03.+Cell+Physiology

=Cell Physiology =

**Explaining what makes up a cell, what genes are, and how genes control what happens in the cell and in our body as well. **
===**Also you will learn how cells communicate with each other, RNA synthesis, the different types of RNA, and what they do to help gene expression. You will also learn about DNA replication, cell division, the cell cycle, and cell death. **===

**Description of a cell:** Cells are the basic unit of structure and function in our body. They make up all living thing.
This video explains what makes up a cell -- This video explains what cells do in our body media type="youtube" key="a6boqEbcJWI?fs=1" height="344" width="425" align="left" media type="youtube" key="u54bRpbSOgs?fs=1" height="345" width="432" align="right"

1. Plasma Membrane and Associated Structures
The plasma membrane (also called the cell membrane) allows selective communication between the intracellular and extracellular compartments and aids cellular movement. It is composed primarily of phospholipids and proteins. The plasma membrane surrounds and gives cell form and it is formed by a double layer of phospholipids that restricts passage of polar compounds.



The plasma membrane participates in the bulk transport of larger portions of the extracellular environment. Bulk transport include the processes of phagocytosis and endocytosis.

**Phagocytosis** serves to protect the body from invading microorganisms and to remove extracellular debris. Largely by neutrophils and macrophages, phagocytosis, is an important immune process that defends the body and promotes inflammation. Phagocytes recognize "eat me" signals on the plasma membrane surface of dying cells.

**Endocytosis** is a process in which the plasma membrane furrows inward, instead of extending outward. Pinocytosis, one form of endocytosis, is a nonspecific process performed by many cells. Another type of endocytosis, receptor-mediated endocytosis, involves a smaller area of plasma membrane and it occurs only in response to specific molecules in the extracellular environment.



**Exocytosis** is a process by which cellular products are secreted into the extracellular environment. Proteins and other molecules produced within the cells that are destined for export are packaged within vesicles by an organelle known as the golgi complex. In the exocytosis process, these secretory vesicles fuse with the plasma membrane and release their contents into the extracellular environment.

**Cilia** are tiny hairlike structures that project from the surface of a cell into the extracellular fluid. Motile cilia can beat like rowers in a boat, stroking in unison. Almost every cell in the body has a single, nonmotile cilium. Cilia is believed to serve sensory functions. Cilia are composed of microtubules and are surrounded by a specialized part of the plasma membrane.



Sperm cells are the only cells in the body that have **flagella**. Flagellum is a single structure that propels the sperm through its environment.

<span style="color: #f23157; font-family: Georgia,serif; font-size: 110%;">**Microvilli** are the numerous folds on the surface area of the cell membrane.






 * <span style="color: #008080; font-family: Georgia,serif; font-size: 120%;">2. Cell Nucleus and Gene Expression **

<span style="color: #1b6c9d; font-family: Georgia,serif; font-size: 110%;">The cell nucleus has two membrane coverings around it. There is the inner membrane and the outer membrane which is on going to the cytoplasm with the plasmic reticulum. The inner and outer membranes are both stuck together by nuclear pore complexes. Each of these nuclear pore complex contains an opening called a nuclear pore that allows small proteins to go through and only some RNA. <span style="color: #1b6c9d; font-family: Georgia,serif; font-size: 110%;">Genes are a part of DNA that code many polypeptide chains.

<span style="color: #1b6c9d; font-family: Georgia,serif; font-size: 110%;">**Cell Signaling**- There are three different ways for cells talk to each other. These include Paracrine, Endocrine, and Synaptic. Paracrine signaling never goes far away. It is also known as the local signaling cell because it only includes the cells of a particular organ. It is known to also control the movements and activities of the cells in that particular organ that it is communicating to.



<span style="color: #1b6c9d; font-family: Georgia,serif; font-size: 110%;">Synaptic signaling is another one that doesn't go too far away. They release neurotransmitters from an axon by a synapse in order to communicate with the targeted cell.



<span style="color: #1b6c9d; font-family: Georgia,serif; font-size: 110%;">The endocrine signaling goes further out in the peripheral nervous system by means of the blood stream to targeted cells.



<span style="color: #008080; font-family: Georgia,serif; font-size: 110%;">Gene expression has two stages: the genetic transcription which is the synthesis of RNA and then the genetic translation which is the synthesis of protien. Each nucleus has at least one dark area called a nucleoli which has all the gene codes in order to produce rRNA. Genetic transcription is the process of coping the DNA code onto a strand of RNA, so the genetic code can be translated into the synthesis of a certain protein. Genetic transcription needs to help of RNA polymerase, which is an enzyme, to transcribe an individual gene. It also breaks the hydrogen bonds that are located between DNA strands. Only one of these two DNA strands will help serve as a guide for RNA synthesis.

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<span style="color: #008080; font-family: Georgia,serif; font-size: 110%;">After a RNA molecule is made it detaches itself from the DNA strand. Then the process of genetic transcription starts all over again. Chromatin, which is a mixture of DNA and protein, is the threadlike substance that makes up chromosomes. A protein inchromatin called acetylation helps make a more open structure so transcription factors can read the DNA. For gene expression there a four RNA needed. They include: precursor messenger RNA (pre-mRNA), messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). Each of these RNAs have a specific duty. Pre-mRNA is changed while in the nucleus to form mRNA. mRNA will hold the code in order to make certian protins. tRNA will be needed to decode the genetic message in mRNA and rRNA is needed to form the structure of ribosomes.


 * <span style="color: #008080; font-family: Georgia,serif; font-size: 130%;">3. Protein Synthesis and Secretion **

media type="youtube" key="TfYf_rPWUdY?fs=1" height="341" width="563" align="center"
 * <span style="color: #571678; font-family: Georgia,serif; font-size: 130%;">A quick over view of Protein synthesis: **
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">A mRNA leaves the nucleus and attaches to the ribosomes.
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">Each tRNA, with a specific base triplet in its anticodon, bonds to a specific amino acid.
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">As the mRNA moves through the ribosomes, complementary base pairing between tRNA anticodons and mRNA codons occurs.
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">As each successive tRNA molecule bonds to its complementary codon, the amino acid it carries is added to the end of a polypeptide chain that is growing.
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">Proteins destined for secretion are produced in ribosomes located on the rough endoplasmic reticulum and enter the cisternae of this organelle.

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 130%; text-align: left;">A quick over view of Protein Secretion:
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">Secretory proteins move from the rough endoplasmic reticulum to the Golgi complex, which consists of a stack of membranous sac.
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">The Golgi complex modifies the proteins it contains, separates different proteins, and packages them in vesicles.
 * <span style="color: #47cc47; font-family: Georgia,serif; font-size: 120%;">Secretory vesicles from the Golgi apparatus fuse with the cell membrane and release their products by exocytosis.

media type="youtube" key="MrHULUxAsGg?fs=1" height="419" width="570" align="center"

**<span style="color: #008080; font-family: Georgia,serif; font-size: 130%;">4. DNA Synthesis and Cell Division **

<span style="color: #571678; font-family: Georgia,serif; font-size: 120%;">**DNA Synthesis** //(DNA Replication)//

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**For a cell to divide, DNA needs to replicate itself. There is an Identical copy of DNA in each of the daughter cells formed by the cell that is divided.**

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">The replication process is initiated at certain points within the DNA, which are targeted by proteins that separate the two strands and initiate DNA synthesis. A group composed of many enzymes and proteins also known as the Helicase is used to go along the DNA molecule and break the hydrogen bonds between the **complementary bases** in order to produce two free strands at a fork in the double-helix. This way the two free strands can bond with new complementary bases (nucleotides) that are available in the nearby plasma. DNA polymerases join the complementary base pair nucleotides together to form a second polynucleotide chain in each DNA that is corresponding to the first DNA strand. You end up with 2 new DNA strands, each having one new strand and one old strand. Thus the original DNA sequence is preserved for future cell generations. <span style="color: #571678; font-family: Georgia,serif; font-size: 70%;">8.



<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**The Cell Cycle**
<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">Unlike the life of organisms which is a straight progression from birth to death, the life of a cell is a cyclical pattern. Each cell is produced as part of its' parent cell. When a daughter cell divides, it turns into two new cells. Which then makes you think that each cell is capable of being immortal as long as its <span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">descendants can continue to divide. But all cells in the body only live as long as the person lives. Some cells do live longer then others, eventually all cells die when their vital functions cease. Most cells in the body are in **interphase**, the non-dividing stage of the cell life cycle.

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: left;"> <span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: left;">**This phase is then subdivided into 3 other phases:**

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**G1- phase-** //(Gap)// **cell performs normal physiological roles**

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">As chromosomes are in their extended form, their genes actively direct synthesis of RNA. Through this process genes control the metabolism of the cell. The cell can also grow in this phase, even though this phase is sometimes described as "resting." The cell still performs normal physiological functions of the tissue in which they are found. The DNA in this phase produce mRNA and proteins as usual. <span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**S- phase-** //(Synthesis)// **DNA is replicated in preparation for division**

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">If a cell needs to divide, it replicates its DNA in this phase. Which was discussed previously above.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**G2- phase-** //(Gap)// **[|chromatin]condenses prior to division**

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">Once the DNA has been replicated the chromatin condenses in this phase to form short, thick structures called chromosomes at the end of this phase. However, these chromosomes have not yet developed into their more familiar forms, which is only become visible at the prophase stage of mitosis.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Cyclins**- are proteins that promote different phases of the cell cycle. They accumulate just prior to mitosis and then are destroyed rapidly during cell division. In the G1-phase an increase concentration of cyclin D proteins within the cell acts quickly to move the cell through this phase. These cyclin D proteins are able to do this by activating usually inactive enzymes called cyclin-dependent kinases. Over activity of genes that codes for cyclins are associated with cancer, including breast and esophagus.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Oncogenes**- are mutated genes that contribute to cancer. They are altered forms of normal proto-oncogenes, which code proteins that control cell division and cell suicide (apoptosis). This gene promotes cancer and other genes called tumor suppressor genes which inhibit its development. An important tumor suppressor gene is called p53 (which is referred to the protein coded by the gene which it's molecular weight is 53,000). **p53** encodes a transcription factor; it halts cell division when DNA is damaged, then either promotes repair of the DNA or apoptosis (cell death). With in 50% of all cancers the mutations in p53 have been found.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Cell Death**
<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">Occurs in 2 ways:

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Necrosis**- occurs when pathological changes kill a cell caused by disease or injury

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Apoptosis**- occurs as a normal physiological response. It is also called programmed cell death. This process helps the body rid from itself cancerous cells with damaged DNA. It is also important in the functioning of the immune system.

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">There are two ways that lead to apotosis: Extrinsic- which extracellular molecules called death ligands bind to receptor proteins on the plasma membrane called death receptors. And Intrinsic- which apotosis responds to intracellular signals. This can be triggered by DNA damage, or by reactive oxygen species that cause oxidative stress. This cellular stress causes a sequence of events that makes the mitochodrial membrane permeable to some molecules, which leak into the cytoplasm and cause the next phase of apoptosis. It involves activation of cytoplamsic caspases (enzymes) sometimes called the "executioner" of the cell, which lead to cell death.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Mitosis**- Is the M phase at the end of the G2 phase of life cycle when a cell divides. Chromosomes are condensed and duplicated. Each consist of two identical strands called chromatids, (which contains a double-helix) that is connected by a centromere. Each chromatid will become separate chromosomes when mitosis has been completed. <span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">media type="youtube" key="nPG6480RQo0?fs=1" height="459" width="526" align="left"//**Mitosis is subdivided into 4 stages:**//

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Prophase**- the chromosomes are visible, the centrioles move apart to opposite poles of the cell. Spindle fibers from each centriole attach to the centromeres of the chromosomes. The nucleolus is no longer visible.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Metaphase**- The chromosomes are lined up at the equator of the cell. The spindle fibers from each centriole attach to the centromeres of the chromosomes. And the nuclear membrane disappears.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Anaphase**- The centromeres split, spindle fibers shorten, and the chromatids separate as each is pulled to opposite poles. Each pole then has a copy of 46 chromosomes.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Telophase**- The chromosomes become longer, thinner, and less distinct. New nuclear membranes form. The nucleolus reappears.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">Then **//Cytokines//** happens and the cytoplasm is divided resulting in the production of two new daughter cells that are genetically identical to each other and to the parent cell as well.

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<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Centrosome**- all animal cells have a centrosome located near the nucleus in interphase. It contains 2 centrioles. The centrosome is duplicated in the G1-phase if the cell is going to divide (or die). Replicates move to opposite poles by metaphase. Microtubles grow from the centrosomes to form spindle fibers (which attach to centromeres of chromosomes). Spindle fibers pull chromosomes to opposite poles during anaphase.

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<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">**Telomeres**- are non-coding regions of DNA at the ends of Chromosomes as seen in the picture on the left. Each time a cell divides, a length of telomere is lost. Because DNA polymerase can't copy the very ends of a DNA strand. When telomeres are used up, the cell becomes senescent. Believed to represent a molecular clock for aging, which ticks down with each division. Germinal (ovary & testes) and cancer cells- can divide indefinitely and don't age. Gamates have the enzyme telomerase, which replaces telomere nucleotides not duplicated by DNA polymerase during divisions.

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 * <span style="color: #571678; font-family: Georgia,serif; font-size: 120%;">Meiosis **<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">- Is also known as the reduction division. The cells go through the same process as Mitosis with phases G1, S, G2. This type of cell division only occurs in the ovaries and testes (gonads) to create ova and sperm (gametes). When a cell is going to divide by either mitosis or meiosis, the DNA is replicated forming chromatids and the chromosomes get shorter and thicker, just as previously described above. When it gets to that point the cell has 46 chromosomes, with each consisting of two duplicate chromatids. But unlike Mitosis the DNA is divided twice after the replication phase.

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">There is one important thing to mention before we go into detail about how meiosis works. The chromosomes seen at the end of the G2-phase are matched in pairs. Each part of the pair appear to be structurally identical. These matched chromosomes are called homolguous chromosomes. Each part of these chromosomes are derived from a chromosome inherited from the mother and the other inherited from the father. These chromosomes do have identical DNA base sequences.There are 22 homologous pairs chromosomes that are autosomal (nonsexual) and 1 pair of sex chromosomes (described as X or Y). Males have one X and one Y chromosomes where as Females have two X chromosomes.

<span style="color: #571678; font-family: Georgia,serif; font-size: 110%;">media type="youtube" key="D1_-mQS_FZ0?fs=1" height="386" width="475" align="left" <span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">**1st division**- the homologous chromosomes line up side by side, instead of single file like in Mitosis, along the equator of the cell. One member of the homologuous pair is pulled to each pole. This gives each daughter cell 23 different chromosomes, which have 2 chromatids.

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">**2nd division**- each daughter cell from the first division then divides. The chromosomes line up in straight line and are divided again into two chromatids. One goes to each new daughter cell, each cell contains 23 chromosomes rather than 46 like the mother cell. Which brings a grand total of 4 new daughter cells being produced from the meiotic cell division of one parent cell.

<span style="color: #571678; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">In Males this division occurs in the testes. Where the one parent cell produces 4 sperm cells. But in the ovaries of Women, which one parent cell also produces 4 daughter cells, only one cell progresses to become a mature egg cell. The other 3 cells die.

<span style="color: #800080; display: block; font-family: Georgia,serif; font-size: 110%; text-align: justify;">**Genetic** **Recombination**- occurs in Prophase 1. Parts of one homologous chromosome are exchanged with its paired homologous, this process is called crossing over. This provides large genetic diversity.

**<span style="color: #000080; font-family: Georgia,serif; font-size: 120%;">Epigenetic Inheritance **

<span style="color: #ab21ab; display: block; font-family: Georgia,serif; text-align: justify;">Genetic inheritance is determined by a sequence of DNA base pairs in chromosomes. However, not all of these genes are active in each cell body. Some genes are switched from active to inactive and back again depending on the particular cell. This activity in the genes is subject to physiological regulation. Some genes may be permanently silenced in all the cells of the body or even in a tissue. This can happen in the gametes (is inherited) or in early embryonic development. Epigenetic Inheritance occurs when gene silencing is passed on to the daughter cells. Gene silencing is enacted by DNA methylation or post-translational modification of histones (which influences how tightly or loosely the chromatin is compacted). Because of these epigenetic changes in the DNA and Histone proteins, even identical twins can have differences in gene expression. Problems with epigenetic inheritance is that it can contribute to diseases such as cancer, fragile X syndrome, and lupus. Because of epigenetic changes in response to differences in their environments.


 * <span style="color: #000080; font-family: Georgia,serif;">To learn more about DNA, RNA and Chromosomes, Meiosis, Mitosis: Check below **
 * [|Build an DNA molecule]**: **[|DNA*:] [|DNA**:][|RNA:]** **<span class="wiki_link_ext">[|Chromosomes] **: **[|Meiosis & Mitosis]**


 * <span style="color: #008080; font-family: Georgia,serif; font-size: 150%;">Essential Questions: **
 * <span style="color: #f23157; font-family: Georgia,serif; font-size: 120%;">-Cells are considered the basic structure and function of the human body. What is meant by this statement? **

<span style="color: #f66609; font-family: Georgia,serif;">This means that without cells in our body's we would not be here. Cells are important for transporting oxygen, blood, nutrients, proteins, and other things that are essential for our body and cells to survive by vessels and veins through out our body. Certain types of cells kill bacteria and infections that get through our skin.


 * <span style="color: #f23157; font-family: Georgia,serif; font-size: 120%;">-Compare and contrast passive and active transport. Include characteristics and examples of each type of transport cells use to maintain homeostasis. Why do cells need to bring molecules in and out of the cell membrane? **

<span style="color: #f66609; font-family: Georgia,serif;">Passive does not require energy to move molecules across the cell membrane from a high to low concentration, while Active does require energy from ATP to move molecules across the cell membrane from a low to high concentration. Cells bring molecules in and out of the cell membrane to try to make it equal pressure in and out of the cell.


 * <span style="color: #f23157; font-family: Georgia,serif; font-size: 130%;">-How do cells communicate? **

<span style="color: #f66609; font-family: Georgia,serif;">Cells communicate to each other by means of signaling each other. There are three different types of signaling they use. These include Paracrine, Synaptic, and Endocrine signaling. Paracrine and synaptic are for signaling other cells close by and endocrine signaling is used for cells far away.


 * <span style="color: #f23157; font-family: Georgia,serif; font-size: 120%;">How does this apply to PTA? **

<span style="color: #f66609; font-family: Georgia,serif;">Cell Physiology applies to PTA's when we have to administer for example a iontophoresis patch which is a patch that has medicine on one side and water solution on the other side. It is placed on the area that hurts and a iontophoresis unit is attached to the patch to activate the medicine. We know through cell physiology when the steroid is working through the synaptic signals, because the patient will feel no pain where the patch has been placed.

<span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">1.[] <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">2.http://www.google.com/images?um=1&hl=en&biw=1345&bih=583&tbs=isch%3A1&sa=1&q=passive+transport+diffusion&aq=8&aqi=g10&aql=&oq=Passive+transport <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">3.http://www.google.com/images?um=1&hl=en&biw=1345&bih=583&tbs=isch%3A1&sa=1&q=Active+trasport+pump&aq=f&aqi=g-sx1&aql=&oq= <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">4.http://www.bothbrainsandbeauty.com/academic-discussions/cell-junctions-703 <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">5.http://www.google.com/images?hl=en&biw=1362&bih=583&gbv=2&tbs=isch%3A1&sa=1&q=synaptic+cell+signaling&aq=f&aqi=&aql=&oq= <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">6.http://www.google.com/images?hl=en&biw=1362&bih=583&gbv=2&tbs=isch%3A1&sa=1&q=paracrine+signaling&aq=f&aqi=g1&aql=&oq= <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">7.http://www.google.com/images?hl=en&biw=1362&bih=583&gbv=2&tbs=isch%3A1&sa=1&q=endocrine+cell+signaling&aq=f&aqi=&aql=&oq= <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">8.Fox, Stuart I. "Human Physiology." New York: McGraw-Hill, 2011. Print <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">9. Ch.3 notes. <span style="color: #00ff00; font-family: Georgia,serif; font-size: 90%;">10.http://highered.mcgraw-hill.com/sites/0073378119/student_view0/chapter3/textbook_images.html