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Last update   11/9/2008  
 
 
 
 
 
       E-Courses

Biology:

Science Description :

The Department of Biology offers undergraduate, graduate, and postdoctoral training programs ranging from general biology to more specialized fields of study and research. The quantitative aspects of biology - including molecular biology, biochemistry, genetics, and cell biology - represent the core of the academic program. Courses are designed to provide a solid background in the physical sciences and to develop an integrated scientific perspective.

 

UnderGraduates Courses:

-   Biological Chemistry II, Spring 2004

Readings
Lecture notes
Assignments

- Minton, Allen P. "The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media." Journal of Biological Chemistry 276, no. 14 (2001): 10577-10580.

- Keating, T. A., and C. T. Walsh. "Initiation, Elongation, and Termination Strategies in Polyketide and Polypeptide Antibiotic Biosynthes." Current Opinion in Chemical Biology 3 (1999): 598-606.

-Ranghan, V. S., A. K. Joshi, and S. Smith. "Mapping the Functional Topology of the Animal Fatty Acid Synthase." Biochemistry 40, no. 36 (2001): 10792-10799.



- Yan, Yunxian. The Flow of Gifts: Reciprocity and Social Networks in a Chinese Village. Stanford, Calif.: Stanford University Press, 1996, pp. 74-97.

- Brown, Michael S., and Joseph L. Goldstein. "Receptor-Mediated Control of Cholesterol Metabolism." Science 191 (1976): 150-4.

-Song, W. S. et al. "Role of Sec61alpha in the Regulated Transfer of the ribosome-nascent chain complex from the signal recognition particle to the translocation channel." Cell 100 (2000): 333-343.

- Suo, Zucai, Huawei Chen, and Christopher T. Walsh. "Acyl-CoA Hydrolysis by the High Molecular Weight Protein 1 Subunit of Yersiniabactin Synthetase: Mutational Evidence for a Cascade of Four Acyl-Enzyme Intermediates during Hydrolytic Editing." PNAS 97 (2000): 14188-14193. (Fidelity in PKS)

- Wang, L, Z Zhang, A Brock, PG Schultz. "Addition of the Keto Functional Group to the Genetic Code of Escherichia coli." Proc Natl Acad Sci 100, no. 1 (January 7, 2003): 56-61. (Methods)

- Newcomb, and Noller. "Direct Hydroxyl Radical Probing of the 16S Ribosome RNA in the 70S Ribosomes from Internal Positions of RNA." Biochemistry 38 (1999): 945-951.

- Ramakrishnan, V. "Ribosome Structure and the Mechanism of Translation." Cell 108 (2002): 557-572.
 

1- Introduction: cell constituents, prokaryotes vs. eukaryotes 

2-Secondary metabolism: PKS, NRPS 

3- Chemistry of PKS and NRPS (cont'd)

              (PDF)

4-Chemistry of PKS and NRPS (cont'd with specific examples)

             (PDF)

5-Biosynthesis of yersiniabactin and cholesterol 

             (PDF)

6- Cholesterol biosynthesis

7-Cholesterol regulation and homeostasis

8- Sensing insoluble molecules 

9-Translation (cont'd)

             (PDF)

10-Elongation, termination, RNA polymerase 

11- Isoleucine tRNA synthetase

(PDF)

12-G proteins: motors 

(PDF)

13-G proteins: switches 

             (PDF)

14-Peptide bond formation; new technologies using the ribosome

(PDF)

1- Prolem set1

          (PDF)

2- Problem set 2

          (PDF)

3- Problem set3

4- Problem set4

           (PDF)

5- Problem set5

           (PDF)

6- Problem set6

 

Graduates Courses:

-   Systems Biology, Fall 2004

Readings
Lecture notes
Assignments

-Equilibrium Binding

                (PDF)

-Lambda Phage


               (PDF)

-Synthetic Genetic Switches

               (PDF)

-Stability Analysis

              (PDF)

-Fine-tuned versus Robust Chemotaxis Models

             (PDF)

-Wrapping up Chemotaxis

            (PDF)

-Genetic Oscillators

            (PDF)

-Genetic Oscillators (cont.)

            (PDF)

 

1- Introduction

           (PDF)

2- Lambda Phage

              (PDF)

3- Multistability (cont.)

             (PDF)

4- Stability Analysis

           (PDF)

5- Fine-tuned versus Robust Chemotaxis Models

       (PDF)

6- Wrapping up Chemotaxis

7- Genetic Oscillators

1- Prolem set1

       (PDF)

2- Problem set 2

3- Problem set3

4- Problem set4

       (PDF)

5- Problem set5

        (PDF)

6- Problem set6

Graduates- UnderGraduate Courses:

-   Neural Plasticity in Learning and Development, Spring 2002

Readings
Lecture notes
Assignments

- In cultures of dissociated rat hippocampal neurons, persistent potentiation and depression of glutamatergic synapses were induced by correlated spiking of presynaptic and postsynaptic neurons.


- Long-term protestation of synaptic transmission in the hippocampus is the primary experimental model for investigating the synaptic basis of learning and memory in vertebrates.

 

- Activity-driven modifications in synaptic connections between neurons in the neocortex may occur during development and learning.

 

- Early visual experience is essential in the refinement of developing neural connections. In vivo whole-cell recording from the tectum of Xenopus tadpoles showed that repetitive dimming-light stimulation applied to the contralateral eye resulted in persistent enhancement of glutamatergic inputs, but not GABAergic or glycinergic inputs, on tectal neurons.                

 

- Calcium ions play crucial signaling roles in many forms of activity-dependent synaptic plasticity.

                 

- Long-term potentiation (LTP) is an enhancement of synaptic strength that can be produced by pairing of presynaptic activity with postsynaptic depolarization.


- Long-lasting forms of learning-related synaptic plasticity require transcription and yet occur in a synapse-specific manner, indicating that there are mechanisms to target the products of gene expression to some but not other synapses of a given cell.


- Formation of glutamatergic synapses entails development of "silent" immature contacts into mature functional synapses. To determine how this transformation occurs, we investigated the development of neurotransmission at single synapses in vitro.

1- Introduction

2- Behavior and Plasticity

3- Synaptic Transmission

             (PDF)

4- Potentiation of Synaptic Transmission

               (PDF)

5- Expression of Plasticity

               (PDF)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1- Prolem set1

       (PDF)

2- Problem set 2

3- Problem set3

4- Problem set4

       (PDF)

For more information visit: www.ocw.mit.edu