Laboratory Course of Biological Chemistry

Course title

CD001000

	HAMASAKI Keita
	LI QINTONG
	MASADOME Takashi

Course description

All the processing in a cell, including genomic DNA replication, metabolic pass way catalyzed by enzymes, are accomplished as the combination of aligned chemical reactions. Molecular biotechnology has been adapted not only in medical, pharmaceutical, foods but even in the fuel or plastic production process. Simply, you might be caught by molecular biology protocols However, you must understand chemistry behind molecular biology and handle it as an engineering. Biological Chemistry Laboratory include training of the experiment with centrifuge, PCR, electrophoresis, chromatography, spectroscopy, and data analysis with the PC application as well

Purpose of class

This laboratory course provides introductive talk, exercises and laboratory training and aims to students understanding for foundation and techniques for the procedure of molecular biology through this course.

Goals and objectives

Understanding for DNA replication by PCR and DNA separation by electrophoresis with performing these experiments.
Understandings for affinity chromatography, gel filtration, UV-visible spectroscopy with performing these experiments.
Understanding for quantitative analysis the enzymatic hydrolysis with performing these experiments.
Uderstand and explain the theory of molecular biological laboratory.

Relationship between 'Goals and Objectives' and 'Course Outcomes'

	report paper 1	report paper 2	report paper 3	examination	Total.
1.	25%				25%
2.		25%			25%
3.			25%		25%
4.				25%	25%
Total.	25%	25%	25%	25%	-

Evaluation method and criteria

Three report paper (25%, each) plus one examination (25%), over 60% of score will give you two credit.

Language

Japanese

Class schedule

	Class schedule	HW assignments (Including preparation and review of the class.)	Amount of Time Required
1.	Foundations of molecular biology, guidance and basis	How to avoide contaminations	200minutes
		Apropriate pipetting
		Significant degit on the calculations
2.	Extraction and purification of genomic DNA from bacterial cell	Prokaryotic cell and eukaryotic cell	200minutes
		Genome and plasmid DNA
		Chemical nature of DNA
3.	Replication of the DNA sequence coding BioH by PCR	Biotin and avidin	200minutes
		Polymerase chain reaction, PCR
		What regulate the velocity of the analyte on the electrophoresis?
4.	Basis of gene analysis and phylogenetic tree	Cloning	200minutes
		DNA sequencing
		Phylogenetic tree of the bacterial 16SrRNA
5.	Report writing for "Extraction and purification of genomic DNA from bacterial cell. Replication of the DNA sequence coding BioH by PCR"	Principle of the purification of genomic DNA from bacterial extract	200minutes
		Principle of the DNA replicarion by PCR
		Principle of DNA quantitative by UV absorption
6.	Purification of fusion protein GFP-BioH by affinity chromatography	Fusion protein and fluorescent protein	200minutes
		Centrifugation
		Affinity chromatography
7.	Further purification of fusion protein GFP-BioH by gel filtration	Gel filtration	200minutes
		Ultraviolet and visible spectroacopy and emission
		Quantitaiton of protein
8.	Study for chemical reacton mechanism with protein data bank	Protein data bank, PDB	200minutes
		Enzyme data bank, DRENDA
		Mechanism of enzyme catalyzed chemical reaction
9.	Report writing for "Purificaiton and quatitation of fusion protein, GFP-BioH"	What determine the velocity of the analyte on the centrifugation?	200minutes
		Princople of the separation of the protein with histidine affinity chromatography.
		The difference in the quatitated amount of the protein determined by absorption at and 475 nm.
10.	Evaluation for the enzymatic activity with para-nitrophenyl acetate as a substrate	Para-nitrophenyl acetate and para-nitrophenolate	200minutes
		The relationship between molecular structure and absorption spectrum
		Measurement of the chemical reaction rate
11.	Evaluation for the enzye inhibition with para-nitrophenyl acetate as a substrate	Chemical action of which inhibit enzymatic activity	200minutes
		Competitive inhibitionaand non competitive inhibition
		Evaluation of the inhibitor
12.	Enzyme kinetics and data analysis with PC application, excel	Michaelis-Menten type of reaction mecanism	200minutes
		Data analysis with reciprocal plot
		Analysis by the least-squares method
13.	Report writing for "Evaluation for the enzye inhibition with para-nitrophenyl acetate as a substrate"	MIchaelis constant and dissociation constant	200minutes
		Affect of GFP in GFP-BioH for enzymatic activity
		Reaction mechanism of competitive inhibition in enzymatic reaction
14.	Examination and answering,	Explain principles in biological chemistry laboratory	200minutes
Total.	-	-	2800minutes

Feedback on exams, assignments, etc.

ways of feedback	specific contents about "Other"
Feedback in outside of the class (ScombZ, mail, etc.)

Textbooks and reference materials

教科書：実験手引き書はscomb2から取得できる
参考書：「理系総合の生命科学」第5版　東京大学生命科学教科書編集委員会　羊土社、「物理化学要論」第7版　P.W. Atkins, Julio de Paura, 東京化学同人

Prerequisites

生物化学、物理化学、有機化学、無機化学、分析化学、有機生物化学を受講することが望ましい。

Office hours and How to contact professors for questions

scomb2「担当教員へのメッセージ」

Regionally-oriented

Non-regionally-oriented course

Development of social and professional independence

Course that cultivates an ability for utilizing knowledge
Course that cultivates a basic problem-solving skills

Active-learning course

Most classes are interactive

Course by professor with work experience

Work experience	Work experience and relevance to the course content if applicable
N/A	実験、実習

Education related SDGs:the Sustainable Development Goals

Last modified : Wed Jul 30 04:04:04 JST 2025