Course Syllabus

Guidelines For Research Proposal

Biochemistry 314

Course Description

This course is an in-depth examination of DNA and RNA structures and how these structures support their respective functions during replication, transcription, and translation of the genetic material. Emphasis is on the detailed mechanims associated with each step of gene expression. Discussions incorporate many recent advances brought about by recombinant DNA technology. Prereq. Biol 210, Chem 302, Biochemistry 311 or permission of instructor; 2 meetings (75 minutes), 1 discussion (50 minutes), 1 lab (4 hours); 4 credits.

Course Syllabus

Textbook: Biochemistry by Voet and Voet, 2nd edition.

 Week  Chapter Reading  Topic
 1  27 Central Dogma of Molecular Biology: Flow of Genetic Information
Genome Structure: DNA/RNA; d.s./s.s.; Size; Linear/Circular
 2  28 Structures of DNA Double Helix: A-, B-, Z-, H-DNA
DNA Supercoiling
Chromatin Organization
 3  31 DNA Replication
DNA Repair and Recombination
 4  28 Forces Stabilizing DNA: Denaturation & Hybridization
Enzymatic Analysis of DNA: Restriction & Modification
Molecular Cloning Techniques
 5  28 Exam #1
Molecular Cloning Techniques
 6  28 DNA Synthesis: Oligonucleotide Technology, PCR Amplification
DNA Sequencing Methods
Footprinting Techniques
 7  26 De Novo Synthesis of Purines and Pyrimidines
Synthesis of Ribonucleotides & Deoxyribonucleotides
Catabolism of Nucleotides & Salvage Pathways
 8    Spring Break
 9  29 RNA: Structures and Cellular Roles
Transcriptional Regulatory Elements: Promoters and Terminators
Exam #2
 10  29 Prokaryotic RNA Polymerase and the Transcription Cycle
Eukaryotic RNA Polymerases
Eukaryotic Transcription & Chromatin Remodeling
 11  29 RNA Processing-Prokaryotes vs. Eukaryotes
Split Genes: Introns and Exons
Splicing Mechanisms: Self-Splicing vs. Spliceosome
 12  29 Transcriptional Regulation: Repression
Transcriptional Regulation: Activation
Protein Synthesis-An Overview
 13  30 Structure and Function of tRNAs and rRNAs
Ribosome Assembly
Deciphering the Genetic Code
 14  30 Suppressor Mutations & tRNA Identity
Translational Regulation & mRNA Stability
Exam #3
 15   Oral Presentation of Research Proposal Projects


Guidelines for Research Proposal

Topic: Choose a topic early in the semester. The topic can be anything related to molecular biology. I need to okay the topic to avoid overlaps in the subject matter among your classmates.

Oral Presentation: About 15 minutes per presentation, on the background material and significance of the project, questions being posed, and what experiments can be performed to clarify them.

Written Proposal: Length should be no more than 12-15 double-spaced pages.

The format of the proposal should be written as a research plan to answer these questions:

A. Specific Aim: What do you intend to do? (1-2 page)

State concisely and realistically what the proposed research intends to accomplish: what hypothesis is to be tested, what question is being addressed.

B. Significance: Why is the work important? (4-5 pages)

Briefly sketch the background to the present proposal; for example, why is the problem you have identified important to study, how does it fit into the larger context of biology. Critically evaluate existing knowledge, and specifically identify the gaps which the project is intended to fill.

C. Preliminary Studies/Progress Report: What has already been done? (2-3 pages)

Provide an account of the preliminary studies in the literature pertinent to the proposal; i.e., the findings that brought out a discrepancy, or led to the question you are interested in examining or resolving.

D. Experimental Design and Methods: How are you going to do the work? (4-5 pages)

Propose an experimental design and the procedures to be used to accomplish each specific aim of the project. Discuss in detail how the proposed experiment will distinguish the various models possible, the hypotheses you have formulated, or the questions you have framed. Each model/hypothesis/question predicts a certain anticipated outcome, so you need to interpret and analyze possible outcomes from the proposed experiments. The "detail" referred to above is concerned with the conceptual one, such as the choice of your experimental approach, controls and/or standards that you may need to include in your experimental set up to allow a critical distinction of the hypotheses, implications of your findings, and further experiments to confirm or disprove the emerging model. Picky details such as buffer compositions, reaction volumes, and exact amount of substrates, etc., etc., are not necessary unless one of the factors is a critical parameter in the proposed experiment (e.g., pH, or choice of metal ion, etc.)

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