BIO 401/501 Advanced  Biological Chemistry

Fall 2016

TENTATIVE TOPIC LIST & Lecture Schedule

FOR SPECIFIC PRE-REQUISITES AND GENERAL DESCRIPTION LOOK HERE

FOR REGISTRATION AND LOCATION INFORMATION, CLICK ON THE APPROPRIATE LINK

Bio 401   Bio 501

Instructors: G. Koudelka, Cooke 607, 645-4940 (koudelka@buffalo.edu);   G. Snyder Cooke 513, 645-4939, (gsnyder@buffalo.edu),
S. Walker (walker47@buffalo.edu) Hochstetter 653 645-2272

Dr. Koudelka is course coordinator, please address all questions about course administration to him.

Learning Objectives/Assessment:

Program Learning Outcome

Depth

Specific outcomes/objectives

Students will develop a broad background in the biological sciences and achieve an understanding and appreciation of basic biological concepts and principles. They will become proficient in five broad areas of biology: evolutionary biology, cell biology, physiology, biochemistry, and genetics.

1

gain a thorough understanding of the structures and function of proteins, enzymes and nucleic acids

 

 

 

Students will acquire laboratory and field skills necessary to answer biological questions and an ability to understand and employ scientific methodologies. They will be able to understand how to obtain, critically evaluate, and communicate experimental results

2

develop critical thinking skills by viewing and analyzing the three dimensional structures of proteins, nucleic acids and their complexes with each other and/or their small molecule substrates.

Students will gain understanding of how to integrate knowledge across biological sub disciplines and to synthesize examples, facts, or hypotheses from more than one level of organization into a coherent whole. They will also obtain the ability to integrate the physical sciences (chemistry, physics, and mathematics) with biology.

2

develop enhanced understanding of the physical forces that shape the structure of biological macromolecules and the interactions between them

Students will develop effective quantitative reasoning skills and be able to operate as a scientist to formulate and test appropriate biological hypotheses. They will be engaged both independently and collaboratively in the scientific process and learn to critically evaluate the veracity and value of published information.

2

develop high level ability to analyze and interpret quantitative data

Students will be able to retrieve information from multiple sources, to analyze this information and communicate it precisely in both written and oral forms.

2

develop expertise in reading scientific literature pertaining to protein, enzyme and nucleic acid structure-function and be able to understand methods and experimental results used in analysis of these macromolecules

 

 


I. Lecture Schedule

  1.  Proteins
  2. Nucleic Acids (click here for information on supplemental material
  3. Enzyme Kinetics
  4. Catalytic Mechanisms

II. Policies & Pre-requisites

III. Tentative Exam Schedule
 

Proteins

Amino acids: estimate protein net charge, analyze hydrophobicity patterns

Aug 29 

Snyder

2

Primary structure : mass spectroscopy :

sequencing / post-translational changes

Aug 31

"

Secondary structure : alpha helices and beta sheets : circular dichroism data

Sept 2

"

Helix stability : effects of  pH, salt, urea, temperature, and protein concentration

Sept 7

"

Tertiary structure : protein data bank, 3-dimensional molecular modeling

Sept 9

"

Charybdotoxin structure : NMR data: intramolecular contacts and folding

Sept 12

"

Charybdotoxin structure: compare folding with related proteins

Sept 14

"

8

Molecular dynamics of protein structures: free energy minimization

Sept 15

"

9

Disulfides: chemistry, cysteine spacing, genetically engineered mutants

Sept 19

"

10

Pancreatic trypsin inhibitor folding : 6 cysteines: sequence of making disulfides

Sept 21

"

11

Pancreatic trypsin inhibitor : differences of structure building in vitro vs. in vivo

Sept 23 

"

12

Chaperonin assisting protein folding: Review for EXAM 9/28/16 at 7PM

Sept 26

 


Nucleic Acids

13

Structural Properties of Nucleic Acid Building Blocks

Sept 28
(Figures)

Koudelka

14

Forces That Stabilize Nucleic Acid Double Helices

Sept 30
(Figures)

"

15

Double Helix Stability and Base Composition

Oct 3
(Figures)

"

16

Assembly and Characteristics of Nucleic Acid Double Helices

Oct 5
(Figures)

"

17

        ""                       ""

Oct 7

"

18

 Protein-DNA Interactions 

Oct 10

19

Unusual DNA Structures/DNA bending 

Oct 12

20

Mechanical Properties of Helices

Oct 14
(Figures)

"

21

Supercoiling and its energetics

Oct 17
(Figures)

"

22

Nucleosomes

Oct 19

(Figures)

"

23

RNA Structure (tRNA) & Sequence-dependent RNA Structure

Oct 21
(Figures)

"

24

Protein-RNA Interactions

Oct 24
(Figures)

"

25

Nucleic Acids Review-

EXAM AT 7PM on 10/31/2015

Oct 26


Enzyme Kinetics

26

Chemical Kinetics:Role of thermal energy

Oct 28

Koudelka

27

Chemical Kinetics: Potential energy, transition states & catalysis

Oct 31

"

28

Reaction order & experimental determination of velocity

Nov. 2

"

29

Steady-State Concepts and Consequences

Nov. 4

"

30(.ppt file)

Deriving rate equations

Nov. 7

"

31

                            

Nov. 9

"

32

Inhibition mechanisms

Nov. 11

"

33

Binding & Equilibrium

Nov. 14

"

34

Kinetics Review

Nov. 16

 

Metabolism

35

Bioenergetics

Nov. 18

Walker

36

Bioenergetics

Nov. 21

"

37

Metabolism-Amino Acids

Nov. 28

"

38

Metabolism-Nucleotides

Nov. 30

"

39

Macromolecular metabolism

Dec. 2

"

40

Macromolecular metabolism

Dec. 5

"

41

Macromolecular metabolism

Dec. 7

"

42

Exam IV- Metabolism

Dec. 9

"

 



BIO 401/501 Advanced  Biological Chemistry

Policies

Prerequisites. This purpose of this course is to give students a rigorous grounding in the fundamental structural, physical and chemical properties of the important biopolymers. These fundamentals will be described in effort to show the roles of these properties in determining the functions these molecules. NOTE: this is an advanced course-a basic class in Biochemistry is a strict pre-requisite; those who choose to remain in the class without the requisite background do so at their own peril.

Grading. This course is cross-listed for both graduate and undergraduate students. The graduate and undergraduate final grades will be determined separately. Graduate students will have additional work assigned. The final grade will be determined from a weighted average of separate evaluations in the four individual sections of the course. Performance in each section will be determined by written exams and, in certain sections, graded homework problems. The grades from each section will be weighted according to the number of lectures in the section. The final grades will generally be determined using the +/- system. The faculty of this course reserve the right to not utilize all grades in the A» F grade range.

Exams. As stated above, there will be four exams, each covering the material presented in one and only one section. The exams will be exclusively of the essay type. The exams will not test rote memory, but instead will examine a student's ability to synthesize and use their knowledge in solving problems. In the past, many exam questions tested the ability to analyze and interpret data from literature. SOME of the exams WILL BE GIVEN IN THE EVENING-NOT DURING CLASS TIME! The exams have been scheduled to be held in the evening of the following dates:

Proteins: Sept 28 (NOTE: NIGHT EXAM)

Nucleic Acids:  October 31 (NOTE: NIGHT EXAM) 

Enzyme Kinetics: Take home –DUE DATE TBD

Metabolism: December 9 (in class)

Required Texts. Lecture notes for most of the lectures will generally be available on UBLearns or distributed by individual faculty. Readings from research literature or monographs to supplement lecture material will be assigned in class and available on UBLearns.