Biology/Chemistry 300 DNA and Protein Biochemistry
 Beloit College > Chemistry > DNA and Protein Biochemistry

DNA and Protein Biochemistry
At the fundamental chemical level, how do cells maintain and extract information from DNA to build and utilize proteins? Considerable emphasis on the chemical basis of biological information storage and processing, structure and function of proteins, enzyme catalysis theory, and quantitative analysis of enzyme kinetics. Three combined class and laboratory periods per week. (Q) Offered each fall.


 Course Information

Required Material:
Donald Voet and Judith Voet. (2010) Biochemistry, 4th ed.
Safety goggles ($2)
Sewn laboratory notebook
Calculator with scientific notation

Inclusivity is a demonstration of equity and social justice through awareness, understanding, and respect for the differences in identity, culture, background, experience, and socialization, and the ways in which these forms of difference impact how we live and learn. Inclusivity requires equitable, institution-wide representation and access to resources. In practice, this manifests itself by each individual being aware of, committed to, and responsible for the well-being and care of all students, staff, and faculty.

This course meets on land that is located on the traditional territory of Indigenous peoples, and we respectfully acknowledge the Potawatomi, Peoria, Miami, Meskwaki, and Ho-Chunk (Winnebago) people who have stewarded this land throughout countless generations. We pay respects to their elders both past and present and, as we gather here for class and lab, we consider the legacies of violence, displacement, and settlement that they have faced. We are always on Indigenous land, and here on the campus we have a constant reminder in the form of the mounds. To recognize the land is an expression of gratitude and appreciation to those on whose territory you reside, and a way of honoring Indigenous people. Land acknowledgments do not exist in a past tense, or outside historical context: colonialism is an ongoing process, and we need to build our mindfulness of our present participation.

Student Evaluation

Daily Check-in (40 x 10 pts. each; drop 3 lowest) 370 points
Exams (3 x 100 pts.) 300 points
Printed Lab Assignments:
  o-Nitrophenol standard curve (20 pts)
  o-Nitrophenol pH titration (20 pts)
  Myoglobin Stability (20 pts)
  Protein Purification (80 pts)
  Noncooperative ligand binding (30 pts)
  Cooperative ligand binding (30 pts)
  Enzyme Mechanism Studies (80 pts)
  Enzyme Active Site Stereoselectivity (30 pts)
300 points
Presentations (2 x 100 pts.) 200 points
Total 1,170 points

Each day of class will have a daily check-in. This will be a short quiz, check of assiged work or reading, or grading of lab notebooks. Points for daily preparation and participation may not be earned without attending the entire class period. Class and lab activities may not be completed outside the regularly scheduled laboratory time. The three lowest daily check-in scores will be dropped. If you miss class or lab for any reason (illness, religious observance, field or athletic trip, family, etc.), that day’s points will be among those dropped. You should save these for when you need them. Missing more than three days of class will negatively affect your grade. The maximum number of absences allowed for this course is six. Missing more than this maximum will result in automatically failing the course.

Grading Scale A (93%-100%) A- (90%-92%)
B+ (87%-89%) B (83%-86%) B- (80%-82%)
C+ (77%-79%) C (73%-76%) C- (70%-72%)
D+ (67%-69%) D (60%-66%) F (less than 60%)
Online Gradebook [Login Required]

If you have a disability and need accommodations, contact Learning Enrichment and Disability Services (LEADS) located on 2nd floor Pearsons (north side), 608-363-2572, learning@beloit.edu or make an appointment through olesena@beloit.edu. For accommodations in my class, you must bring me an Access Letter from the Director of LEADS and then we will discuss how to implement the accommodations. Contact that office promptly; accommodations are not retroactive.

Free peer tutoring is available for most classes. For a tutor, apply by going to your Portal, to the Student Life tab, and then apply using the Tutoring Forms (on left) and Request a Tutor. If you have any questions, contact LEADS.

If you want an Organizational Tutor, they are available in the Library on Sundays through Thursdays from 6-9 pm.

Office hours for this course are on Mondays, Wednesdays, and Fridays from 1:30 to 2:00 p.m. in Sanger 302 or 308.

Previous Quizes
Previous Exams
Error Propagation
How to Polish Graphical Figures
Schedule:

 Part 1: What is a protein?

Date Topic/Activity Reading
August 26 (1) Chemical Review and Amino Acids pp. 67-73
August 28 (2) Beer's Law [Example Polished Figure] Nonlinear Fitting Paper
August 30 (3) o-nitrophenol pKa Determination pp. 45-50
September 2 (4) Primary and Secondary Protein Structure pp. 221-232
September 4 (5) Tertiary and Quaternary Protein Structure pp. 245-257 and pp. 266-271
September 6 (6) 3D Printing Protein Models
September 9 (7) Protein Structure Stability and Introduction to Enzyme Presentations pp. 259-266
September 11 (8) Stability of Mb Structure pp. 323-324 and Mb Structure Stability Paper
September 13 (9) Exam 1 Exam 1 Paper
Exam 1 Digitized Data

 Part 2: Where do proteins come from?

Date Topic/Activity Reading
September 16 (10) DNA structure and Nucleobases pp. 82-90 and Molecular Structure of Nucleic Acids
September 18 (11) Transcription pp. 1260-1276
September 20 (12) Translation pp.1338-1398
September 23 (13) Chicken Liver Mitochondria Preparation pp. 129-146
September 25 (14) Ammonium sulfate fractionation and Dialysis Succinate Dehydrogenase Purification
September 27 (15) PAGE Analysis of Proteins and Chromatography Discussion [Gel Photos] pp. 146-152
September 30 (16) Enzyme Presentation Practice Talks and Painting Models
October 2 (17) Enzyme Presentation Practice Talks and Painting Models
October 4 (18) Enzyme Activity Determination and Protein Concentration Determination Bicinchoninic Acid Protein Assay
October 7 (19) Preparing an Enzyme Purification Report [Example Error Propagation]
October 9 (20) Class Enzyme Presentations
October 11 (21) Exam 2 Exam 2 Paper
October 14-18 Midterm Break

 Part 3: How do proteins function?

Date Topic/Activity Reading
October 21 (22) Introduction to Noncooperative Ligand Binding A Guide to Simple and Informative Binding Assays
October 23 (23) How tightly does azide bind to Myoglobin? Chapter 10
October 25 (24) Introduction to Cooperative Ligand Binding Chapter 10
October 28 (25) Cooperative Ligand Binding Continued (MWC model) Chapter 10
October 30 (26) Exploring Hemoglobin Adaptations Mechanisms of Hemoglobin Adaptation to High Altitude Hypoxia
November 1 (27) Exploring Woolly Mammoth and Elephant Hemoglobins [Data Table] Regulating the Effect of Temperature and Allosteric Effectors on Wolly Mammoth Hb
November 4 (28) Bovine Blood Oxygenation Experiement Chapter 10
November 6 (29) Introduction to Kinetics and Poster Project pp. 482-492
November 8 (30) Determine VMax, KM, and kcat
       [LabQuest Setup for Kinetic Data Collection]
November 11 (31) Enzyme Inhibition and Mutltiple Substrate/Product Kinetics pp. 492-503
November 13 (32) Enzyme Kinetic Inhibition Experiements
November 15 (33) Enzyme Kinetic Inhibition Experiements
November 18 (34) Enzyme Kinetic Inhibition Experiements
November 20 International Symposium
November 22 (35) Modes of Catalysis pp. 506-516
November 25 (36) Statistical Modeling Workshop and Poster Review
November 27 (37) Poster Review
November 29 Thanksgiving Break
December 2 (38) Enzyme Active Site Stereoselectivity [Day 1] pp. 470-474
December 4 (39) Enzyme Active Site Stereoselectivity [Day 2] Plapp et al. (2014)
December 6 (40) Enzyme Active Site Stereoselectivity [Day 3] Oppenheimer et al. (1971)
December 9 (41) Enzyme Poster Presentations
December 11 (42) Course Evaluations and [Enzyme Kinetics Project Due]
December 14 Final Exam (2:00 p.m. to 5:00 p.m.)
Final Exam Paper

Last edited on November 7, 2019 by Ted Gries

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