CHEM523

Section 001

Fall 2022

Lecture Files

PowerPoint files and any audio recordings of the lectures may be found on this page. All files are intended for use by students enrolled in CHEM523 at Winthrop University and are the sole copyright of the instructor. Any use by unauthorized personnel without the express written consent of the instructor is forbidden. Enjoy!

Topic 1: Intermolecular Forces, their Coulombic energies and Thermodynamics

• Lecture Powerpoint file

Topic 2: Amino acids and pKa values

• Lecture Powerpoint file

• MP3 audio file of lecture Friday, 26 August lecture

After this lecture, you should know:

1. The structure and physicochemical properties of the 20 naturally occurring amino acids
2. The 9 amino acids that typically take part in enzyme-catalyzed reactions
3. How to condense two amino acids together to make a peptide bond

• MP3 audio file of Monday, 29 August lecture

After this lecture, you should know:

1. Features of the peptide bond
2. The directionality and how to name peptides
3. What Ramachandran angles are, what a Ramachandran plot is, the two regions that amino acids are most likely to populate on a Ramachandran plot and what that means for secondary structure
4. The 3 types of secondary structure and characteristics of each
5. Why Proline can never be part of a secondary structure
6. The 4 levels of protein structure and features of each
7. The difference between a motif and a domain and why domains can be considered as evolutionary units

• MP3 audio file of the end of Chapter 2 from 31 August

After this lecture, you should know:

1. The details of the Anfinsen Experiment
2. The details of the Protein Folding funnel
3. The order of steps in protein folding going from the polypeptide chain exiting the ribosome to forming the molten globule due to the hydrophobic effect to forming secondary structures to forming tertiary and quaternary structures (if necessary)
4. What is meant by the term "intrinsically disordered protein"

Topic 3: Proteins and Proteomes

• Lecture Powerpoint file

• MP3 audio file of the beginning of Chapter 3 from 31 August

After this lecture, you should know:

1. The steps necessary to prepare a solution to purify a protein from it: Lysing a cell, centrifuging out the cell debris, salting out, dialysis

2. The three types of column chromatographic methods necessary to purify a protein. What you must consider for each method, how you elute the protein in each method

• MP3 audio file of the second half of Chapter 3 from 2 September

After this lecture, you should know:

1. What SDS-PAGE is and what you can learn from a SDS-PAGE gel

2. Antibodies: What an Fc and the Fab are

3. What ELISA stands for, the two types of ELISA techniques and the best use for each type

4. What a Western blot is and what you can learn from one

5. What a 2D-gel is and waht you can learn from a two-dimensional gel experiment

6. What MALDI-TOF means, the basics of the instrument and what you can learn from a MALDU-TOF mass spectrogram

Topic 4: Hemoglobin Structure and Function

• Lecture Powerpoint file

• MP3 audio file of lecture from 7 September

After this lecture, you should know:

1. The coordination state of Fe+2 and what a porphyrin ring is

2. How myoglobin and hemoglobin bind the porphyrin ring and what the proximal and distal histidines do

3. The roles of myoglobin in organisms

4. The role of hemoglobin in organisms

5. The difference between myoglobin and hemoglobin

6. The evolutionary relationshiip between myoglobin and hemoglobin

7. What divergent and convergent evolution mean

• MP3 audio file of lecture from 7 September

After this lecture, you should know:

1. The relationship between Kd, the pO2 values necessary to give fractional saturation values of 50% for myoglobin and hemoglobin and how that directly relates to the function of each protein.

2. Explain the fractional saturation curve knowing the arterial and venous pO2 values and how similar they are to the p50 values of each protein

3. What cooperativity is, what is required to exhibit cooperative behaviour and the two models of cooperativity

4. The basis of cooperativity in hemoglobin with EXACT chemical changes occurring in the subunits as oxygen binds

5. Allosteric effectors of hemoglobin (and understanding that allostery and cooperativity are different things)

Topic 5: Enzyme Kinetics

• Lecture Powerpoint file

• MP3 audio file of Chapter 8 Part 1

After this lecture, you should know:

1. What an enzyme is
2. How an enzyme lowers the activation energy of a reaction
3. The two components of an active site and what each does

• Zoom recording of 19 September Lecture on Chapter 8 Part 2(NOTE: You will have to download the file while on campus in before you can play it, it will not stream from the web server)

After this lecture, you should know:

1. What Vo, Km and Vm are
2. What the Steady State assumption is, both in terms of explaining it and mathematically
3. What the Michaelis-Menton equaiton is and what a plot of the equation looks like
4. What a Lineweaver-Burk or double-reciprocal plot looks like and what the linear regression equation of the plotted data can tell you
5. What the kcat of an enzyme is
6. What you can do with kcat/Km and what it means

From this point until the end of class, all audio recordings and any Zoom videos of lectures will appear on the course Blackboard site only. These files are too large to be streamed from the departmental server, but can be streamed from the University Blackboard server

Topic 6: Catalytic Strategies

• Lecture Powerpoint file

After these lectures, you should know:

1. The three rules of biochemical reaction mechanisms
2. The reaction mechanism for serine proteases
3. The reaction mechanism for carbonic anhydrase
4. The difference between convergent and divergent evolution using specific examples from the serine proteases

Topic 7: Regulatory Strategies

• Lecture Powerpoint file

• Insulin Tyrosine Kinase Receptor mini-lecture

After this lecture, you should know:

1. The 5 ways that enzyme activities can be regulated
2. Examples of each type of regulation
3. The importance of phosphorylation in causing conformational changes using the insulin receptor tyrosine kinase as an example
4. How kinases and phosphatases work together to regulate enzyme activities in the cell

Topic 8: Carbohydrates

• Lecture Powerpoint file

Topic 9: Lipids and Membranes

• Lecture Powerpoint file

Topic 10: Nucelotides and nucleic acids

• Lecture Powerpoint File

After this lecture, you should know:

1. What nucleopsides and a nucleotides are and their base structure (not the nitrogenous base)
2. How nucleotides are joined together
3. The structure of B-form DNA
4. What supercoling is and why it matters

Topic 11: DNA Replication

• Lecture Powerpoint File

Topic 12: RNA Replication

• Lecture Powerpoint File

Topic 13: Protein synthesis

• Lecture Powerpoint File

Topic 14: Gene regulation in Prokaryotes

• Lecture Powerpoint File