Animations

[heading style=”2″] ANIMATIONS [/heading]

Please Note: You may need the latest version of Adobe Flash Player and Quicktime Player installed in order to view some of the animations. You can download the latest versions for free by clicking on the links above.

 

 HUMAN ANATOMY & PHYSIOLOGY

 

[EXPAND Heart Anatomical Structures]

Roll over the heart illustration to identify anatomical structures and hear pronunciations. In the human body, the heart is usually situated in the middle of the thorax with the largest part of the heart slightly offset to the left (although sometimes it is on the right, (dextrocardia), underneath the breastbone. The left lung is smaller than the right lung because the heart occupies more of the left hemithorax. The heart is enclosed by a sac known as the pericardium and is surrounded by the lungs. The mediastinum, a subdivision of the thoracic cavity, is the name of the heart cavity. The function of the right side of the heart (see right heart) is to collect de-oxygenated blood, in the right atrium, from the body and pump it, via the right ventricle, into the lungs (pulmonary circulation) so that carbon dioxide can be dropped off and oxygen picked up (gas exchange). This happens through a passive process called diffusion. The left side collects oxygenated blood from the lungs into the left atrium. From the left atrium the blood moves to the left ventricle which pumps it out to the body. Acknowledgement: LearnersTv
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[EXPAND Cardiac Physiology]

A basic understanding of cardiac physiology is essential to interpreting the physical finding during a cardiac exam. Each pump or beat of the heart consists of two parts or phases – diastole and systole. During diastole the ventricles are filling and the atria contract. Then during systole , the ventricles contract while the atria are relaxed and filling. A more detailed understanding of the of cardiac physiology can be obtained by examining in detail the simultaneous pressure characteristics in the aorta, left atrium (atrium) and left ventricle (ventricle) through one cardiac cycle. Acknowledgement: LearnersTv
Click here to see animation.

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[EXPAND Cardiac Arrythmias]

Cardiac arrhythmia is any of a group of conditions in which the electrical activity of the heart is irregular or is faster or slower than normal. In adults the normal resting heart rate ranges from 60 beats per minute to 100 beats per minute. The normal heart beat is controlled by a small area in the upper chamber of the heart called the sinoatrial node or sinus node. The sinus node contains specialized cells that have spontaneous electrical activity that starts each normal heart beat. In an adult, a heart rate faster than 100 beats/minute is considered tachycardia. A slow rhythm, known as bradycardia (less than 60 beats/min), is usually not life threatening, but may cause symptoms. Acknowledgement: LearnersTv
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[EXPAND Artherosclerosis]

Atherosclerosis is a disease in which fatty material is deposited on the wall of an artery. Normally the walls of an artery are smooth, allowing blood to flow unimpeded. However, if damage occurs to inner lining, fat, cholesterol, platelets and other substances may accumulate at a damaged section of the arterial wall. Eventually, the tissue builds-up and a plaque if formed, narrowing the lumen of the artery. Where the narrowing is severe, there is a risk that the vessel can become blocked completely if a thrombus forms in the diseased segment. Acknowledgement: LearnersTv
Click here to see animation.

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[EXPAND Cloning]

Cloning is the process of creating an identical copy of something. It collectively refers to processes used to create copies of DNA fragments (molecular cloning), cells (cell cloning), or organisms. This animation introduces you to the concept of “molecular scissors” which are used to cut the DNA into fragments. This can be done using enzymes called restriction endonucleases (or restriction enzymes), that digest DNA at sequence-specific sites. Acknowledgement: LearnersTv
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[EXPAND Neurons]

The following work has been created by Dr. Patricia Stewart, Linda Wilson-Pauwels and Teddy Cameron and is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives License2.0.

[EXPAND A. Axonal Transport]

[EXPAND A.1 Kinesin and Dynein motors]
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[EXPAND A.2 Kinesin and ATP hydrolysis]
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[EXPAND A.3 Transport of vesicles and mitochondria]
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[EXPAND A.4 Transport of mitochondria]
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[EXPAND A.5 Transport of endosomes]
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[EXPAND A.6 Neurotrophic factors]
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[EXPAND A.7 Transport of microfilaments and microtubules]
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[EXPAND B. Ion Channels]

[EXPAND B.1 Specific channels]
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[EXPAND B.2 Non-specific channels]
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[EXPAND B.3 Passive channel]
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[EXPAND B.4 Gated channel]
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[EXPAND B.5 Voltage gated channel]
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[EXPAND B.6 Mechanically gated channel]
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[EXPAND B.7 Phosphorylation gated Channel]
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[EXPAND B.8 Indirectly gated channel]
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[EXPAND B.9 Chorlide transporter]
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[EXPAND B.10 Na+K+ATPase pump]
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[EXPAND B.11 Glutamate transporter]
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[EXPAND C. Neurotransmitter Release]

[EXPAND C.1 Vesicle loading, docking and exocytosis ]
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[EXPAND C.2 Membrane re-uptake and refilling]
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[EXPAND C.3 Kiss & Run hypothesis]
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[EXPAND C.4 Neurotoxins]
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[EXPAND C.5 Ca+ channel blockers]
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[EXPAND D. Removal of Neurotransmitter]

[EXPAND D.1 Diffusion ]
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[EXPAND D.2 Acetylcholinesterase inhibitor]
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[EXPAND D.3 Re-uptake transporter pumps]
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[EXPAND D.4 Neurotoxins]
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[EXPAND Cell Structure]

The three cells you will be studying in this unit are prokaryote, animal and plant. At the end of the lesson you should be able to recognize the differences between prokaryotic and eukaryotic cells, differences between animal and plant cells and understand the function of the organelles in these different cells. Press the button on the right that corresponds to the section you want to learn first or press “Continue”. Acknowledgement: LearnersTv
Click here to see animation.

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[EXPAND How Enzymes Act As Catalysts]

Life from a biochemist’s viewpoint is simply a coordinated series of reactions. Energy changes occur during reactions, and in fact, it is these changes in energy that drive reactions. In this animation you will be shown how reactions are driven by energy changes, and how enzymes, act as catalysts, increase the rates at which reactions take place. Acknowledgement: LearnersTv
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DEVICES & INSTRUMENTATION

 

[EXPAND Fluorescence Microscopy]

In fluorescence microscopy, a specimen is typically labeled with a fluorescent molecule, or fluorophore. When illuminated with light of a specific wavelength, the fluorophore can be excited and will subsequently emit light of a longer wavelength. This emitted light is detected by a CCD, and the image is captured.
Click here to see animation.

The light source for the fluorescence microscope often produces a wide spectrum of light, and an excitation filter can be used to limit the illumination light to a specific wavelength range appropriate for the sample. An emission filter is useful for blocking any light outside of the range of the emitted wavelength, thus improving the signal to noise ratio of the acquired image. The animation above illustrates the light path in an upright microscope. Using a filter wheel, as shown in the animation below allows for rapid imaging of two different fluorophores.

Click here to see animation.

The CCD (charge-coupled device) is made up of a two-dimensional array of photodiodes which convert light into electrical charge. When the exposure is completed, the charges are transferred, one-by-one, into an amplifier and converted into a voltage. Each photodiode in the CCD gives rise to a pixel in the final image, where the recorded voltage values are converted to black/white pixel intensities. The resolution of the final image is directly proportional to the number of photodiodes in the CCD. This is illustrated in the animation below. Acknowledgement: This work by Janet Iwasa is licensed under aCreative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Click here to see animation.

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[EXPAND Chromatography and Gel Electrophoresis]

Chromatography is the collective term for a family of laboratory techniques for the separation of mixtures. It involves passing a mixture dissolved in a “mobile phase” through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid, ribonucleic acid, or protein molecules using an electric current applied to a gel matrix. Acknowledgement: LearnersTv
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 MOLECULAR BIOLOGY OF THE CELL

 

[EXPAND Mechanism of Chromosomal Instability]

Chromosomal instability (CIN), or the tendency to lose or gain whole chromosomes, is a hallmark of cancerous cells. These series of animations illustrate how CIN occurs in cells with multiple centrosomes.

In normal cell division, the two centrosomes, which are located at opposite poles, each attach to the kinetochore of one of the two chromatids of a chromosome. As cell division progresses, the sister chromatids are pulled apart and segregate to different daughter cells. It is also possible, however, for centrosomes at different poles to attach to the same kinetochore, creating what’s known as a merotelic attachment. These merotelic attachments, if not fixed quickly enough, can result in lagging chromosomes and the formation of micronuclei.
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In cells with multiple centrosomes, a multi-polar spindle is often formed. In many cases, these spindles resolve into bipolar spindles and undergo cell division. Depending on how the kinetochore attachments were made and how the centrosomes segregate, this may result in having one or more merotelic chromosomes. In the case where two centrosomes at the same pole attach to a single kinetochore (known as a syntelic attachment), chromosome segregation proceeds as normal. Acknowledgement: This work by Janet Iwasa is licensed under aCreative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Click here to see animation.

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[EXPAND Proteasome Structure and Function]

The proteasome is a large, highly conserved protein complex whose main function is to enzymatically degrade target proteins. The eukaryotic proteasome houses six protease sites that are located deep within the barrel-shaped 20S core particle. Each core particle is built from two outer rings formed from seven alpha subunits, and two inner rings formed from seven beta subunits. The N-termini of the alpha subunit rings on either end of the core particle form a gate which can open to allow passage of target proteins into the proteasome core.
Click here to see animation showing proteasome-mediated degradation of a target protein.

Gate opening is regulated by association with the 19S regulatory particle (RP), which is composed of two major parts: a lid and a base. The base is made up of six ATPases which form a ring. The C-terminal tails of the ATPases fit into “pockets” in the core particle, causing a conformational change and resulting in gate opening.

How the heptameric core particle and hexameric base interact is not well understood. The “wobble” hypothesis suggests that the regulatory particle may rock back and forth while bound to the core particle, such that only a subset of C-terminal tails in the base associate with the pockets in the core particle at any given moment.
Click here to see the regulatory particle “wobbling” as it interacts with the core particle.

In eukaryotes, proteins are tagged for degradation with chains of proteins known as ubiquitin. The ubiquitin tag is recognized by subunits in the lid of the proteasome, and is thought to be eventually removed as the target protein enters the proteasome for degradation. Meanwhile, the protein unfolds and enters the central channel and is cleaved into short peptides of 3 to 15 amino acids in length. These peptides eventually exit the proteasome through one or both open pores. Acknowledgement: This work by Janet Iwasa is licensed under aCreative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Click here to see an animated introduction to proteasome structure.

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[EXPAND Protein Translocation]

Protein translocation is the process by which peptides are transported across a membrane bilayer. Translocation of proteins across the membrane of the endoplasmic reticulum (ER) is know to occur in one of two ways: cotranslationally, in which translocation is concurrent with peptide synthesis by the ribosome, or posttranslationally, in which the protein is first synthesized in the cytosol and later is transported into the ER. Both means of translocation are mediated by the same protein channel, known as Sec61 in eukaryotes and SecY in prokaryotes and archaea.

Cotranslational translocation

Proteins that are targeted for translocation across the ER have a distinctive amino-terminal signal sequence (shown in yellow in the animation) which is recognized by the signal recognition particle (SRP). The SRP in eukaryotes is a large ribonucleoprotein which, when bound to the ribosome and the signal sequence of the nascent peptide, is able to arrest protein translation by blocking tRNA entry.

The ribosome is targeted to the ER membrane through a series of interactions, starting with the binding of the SRP by the SRP receptor. The signal sequence of the nascent peptide chain is then transferred to the protein channel, Sec61. The binding of SRP to its receptor causes the SRP to dissociate from the ribosome, and the SRP and SRP receptor also dissociate from each other following GTP hydrolysis. As the SRP and SRP receptor dissociate from the ribsome, the ribosome is able to bind directly Sec61.

The Sec61 translocation channel (known as SecY in prokaryotes) is a highly conserved heterotrimeric complex composed of α-, β- and γ-subunits. The pore of the channel, formed by the α-subunit, is blocked by a short helical segment which is thought to become unstructured during the beginning of protein translocation, allowing the peptide to pass through the channel. As shown in the animation, the signal sequence of the nascent peptide intercalates into the walls of the channel, through a side opening known as the lateral gate. During translocation, the signal sequence is cleaved by a signal peptide peptidase, freeing the amino terminus of the growing peptide.
Click here to see animation.

Posttranslational translocation in eukaryotes

During cotranslational translocation, the ribosome provides the motive power that pushes the growing peptide into the ER lumen. During posttranslational translocation, additional proteins are necessary to ensure that the peptide moves unidirectionally into the ER. Eukaryotes and prokaryotes have evolved different mechanisms to ensure the successful translocation of synthesized peptides.

In eukaryotes, posttranslational translocation requires the Sec62/Sec63 complex (shown in green in the animation) and the chaperone protein BiP (shown in purple/blue).

BiP is a member of the Hsp70 family of ATPases, a group which is characterized as having an N-terminal nucleotide-binding domain (NBD), and a C-terminal substrate-binding domain (SBD) which binds to peptides. The nucleotide binding state of the NBD determines whether the SBD can bding to a substrate peptide. While the NBD is bound to ATP, the SBD is in an open state, allowing for peptide release, while in the ADP state, the SBD is closed and peptide-bound. In the animation, the ATP-bound NBD is shown in purple, and the ADP-bound state is shown in blue.

The primary role of the membrane protein complex Sec62/Sec63 is to activate the ATPase activity of BiP via a J-domain located on the lumen-facing portion of Sec63. The SBD of BiP binds non-specifically to the peptide as it enters the ER lumen, and keeps the peptide from sliding backwards in a ratchet-type mechanism.

In the animation, the structure of BiP is approximated using the structure of hsc70 (1YUW), and the J-domain of Sec63 is based on that of auxilin (2QWN).
Click here to see animation.

Posttranslational translocation in prokaryotes

In prokaryotes, translated peptides are actively pushed through the SecY channel by a protein called SecA. SecA is composed of a nucleotide-binding domain (medium green), a polypeptide crosslinking domain (dark green), and helical wing and scaffold domains (light green).

During translocation, a region of the helical scaffold domain forms a two-finger helix which inserts into the cytoplasmic side of the SecY channel, thereby pushing the translocating peptide through. A tyrosine found on the tip of the two-finger helix plays a critical role in translocation, and is thought to make direct contact with the translocating peptide.

The polypeptide crosslinking domain (PPXD) forms a clamp which is thought to open as the translocating peptide is being pushed into the SecY channel by the two-finger helix, and close as the two-finger helix resets to its “up” position. The conformational changes of SecA are powered by its nuclease activity, with one ATP being hydrolyzed during each cycle. Acknowledgement: This work by Janet Iwasa is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Click here to see animation.

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[EXPAND Hemoglobin: Studying the T to R Transition]

Hemoglobin, a tetrameric protein found in high concentrations in red blood cells, is responsible for binding and transporting oxygen in the body. Each hemoglobin protein is made up of four subunits – two alpha subunits and two beta subunits – and each subunit is capable of binding to an oxygen molecule via its heme group.

Structural studies have shown that hemoglobin exists in one of two conformations, known as T (taut) and R (relaxed). Deoxygenated hemoglobin (blue) is found in the T state, and oxygen binding (red) triggers the transition to the R state. The animation on the right shows a close-up view of the heme group (white, in ball and stick representation) in one of the hemoglobin subunits. In the deoxygenated (T) state, the iron atom is non-planar with the rest of the heme group due to its association with a histidine side chain. Oxygen binding causes the iron atom in the heme to move such that it becomes planar with the rest of the heme group, which then pulls the histidine, causing a larger scale structural change in the protein.
Click here to see animation.

Hemoglobin can be thought of as a tetramer made up of two alpha-beta dimers. The conformational change that occurs during the T to R transition takes place primarily in the positions of these two dimers relative to one another (rather than between the alpha and beta subunits within the same dimer). This is illustrated in the last (black and white) segment of the animation on the right.

The T to R transition requires that at least two of the hemoglobin subunits be bound by oxygen. Since hemoglobin in the T state only has a low affinity for oxygen, the conformational change can only occur under relatively high oxygen concentrations (such as in the lung capillaries). In the R state, hemoglobin binds to oxygen with much greater affinity, leading to any remaining deoxygenated subunits quickly binding to oxygen. This concept is shown in the center animation on the right.
Click here to see animation.

Oxygen-rich red blood cells in the lungs must circulate throughout the body to provide tissues with oxygen for metabolic processes. There are several key molecules that contribute to the ability of hemoglobin to unload oxygen into oxygen-hungry tissues.

Protons are important allosteric effectors of hemoglobin. At relatively low pH (such as in respiring muscle tissues), hemoglobin has a lower affinity for oxygen than it does at higher pHs (such as in the lung tissue).

Another allosteric regulator of the T to R transition is 2,3-DPG. As shown in the animation on the right, 2,3-DPG can bind in the central pocket of hemoglobin when hemoglobin is in the T state. Binding of 2,3-DPG is mediated by a rosette of amino acid side chains from both beta subunits. By this mechanism, 2,3-DPG stabilizes the T state and lowers the affinity of hemoglobin for oxygen. Upregulation of 2,3-DPG increases the delivery of oxygen to tissues in low-oxygen conditions. Acknowledgement: This work by Janet Iwasa is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Click here to see animation.

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[EXPAND Clathrin-mediated Endocytosis]

Endocytosis is the process by which cells are able to internalize membrane and extracellular materials through the formation of a vesicle. The process of membrane budding to form a vesicle is generally mediated by a protein coat, which acts both as a means to deform the membrane and to concentrate specific types of proteins inside the nascent vesicle. Clathrin is a coat protein that has been shown to function in receptor-mediated endocytosis events at the plasma membrane.

The animation below shows the process of clathrin-mediated endocytosis. Iron-bound transferrin is bound to its receptor on the exterior cell membrane. The transferrin receptor in turn binds to adaptor proteins in the interior of the cell, triggering the formation of a clathrin cage around the bound transferrin receptors. Soon after the vesicle has budded off the membrane, clathrin cage disassembly begins. Disassembly is mediated by HSC70, and its cofactor auxilin. Acknowledgement: This work by Janet Iwasa is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Click here to see animation.

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[EXPAND Role of Dynein in Yeast Mitosis]

Dynein is a large molecular motor that transports cargo along microtubules in the cell. Unlike kinesins, which travel towards the fast-growing plus end of the microtubule, dynein “walks” in the minus end direction. Dyneins are classified as belonging to one of two groups: axonemal (or flagellar) dynein, which is a component of cilia and flagella, and cytoplasmic dynein.

In the budding yeast Saccharomyces cerevisiae, dynein plays a critical role in positioning the mitotic spindle during mitosis. At metaphase, dynein is localized the spindle pole body (shown in orange in the animation) of the daughter cell, and is eventually targeted towards the plus end of an astral microtubule. When the astral microtubule plus end encounters a target at the bud cortex (which includes the protein Num1), dynein is transferred from the microtubule to the cortical target (shown in red) and becomes active (indicated by the change in color from black to green). The activated dynein, which is anchored to the cortex, pulls the microtubule towards the bud cortex, causing the mitotic spindle to move into the bud neck. Acknowledgement: This work by Janet Iwasa is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Click here to see animation.

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[EXPAND Glycolysis]

Oxidation of glucose is known as glycolysis.Glucose is oxidized to either lactate or pyruvate. Under aerobic conditions, the dominant product in most tissues is pyruvate and the pathway is known as aerobic glycolysis. When oxygen is depleted, as for instance during prolonged vigorous exercise, the dominant glycolytic product in many tissues is lactate and the process is known as anaerobic glycolysis. The pathway of glycolysis can be seen as consisting of 2 separate phases. The first is the chemical priming phase requiring energy in the form of ATP, and the second is considered the energy-yielding phase. In the first phase, 2 equivalents of ATP are used to convert glucose to fructose 1,6-bisphosphate (F1,6BP). In the second phase F1,6BP is degraded to pyruvate, with the production of 4 equivalents of ATP and 2 equivalents of NADH. Acknowledgement: LearnersTv
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[EXPAND Protein Folding]

With all the known details of protein structure from X-ray and NMR studies, one might expect that we would understand how proteins fold up into structures. Unfortunately, this is not the case, and the “protein folding issue” is still largely an unsolved and central question for biochemistry. Acknowledgement: LearnersTv
Click here to see animation.

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[EXPAND Protein Synthesis]

Protein synthesis is the creation of proteins using DNA and RNA. Protein Synthesis is a two step process. Transcription – Protein synthesis starts in the nucleus, where the DNA is held. DNA structure is two chains of sugars and phosphates joined by pairs of nucleic acids; Adenine, Guanine, Cytosine, and Thymine. Similar to DNA replication, the DNA is “unzipped” by the enzyme helicase, leaving the single nucleotide chain open to be copied. RNA polymerase reads the DNA strand, and synthesizes a single strand of messenger RNA (mRNA). This single strand of mRNA leaves the nucleus through nuclear pores, and migrates into the cytoplasm where it joins with ribosomes.Where protein synthesis occurs by the formation of amino acids. Note: in the new RNA strand, the nucleotide Uracil takes the place of Thymine. Translation – the process of converting the mRNA codon sequences into an amino acid polypeptide chain. 1. Initiation – A ribosome attaches to the mRNA and starts to code at the FMet codon (usually AUG, sometimes GUG or UUG). 2. Elongation – tRNA brings the corresponding amino acid to each codon as the ribosome moves down the mRNA strand. 3. Termination – Reading of the final mRNA codon (aka the STOP codon), which ends the synthesis of the peptide chain and releases it. Acknowledgement: LearnersTv
Click here to see animation.

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[EXPAND DNA Replication]

DNA replication is the process of copying a double-stranded DNA molecule. This process is important in all known life forms and the general mechanisms of DNA replication are not the same in prokaryotic and eukaryotic organisms. As each DNA strand holds the same genetic information, both strands can serve as templates for the reproduction of the opposite strand. The template strand is preserved in its entirety and the new strand is assembled from nucleotides. This process is called semiconservative replication. The resulting double-stranded DNA molecules are identical; proofreading and error-checking mechanisms exist to ensure extremely high fidelity. In a cell, DNA replication must happen before cell division. Prokaryotes replicate their DNA throughout the interval between cell divisions. In eukaryotes, timings are highly regulated and this occurs during the S phase of the cell cycle, preceding mitosis or meiosis I. The replication fork is a structure which forms when DNA is being replicated. It is created through the action of helicase, which breaks the hydrogen bonds holding the two DNA strands together. The resulting structure has two branching “prongs”, each one made up of a single strand of DNA. In DNA replication, the lagging strand is the DNA strand at the opposite side of the replication fork from the leading strand. It goes from 3′ to 5′ (these numbers indicate the position of the molecule in respect to the carbon atoms it contains). When the enzyme helicase unwinds DNA, two single stranded regions of DNA (the “replication fork”) form. DNA polymerase cannot build a strand in the 3′ → 5′ direction. Thus, the strand complementary to the 3′ → 5′ template strand (known as the lagging strand) is synthesized in short segments known as Okazaki fragments. Acknowledgement: LearnersTv
Click here to see animation.

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[EXPAND Cell Death or Apoptosis]

Programmed cell death is an induced and orderly process in which the cell actively participates in its own demise. The morphological process resulting in programmed cell death is called apoptosis. Apoptosis is easily distinguished from necrosis (cell death from external injury) by a number of morphological criteria presented in this animation. From the viewpoint of the immune system, an important feature of apoptotic death is the engulfment of the dead cell by surrounding phagocytic cells, because this prevents an inflammatory response. There are many instances in which apoptosis is used to remove unwanted lymphocytes. For example, several days after their stimulation, activated peripheral T cells are induced to die via apoptosis, thus ensuring the removal of a highly proliferative cell population that is secreting inflammatory cytokines. In addition, CTLs kill target cells by inducing apoptosis in the target population. Acknowledgement: LearnersTv
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