Welcome to Biochemistry 432/832. Instructors: Vadim Gladyshev Lori Allison Teaching Assistant: Yun Jeong Kim [email protected] Class web page : http://www-class.unl.edu/bioc432/bioc432.htm Tuesday/Thursday 11.00-12.15 pm Beadle Center Auditorium. Outline. Information Syllabus
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Introduction to the course
Introduction to metabolism
Overview of glycolysis
THE LITERATURE OF BIOCHEMISTRY
THE FIELD OF BIOCHEMISTRY
YOUR OWN FIELD OF RESEARCH
KEY WORD SEARCH
WHERE TO SEARCH?
How to Read a Research Article
Composition of a full paper
Composition of a communication
What to read?
National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov
Access to the primary literature (Pubmed) http://www.ncbi.nlm.nih.gov/PubMed/
On-line journals J. of Biol. Chemistry http://www.jbc.org/
Proc. of the Nat. Acad of Sci. USA http://www.pnas.org/
Sequences (Entrez) http://www.ncbi.nlm.nih.gov/Entrez/
Clusters of orthologous groups (COS) http://www.ncbi.nlm.nih.gov/COG/
You are welcome to come without an appointment, but it is better to E-mail or call before you come
You are responsible for all material covered in the chapter that is discussed in the class. You will have the reading assignment for each class period except exams.
Some sections of certain chapters may be excluded from the reading assignments and exams, and if it happens, I will tell you beforehand.
No excuses for missing exams. Medical school interview is not an excuse.
Recent scientific papers that describe discoveries or breakthroughs in areas being covered during the course, will be discussed and corresponding concept questions may be included in the exams and bonus questions.
Methods to study: read the chapter (reading assignment) before the respective class period. First, you could read quickly the chapter to get an idea what is it about. The second time you read, pay a particular attention to concepts, but knowledge of details may also be necessary. After the class, read the chapter again and also read the lecture notes. It should be enough for a good performance on exams.
Metabolism is a sum of chemical changes that convert nutrients into energy and finally to complex finished products of cells (The process through which organisms acquire and utilize energy for their function)
Do we know all metabolic pathways?
building blocks – common intermediates -
Metabolic pathways are irreversible (because they
must be regulated)
Metabolic pathways have (first) committedstep
Metabolic pathways are regulated
Metabolic pathways are compartmentalized
Principles: anabolic and catabolic pathways must differ in at least one step in order to be regulated
Anabolic & catabolic pathways
involving the same product are
not the same
Some steps may be common
Others must be different- to ensure
that each pathway is spontaneous
This also allowsregulation
mechanisms to turn one pathway
and the other off
Metabolic pathways are compartmentalized
Mitochondria (TCA cycle, OxPhos, fatty acid oxidation, amino acid breakdown)
Cytosol (glycolysis, fatty acid biosynthesis, pentose phosphate cycle)
Nucleus (DNA replication, transcription, RNA processing)
ER (Rough ER: synthesis of membrane and secretory proteins, smooth ER: lipid and steroid biosynthesis)
Golgi (posttranslational processing of proteins)
- The enzymes may be separate
- Or may form a multienzyme complex
- Or may be a membrane-bound system
- New research
complexes are more
common than once
Understanding of pathways:
Sequence of reactions
Mechanisms of each reaction
Regulation of pathways
Inhibitors (accumulation of intermediates)
Genetic defects (also accumulation of intermediates)
Genetic manipulations: animals (transgenic, knockout), expression in certain tissues
Emerging methods: sequence methods (genome projects),
bioinformatics, high throughput gene expression methods
(microarray analyses - hybridizations on membranes, slides, chips)
Catabolic and anabolic pathways, occurring simultaneously, must act as a regulated, orderly, responsive whole
NAD+/NADH ratio: 725 Concentration: 0.5 mM
NADP+/NADPH ratio: 0.015 Concentration: 0.2 mM