Explain the relationship between genotype and key genetic processes that create phenotypic diversity

Biology

Biology is the scientific study of life. Studying biology is an opportunity to ask exciting questions about the world that surrounds us. It is an opportunity to dig into some of humanity’s deepest questions about our origins, our planet’s history, and our connections to other living beings (big and small/extant or extinct). It is also an opportunity to dive into a world of practical problem solving and to think hard about possible solutions for improving health care, maintaining sustainable food supplies, and producing renewable energy technologies. Studying biology helps us understand issues and address everyday problems. For instance, you can better understand how what you eat and the amount you exercise influence your health when you understand the biochemical reactions that describe how the food (matter) is transformed, how it and your body store energy, and how this energy can be transferred from the food to your muscles. Deciding whether or not to buy products labeled with terms like “antimicrobial” or “probiotic” can be easier if you understand what the microbes, which live in, on, and around us, do. Understanding the biochemical principles that describe the changes that happen to eggs as they cook can help us understand how similar physical processes may be central to the cellular stress response and some diseases. Your eye color can be better appreciated with an understanding of the genetic and biochemical mechanisms that link genetic information to physical traits. Studying biology even helps us understand things that are “out of this world.” For instance, understanding the requirements for life can help us look for life in places like Mars or deep in Earth’s crust. When we understand how to properly “rewire” cellular decision-making networks, we may finally be able to regenerate functional limbs or organs from someone’s own tissue, or reprogram diseased tissues back to health. There are many exciting opportunities. The key point is that mastering a few basic principles helps you understand and think more deeply about a wide array of topics. Keep this notion in mind throughout the course.

Biology: an interdisciplinary science

Questions in biology span size scales in excess of ten orders of magnitude, from the atomic makeup and chemical behavior of individual molecules to planetary-scale systems of interacting ecologies. Whatever the scale of interest, to develop a deep and functional understanding of biology, we must first appreciate biological concepts. This involves integrating important ideas and tools from across the spectrum of science, including chemistry, physics, and mathematics. Biology is truly an interdisciplinary science.

The potential application of knowledge is broad

Some people may think studying biology is only about medicine—however, it can lead to or influence many different careers. Biology has applications that are both vast and wide-ranging.Applications include treating (human or other animal) patients, improving agricultural practices, developing new building materials, writing new energy policies, remedying global climate change, creating new works of art—the list goes on and on. For the curious, biology has plenty of unexplored mysteries.

As you study biology, appreciate its exciting questions and topics and be open-minded. Even though course topics may not always seem related at first, they likely are. Being open-minded helps you discover and appreciate the connections between the course’s topics and your interests. Discovering how seemingly different topics interrelate can give you a deeper appreciation for the things you enjoy and maybe even spark a new passion.

BIS2A—from molecules to cells

BIS2A focuses on the cell, one of the most fundamental units of life. Cells can be as simple as the disease-causing bacterium Mycoplasma genitalium, whose genome encodes just 525 genes (only 382 of which are essential for life), or as complex as a cell belonging to the multicellular plant Oryza sativa (rice), whose genome likely encodes ~51,000 genes. However, in spite of this diversity, all cells share some fundamental properties. In BIS2A, we explore basic problems that must be dealt with by all cells. We study the building blocks of cells, some of their key biochemical properties, how biological information is encoded and expressed in genetic material, and how all this combines to make a living system. We will also discuss some of the ways in which living systems exchange matter, energy, and information with their environment (including other living things). We focus primarily on core principles that are common to all life on Earth, and due to biology’s large breadth, we put these ideas into a variety of contexts throughout the quarter.

Welcome to BIS2A

Welcome to Biological Sciences 2A at UC Davis. BIS2A is a 5-unit course with either three 50 minute or two 1 hour and 50 minute lectures (depending on the quarter) plus a 2-hour discussion each week. BIS2A is the first of three courses in the lower division core sequence in the biological sciences. BIS2A provides a foundation in key biological concepts that are of use across a broad spectrum of majors. Students are introduced to the fundamental chemical, molecular, genetic, and cellular building blocks of life, biological mechanisms for the recruitment and transfer of matter and energy, basic principles of biological information flow and cellular decision making, and core concepts underlying the relationships between genetic information and phenotype.

It is important to realize that BIS2A is not a survey course in biology. Biology is an exciting, broad, and dynamic field. It is critical for students in biology or related fields to develop a strong conceptual foundation and to demonstrate their ability to use it in contexts that may be novel to them. Students in BIS2A will be asked to begin developing the ability to identify and articulate the key scientific and biological questions that are at the core of the course content. Students will be expected to learn and use correct technical vocabulary in their discussions of course content. Students will be expected to begin conceptualizing course content from a question-driven and problem-solving perspective.

Yes, BIS2A will require you to work hard, but we also hope that you will have fun discovering new aspects of biology and exploring the many unanswered questions concerning what it means to be alive.

The main course learning objectives include:

· Apply principles of chemistry and bioenergetics in the context of biological systems to describe how cells acquire and transform matter and energy to build and fuel various life sustaining processes, including chemical transformations of elemental compounds, cellular replication, and cellular information processing.

· Explain the relationship between genotype and key genetic processes that create phenotypic diversity.

· Describe the processes regulating the management of cellular information; how information is stored, read, rearranged, replicated; how cells interact with their environment and how these processes can control cellular physiology.

Who should I ask when I have questions about the course?

1. General information about the course: The syllabus provides most of this type of information. For the quickest answers to many of your questions, we highly recommend looking at the syllabus before contacting one of the staff.

2. General information about topics in BIS2A: The BIS2A Learning Center (BLC), which is in RM 2089 SLB, is a resource center for all BIS2A students. The BLC is staffed by the instructors and teaching assistants associated with all BIS2A sections. Any BIS2A instructor or TA having office hours in the BLC should be able to answer general questions about the lecture and discussion material. If they can’t answer your questions, they will be happy to refer you to someone who can.

3. Lecture material and Nota Bene assignments: Your Lecture TA is a great source of information about the lecture material and any lecture related reading specific to your section of BIS2A.

4. Discussion material: Your discussion TA is the best source of information about the discussion material present in your specific discussion section.

5. All course content related material: Your instructor is a great resource for questions about course related material. Find your instructor after class and go to their office hours whenever possible.

Some of your responsibilities

BIS2A is a team effort. Several professors are involved in developing the course content and assessment materials. There are also teaching assistants, who not only run the discussion sections, but also provide insights into which concepts students find the most difficult.

Please keep up with your responsibilities as a student. Do the assigned reading and start to learn new vocabulary before coming to class. Come to class prepared to engage – your instructor will assume that you have read the material before class and that the lecture will not be your first exposure to the content. After class, review your notes, the podcast, and the post-study guide. Seek out assistance immediately when you need it. If everyone in the class can conscientiously do these things, we’ll all have fun this quarter (even while working hard) and be a happy and smarter bunch at the end of the term!

Active learning in BIS2A

In every lecture, we will ask you to answer questions, either in a small group or individually. These questions serve several purposes:

Functions of in-class questions

· Questions stimulate students to examine a topic from a different perspective, one that the instructor considers relevant to their learning.

· Questions act as mini “self-tests” for students. If you are uncertain about what question is being asked or how to answer it, this is a good time to (a) ask the instructor for clarification and/or (b) take note to review this immediately after class with a TA, the instructor, classmates, or the internet. If the instructor took the time to ask you the question in class, this is a big clue that he/she thinks that both the question and the answer are important.

· Some in-class questions will ask students to formulate questions themselves. This is typically an exercise that is designed to force the student to reflect on and try to articulate the point of the lesson. These are critical exercises that force you to think more deeply about a topic and to place it in the broader context of the course.

· Some questions may ask the student to interpret data or to create a model (e.g., perhaps a picture) and to communicate what they see to the class. This exercise asks the student to practice explaining something out loud. This can be a great self-test and learning experience, both for the person answering and fellow students who should also be using the time to examine how they would have answered the question and how that compares with the feedback of the instructor.

· Questions in the discussion that follows and the thought process involved in solving a problem or answering the questions are opportunities for the instructor to model expert behavior in an interactive way—sometimes it is equally important to understand HOW we arrive at an answer as it is to understand the answer.

Some questions are designed to stimulate thought and discussion rather than to elicit a discrete answer. If called on, you should not feel compelled to have one “right” answer!! Understanding this is very important. Once you realize that it is perfectly acceptable (and sometimes desirable) to not know all of the answers (if you did, what would be the point of coming to class?), it can take away a lot of the anxiety of getting called on. While it is okay to not know “the answer”, it is nevertheless important for you to attempt to make a contribution to the discussion. Examples of other meaningful contributions might include: asking for clarification; associating the question with another class topic (trying to make connections); and expressing what you are comfortable with and what confuses you about the question. Don’t be afraid to say “I don’t know”. That’s perfectly okay and even expected sometimes. Be prepared for the instructor to follow up with a different question, however, that will try to either highlight something that you likely do know or to ask for your help with identifying a point of confusion.

Getting ready for lecture

To help you get ready for each lecture, we provide study guides that include instructions on how to prepare for class. You should do your best to complete the assigned reading and suggested “self-assessments” before coming to class. This will ensure that you are ready for discussions and that you can make the most of your time during class. We do not expect you to be an expert before lecture, but we do expect you to do the pre-reading and by doing so make yourself familiar with the required vocabulary and spend some time thinking about the concepts that will be discussed. We will build on that basic knowledge in lecture. If you do not have at least some of the basic building blocks before hand, you will make less efficient use of your time in class. We cannot emphasize too strongly that YOU have the primary responsibility for learning the material in this (or any other) course. Although we are invested in your success, your instructors and TAs cannot magically implant knowledge. Like any other discipline that requires mastery (e.g., sports, music, dance, etc.), we can help guide you and critique your performance, but we can not replace the hours of practice necessary to become good at something. You would never expect to become a proficient pianist by going to lessons once or twice a week and never practicing. To most of us, it seems self-evident that you need practice to become good at something like music, art, or sports. It should not be surprising that the same rule applies with learning biology or any other academic subject. We see ourselves as your coaches for this class; we want all of you to succeed. However, for this to happen, you have to take your practice seriously. This means coming to class prepared, participating in class, studying the material covered in class as soon as possible, identifying where you are uncertain and getting help to clarify those topics as soon as possible, and trying to make thoughtful contributions to the online discussions (not just the bare minimum required to “get the points”). Bottom line: you need to be active participants in your learning.

Knowledge and Learning

Teaching and Learning Science

Teaching and learning science are both challenging endeavors. As instructors, we need to communicate complex, highly interconnected concepts that will serve as a foundation for all your future studies. We also want our students to demonstrate mastery of these ideas at a high level. As students, you need to learn a large new vocabulary, create mental models on which you can “hang” the new conceptual knowledge, and demonstrate that you can actually use this new knowledge. The process challenges both the instructor and the student. Although the process involves hard work, it can also be incredibly rewarding. There is nothing more satisfying for an instructor than those “Aha!” moments when a student suddenly understands an important concept.  In BIS2A we face some interesting teaching and learning challenges. One key challenge is that we discuss physical things and ideas that exist or happen on time and/or size scales that are not familiar to most students. What does this mean? Consider the following example:

EXAMPLE:  SOME CHALLENGES ASSOCIATED WITH CREATING MENTAL MODELS

An instructor teaching wildlife biology may want to talk about concepts in evolution by using bird beaks as a starting point for discussion. In this case, the instructor does not need to spend time creating mental pictures of different shaped bird beaks (or at the very least only needs to show one image); most students will readily draw on their past knowledge and everyday lives to create mental pictures of duck, eagle, or wood pecker beaks and infer the different functional reasons why Nature might have selected different shapes. As a consequence, the students will not need to expend any mental effort imagining what the beaks look like and can instead focus all of their energies on the core evolutionary lesson.  More colloquially: If you are asked to think about something new that is closely related to something you already know well, it is not too difficult to focus on the new material. By contrast, in BIS2A we ask students to think about and discuss things that happen on the atomic, molecular and cellular scales and at rates that span microseconds to millennia. Most students, we will guess, have not lived life on the micro to nanometer scale. Yet, this length scale is where most of the events common to all biological systems takes place. Beginning students, who have not thought much about how things happen at the molecular scale, lack mental models upon which to add new information. This starting point places a burden on both the student and the instructors to create and reinforce NEW mental models for many of the things we talk about in class. For instance, to really talk about how proteins function, we first need to develop a common set of models and vocabulary for representing molecules at the atomic and molecular levels. Not only do these models need to find ways of representing the molecule’s structure, but the models must also contain abstract ideas about the chemical properties of molecules and how these molecules interact.Therefore, students in BIS2A need to put some effort into constructing mental models of what proteins “look” like and how they behave at the molecular scale. Since the entire course centers around biomolecules and processes that happen at a microscopic scale, a similar argument can be made for nearly every topic in the class.

NOTE: POSSIBLE DISCUSSION

How do you interpret the term mental model and why do you think that it is important for learning?

 

Some of the in-class and study guide exercises are designed to help with meeting this challenge; most students have found them very useful. However, some students are more accustomed to studying for exams by memorizing information rather than understanding it. (It’s not their fault; that’s what they were asked to do in the past). As a result, if the problems are approached with the “memorize-at-all-costs” attitude some of the BIS2A exercises may initially seem pointless. For instance, why are your instructors asking you to repeatedly draw some of the concepts described in class? What multiple-choice question could that exercise possibly prepare you for? While it is true that some of your instructors won’t ask you to draw complicated figures on an exam, these drawing exercises are not trying to prepare students for one specific question. Rather the instructor is trying to encourage you to begin creating a mental model for yourself and to practice using it.  The act of drawing can also serves as a “self test.” When you force yourself to write something down or to create a picture describing a process on paper, you will be able to independently assess how strong your conceptual grasp of a topic really is by seeing how easy or hard it was to put your mental image of something onto paper. If it is hard for you to draw a core concept or process from class WITHOUT EXTERNAL ASSISTANCE, it is likely that you need more practice. If it is easy, you are ready to add new information to your model. Throughout the course, you will continue to add new information to your mental model or to use the concept represented in your mental model in a new context. Keep your drawings – or other self-testing mechanisms – current. Don’t fall behind.  Incidentally, the presentation of a course concept on an exam in a context that the student has never seen before is NOT an evil plot by the instructor. Rather it is a way for the instructor and student to assess whether the concept has been learned and whether that knowledge can be used/transferred by the student outside of the specific example given in class or in the reading. Asking the student to repeat the latter would represent an exercise in memorization and would not be an assessment of valuable learning and independent thinking or a representation of what happens in real life.  IMPORTANT: The idea that students in BIS2A will be tested on their ability to USE concepts in specific contexts that they haven’t seen before is critical to understand! Take special heed of this knowledge. Developing usable conceptual knowledge takes more discipline and work than memorizing. The quarter also moves VERY fast and concepts are layered one on top of the other.  If you get too far behind, it is very, very difficult to make up for lost time two or three days before an exam. Be as disciplined as you can and keep up with course materials.

 

So, some concepts are hard to teach and to understand. What are we to do? Something instructors and students both do is to use various communication tricks to simplify or make abstract ideas more relatable. We use tools like analogies or simplified models (more on the importance of these shortly) to describe complex ideas. Making things more relatable can take various forms. Instructors might try to use various simlies or metaphors to take advantage of mental pictures or conceptual models that students already have (drawn from everyday life) to explain something new. For instance, the thing X that you don’t understand works a little like thing Y that you do understand. Sometimes, this helps ground a discussion.Another thing you might catch an instructor or student doing is anthropomorphizing the behaviors of physical things that are unfamiliar. For example we might say molecule A “wants” to interact with molecule B to simplify the more correct but more complex description of the chemical energetics involved in the interaction between molecules A and B.Anthropomorphisms can be useful because, like similes and metaphors, they attempt to link the creation of new ideas and mental models to concepts that already exist in the student’s brain.

While these tools can be great and effective they nevertheless need to be used carefully – by both the instructor and the student. The main risk associated with these simplifying tools is that they can create conceptual connections that shouldn’t exist, that lead to unintended misconceptions, or that makes it more difficult to connect a new concept. So while these tools are valid, we – students and instructors – also need to be vigilant about understanding the limits these tools have in our ability to learn new ideas. If these pedagogical tools are useful but their use also carries risk, how do we proceed?   The remedy has two parts:  1. Recognize when one of these “simplifying” tools is being used and  2. Try to determine where the specific analogy, metaphor etc. works and where it fails conceptually.   The second instruction is the most difficult and may prove challenging for learners, particularly when they are first exposed to a new concept. However, the act of simply thinking about the potential problems associated with an analogy or model is an important metacognitive exercise that will help students learn. In BIS2A your instructors will occasionally expect you to explicitly recognize the use of these pedagogical tools and to explain the trade-offs associated with their use. Your instructors will also help you with this by explicitly pointing out examples or prodding you to recognize a potential issue.

 

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