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QofQuimica

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This thread will function analogously to the physical science and organic chemistry explanations threads. We will be adding new posts periodically on cell and molecular biology topics that many students find difficult. Students are requested to please NOT post questions here. If you would like to ask a molecular biology or biochemistry question, you should post it in the Biochemistry, Cell Biology, and Genetics Question Thread.

Here is a list of all of the posts in this thread alphabetized by topic:

Table of Contents:
 

QofQuimica

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For all of the pre-health tests (MCAT, PCAT, DAT, and OAT), you should be able to follow the generation of ATP in each step, and also the energy carrier reduction (NAD and FAD) in each stage. You do NOT need to memorize any enzymes or pathway intermediates; they will make you do that in your professional school biochem class. You should also know that oxygen is the final electron acceptor of the electron transport chain, and that anaerobic respiration is insufficient to sustain human life. In addition, fermentation produces lactic acid as a byproduct in humans, and ethanol in yeast. Finally, you should know where in the cell each stage of respiration occurs. Here is a list of the energy conversions for each stage and where in the cell they take place:

Glycolysis: (anaerobic, occurs in the cytoplasm)
  • 2 net ATP (4 total made, but 2 needed to complete this stage)
  • 2 NADH produced (making 4 ATP in ETC for eukaryotes and 6 ATP for prokaryotes)

Fermentation: (anaerobic, occurs in the cytoplasm)
  • 0 ATP; its main purpose is to reoxidize the NADH produced in glycolysis

Pyruvate Decarboxylation: (aerobic, occurs in the cytoplasm for prokaryotes, mitochondrial matrix for eukaryotes)
  • 0 ATP produced
  • 2 NADH produced (making 6 ATP in ETC)

TCA Cycle: (aerobic, occurs in the cytoplasm for prokaryotes, mitochondrial matrix for eukaryotes)
  • 2 ATP produced
  • 6 NADH produced (making 18 ATP in ETC)
  • 2 FADH2 produced (making 4 ATP in ETC)

Electron Transport Chain (ETC): aerobic, occurs across the inner cell membrane for prokaryotes, inner mitochondrial membrane for eukaryotes
  • NADH oxidation back to NAD and FADH2 oxidation back to FAD occur along with ATP production, allowing the earlier stages to continue

Summary: 36 net ATP produced in eukaryotes, 38 net ATP produced in prokaryotes (because the electrons from the NADH produced from pyruvate decarboxylation do not have to be transported across the mitochondrial membrane in prokaryotes; doing this causes a net loss of two ATP in eukaryotes)
 

QofQuimica

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I will post further details about them at a later time, but for MCAT, DAT, OAT, and PCAT biology, you should know the structure and function of the following organelles:

  • nucleus
  • cell membrane
  • cytosol (cytoplasm)
  • cytoskeleton (microtubules, microfilaments, and intermediate filaments)
  • endoplasmic reticulum
  • Golgi apparatus
  • vesicles
  • vacuoles
  • ribosomes
  • lysosomes
  • microbodies
  • mitochondria
  • chloroplasts
  • cell wall
  • centrioles

You should also know that prokaryotes do NOT have any membrane-bound organelles, such as a nucleus, mitochondria, or Golgi apparatus.
 
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Flash cards can work for memorization, but I consider them a waste of time. The amount of time you spend making them could be better used working to understand the big picture of what's going on with metabolism.

The MCAT is not about memorization. The MCAT is about critical thinking. You must UNDERSTAND the equations and concepts, not merely memorize them.

All the concepts that are tested on the MCAT are fairly simple, but the MCAT will ask you questions in such a way that if you don't have a rock solid understanding of the concepts, and have merely memorized them, you will not be able to answer them.

You have to know very little about metabolism for the MCAT anyway, so there would be hardly anything to memorize. Just know the big picture, and the details you need to know will be easy to remember! They're crucial to the big picture!

So how to do this? Review books by Kaplan and TPR will give you tons more info than you really need, but they can help you to understand what's really going on with metabolism, or whatever you're studying. You just have to be able to let go of all the minutiae, which can be hard for those of us who tend to get bogged down in details. EK can give you a solid, bare-bones review. You DO have to know pretty much everything they tell you. It's up to you!
 

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Operons in prokaryotes consist of groups of genes that typically work together and are all controlled by one promoter, which is in turn controlled by an operator region. This means that all of the genes in the operon are turned on and off together.

As far as inducible operons go, the first example that comes to mind is the lac operon. The genes in the operon, lac Z, Y, and A, code for proteins that DEGRADE/utilize lactose. These genes are preceeded by an operator region. the operator region is the "control region" of the operon. With the lac operon, in the absence of lactose, an inhibitor (protein) binds to the operator region DNA, and the operon is effectively turned off because the inhibitor interferes with RNA polymerase binding. When lactose is around, it binds the inhibitor and releases it from the operator DNA. Once the repressing inhibitor is removed, RNA polymerase can bind and transcribe the operon (the Z,Y and A genes), and the operator is considered "induced" or turned on. If you look at this from the standpoint of the cell, it makes sense. The cell only needs the proteins that utilize lactose when lactose is around, right? So it's set up that the genes that utilize lactose are only "turned on" when there is sufficient lactose in the cell (ie. the cell doesn't waste energy making proteins it doesn't need).

For repressible operons, the tryptophan operon comes to mind. In this operon, the genes for tryptophan (Trp) SYNTHESIS are grouped together. These genes are also preceeded by an operator region that controls expression of the operon. However, in this operon, there is a repressor that is only active (i.e., it will only bind the operator) when it is also bound to Trp. This means that there has to be a relatively high level of Trp in the cell to bind the repressor which will then turn off the genes for Trp production. This also makes sense from the standpoint of the cell....if you need more Trp, the genes will be turned on until there is enough Trp in the cell. When there is enough Trp in the cell, the genes will be turned off.
 

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Please excuse me if the material is slightly long or beyond the scope of MCAT. But, I think, this should summarize most of eukaryotic transcription. For the purposes of this post, I'm only going to summarize RNA pol II (mRNA synthesis) mediated transcription. RNA pol I regulates rRNA synthesis and Pol III regulates 5s RNA and tRNA synthesis.

The mechanism of gene transcription by RNA pol II follows 3 general steps, initiation, elongation and termination. These 3 steps are followed by RNA processing.
Initiation
In eukaryotes initiation is regulated by the presence of regulatory regions, promoters and enhancers. Common promoter elements are the TATA and CCAAT boxes, found upstream of the transcription start site. Enhancers can be found upstream, downstream, or within the coding region
Promoters are recognized by basal transcription factors and are necessary for initiating transcription, while enhancers, as the name suggests are necessary for enhancing transcription and also for regulating and mediating cell and tissue specific transcription.
The basal transcription factors (TFs) such as TFIID, along with other TFs, recruit RNA pol II to the promoter element and initiate basal transcription.
Other enhancer elements and TFs mediate higher levels of transcription.
Elongation
During elongation, RNA pol II moves along the DNA, close to the bubble that represents separation of the two strands of DNA. As the enzyme moves forward along the bubble, RNA is synthesized in the 5’ to 3’ direction. DNA ahead of the bubble is unwound and behind it is rewound. Elontation continues until the enzyme reaches a termination point.
Termination
If I may, termination in eukaryotic genes is not very specific. Pol II continues to transcribe RNA for a few thousand (1000-2000) bases past the end of the mature mRNA. The exact end is determined during RNA processing.
Processing
RNA processing is characterized by capping at the 5’ end, polyadenylation at the 3’ end and intron splicing.
5' Capping
A methylated guanine nucleotide is added to the 5’ end of the mRNA in a 5’ to 5’ phosphodiester linkage. This capping is essential for mRNA recognition by ribosomes during translation.
3' Polyadenylation
A polyadenylation signal (AUAAA) is present in most of the mRNA transcripts and this signal is reconized by an enzyme that cleaves the transcript about 20 nucleotides downstream and adds a series of As (~200) to the 3’ end. These As are added without the need for a template and prevent the mRNA from degradation.
Splicing
Removal of the introns from the pre-mRNA to yield mature mRNA is called splicing. Splicing is carried out by spliceosomes that contain at least 5 known small nucleotide ribonucleoproteins (snRNPs). These snRNPs contain small nuclear RNAs (snRNAs) and together they detect intron/exon boundaries and cleave the RNA at those specific junctions. The spliced RNA is then joined together to form the mature mRNA transcript.

Salient points of eukaryotic mRNA transcription:
1) occurs in 5’ to 3’ direction
2) mRNA synthesis regulated by RNA pol II
3) mRNA synthesis involves initiation, elongation and termination followed by processing to make the mature transcript.
4) Initiation is mediated by promoters and enhancers, and elongation by the RNA pol II. Termination in eukaryotes occurs way downstream and is not very specific, unlike in prokaryotes.
5) mRNA processing to produce the mature trancript involves 5’ capping, 3’ polyadenylation and intron splicing.
 

travelbug73

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Please feel free to add if I may have missed anything or correct if I'm even partially wrong.

tRNA molecule
• Single chain, contains 73-93 ribonucleotides
• Contains many unusual bases such as inosine, pseudouridine
• tRNA is L shaped
• 5’ end is phosphorylated
• 3’ end ends in CCA and contains the amino acid attachment, it is at one end of the L
• The other end of the L, far from the amino acid end, is the anticodon loop


The process of translation, like transcription, is also divided into three phases:
initiation, elongation and termination. These three phases are regulated by initiation, elongation and termination factors respectively.

Initiation

Initiator tRNA (tRNAi) that carries methionine is the only tRNA capable of initiating translation. An initiation complex called 43S, comprising methionine tRNAi, the small 40S ribosomal subunit, and initiation factors such as eIF2. The 43S complex is recruited to the 5’ end of the mRNA by eIF4E. This complex now scans the mRNA in the 5’ to 3’ direction to find the first 5’-AUG-3’. Scanning is an ATP dependent process. As soon as the met-tRNAi finds the first AUG, the larger ribosomal subunit is recruited and this recruitment is mediated by eIF5. Assembly of the large ribosomal subunit completes the initiation step. The large subunit has 3 binding sites, E, P and A and the first codon (AUG) is aligned at the P site.

Elongation

Elongation begins with the delivery of an amino-acyl tRNA (corresponding to the appropriate codon on the mRNA) to the A site on the ribosome by EF-Tu and this is followed by GTP hydrolysis. A peptide bond, catalyzed by peptidyl transferase, is formed between methionine and the aminoacyl tRNA by the transfer of methionine to the A site, leaving the deacylated tRNA at the P site. The next step of elongation is translocation, where, the deacylated tRNA moves to the E site, the dipeptidyl-tRNA (met + aminoacyl tRNA) moves to the P site and the mRNA moves forward by 3 bases, thereby aligning the next codon for the appropriate aminoacyl tRNA. Translocation is mediated by elongation factor G. A and E sites cannot be occupied at the same time, therefore, as soon as the A site is occupied, the E site containing the deacylated tRNA is emptied. Elongation proceeds in this fashion until a stop codon is encountered.

Termination

Normally, tRNAs do not have anticodons corresponding to the stop codons (UAA, UAG or UGA. At termination the polypeptide chain is at the P site and the stop codon is at the A site. Stop codons are recognized by proteins called release factors (RFs) or termination factors. Peptidyl transferase is activated when an RF binds to a termination codon at the A site. The activated peptidyl transferase hydrolyzes the bonds between the polypeptide and the tRNA at the P site. The released polypeptide chain, tRNA and mRNA leave the ribosome in that order. The ribosome dissociates into its subunits ready for another round of protein synthesis.

Summarizing eukaryotic protein translation

• mRNA is always translated in the 5’ to 3’ direction
• proteins are synthesized in the amino to carboxyl direction
• several ribosomes can simultaneously translate an mRNA molecule and such an mRNA molecule (with many ribosomes attached) is called a polysome or a polyribosome
• amino acids are added sequentially to the carboxyl end of a polypeptide chain
• aminoacyl tRNAs are the activated precursors in which the carboxyl group of an amino acid is attached to the 3’ hydroxyl group of a tRNA
• the above step is catalyzed by an aminoacyl tRNA synthetase and is driven by ATP
• initiator tRNA, met-tRNAi, occupies peptidyl (P) site, the next aminoacyl tRNA, added during elongation, occupies the aminoacyl (A) site
• peptide bond is formed between carboxyl group of met and aminoacyl tRNA
• dipeptidyl tRNA moves from A to P site
• deacylated tRNAi moves to E (exit) site and leaves ribosome
• a new aminoacyl tRNA occupies A site
• elongation proceeds until stop codon is encountered
• stop codon (UGA, UAA, or UAG) recognized by release factors that facilitate release of the completed polypeptide from the ribosome
 

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Note: this explanation is best understood if you have a Lineweaver-Burke plot and a velocity vs. concentration graph available while reading it.

When you look at an enzyme reaction, you're really looking at two reactions:

E+S <--> ES --> E + P

So in those rxns, E is the enzyme, S is the substrate, and P is the product. You'll notice that substrate binding is reversible, so you could say that we're looking at three possible reactions. Call the first forward reaction R1. Call the reverse of that reaction R2. Call the release of product from the enzyme R3.

So what happens with the Michaelis constant, Km, is that you make a ratio out of the rates of those three reactions to come up with a ratio for the overall reaction. That ratio is (R2+R3)/R1. So take a look at that ratio, and think about this: R2 and R3 are the two reactions that remove the substrate from the enzyme, and R1 is the reaction that binds the substrate to the enzyme. This means that Km is a ratio of separation:binding. So Km is related to the affinity of the enzyme for the substrate.

Now look at the velocity vs. concentration curve. Km is the substrate concentration at 1/2 of Vmax. Remember that Vmax is the mechanical limit of the enzyme -- it's churning out the product as fast as it possibly can. So look at a pair of enzymes, one with a high Km, and one with a low Km. An enzyme with a low Km reaches 1/2 Vmax at very low concentrations, because the enzyme has a high affinity for the substrate. An enzyme with a high Km, though, doesn't have a strong affinity for the substrate, so it takes a lot more of the substrate to get the enzyme up to 1/2 Vmax.

Now look at the Lineweaver-Burke plot of 1/Vo vs. 1/[substrate], aka the double reciprocal plot. The important things to remember about Lineweaver-Burke plots are the x and y intercepts. The x-intercept = -1/Km, and the y-intercept = 1/Vmax. Just learn these, and I'll help you make sense of them by discussing inhibition.

InhibitionThe best way to understand these graphs is to look at what happens with different types of inhibition.

First, think about competitive inhibition. You've got another substrate competing for the same enzyme. So what changes? Well, the enzyme suddenly has something else it can bind to, so its affinity for the substrate is reduced. At the same time, if you cram in enough substrate to overwhelm the competition, you can eventually reach Vmax. So in competitive inhibition, Km increases while Vmax remains the same. Look at your V/ graph, and the curve will stretch, because it takes a lot more substrate to get that Km at 1/2 Vmax. Look at your Lineweaver-Burke plot. The y-intercept stays the same because Vmax doesn't change. But Km has gone up, which means that -1/Km has gotten closer to zero, increasing the slope of the line and rotating it on the y-axis.

Now look at noncompetitive inhibition. In noncompetitive inhibition, you have something binding to another site on the enzyme, changing the structure of the binding site, and thus affecting the amount of enzyme that is able to bind substrate. This means that Vmax is reduced. Km, the affinity of the functional enzyme, remains the same, though. Looking at the V/ curve, you simply squish the maximum down. Looking at Lineweaver-Burke, Km is the same, so your x-intercept doesn't move. Vmax is smaller, so 1/Vmax is larger. This means that your line will have a higher slope and rotate on the x axis.

There are other conditions possible, but that covers the basics. Oh, and notice I didn't actually mention the Michaelis-Menten equation or the Lineweaver-Burke equation. Questions involving those are memorization w/plug & chug calculation. Understanding what happens on the graphs is much more intuitive.
 

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Cells of the Immune System: derived from the hematopoietic stem cell

1. Lymphoid Lineage

T lymphocytes (T cells, made in the thymus)

B lymphocytes (B cells, made directly from the bone marrow)

Natural Killer cells (NK cells)

2. Myeloid lineage

Monocytes that give rise to macrophages

Langerhans cells and Dendritic cells

Megakaryocytes that give rise to Platelets

Granulocytes (eosinophils, basophils and neutrophils)


Primary lymphoid tissues: bone marrow and thymus

Secondary lymphoid tissues: spleen, lymph nodes


Leukocyte migration: T and B cells leave the thymus and bone marrow respectively as naïve lymphocytes, migrate into the blood and then into the secondary lymphoid tissue. Antigen presenting cells (APCs), such as dendritic cells, also derived from the bone marrow, migrate into tissues, take up antigen and bring it back to the secondary lymphoid tissues to present the antigen to the T and B cells. The T and B cells are now primed or activated and they migrate to the sites of infection and inflammation to mount an attack.

Immune Response

Pathogens usually have two locations: Extracellular and Intracellular

Extracellular Pathogens are targeted by antibodies by at least one of three processes: Neutralization, Opsonization and Complement Activation

Neutralization: antibody may bind to bacterial toxin and neutralize, thereby preventing the pathogen from interacting with host cells. These antibody tagged toxins are later degraded

Opsonization: Antigens are coated with antibodies and are targeted for phagocytosis.

Complement Activation: Antibodies coat bacterial cells and these antibodies act as receptors for the first protein of the complement system, eventually forming a protein complex leading usually to phagocytosis.

Antibodies in each class have different sites of action and therefore vary in their effectiveness in neutralization, opsonization and complement activation.

Intracellular Pathogens are targeted by a T-cell mediated response. There are two intracellular locations:

Cytosol (continuous with nucleus via nuclear pore): site of all viruses and some bacteria

Vesicular System (ER, Golgi, endosomes, lysosomes etc): site of some bacteria and some parasites

There are also two T cells and the intracellular location determines the type of T cell.

Cytotoxic T cells (Tc or CTL): Express CD8 and kill pathogens in cytosol

Helper T cells (Th): Express CD4 and are again of two kinds

Inflammatory Th1 that kill vesicular pathogens

Th2 (True helper cells) are involved in antibody production by B cells against T-dependent antigens on extracellular pathogens.


Both antibody (humoral) and cell-mediated responses contribute to eliminating the pathogen.
 

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CELL CYCLE (Mitosis and Meiosis will follow in later posts)

There are two main phases to eukaryotic cell division: DNA doubling in S (synthetic) phase and halving of that genome in M (mitotic) phase. The S and M phase are interspersed with G1 (between M and S) and G2 (between S and M) phases. Therefore, it is G1, S, G2 and M.

So, what happens at each of these phases?

G1: growth and preparation of chromosomes for replication

S: DNA synthesis

G2: preparation for mitosis

M: Mitosis

Any stage other than mitosis is usually called the interphase.

What are some of the key players in cell cycle regulation?

Cyclins:
Cyclin D (G1 cyclin)
Cyclins E and A (S-phase cyclins)
Cyclins B and A (Mitotic cyclins)

The levels of these cyclins change depending on the stage of the cell cycle.

Cyclin-dependent kinases (Cdks)

Cdk4 is a G1 dependent Cdk
Cdk2 is an S-phase Cdk
Cdk1 is an M-phase Cdk

Cdks must bind to the appropriate cyclin to be activated. Their levels remain fairly constant throughout the cell cycle. However, the rise and fall of the cyclins determines Cdks’ activation. For example, Cdk4 is only activated when the level of G1 cyclins rises and thus prepares the cell for chromosome replication.


We all know that every cell has to encounter various check points to progress through each of these phases, so what are some examples of such check points?

DNA damage checkpoints: present at G1 (p53), S phase, G2 and at mitosis (MAD)
Spindle checkpoints (proteins such as kinesin):
arrest cells in metaphase if spindle fibers not properly attached to kinetochore
block cytokinesis by detecting improper spindle alignment
induce apoptosis if damage irreparable

What is G0?
When a cell exits the cell cycle at G1, either temporarily or permanently, it is said to be in G0. Many times cells in G0 are terminally differentiated and will not enter cell cycle, while other cells such as lymphocytes will reenter cell cycle upon stimulation (presence of antigen). During G0, genes needed for mitotic division are repressed. Most cancer cells cannot enter G0 and therefore replicate indefinitely.
 

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Interphase precedes both mitosis and meiosis and is the period between cell divisions during which time the chromosomes replicate and the chromosomes are not visible (loosely packed). During interphase, two pairs of centrioles lie next to each other, just outside the nucleus.

Mitosis is a process where in, one parent cell gives rise to two identical daughter cells. Mitosis can be divided into four stages: Prophase, Metaphase, Anaphase and Telophase.

Prophase: Chromosomes (two identical copies) condense, each chromosome has two arms and each copy of chromosome is called Chromatid. Spindle fibers form at centriole and centriole begin to separate. In addition, nuclear membrane disappears.

A short period just before metaphase, called prometaphase, comprises movement of centrioles to opposite ends of the cell and attachment of spindle fibers to each of the chromatids.

Metaphase: Chromosomes line up along an imaginary line, called the metaphase plate that divides the cell into two. The spindle fibers begin to pull the chromosomes to the opposite ends of the cell.

Anaphase: Spindle fibers separate sister chromatids to opposite ends of the cell.

Telophase: Chromatids, now called chromosomes move to each pole and new nuclear membranes form.

Once mitosis is complete, the rest of the cell divides, by a process called cytokinesis (division of the cytoplasm) and cell division is complete.


Meiosis is a type of cell division that is specific to reproduction and results in 4 daughter cells that have half the number of unidentical chromosomes (genetic information is contained from both parents). Meiosis is divided into two phases: Meiosis I and Meiosis II.

Meiosis I: comprises Prophase I, Metaphase I, Anaphase I and Telophase I

Prophase I: Chromosomes attach to nuclear membrane and pair up with corresponding chromosome (to from a tetrad) from the other parent. Homologous recombination occurs between chromosome pairs and genetic material exchange takes place.

Prometaphase I: Similar to prometaphase I in mitosis except, one chromosome (instead of chromatid) from the homologous pair is attached to each centriole. Therefore, 23 chromosomes (in humans) attach to fibers from one centriole and remaining 23 attach to the fibers from the other centriole.

Metaphase I: Chromosome pairs line up along the metaphase plate on either side.

Anaphase I: Chromosome pairs separate. One half of the chromosomes goes to one pole and the other half to the other pole.

Telophase I: Chromosomes reach opposite ends of the cell and a nuclear membrane forms marking the end of Meiosis I.

There is a major distinction between sperm and egg cells at this stage. While in sperm cells the cytoplasm is equally divided between the two emerging daughter cells, in oocytes, the cytoplasm is concentrated in one of the emerging daughter cells resulting in a large and a small daughter cell called the polar body.

Telophase I is followed by cytokinesis resulting in two daughter cells in case of sperms and one large cell and one small cell (polar body) in the case of the egg (primary oocyte to be precise).


Meiosis II follows a very short Interphase II but chromosome replication does not take place unlike in Mitosis and Meiosis I.

Meiosis II can also be divided into four phases: Prophase II, Metaphase II, Anaphase II and Telophase II. Meiosis II is very similar to Mitosis

Prophase II: Chromosomes condense, spindles form centrioles begin to separate and the nuclear membrane disappears. There is no homologous recombination.

Prometaphase II: Spindle fibers attach to chromatids and centrioles move to opposite ends of cell.

Metaphase II: Chromosomes align along the metaphase plate and fibers begin to pull at the chromosomes.

Anaphase II: Sister chromatids are pulled apart toward opposite ends of the cells.

Telophase II: Chromatids arrive at opposite poles, nuclear membranes form. Again, as in Telophase I, in the female cell, the emerging daughter cells will have unequal distribution of the cytoplasm resulting in one large and another small cell. The resulting large cell becomes the egg or ovum and the smaller cell is called the polar body. The first polar body formed at the end of Meiosis I also divides to form two polar bodies. Therefore, in females, at the end of Meiosis, there is one egg cell and three polar bodies.

Cytokinesis follows Telophase II to mark the completion of cell division.

Main differences between Mitosis and Meiosis I:

Prophase

Mitosis: Chromatids of chromosome begin to separate. There is no exchange of any genetic material
Meiosis I: Pairing of homologous chromosomes, tetrad formation and homologous recombination (exchange of genetic material) take place

Metaphase

Mitosis: Chromosomes line up along metaphase plate
Meiosis I: Chromosome pairs line up along metaphase plate

Anaphase

Mitosis: Sister chromatids pulled to opposite ends of cell
Meiosis I: Separation of chromosome pairs to opposite ends of cell

Telophase and Cytokinesis

Mitosis: Two daughter cells with identical chromosomes and exact number of chromosomes as parent cells
Meiosis I: Two daughter cells with chromosomes from both parents and half the number as parent cells and this is followed by Meiosis II

PS: Opposite ends of cell and opposite poles have been used interchangeably
 
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