Biochemistry for Biology

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A course of the

Please refer also to the main topic:Biochemistry wiki for Biochemistry for Chemistry and for Medicine and Pharmacy.

You are invited to improve thoughtfully upon these subjects. Please refer to the Discussion page for proposals, discussion and comments.

Learning Projects

Lesson 2: Amino Acids

General Structure of an amino acid

All amino acids have the following general structure:

Image link: http://img222.imageshack.us/img222/4723/aminoacidwithgroup.jpg

• Area in Green is the amino group - NH2
• Area in Beige is the carboxyl group - COOH

The 'R' is the variable region. Different amino acids have different groups attached in the R region, this is what gives each group of amino acids essentially it own specific function and shape.

Essay and Discussion Themes

1. w:Digestion and absorption
2. Kidney
3. w:Nerve impulse, transmission, w:neuromuscular junction and modulators.
4. w:The origin of life on Earth
5. The possible origin of life outside Earth (w:Astrobiology)
6. Iron, w:Heme
7. w:Coagulation
8. Voluntary w:Muscle (item) metabolic peculiarities (item, item, item) and the w:neuromuscular junction
9. w:Connective tissue (w:collagen, w:elastin, w:reticulin)

...

• Vitalism - Is vitalism dead? Is mechanicism firmly established? Are all life processes, including consciousness, emotions, feelings (sentiments), and the sense of being oneself (Self) chemical and organic processes and functions, as neurologist António Damásio says ([1], [2], [3])? Is there a life force that drives the processes of the emergence of life on Earth, growth, tissue differentiation, morphogenesis ([4][5]) and of tissue repair? Something like the egyptians Ka ([6]) ? It's true that the controversy between materialism and idealisms has thousands of years and is likely to stay around; but what do you think yourself?

Topics and Learning Materials

Basics The International System of Units, item Nomenclature of organic chemistry,item, w:Logarithms w:Nuclides w:Radioactive decay w:gas laws, Gases and Gas Laws w:Partial pressure and w:mole fraction w:Osmosis w:Diffusion pH (needs a little more) Buffers Biomolecules -- Structures, classification and properties of: w:Nucleic acids w:Amino acids w:Protein w:Carbohydrate w:Lipid Laboratory and Analytical Methods Simple (glass) laboratory equipment and how to use it Laboratory safety w:Size exclusion chromatography UV-VIS Spectrometry IR spectrometry Centrifugation and w:Ultracentrifugation w:Electrophoresis w:Chromatography Gas chromatography and mass spectrometry Gamma counting Beta counting w:Enzyme assays w:PCR Metabolic pathways Proteins In vivo nucleic acids synthesis Nucleic acid degradation, pyrimidine and purine catabolism w:Peptide bond In vivo protein synthesis w:Micronutrients and w:Vitamins w:Enzymes Regulation of metabolic pathways Associated: w:Hemoglobin, gas transportation

Amino acids w:Decarboxylation w:Transamination General amino acid synthesis General amino acid catabolism Special amino acid metabolism Amino acid interconversion w:Urea cycle, item Gamma-glutamyl cycle Associated: w:Gout,w:Maple syrup disease Carbohydrates w:Glycolysis Krebs' cycle w:Pyruvate decarboxylation The ATP cycle w:Oxidative phosphorilation w:C4 carbon fixation w:Photosynthesis w:Calvin Cycle Dickens-Horecker cycle Hexose interconversions w:Neoglucogenesis w:Glycogenesis w:Glycogenolysis w:Cori cycle Carbohydrate regulation mechanism: w:glucagon and w:insulin Associated: ... Lipids w:fatty acids Essential fatty acids, item, poly-unsaturated fatty acids (w:PUFA); w:eicosanoids: w:prostaglandins, w:thromboxanes, w:prostacyclin and w:leukotrienes. The w:lipid bilayer, item, and transport across it w:Lipid peroxidation Acylglycerols Triacylglycerols Sn system w:Carnitine and membrane transport of fatty acids w:Fatty acid oxidations w:Beta oxidation w:Ketogenesis Lipid synthesis (w:lipogenesis) w:Arachidonic acid cascade and the eicosanoids (above) Associated: ... w:Lipoproteins and cholesterol The serum lipoprotein transport system w:Cholesterol metabolism, regulation and transport Lipoprotein metabolism w:Chylomicra and w:VLDL w:LDL and w:HDL Regulation of lipoprotein metabolism w:History of Biochemistry

Books

By alphabetical order of the first author's surname.

General Biochemistry

• Garrett, R, Grisham, C. "Biochemistry". Sanders College Publishing. Fort Worth, TX. 1999. ISBN 0-03-022318-0. Online at http://www.web.virginia.edu/Heidi/home.htm

• Nelson DL, Cox MM. "Lehninger Principles of Biochemistry". Worth Publishers. New York. 2000. ISBN 1-57259-153-6. http://worthpublishers.com/lehninger

• Osgood M, Ocorr K. "The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry Study Guide and Solution Manual". Worth Publishers. New York. 2000. ISBN 007-1256300-9.

• Biochemistry Wikibook

• The more general Entrez

• Online Biology Book [7] or [8]

• Exercises

Other resources

UH tutorial [9]

Interactives [10]