucleosome octamer is what DNA wraps around so we can condensed chromatin into the nucleus. Around 1 nucleosome we have 146 base pairs of DNA that wraps around 1.75 times. DNA is negatively charged and histones are positively charged. They attract and come together.

  • A singular histone is made of a globular core, an N terminus and a C terminus. Remember we read from N terminus to the C terminus.

• How to modify:

  • 1) Histone writers: Enzymes that catalyse formation of a particular histone modification.

  • 2) Histone erasers: Enzyme that remove the histone modification

  • 3) Reading the code: translating a histone modification into an effect on gene expression. There is a direct and indirect way of reading the histone code.

    • Direct: that modification directly alters the interaction of the histone protein with DNA and/or other histones.

    • Indirect: reader proteins act at the interface between the modifier and the effect on gene expression.

1. Acetylated histones usually result in which of the following?

A. Production and assembly of ribosomes

B. Increase in transcription/ gene expression

C. Decrease in transcription/ gene expression

D. Increase in protein degradation

E. Decrease in protein degradation

B. Increase in transcription/ gene expression

Which of the following is true about epigenetic gene regulation?

A. DNA methylation increases during the induction of induced pluripotent cells.

B. The establishment of X-inactivation is essential to maintain embryonic stem cells.

C. Histone methylation can be maintained through cell divisions, thereby playing a role in epigenetic

inheritance.

D. DNA methylation can be reversed by protein phosphatase.

E. X-inactivation always occurs on the maternal X chromosome in males.

C. Histone methylation can be maintained through cell divisions, thereby playing a role in epigenetic

inheritance.

Mitosis

• A type of cell division, responsible for many of our bodies functions.

• we are made of many cells, in our cells there’s out nucleus with DNA, our bodies instructions.

• We have 46 chromosomes that make 23 pairs

• Almost all our cells are diploid, except sex cells.

• Mitosis takes place over these phases:

  • Prophase

  • Metaphase

  • Anaphase

  • Telophase

• Most of their lives cells are in interphase, their in between episodes of mitosis, during interphase the long strings of DNA are folded in the form of chromatin. To get ready for division a set of protein cylinders called the centrosomes duplicates itself. All of the DNA begins to replicate itself now we enter phase 1..

• Prophase:

  • the chromatin condenses into chromosomes and the two copies of DNA made stick together. These are called the chromatids, they meet in the middle, at the centromere. Now the nuclear envelop disintegrates and the centrosomes peel away from the nucleus and head to opposite ends of the cells, as they go, they leave behind a wide trail of protein ropes called microtubules. These provide structure to the cell.

• Metaphase:

  • the chromosomes attach to the microtubules by their centromeres and get moved by motor proteins. The chromosomes line up right down the middle of the cell.

• Anaphase:

  • Motor proteins pull so hard on the ropes that the X shaped chromosomes split back into singles and get pulled towards either end of the cell.

• Telophase:

  • Each of the new cell structures are reconstructed, nucleus and membranes form, and the chromosomes become chromatin again. Then the cell begins to crease and start to split into two, this is called cleavage.

• Cytokinesis:

  • the splitting of the two cells, the two new nuclei move apart from each others and the cells separate. Now we have two new cells and these clones are called the daughter cells of the parent cell.

Cell cycle

• Interphase

  • G1: cells grow

  • S: DNA replication of cells

  • G2: Cell grows more in preparation for mitosis

• M phase

  • mitosis

• Checkpoints

  • G1: checks if the cell is growing well enough, is its DNA damaged, does the cell have the resources it needs?

  • G2: checks if DNA was replicated correctly back in S phase, does it have resources to continue?

  • M: checks in the stage metaphase if the chromosome are lined up correctly in the middle.

• Apoptosis:

  • a damaged cell will self distrust

Cell division in bacteria takes place mainly by

A. mitosis

B. binary fission

C. sporulation

D. meiosis

E. None of the above

B. binary fission

2. A group of cells is assayed for DNA content immediately following mitosis and is found to have an

average of 12 picograms of DNA per nucleus. Those cells would have __________ picograms at the end

of the S phase and __________ picograms at the end of G2.

A. 12, 12

B. 12, 24

C. 24, 24

D. 24, 12

E. 16, 24

C. 24, 24

3. Cancer is characterized by runaway cell division. Several scientists think drugs that disrupt normal

microtubule function could be important anti-cancer compounds. What is the most likely explanation?

A. These drugs would disrupt DNA replication.

B. These drugs would lower ATP production in the mitochondria altering G1 phase.

C. These drugs would disrupt mitosis.

D. These drugs would disrupt actin filaments.

E. These drugs would disrupt the nuclear membrane.

C. These drugs would disrupt mitosis.

Double stranded DNA repair

• double stranded breaks can occur due to ionizing radiation, there are two ways to repair this

  • non-homologous end joining

  • homologous recombination

• 1. Non-Homologous End Joining (NHEJ)

  • This repair mechanism directly joins the broken ends of DNA.

  • It does not require a homologous template.

  • It’s a quick but error-prone process — small insertions or deletions (indels) can occur at the break site.

  • Often described as a “glue it back together” method — useful but crude.

  • Occurs mainly before the S phase of the cell cycle (when a sister chromatid isn't yet available).

  • Requires proteins like Ku and DNA ligase IV.

  • Defects in ATM (ataxia-telangiectasia mutated) protein, which is involved in recognizing DSBs, can impair this pathway and lead to disorders like ataxia-telangiectasia — a severe genetic condition with neurodegeneration and cancer risk.

  2. Homologous Recombination (HR)

  • This is a high-fidelity repair process.

  • It uses a sister chromatid as a template to accurately restore the DNA sequence.

  • Mainly occurs after DNA replication (S and G2 phases) when a sister chromatid is available.

  • Involves proteins like BRCA1/2, Rad51, and others.

  • Because it uses a template, HR is much more accurate than NHEJ.

  • Defects in HR proteins (e.g., BRCA mutations) are linked to cancers, especially breast and ovarian cancer

DNA repair

Repair Type	Fixes	Key Features
Mismatch Repair (MMR)	Mismatched bases after DNA replication	Uses template strand to excise and replace wrong base
Base Excision Repair (BER)	Small, non-helix-distorting base damage (e.g., deamination, oxidation)	Removes and replaces a single damaged base
Nucleotide Excision Repair (NER)	Bulky lesions (e.g., thymine dimers, adducts)	Removes a short single-stranded DNA segment
Direct Repair	Specific types of base damage (e.g., methylation)	Enzyme directly reverses chemical modification
Homologous Recombination (HR)	Double-strand breaks (DSBs)	Error-free; uses sister chromatid as template
Non-Homologous End Joining (NHEJ)	Double-strand breaks (DSBs)	Error-prone; ligates broken ends without template

DNA damage checkpoint and p53

• When there is a double stranded break, it would be dangerous for this DNA to replicate, so the cell tries to repair this damage, this is regulated by p53. When p53 is phosphorylated it becomes available, it has many transcription targets, p53 encourages cell death, to regulate the cell cycle.

Cell cycle, RB and P53

• The genes that code these proteins are tumor suppressing proteins

• Cell cycle

  • interphase and Mitosis

  • further broken down:

    • Interphase: G1, S phase, G2 phase

    • Mitosis: prophase, metaphase, anaphase, telophase

  • Cell cycle starts in the G1 phase, as the cell matures it goes through S phase and then G2, then mitosis occurs.

  • Mitosis; the part of the cell cycle in which the nucleus and cytoplasm of the parent cell split into two genetically identical cells (daughter cells) (in mitosis they’re genetically identical, in meiosis they are not). Once Mitosis has occurred any DNA changes or mutation which were not corrected become permanent.

  • Interphase: the cell grows, replicates DNA and synthesizes new proteins in preparation for mitosis. Made of several phases, G1(prepping for DNA replication), S(DNA is replicated), G2(cell synthesizes proteins required for mitosis) , G0 (resting phase)

• Cell cycle checkpoints:

  • Extremely important:

  • Checks to see if no DNA errors are present which can potentially be passed down to the future daughter cells. If these problems cannot be fixed, cells will be destroyed. These quality checkpoints are called, cyclins or cyclin dependent kinases.

  • Cyclins are proteins which bind to enzymes called cyclin dependent kinases.

  • Each type of cyclin increases in concentration depending on which part of the cycle we’re in. Ex. the cyclin E checkpoint which allows the cell to pass from G1 phase into S phase.

• Cyclin Dependent Kinases

  • enzymes that activate proteins required for progression through the cell cycle and its checkpoints. CKDs must first interact with cyclins to form a cyclin-CKD complex. So cyclins must be present in the intercellular space.

• The types of checkpoints (there are more checkpoints than this):

  • G1/S checkpoint: this checkpoint between in the transition from G1—S, this is where the cell decided whether or not to undergo mitosis and divide, or not divide and go into the G0 phase. This process is mediated by the cyclin E/CKD2 complex, and two regulatory proteins retinoblastoma protein (RB) and E2F.

  • G2/M checkpoint

  • Spindle checkpoint: occurs in mitosis, between metaphase and anaphase, this is making sure the chromosomes are positioned appropriately.

• Retinoblastoma protein

  • prevents excessive cell division by inhibiting cell cycle progression. RB is inactivated by phosphorylation, it’s normally bound to E2F, when the cell isn’t dividing. Once E2F is released it is able to bind the promoter of genes which is able to code for DNA replication enzymes like DNA polymerase.

1. You found that a small deletion was generated after DNA repair. What is the possible mechanism

mediating this process?

A. Mismatch repair

B. Non-homologous end joining

C. Homologous recombination

D. Base excision repair

E. Nucleotide excision repair

B. Non-homologous end joining

Meiosis

• we get a pair of homologous chromosomes from each of our parents.

• Haploid cells, half the full set of chromosome, so 23, they need to combine to get to the 46

• Meiosis: specialized diploid cells split in half twice. Like mitosis, meiosis goes through prophase, metaphase, anaphase and telophase but they also go through prophase 2, metaphase 2, anaphase 2 and telophase 2.

• The raw materials for this process are in your ovaries or testes. They’re diploid cells called either primary oocytes or primary spermatocytes. Men produce sperm all throughout their adult lives, while women are born with a certain amount of eggs that’s they’ll release over time throughout puberty.

  • Interphase, everything is replicating itself

  • Prophase 1: centrosomes head to opposites of the cell and unspool the microtubules, and the DNA clump up into chromsomes, they’re link to their complimentary chromosome, forming that X shape, each arm is called a chromatid. Includes two additional steps, crossover and homologous recombination. Each double chromosome line up next to its homolog, aka the pair form ur mom and the pair from your dad. This adds up to 4 chromatids, one chromatid from each X gets tangled up with the other, this is crossover, then they exchange DNA, that’s recombination. Now all four chromatids are different. There’s one pair of chromosomes that doesn’t always go through the crossover or recombination, this is the 23 pair and this is the sex chromosomes. Female is two XX, since they;re the same they can do crossover and recombination. However if you’re male, you have Xy chromosomes, the X wants nothing to do with y because they are not homologous, so they don’t match up, half of the 4 resulting sperm will be x and the other half will Y.

  • Metaphase 1: the chromosomes line up with their partner and the pairs get pulled apart and migrate to either end of the cell that’s Anaphase 1.

  • Telophase 1: the nuclear membrane reform, the chromosomes become chromatin again, we have cleavage, the two new nuclei pull a part from one another, this is cytokinesis and now we have two haploid cells each with 23 double chromosomes, that are new, unique combinations.

  • Here we have the second phase, which is almost identical to mitosis.

  • Prophase 2: the DNA clumps up again to chromosomes and the microtubules are put back in place

  • Metaphase 2: the chromosomes are lined up in the middle of the cell

  • Anaphase 2: the chromatids are pulled apart into seperate single chromosomes. The crease forms for cleavage, and the final separation of cytokinesis leads to four new cells with 23 single chromosomes each!

Meiosis more clear

Meiosis: Making Haploid Cells for Reproduction

• Humans have 46 chromosomes, or 23 pairs — one set from each parent.

• To pass on genetic material, we must create haploid cells (gametes: sperm or egg) with only 23 chromosomes.

• Meiosis is the process that creates these haploid cells by dividing a diploid cell twice, resulting in four unique daughter cells.

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Where It Starts

• This happens in the ovaries (eggs) or testes (sperm).

• The starting diploid cells are:

  • Primary oocytes (females)

  • Primary spermatocytes (males)

• Men produce sperm throughout life, but women are born with all their eggs, releasing one each cycle during puberty.

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Interphase (Before Meiosis Starts)

• DNA is replicated, so each chromosome now consists of two sister chromatids.

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📍 Meiosis I: Reduction Division

(This is where the chromosome number is cut in half)

Prophase I

• Chromosomes condense.

• Centrosomes move to opposite poles, and spindle fibers form.

• Homologous chromosomes (one from each parent) pair up.

• Crossing over and homologous recombination occur:

  • Matching chromatids swap DNA, mixing up genetic material.

  • This creates genetic diversity.

• Note: the 23rd pair (sex chromosomes) behaves differently:

  • Females (XX): crossover can occur.

  • Males (XY): X and Y are not homologous, so no crossover. Half of sperm get X, half get Y.

Metaphase I

• Homologous pairs line up in the middle of the cell.

Anaphase I

• Entire chromosomes (with both sister chromatids) are pulled to opposite sides.

Telophase I + Cytokinesis

• Nuclear membranes may reform.

• Cell divides into two haploid cells — each with 23 chromosomes, but those chromosomes are still duplicated (two chromatids).

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📍 Meiosis II: Separation of Sister Chromatids

(Just like mitosis, but starting with haploid cells)

Prophase II

• Chromosomes condense again.

• New spindle fibers form.

Metaphase II

• Chromosomes line up in the center.

Anaphase II

• Sister chromatids are pulled apart to opposite ends.

Telophase II + Cytokinesis

• Nuclei reform.

• Cells divide → Four unique haploid cells, each with 23 single chromosomes

1. How does mitosis differ from meiosis?

a. Crossing over occurs in mitosis, but not in meiosis I.

b. Sister chromatids separate in mitosis but not in meiosis II.

c. The nuclear envelope disappears only in meiosis I.

d. Mono-orientation of sister kinetochores takes place in meiosis I but not in mitosis.

e. Homologous recombination only occurs in mitosis.

2. Meiotic recombination results in

a. Chiasmata formation in meiosis I

b. Changes in the combinations of genes on each chromosome

c. Changes in combinations of exons on each chromosome

d. DNA replication in premeiotic S phase

e. Changes in the order in which genes are present on the chromosome

What is the key difference between male and female meiosis in mammals?

• Male meiosis: Continuous, symmetrical divisions, takes ~25 days per cycle.

• Female meiosis: Begins during embryonic development, arrested in prophase I until ovulation, resumes at fertilization; involves asymmetrical divisions (produces polar bodies).

What is the purpose of epigenetic reprogramming in the mammalian germline?

To erase and reset epigenetic marks, enabling pluripotency and full developmental potential in the next generation.

What is pluripotency?

The ability of a cell to differentiate into any cell type in the body. Found in embryonic stem cells and induced pluripotent stem cells (iPSCs).

What happens to female oocytes after meiosis begins during embryonic development?

They enter meiotic arrest at prophase I, remaining dormant until ovulation. This arrest can last decades (up to ~50 years).

What are polar bodies, and what is their significance?

Polar bodies are small cells produced during asymmetric division in oogenesis. They help discard extra chromosomes and preserve cytoplasm in the egg.

What is the function of epigenetic regulation during somatic cell differentiation?

It ensures heritable patterns of gene expression, locking in a cell's identity by adding epigenetic modifications (like methylation or histone changes)

Meiotic arrest in females

In female mammals, oocytes begin meiosis during embryonic development but pause in prophase I. They can remain in this arrested state for decades, resuming meiosis upon ovulation and fertilization.

Asymmetrical division in oogenesis

Oocytes divide asymmetrically to conserve cytoplasm, forming one large egg cell and small polar bodies. This ensures the egg has enough resources to support early development.

Epigenetic reprogramming

The process of erasing and resetting epigenetic marks (like DNA methylation or histone modification) to restore pluripotency. Essential during fertilization and iPS cell generation.

Spermatogenesis

The continuous, symmetrical process of forming sperm in males. It involves DNA replication, meiosis, and maturation, taking about 25 days per cycle.

Ovarian reserve

The total number of oocytes present in a female at birth. This reserve declines with age and determines fertility and the timing of menopause.

Embryonic stem cells (ES cells)

Pluripotent cells derived from the inner cell mass of the blastocyst. They can differentiate into all cell types of the body.

Induced pluripotent stem cells (iPS cells)

Somatic (adult) cells that have been reprogrammed back to a pluripotent state using transcription factors like Oct4, Sox2, Klf4, and c-Myc.

Epigenetic regulation during development

Refers to the gain or loss of chemical modifications on DNA/histones that control gene expression. Crucial for determining cell fate and maintaining identity.

1. What is the primary purpose of epigenetic reprogramming in the mammalian germline?

a. To enhance gene expression for rapid embryonic development

b. To preserve the epigenetic marks acquired during the parent's lifetime

c. To erase and reset epigenetic marks, enabling full developmental potential in the next generation

d. To introduce mutations that increase genetic diversity

c. To erase and reset epigenetic marks, enabling full developmental potential in the next generation