Lecture #1

Welcome to Advanced Biochemistry and Molecular Biology
In our first lecture we will review biological systems and some
of the chemical structures and nomenclature that we need to be familiar with. Lectures are downloadable as both a pdf and powerpoint file. Problem sets are downloadable as pdf files.

I reserve the right to alter content up to 48 hours before a lecture to correct errors or update material!! So please check the website 48hrs before the actual class period.

The first Lecture is essentially a review of biochemistry subject matter and what I expect you to know based on the requirements for this class. This is essentially chapters 1-4 in Voet and Voet plus any additional reading that is listed below.

Lecture_1.ppt ; Lecture_1.pdf ; Problem_set_1.pdf ;

Additional Reading -
Article_1.pdf ;

 

Lecture #2

In this lecture we introduce two important topics that must be
addressed before we can talk about protein/enzyme structure.
First we will review thermodynamics and discuss this in the
context of what forces are driving protein folding. Then we will
begin to discuss the fundamental procedures used in protein purification. This is described in Chapter 6 of Voet and Voet.

Lecture_2.ppt ; Lecture_2.pdf : Problem_set_2.pdf

 

Lecture #3

Now that we have an understanding of the thermodynamics of protein folding and how proteins are isolated, we will discuss the covalent and three dimensional structures. We will also consider the theory and experiments behind protein folding. This is essentially chapters 7, 8, and 9 from Voet and Voet.

Lecture_3.ppt ; Lecture_3.pdf ; Problem_set_3.pdf

Spectroscopy.pdf ; Protein_Folding.pdf

Lecture #4

Structural information is extremely important in research today.
In this lecture we cover structure determination by NMR and
X-ray crystallography. It is important to have a general understanding of how these two techniques are performed as well as what their strengths and weaknesses are. This is especially true given that many of the mechanisms we discuss are built largely on structural information.

Lecture_4.ppt ; Lecture_4.pdf ; Problem_set4.pdf

Additional information on protein motifs ; Motifs_1.ppt

For those who have never been exposed to Nuclear Magnetic
Resonance (NMR) or just want to review; NMR_primer.pdf

Lecture #5

In this lecture we will begin to explore enzyme kinetics with respect to both ligand binding and catalysis. It will become clear how a complete kinetic analysis can reveal important mechanistic information about an enzyme-catalyzed reaction. Due to the desire to impart a complete understanding of enzyme kinetics and the substantial information that is available on the topic, this lecture may run into two class periods.

Lecture_5.ppt ; Lecture_5.pdf ; Enzyme.ppt ; Problem_set_5.pdf

Some useful reading includes Chapters 13 and 14 of
Voet and Voet as well as Kinetics_1.pdf


Lecture #6

The form and function of cellular membranes is extremely important to a healthy organism. Unfortunately, due to the difficulty associated with isolation and characterization of membrane proteins, this is clearly an under-investigated area of research. We will spend the next two lectures discussing membrane structure and function. A problem set for both lectures will then be presented.

Lecture_6.ppt ; Lecture_6.pdf ;

Reading;
Chapter 12, of Voet and Voet
Membrane_1.pdf
Membrane_2.pdf
Membrane_3.pdf
Cryo_EM.pdf

Lecture #7

In this lecture we will continue our discussion of the cell membrane. In particular we will focus on the power of the membrane with respect to free energy and some important mechanisms for transport across the cell membrane.

Lecture_7.ppt ; Lecture_7.pdf ; Problem_Set_6-7.pdf

Reading;
Chapter 20, of Voet and Voet
membrane_4.pdf
membrane_5.pdf


Lecture #8

Oxidative phosphorylation is central to oxidative metabolism in all living cells. We have discussed membrane structure, however, before we can discuss this energy-generating process we must know a little bit more about the role of metals in biology.

Lecture_8.ppt ; Lecture_8.pdf ;

Reading;
Transition_metals.pdf

Lecture #9

Having a better understanding of bioinorganic chemistry we can now discuss some of the more important aspects of one of the most highly conserved processes in Nature, oxidative phosphorylation.

Lecture_9.ppt ; Lecture_9.pdf ; Problem_Set_8-9.pdf

Reading;
Chapter 22 of Voet and Voet
ETC_1.pdf
ETC_2.pdf

 

Lecture #10

In this lecture we will discuss the key aspects and structure-function relationships at work in photosynthesis, an extremely important biochemical process.

Lecture_10.ppt ; Lecture_10.pdf

Problem_set_10.pdf

 

 

Supplemental Lecture

"Oxygen and Iron; Enzyme Mechanisms and Evolutionary Implications"

Lecture_11.ppt ; Lecture_11.pdf

 

Supplemental Lecture #2

"Structure and Functional Diversity in Heme Monooxygenases: The NOS Story"

Supp.ppt : Supp.pdf