Virtual biology

The title of the Project: Gene expression  This virtual laboratory is intended for use in 11th grade classes on the following topics: Purpose of the virtual laboratory work: Virtual experiment This virtual simulation of PhET allows you to visualize the complex process of gene expression at the cellular level in a simplified form. 1.Run the simulation. You will be given a choice of three different modes: Expression, mRNA, Multiple cells. Select the Expression mode. 2.On the screen you can see a long double-spiral DNA sequence and one particle isolated in its center-a gene. The gene consists of two different regions: regulatory and transcribed. The regulatory region is the place where transcription factors bind, and the transcribed region is the main DNA reading region that binds to RNA polymerase. 3.Now familiarize yourself with the symbols (take a look at the terminology below). 4. Gene expression consists of two main stages: transcription and translation. Transcription is the process of synthesizing an RNA molecule from a DNA molecule by RNA polymerase, resulting in the formation of an informational RNA(mRNA). Translation is the process of protein synthesis involving a ribosome from an mRNA  molecule. Table 1. 5. Start experimenting. Drag the positive transcription factor from the toolbox to the regulatory region of “gene 1” by pressing and holding the left mouse button. 6.To start the transcription process, place the enzyme RNA polymerase at the beginning of the transcribed region. RNA polymerase immediately begins to synthesize mRNA, a complementary strand of DNA. This manipulation can be repeated indefinitely. 7.To stop transcription, replace the activating factor with a negative transcription factor. You will notice that the transcription process will stop because the repressor blocks the RNA polymerase, preventing it from binding with the transcribed region. 8.To start the translation process, install the ribosome complex at the end of the formed mRNA chain. You will notice how the ribosome will begin to synthesize a protein molecule, moving along the mRNA. 9.Add the resulting protein to the collection. Note that an unlimited number of proteins can be obtained from a single mRNA chain. 10.To stop the formation of proteins, bind the mRNA destroyer enzyme to the mRNA sequence. You will notice how the enzyme splits it into smaller fragments. This completes the expression of the 1st gene. 11.Click the “Next gene” button to start expressing the next gene. You may notice that it is longer than the previous one. Accordingly, the mRNA chain formed from it will be longer. Note that this gene requires two factors to activate transcription. 12.Perform the expression of the last gene by following the instructions provided above. Conclusion The virtual laboratory for gene expression provides a unique opportunity to visually study the complex processes of gene expression, as well as to investigate the influence of various factors on it. Terminology Gene – Ген – Ген Protein – Белок – Ақуыз Positive transcription factor – Активный фактор транскрипции(Индукторы) – Транскрипцияның белсендірілген факторы(Индукторлар) Negative transcription factor – Негативный фактор транскрипции(Репрессоры) – Транскрипцияның өшірілген факторы (Репрессорлар) RNA-polymerase – РНК-полимераза – РНҚ-полимераза Ribosome – Рибосома – Рибосома mRNA destroyer – расщеплитель мРНК – аРНҚ ыдыратқыш Regulatory region – Регуляторный участок – Реттелуші аймақ Transcribed region – Транскрибируемый участок – Транскрипциялық аймақ

The title of the Project: Mendel’s laws. Monohybrid and dihybrid cross This virtual laboratory is intended for use in 9th grade classes on the following topics: Purpose of the virtual laboratory work: Practical part 1. Start the simulation. You will be given a choice of two modes: “Intro” and “Lab”. 2. Select the “Lab” mode. You will see a white bunny hopping around and food supplies (green plants), in a desert environment with a brown background. 3. Review the settings. generation counter, tracks breeding and environmental events. Equator, warm habitat, represented as a brown background Alaska, a cold habitat, represented as a snowy white background reset button or reset simulation simulation acceleration button, you can speed up the time by pressing and holding this button play/pause button button to add a breeding pair Virtual experiment No. 1: Monohybrid cross 4. Now start experimenting. In the upper right part of the screen are mutations that are expressed in the phenotype of rabbits in the form of brown fur, floppy ears and long teeth. First, examine just one trait. For example, select the brown fur mutation as the dominant trait. Then add a breeding mate to the rabbit. Press pause. 5. Change the radio button to Pedigree. The Alleles section shows the mutant dominant allele – brown fur (F) and the normal recessive allele – white fur (f). Please note that dominant traits are indicated in capital Latin letters, and recessive traits are indicated in lowercase letters. You can also click on any rabbit to see its pedigree. The example shows a parent with dihomozygous recessive alleles (ff). 6. Click Play. Wait until the individuals of the first generation (Generation 1) appear. In each generation, one pair of rabbits produces four young rabbits. Among the individuals, a rabbit with brown fur appears. Click on him to see his pedigree. This pedigree shows that as a result of the mutation that occurred, a heterozygous offspring (fF) was born from dihomozygous (ff) parents. 7. In an equatorial environment, rabbits with a brown color will have an advantage over white ones, as they will blend better with the background. This will make them less visible to predators, increasing their chances of survival. To prove this hypothesis, add predators (wolves) to the environment. To do this, check the box next to the wolf picture in the Environmental factors section. 8. A pack of wolves appears on the screen, eating white rabbits and now their numbers become much smaller. As a result, brown rabbits gradually become dominant in a given habitat. 9. Speed up the simulation and observe the population for at least 10 generations (Generation 10). Then fill out the table below. To get data on the number of both individuals in the form of a proportion, change the radio button to the Proportions item. Click the icon to compare data from previous generations. Dominant Total Population White Fur Population Proportion % (White Fur/Total) Brown Fur Population Proportion % (Brown Fur/Total) Generation 1 Generation 2 Generation 3 Generation 4 Generation 5 Virtual experiment No. 2. Mendel’s laws 10. Reset the parameters and run the simulation again. Now select the same mutant trait as recessive. Then add a breeding mate to the rabbit. 11.Pause the simulation after the first generation appears. All rabbits are white, which corresponds to Mendel’s first law, which states: all descendants of the first generation obtained from crossing homozygous parents will be identical in genotype (100%) with respect to a specific gene and will have the characteristics of one of the parents. 12.Press pause after receiving the third generation. In this generation, for the first time, a recessive trait (ff) appears in the phenotype of 25% of the offspring. This corresponds to Mendel’s second law, the law of Independent Assortment, which states: when crossing two heterozygous hybrids of the first generation, segregation is observed in the second generation: In our case, the splitting of characters occurred only in the third generation, since in the first offspring only one individual underwent a mutation. 13. Repeat Step 9 and fill in the table with data for the recessive trait. Recessive Total Population White Fur Population Proportion % (White Fur/Total) Brown Fur Population Proportion % (Brown Fur/Total) Generation 1 Generation 2 Generation 3 Generation 4 Generation 5 Virtual experiment No. 3: Dihybrid cross 14. Reset the parameters and run the simulation again. Add a breeding pair to your rabbit and wait until the first and second generations appear on the screen, then select two of the three mutations as Dominant. For example, brown fur (FF) and long teeth (TT). 15. After the third generation appears, press pause and analyze the data. 16. In the fourth generation, you will notice rabbits with brown fur (F) and long teeth (T) in the population. Add environmental factors, for example, add Wolves and replace the food with Tough food. 17. Hypothesis: brown rabbits have an advantage over white rabbits, since they can be invisible to predators, and rabbits with long teeth have an advantage over rabbits with normal teeth, since they can eat tough food. According to the hypothesis, under the conditions that we have chosen for the population, rabbits with both dominant traits, that is, brown rabbits with long teeth (FFTT, FfTt), will be able to survive. Use different simulation options to add variety to your challenges. Remember, the key is to actively experiment, observe, and analyze to understand how natural selection shapes populations. Conclusion This virtual laboratory is an effective tool for studying the laws of dihybrid crossing and allows students to gain in-depth knowledge and skills in the field of genetics. Terminology Natural selection – Естественный отбор – Табиғи сұрыпталу  Mutation – Мутация – Мутация Dominant trait – Доминантный признак – Доминантты белгі Recessive trait – Рецессивный признак – Рецессивті белгі Brown fur – Коричневый мех – Қоңыр жүнді White fur – Белый мех – Ақ жүнді Straight ears – Прямые уши – Тікқұлақты Floppy ears – Висячие уши – Салпаңқұлақты Long teeth – Длинные зубы

The title of the Project: Membrane potential of a neuron Purpose of the virtual laboratory work: Theoretical part Every living cell carries an electrical charge. This charge arises from the movement of charged particles called ions, flowing in and out of the cell. When at rest, the cell membrane holds a negative charge inside and a positive charge outside. This difference, known as the membrane potential (resting potential), typically measures around -70 mV in neurons. When a neuron receives a nerve impulse, its membrane charge briefly changes. This shift, called the action potential, typically reaches around 110-120 mV in neurons. Sources: Practical part In this virtual simulation, you will control the process of a nerve impulse passing through a neuron. Step 1. Familiarize yourself with the legend. The “Legend” section on the right side of the screen shows the symbols and their names like sodium and potassium ions, sodium and potassium gated channels and leak channels (Check out the glossary of terms below) Step 2. In the “Show” section below, you can: Step 3. The zoom slider is located on the left side of the screen. Use it to zoom in or out of the object. Step 4. The current scene you are observing is the process occurring on the neuron membrane at rest. This means that most of the Na+ and K+ channels are gated. Pay attention to their concentration values and you will notice that: Step 5. Observe the effect of a nerve impulse on the neuron membrane. Click the “Stimulate neuron” button. Step 6. Analyze the changes. You may notice that the membrane charges have shifted. This means that the resting potential has shifted to the action potential. In real-time, this process happens very quickly. These actions will help you slow down the process and get a better look at it. Step 7. Study the stages of action potential generation: Depolarization: All processes in our brain are based on this complex reaction. Normally, millions of nerve impulses are transmitted from one neuron to another in the brain within milliseconds. This is how processes such as: Step 8. To see the stages of the action potential passage in the form of a chart, check the box next to the Potential chart and click the Stimulate neuron button again. Conclusion: This simulation allowed students to visualize the complex processes occurring in a neuron and to understand how these processes are related to the transmission of information in the nervous system. Terminology Neuron-Нейрон-Жүйке жасушасы Membrane potential-Мембранный потенциал-Мембраналық потенциал Sodium ion-Ион натрия-Натрий ионы Potassium ion-Ион калия-Калий ионы Sodium gated channel-Закрытый натриевый канал-Жабық натрий каналы Potassium gated channel-Закрытый калиевый канал-Жабық калий каналы Sodium leak channel-Канал утечки натрия-Ашық натрий каналы Potassium leak channel-Канал утечки калия-Ашық калий каналы All ions-Все ионы-Барлық иондар Charges-Заряды-Зарядтар Concentrations-Концентрации-Концентрациялар Potential chart-График потенциала-Потенциал графигі

The title of the Project: Natural selection This virtual laboratory is intended for use in 8th grade classes on the following topics: Purpose of the virtual laboratory work: Theoretical part The environment encompasses all living (biotic) and non-living (abiotic) factors that interact and influence each other in complex ways. Take a hare in a forest; it directly interacts with plants and foxes, but also indirectly interacts with the soil and its moisture (through the plants). Every plant and animal exemplifies fitness in its own way, with those unable to adapt ultimately perishing [1]. Imagine a new coloration arises in an organism due to a mutation. If this color renders it invisible to predators, it gains a survival advantage. This organism will leave more offspring due to enhanced protection, and its descendants will inherit the beneficial coloration, further increasing their survival and reproductive success compared to their differently colored counterparts. Consequently, over several generations, the entire population or a significant portion of it will adopt the advantageous coloration. These adaptations, acquired through random mutations and inherited variations, become permanently fixed within their gene pool. In contrast, if a mutation results in a coloration that makes the organism more conspicuous to predators, it will likely perish quickly [2]. Sources: Practical part: The “Natural Selection” simulation from PhET allows you to explore how environmental pressures and mutations can influence the evolution of a virtual bunny population. It demonstrates the core principles of natural selection, where traits that offer survival advantages become more common in successive generations. 1. Start the simulation. Choose between “Intro” and “Lab” modes. 2. Select “Intro” mode. Observe a white rabbit hopping amidst green plants (food) in a desert environment (e.g., sand) with a brown background. Click the “” button to initiate breeding. Now you have two rabbits. 3. Watch the population increase (4 rabbits added each generation). A generation counter “” displays at the top of the screen. 4. Hold down the “” button for faster breeding. Remember, as the 6th generation progresses, power reaches its peak and the simulation ends. Click the reset “” button to restart. Virtual Experiment No. 1 5. Now begin experimenting. At the top right, find the brown fur mutation in rabbits. Select this trait as Dominant. 6. Rabbits with brown fur appear among the individuals. In an equatorial environment, brown rabbits blend better with the background, making them less visible to predators and increasing their survival. To test this hypothesis, introduce wolves (predators) by checking the box next to their image in the “Environmental Factors” section. 7. Wolves hunt white rabbits, shrinking their “hunting grounds.” Consequently, brown rabbits gradually become more common in this habitat. 8. Monitor the population for at least 10 generations. Change the radio button on the “Proportions” item to display population ratios. 9. Reset and repeat steps 5-8. This time, test the impact of limited food resources by selecting the “Limited Food” option in “Environmental Factors” instead of “Wolves”. 10. Observe the population for 10 generations. Then, compare the population trends and data between the wolf and limited food experiments. What changes did you observe? Virtual Experiment No. 2 11. In this experiment, observe the population scenario development in a snowy habitat. Start the simulation again and change the environment at the top from Equator “”  to Alaska “”. Now, a white rabbit is hopping around on a white background. Introduce breeding. 12. Repeat steps 5-8 of the first experiment for this environment. Wolves would struggle to find white rabbits here, but brown rabbits, more visible against the snow, would be easier prey. Therefore, the brown fur mutation, previously advantageous, might now be detrimental. 13. Evaluate the results compared to the first experiment. 14. Reset and run the experiment with the Limited Food scenario. Compare the results with the first experiment. Did you notice any changes? Remember, the key is to actively experiment, observe, and analyze to understand how natural selection works in shaping populations. Conclusion: In this virtual laboratory students observed how natural selection operates in real-time, making it a valuable tool for both educational and scientific purposes, promoting understanding of evolution, fostering critical thinking, and contributing to the study of this fundamental biological process. Terminology Natural selection – Естественный отбор – Табиғи сұрыпталу  Mutation – Мутация – Мутация Dominant trait – Доминантный признак – Доминантты белгі Recessive trait – Рецессивный признак – Рецессивті белгі Brown fur – Коричневый мех – Қоңыр жүнді White fur – Белый мех – Ақ жүнді Straight ears – Прямые уши – Тікқұлақты Floppy ears – Висячие уши – Салпаңқұлақты Long teeth – Длинные зубы – Ұзын тісті Short teeth – Короткие зубы – Қысқа тісті Environmental factors – Факторы окружающей среды – Қоршаған орта факторлары Wolves – Волки – Қасқырлар Limited food – Ограниченные пищевые ресурсы – Шектелген қоректік ресурстар Tough food – Жесткие пища – Қатты қорек Population – Популяция – Популяция Proportions – Пропорции – Пропорциялар Pedigree – Родословная – Шежіре Alleles – Аллели – Аллельдер Generation – Поколение – Ұрпақ

The title of the Project: Color vision Purpose of the virtual laboratory work: Practical part This virtual simulation helps you understand how different colored lights appear to human eyes. 1. Turn on the simulation. You will be given a choice of two modes: Single Bulb and RGB Bulbs. 2.Observe a human face with thought bubbles, representing someone’s perception of light. On the right, find a flashlight with different bulb and filter colors. Single Bulb Screen 3. Choose a single bulb color (e.g., red). See how the person perceives only that color. Change the bulb to yellow or blue, and witness the shift in their perception. 4. Turn on “photon view” to see all the invisible lights the person absorbs. 5. Shine white light. Notice both the white light and the person perceiving it as white. Now activate “photon view” to reveal the secret: a mixture of all colors combined by our brain to create white. 6. Apply a filter to white light. Watch as the person sees only the filtered color (e.g., yellow). “Photon view” shows all colors present, but only yellow reaches the eye. RGB Bulb Screen 7. Now switch to the RGB bulb screen. There are three primary colors of light: red, green and blue. These colors form the basis of the RGB color model, which is used to create images on TV or computer monitors. Its name is an abbreviation created from the first letters of the colors (Red, Green, Blue). When combined they create countless other colors. Screens use these colors in different proportions to display different shades. 8. See how combining primary colors produces new ones: Red + Green = Yellow Red + Blue = Magenta Green + Blue = Cyan Red + Green + Blue = White 9.Remember: This simulation demonstrates how our brains interpret the light we see, creating the vibrant world of colors we experience. Conclusion: The virtual lab provided an interactive and engaging way to learn about the science behind color vision and light manipulation. By combining visual elements, clear explanations, and hands-on exploration, it deepened the student’s understanding of these concepts. Terminology Color vision – Цветовое зрение – Түсті көру Single bulb- Одна лампа – Бір шам RGB bulbs – Лампы RGB – RGB шамдары monochromatic light – монохромный свет – монохромды жарық white light – белый свет – ақ жарық bulb color – цвет лампы – шам түсі filter color – цвет фильтра – фильтр түсі beam –  луч – сәуле photon – фотон – фотон