Instructor:                Dr. Inder M. Saxena

Office:                        NMS 4.312

Office hours:            M         10:00 – 12:00 noon

                                    W        11:00 – 12:00 noon

(or by appointment)

E-mail:                       imsaxena@austin.utexas.edu 



LECTURE                                        T, Th              3:30 - 5:00 PM          (WEL 2.304)

                                    Unique #

DISCUSSION           49810             M                     8:00 - 9:00 AM          (RLM 5.112)

                                    49815             M                     9:00 - 10:00 AM        (GDC 2.502)

                                    49820             W                    9:00 - 10:00 AM        (SZB 284)

                                    49825             W                    10:00 - 11:00 AM     (SZB 284)


Course objectives

The objective of this course is to provide an overview of cell structure and function at the molecular level and discuss

specific cellular processes including the cell cycle, cell death, and cancer.  The course will focus on developing an

understanding of the nature and function of a large number of proteins and methods used for their analyses.


Text Book

Molecular Biology of the Cell (Fifth Edition, 2008)

B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter

Garland Science


Problems and Solutions

Molecular Biology of the Cell, Fifth Edition

The Problems Book (2008)

J. Wilson and T. Hunt

Garland Science


Lecture material


        Slides -    Chapter 1 – Universal features of cells

                                List of topics

                                Problems – 1-1 to 1-12         

Articles – Towards synthesis of a minimal cell

A giant step towards artificial life

                                                Essential genes of a minimal bacterium

                                                Minimal bacterial genome

                                                Determination of the core of a minimal bacterial gene set

                        Chapter 1 – Diversity of genomes and the tree of life

                                Article – Eukaryotic evolution, changes and challenges

                                                Ancient invasions: from endosymbionts to organelles

                        Chapters 3 and 6 – Protein structure

                                List of topics – Chapter 3

                                List of topics – Chapter 6

                                                GroEL-GroES ATP-directed reaction cycle

                                Problems – 3-1 to 3-10, 3-15 to 3-18; 6-10, 6-11

                                                - The Gene Gateway Workbook (work on activities 4 and 5)

                                                - The Protein Data Bank

                        Chapter 3 – Protein function

                        Chapter 8 – Tools for protein analysis

                                                List of topics

                                Problems – 8-1, 8-2, 8-5 to 8-8, 8-10

                                Articles – Nuclear reprogramming to a pluripotent state by three approaches

                                                Bimolecular Fluorescence Complementation (BiFC) analysis                                              

                        Chapter 9 – Visualizing cells

                                                List of topics

                                Problems – 9-2 to 9-12

                                                Milestones in light microscopy (timeline)

                        Chapter 10 – Membrane structure

                                                List of topics

                                                (Membrane proteins of known 3-D structure)

                                Problems – 10-1 to 10-5, 10-7 to 10-10

                        Chapter 11 - Membrane transport

                                                List of topics

                                Problems – 11-1 to 11-6, 11-9

                                Web link -       Nobel lecture by Roderick MacKinnon

                                                        (Potassium channels and the atomic basis of selective ion conduction)

                                                                                    Video - “Potassium Channels” – a lecture by Roderick MacKinnon

                                                                   Article – Principles of Selective Ion Transport in Channels and Pumps

                                                                   Article – Crystal structure of the Na+, K+ - ATPase in the Na+ - bound state

                                                                    Calcium pump - movie

                                Inactivation Presentation - Trent Hodgson

                                Ion flow across cellular membranes and the Nernst equation – Presentation by Myra Dioquino

Chapter 12 – Intracellular Compartments and Protein Sorting   

                        List of topics

        Problems – 12-1 to 12-7, 12-9, 12-11, 12-13 to 12-17

                                Proteomic analysis of the secretome of Leishmania donovani – for class discussion

Review -                  Unfolded Protein Response

                                                                Membrane-protein integration and the role of the translocation channel

                                Perspectives –       Membrane Protein Insertion and Stability (R. MacKinnon)

                                                                Membrane Insertion of a Potassium-Channel Voltage Sensor

                        Chapter 13 – Intracellular vesicular traffic

                                                List of topics

                                Problems – 13-1 to 13-8, 13-10 to 13-15

2013 Nobel Prize in Physiology or Medicine: Machinery regulating vesicle traffic, a major transport system in our cells

                                                Article: Maturation of Golgi cisternae directly observed

                                                            Molecular anatomy of a trafficking organelle

                                                Review: The mechanisms of vesicle budding and fusion

                                                              The distribution and targeting of neuronal voltage-gated ion channels

                        Chapter 15 – Mechanisms of cell communication

                                                List of topics

                                                A Few Good Domains

                                                c-di-GMP signaling in bacteria

                                                From minimalism to maximalism

Chapter 16 – The cytoskeleton

                        List of topics

                                                Actin filaments – analyze the data

                                Problems – 16-1 to 16-10

                        Chapters 17 – The cell cycle

                                                List of topics         

                        Chapter 18 – Apoptosis

                                                List of topics         

                        Chapter 19 – Cell junctions, cell adhesion, and the ECM

                        Chapter 20 - Cancer

A few assignments

Articles and web sites  

        Article: How cells connect their plumbing? (research news; research article)

        Web site: NCBI

        Dynamic Gene

        Interview with a protein

        The Cell Biology of synaptic plasticity: AMPA receptor trafficking

        Cell Biology of Human Diseases

Animations and movies

        Visualization of molecular processes

        An animated model of protein targeting and translocation

        The dynamics of protein translocation

        Control of the Cell Cycle Game

            Cellular Visions: The Inner Life of a Cell (video with commentary)


          Swimming E. coli - movies


News items

        Detailed Picture of How Nutrients and Other Molecules Get Into Cells


Lecture topics



Lecture topics                                                                                   Chapter(s)



Universal features of cells and the diversity of living forms                 1

Proteins – structure and function                                                             3

Proteins – folding, misfolding, and destruction                                      6

Methods for study of proteins and cells                                                   8, 9

Biological membranes – structure                                                            10

Membrane transport                                                                                    11

Intracellular compartments and protein sorting                                      12

Intracellular vesicular traffic                                                                       13

Mechanisms of cell communication                                                         15

The cytoskeleton                                                                                          16

The cell cycle                                                                                                17

Apoptosis                                                                                                      18

Cancer                                                                                                           20