Biochemistry Class Notebook

Marion Carroll | Homework Paradise

2011-12-29T09:38:00.000-08:00

Marion Carroll | Homework Paradise

Since leaving the classroom I have been longing to help students academically with their questions and concerns in basic chemistry. biology and biochemistry. Homework Paradise might be a way to do that. Give this a try. This portal is new to me so I will see how this goes and if it is useful in providing you with the help you seek. If so, I will begin promoting myself and you can help by submitting your own review. Thanks. Good luck!

Dr. Carroll

Summer time...and the livin' is easy...

2010-07-04T11:27:00.000-07:00

That's right. All done for another summer of kicking back, relaxin', readin', writing and some overall reflectin'. Things are looking up since the last time summer came around. Hope you enjoy yours in spite the challenges. God will bless in due time.

The Inner Life of the Cell

2010-06-26T12:05:00.000-07:00

Better know this stuff!

Introduction to Biochemistry

2010-06-25T19:30:00.000-07:00

I welcome your comments here after or before your class. Suggestions for topics and clarification may be and are encouraged to be posted here. You can be anonymous or you may identify yourself. I especially would like to see comment strings, that is, what you think about what someone else has said. Come here often to review material covered in lecture.

Chapter 1 part 1

2010-06-23T19:20:00.000-07:00

Much of chapter 1 is a review of material you should have seen before with respect to thermodynamics and Gibbs Free Energy.

Chapter 1 part 2

2010-06-20T19:10:00.000-07:00

Chapter 1 contains a discussion of thermodynamics. Your comments are always welcomed. Enthalpy, entropy and free energy changes lie underneath all biochemical reactions driving them to completion and initiating the next reaction. Carefully read your chapter and search for other sources to reinforce these concepts.

Thermodynamics....huh?

2010-06-18T05:42:00.000-07:00

So here's a little description of what I believe explains the difference between
&Delta G and &Delta G⁰.

Gibb's Free Energy

pH and Amino Acid Titration

2010-06-15T04:20:00.000-07:00

Here is a quick review of pH, pK and pI that will be important when we begin Chapter 4: amino acids.Amino Acid Titration.

For Window Media Players

Chapter 4: Amino Acids

2010-06-12T23:00:00.000-07:00

Here is a summary of some important details concerning amino acid structure and properties. You should also be able to download theses videos for free from the iTunes music store if you have an account. You will find it in the Podcast section under "Biochemistry Class Notebook".

Stevie...what more can I say.

Chapter 7

2010-06-10T06:09:00.000-07:00

After discussing amino acids, protein primary, secondary and tertiary structure, we will discuss protein structure and function using hemoglobin: the classical allosteric protein.

The Bohr Effect

2010-06-09T05:11:00.000-07:00

Here's a brief overview of the most challenging topic in chapter 7, The Bohr Effect.

Michaelis-Menton Kinetics after Exam II

2010-06-05T06:44:00.000-07:00

Here is the first of 2 installments on our Enzyme Kinetics lectures. Use this for a quick review of the terms K_M, V_MAX, K_cat, K_S and enzyme efficiency. More description of the Linweaver-Burke and inhibition will follow in the 2nd installment.

Enzyme Inhibition

2010-06-01T20:28:00.000-07:00

Hope you listen in on this description of the 3 common enzyme inhibition profiles, it may prove helpful on Exam III.

Biochem Lab Fall 2009

2009-08-31T10:59:00.000-07:00

BIOCHEM LAB: Spectrophotometry of Riboflavin Part I

2009-08-26T05:35:00.000-07:00

(click the title to play or right click it to download and play in Quicktime)

The first experiment in Biochemistry lab this coming week is the Spectrophotometry of Riboflavin. Take a look at the Spectrophotometry of Riboflavin, Part I before coming to class.

If you're having trouble downloading and viewing the link on the title then this link will redirect you to the source file and you should be able to hear and see it there.

BIOCHEM LAB: Spectrophotometry of Riboflavin Part II

2009-08-25T23:14:00.000-07:00

(click the title to play or right click to download and play in Quicktime)

The first experiment in Biochemistry lab this coming week is the Spectrophotometry of Riboflavin. Take a look at the Spectrophotometry of Riboflavin, Part II video before class.

If you're having trouble downloading and viewing the link on the title then this link will redirect you to the source file and you should be able to hear and see it there.

BIOCHEM LAB: pH Determination

2009-08-24T15:09:00.000-07:00

Read your manual and do your calculations before class. Let me know if you have trouble viewing the Quicktime movie.

BIOCHEM LAB: Titration of an Amino Acid

2009-08-23T20:44:00.000-07:00

The amino acid titration experiment is described in this 20 minute video. CLICK the title to download and play a windows media file (not very good). Here you can download and play the quicktime file or get it from iTunes. Finally to accommodate all of you you may be able to view this video below. Go through it before taking the bonus quiz.

Protein Concentration Determination

2009-08-22T04:47:00.000-07:00

In the Experiment IV video will take a stock solution of BSA to generate a standard curve to use to determine the concentration of an unknown concentration of BSA. BSA is a standard size protein and is used regularly as a control to compare and determine concentrations of many different types of pure proteins. Can you tell me what BSA stands for?

Protein Characterization and PAG Electrophoresis

2009-08-21T21:49:00.000-07:00

Experiment VI and part of Experiment VII are described in this video. There is forthcoming the actual loading, running, staining and destaining of the gel before the final so stay tuned. You can access this video from iTunes or click the title here and view it or download it from my archives if having trouble viewing here. It may be necessary to wait until the video completes buffering to get a smooth view.

Polyacrylamide Gel Loading, Running and Drying

2009-08-21T21:07:00.000-07:00

This one is a little long but it covers the entire steps for diluting samples, adding them to the gel, staining/destaining and eventually drying the gel. Worth the time.

If you wish to download click here or get it from iTunes.

Determination of Catalase Activity

2009-08-20T21:51:00.000-07:00

Experiment VIII utilizes one of the fastest enzymes in biochemistry called catalase and its common household substrate none as hydrogen peroxide. Peroxide generates free oxygen radicals that can be damaging to tissues. Catalase along with other free radical scavengers and neutralizers converts peroxide into water and oxygen very efficiently. What factors effect the efficiency of catalase activity?

You can click the title here and view the video in my archive, you can download from iTunes of view here. You will have a better viewing experience if you wait for the video to buffer.

Alkaline Phosphatase Experiment #9

2009-08-19T14:27:00.000-07:00

Get it from Blackboard if unable to view here.

Blackboard Academic Suite

DNA Replication part I

2009-03-21T05:53:00.000-07:00

In my absence begin to review eukaryotic DNA replication in Chapter 24 using the following notes as your guide. There are 3 parts that cover the first half of this chapter on DNA replication. A second set will follow to cover DNA repair mechanisms

Part I

DNA Replication part II

2009-03-20T17:53:00.000-07:00

Chapter 24 DNA Replication part III

2009-03-01T10:55:00.000-08:00

Welcome back!

2008-08-22T13:00:00.000-07:00

Summer's over so let's get back to work. I hope to provide you with some insight into your biochemistry experiments here as well as recycle the notes on lecture topics. To start off the semester lets have a party...a Chemistry Party. (be warned, some reaction may be disturbing in the following video!)

We Need Your Data!!

2008-03-31T07:45:00.000-07:00

Are you a graduating senior or alumni from Xavier in Chemistry? We need you to fill in the survey. (click the title to redirect you)

Across Curriculum Thinking...I expect you there!

2008-03-21T13:09:00.000-07:00

Much of our perceived and anticipated reality has been shaped and mimicked in film and television. Let's hope we don't make it this far...but whose to stop us?

Join me at the ACT Brown Bag in the UC on Wednesday, March 26th, 2008 to face consequences that seem inevitable.

Oh Well. I think SKYPE did not let USTREAM use my sound card. Sorry. "Technical problems" is my middle name. Yeah but aren't I just adorable!

cAMP activation of PKA: Dr. Choel Kim, UCSD

2008-02-26T17:54:00.000-08:00

Many thanks to Dr. Choel Kim, Structural Biologist from UCSD for addressing my Introduction to Biochemistry class here at Xavier University of Louisiana. We are discussing protein function in class and Dr. Kim's explanation and illustrations of the intricacies of cAMP binding to PKA described in the research lab of Dr. Susan Taylor have helped many students in my class to see the dynamics of protein structure and function and small molecule binding.

I wish to extend my thanks also to Dr. Susan Taylor, in whose lab Dr. Kim has done this work. Dr. Taylor encouraged my efforts to hold this virtual lecture via Skype and with the exception of the "red" screen pictured here Dr. Kim came through marvelously. Our IT has managed to correct the "red" screen issue for my next presentation. Thanks Yamlak, Carl and Devin.

I'd also like to thank my students for their attention. They've endure my eccentricities with audio and video tools for study only when comforted in the knowledge that "it won't be on the test"...so they think. Remember, BONUS points go only to the prepared mind.

Sickle Cell Anemia: Novel Small Molecule Therapy Shows Benefit Via Hydration Of Red Blood Cells

2008-02-10T07:29:00.000-08:00

ScienceDaily

(2008-02-10) -- Researchers are identifying innovative therapeutics for sickle cell anemia that focus on specific factors in the disease's progression, such as the important role of hydration of the red blood cells. A novel small molecule therapy called senicapoc showed efficacy in maintaining hydration of red blood cells and increasing hemoglobin levels in patients with sickle cell anemia.

PKA Structure and Function: Susan S. Talyor

2008-01-31T22:02:00.000-08:00

You are assigned to read this paper published in PNAS vol 104 no. 1, January 2nd, 2007 out of the laboratory of Susan S. Taylor, Professor of Pharmacology, UCSD, Department of Chemistry and Biochemistry. Read, review, read and read again. Here is an exquisite illustration of the science of protein structure and how the intricate dynamics of the hierarchical protein structure contributes to its function and to an understanding of how best to effectively treat disease and irregular biochemical processes.

Ignore the dates as they apply to last semester.

One of my all-time favorite artists...Pat Metheny

Click to download from Archive.org

Protein folding

2008-01-31T13:39:00.000-08:00

Simulations of the villin headpiece

The villin headpiece is a small, 36-residue alpha helical protein. It has been heavily studied experimentally and by simulation since is perhaps one of the smallest, fastest folding proteins. It has a hydrophobic core made of 3 phenylalanines, but also has two groups (a tryptophan and another phenylalanine) which are hydrophobic, but are solvent exposed (for functional reasons). Duan and Kollman simulated 1 microsecond of MD time, in a ground breaking simulation. D. Lucent, V. Vishal, V. S. Pande. Proceedings of the National Academy of Sciences (2007)

Join the Folding@Home project!

New Buffer Resists PH Change, Even As Temperature Drops

2008-01-23T20:03:00.000-08:00

ScienceDaily (2008-01-16) -- Researchers at the University of Illinois have found a simple solution to a problem that has plagued scientists for decades: the tendency of chemical buffers used to maintain the pH of laboratory samples to lose their efficacy as the samples are cooled. The research team, headed by chemistry professor Yi Lu, developed a method to formulate a buffer that maintains a desired pH at a range of low temperatures.

Biochemistry 4130 Lecture and Lab

2008-01-12T12:51:00.000-08:00

From this virtual class my students will have access to short focused presentations
of the lecture material for the week. I will be posting to this blog
as well as XU's Blackboard material for quiz and test preparation in lecture and maybe even biochem labs. Be prepared! I'll also post interesting articles and discoveries as I see them. Check out the historical timeline to the present. Otherwise view the YouTube version.

A voice that could launch a thousand ships...well at least mine.
Corinne Bailey Rae

This video is depicting activity within capillaries and a single cell. I think its cool.

Proteins hard at work!

2008-01-11T22:49:00.000-08:00

Science Daily

ScienceDaily (Jan. 12, 2008) — Scientists at Washington University School of Medicine in St. Louis have used yeast cells to better understand a collection of proteins associated with the formation of actin networks, which are essential to cell movement.

Biochemistry Timeline....

2008-01-11T21:53:00.000-08:00

If some of you have trouble viewing the Timeline I displayed on the first day of class (see previous post). Here you are courtesy of YouTube...maybe!

Chapter 2

2008-01-10T23:08:00.000-08:00

Chapter 4 amino acid quiz coming soon!

Water...

2008-01-10T22:25:00.000-08:00

Here is a summary of Chapter 2prt1 with some hint to a few important considerations in Chapter 4 on amino acids. Give a listen. It may be useful to some of you and if so I'll continue providing these summaries. Good luck on Exam I coming 9/19!

Divided this summary into two videocasts:

Water part 1

Water part 2

Broadband download

Condensation 101

2008-01-10T14:18:00.000-08:00

A quick review of the condensation reaction...do you know your amino acidscondensation of amino acids. It's not that tough!