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
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 |
Amino acids: estimate protein net charge, analyze hydrophobicity patterns |
Aug 29 |
Snyder |
2 |
Primary structure : mass spectroscopy : sequencing / post-translational changes |
Aug 31 |
" |
3 |
Secondary structure : alpha helices and beta sheets : circular dichroism data |
Sept 2 |
" |
4 |
Helix stability : effects of pH, salt, urea, temperature, and protein concentration |
Sept 7 |
" |
5 |
Tertiary structure : protein data bank, 3-dimensional molecular modeling |
Sept 9 |
" |
6 |
Charybdotoxin structure : NMR data: intramolecular contacts and folding |
Sept 12 |
" |
7 |
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 |
Sept 28 |
Koudelka |
|
14 |
Sept 30 |
" |
|
15 |
Oct 3 |
" |
|
16 |
Oct 5 |
" |
|
17 |
Oct 7 |
" |
|
18 |
Protein-DNA Interactions |
Oct 10 |
|
19 |
Unusual DNA Structures/DNA bending |
Oct 12 |
|
20 |
Oct 14 |
" |
|
21 |
Oct 17 |
" |
|
22 |
Nucleosomes |
Oct 19 (Figures) |
" |
23 |
RNA Structure (tRNA) & Sequence-dependent RNA Structure |
Oct 21 |
" |
24 |
Protein-RNA Interactions |
Oct 24 |
" |
25 |
Nucleic Acids Review- EXAM AT 7PM on 10/31/2015 |
Oct 26 |
Enzyme Kinetics
26 |
Oct 28 |
Koudelka |
|
27 |
Chemical Kinetics: Potential energy, transition states & catalysis |
Oct 31 |
" |
28 |
Nov. 2 |
" |
|
29 |
Nov. 4 |
" |
|
Nov. 7 |
" |
||
31 |
“ “ |
Nov. 9 |
" |
32 |
Nov. 11 |
" |
|
33 |
Nov. 14 |
" |
|
34 |
Kinetics Review |
Nov. 16 |
|
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.