Biology

Welcome to this course!

Interdisciplinary Topics in Biology is opened for DII students, this page is the main page of this course, established by ALL students that take part in this course in spring, 2015.

Click here to the wiki page.

通知：

对于新近加入此课程的同学，请注意，我们有一个QQ群：379124589。由于需要维护此wiki，因此我们需要让每一位同学贡献自己的力量。我们现在有五个小组，每组负责一周的工作。具体分组情况请点击此链接下载。请加入QQ群后，自行选择加入某一小组，并与该组负责同学联系，组长会分配任务:)

此外，我申请了一个顶级域名，同学们可以键入: njubiology.com，会自动跳转到课程主页，此外键入wiki.njubiology.com会自动跳转到wiki页。

Wiki page

If you want to know more details about this course, please goto Wiki page. The wiki is the textbook of this course organized by us.

Course introduction

This coure has 2 parts:

• Biological diversity, molecular evolution, logic of cellular metabolism (April 4-May 12)
  Instructor: Prof. Wouter D. Hoff(email: wouter.hoff@okstate.edu)
  Department of Microbiology & Molecular Genetics, Oklahoma State University

• Protein Structure, folding and interactions (May 13-June 20)
  Instructor: Prof. Junpeng Deng(email: junpeng.deng@okstate.edu)
  Department Biochemistry & Molecular Biology, Oklahoma State University

Weekly lecture schedule:

Twice a week a 2-hour lecture (so a total of four 50 minutes lectures per week)

Examination:

Four brief written exams (planned in weeks 3, 5, 8, and 11), each contributing equally to the final grade for the course, with each exam focusing on the material covered in the preceding ~3 weeks.

Homework assignments:

Homework assignments will be given at the discretion of the instructors to help students master the material covered in class.

Text book:

Biochemistry, 4th Ed., D. Voet & J. G. Voet; additional handouts and reading assignments provided in class.

Course Part 1

Course Description:

This course will take an interdisciplinary approach to connect classic and recent discoveries in biological diversity, molecular evolution, and cellular metabolism. A mix of classic core concepts, recent advances, current research, and gaps in knowledge will be discussed. The course will aim to emphasize scientific creativity and critical thinking about these topics, and will strive to have students integrate the topics discussed into their current knowledge so that students are ready to utilize this knowledge in real-life research.

Learning Objectives

• Students will be encouraged to develop study habits in which they critically evaluate new concepts and knowledge presented in class, and connect this new knowledge with what the student learned previously.

• Students will learn about key molecular tools in studying biological diversity and the remarkable findings uncovered by these tools.

• Students will learn to think about how molecular evolution proceeds, how this can be studied, and how evolution can be accelerated.

• Students will be able to understand the “energy core” and “information core” of the cell and how to critically think about topics in bioenergetics and cellular signaling.

Course Outline (subject to possible changes):

• Week 1 Introduction & biological diversity.
  A scientific approach to studying as a science major.
  How to discover and analyze biological diversity?
  What surprising and important insights were obtained using this approach?
  The tree of life and the uncultured majority.
  The wonders and problems of phylogenetic trees.

• Week 2
  A brief history of life.
  LUCA, ribozymes, the time line for life on the planet.
  How to define a biological species? What is a bacterial species?

• Week 3
  Climbing mount improbable.
  How does molecular evolution occur?
  Can we distinguish different “types” of molecular evolution?
  Is the mutation rate in cells always constant? How to speed up evolution?
  Microbial games, competition and cellular cooperation.

• Week 4
  Foundations of metabolism.
  How do cells make a living? How many ways are there to make a living as a cell?
  How do cells “generate” energy needed to live? How can we quantify this?
  Where did oxygen in in atmosphere and coal in the ground come from?

• Week 5
  Cellular networks.
  Metabolic networks and signaling networks. What is in a cell? The “energy core” versus “information core” of a cell. How do cells make decisions? Which decisions? Implications of finite cell size.

Course Part 2

Course Description:

Properties of amino acids and the peptide bond and the forces that drive protein folding into their 3D and quaternary structure; methods to study protein structure and function; and enzyme reaction mechanisms.

Learning Objectives

• You will develop an appreciation for the properties of amino acids and the peptide bonds and the forces that drive the folding of polypeptides into specific three dimensional structures. You will learn how proteins are organized into higher ordered structures, how proteins evolved and methods for predicting, determining protein structure and function, methods for charactering protein interactions.
• You should be able to extrapolate knowledge that is presented in lectures, and discussions for solving theoretical problems, and be able to interpret the meaning of sets of theoretical data that is presented. This does not mean that you must memorize every bit of information, but rather that you should understand the underlying logic of how cellular processes are studied and how this knowledge can be applied to solve important scientific questions.
• More generally, this course aims to prepare you to be a scientist. You will develop skills in seeking more advanced information in the scientific literature and in your own lab work. For this course, this means that you should be able to appreciate the experimental foundations of the study of macromolecules and molecular biology. You should be able to critically assess the limits of this knowledge, and to creatively think about how you could gain further information through new experimentation and interpretation of new data. Finally, it is vital that you can communicate your own thoughts effectively, both in written and oral forms: that is to know the language and terminology used in this field of study.

Course Outline (subject to possible changes):

• Lecture 1 Introduction to Proteins and Thermodynamics
• Lecture 2 Water Structure, weak bonds
• Lecture 3 Amino Acids
• Lecture 4 Side Chains, ionization separation, detection
• Lecture 5 Protein structure: Primary. Methods in analysis
• Lecture 6 Protein Structure: secondary. Methods in analysis
• Lecture 7 Protein Structure: Tertiary and stability
• Lecture 8 Protein structure: Quaternary. Examples
• Lecture 9 Protein purification
• Lecutre 10 Protein folding and dynamics
• Lecture 11 Protein structure modeling: homology and ab initial modeling
• Lecture 12 Protein prediction, Secondary structure, protein motifs, blocks, folds
• Lecture 13 X-ray crystallography: protein crystals and crystallization
• Lecture 14 X-ray crystallography: X-ray diffraction theory and structure determination, validation
• Lecture 15 Intrinsically Disordered proteins (IUP)
• Lecture 16 Post Translational modification on proteins (PTM)
• Lecture 17 Protein:Protein interactions
• Lecture 18 Protein: nucleic acids interactions
• Lecutre 19 Protein:small molecule interactions, Structure Based Drug Design (SBDD)
• Lecture 20 Mutational analysis : protein stability and folding.
• Lecture 21 Enzymes: Kinetics
• Lecture 22 Enzymes: mutisubstrate, inhibition, allosteric effects
• Lecture 23 Enzyme mechanisms: examples
• Lecture 24 Biological membranes

Here is the link to online Protein Structure course .