Biochemistry

Lesson 2: /Amino Acids/
 General Structure of an amino acid 

All amino acids have the following general structure:

Image link: https://archive.is/20130707075958/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
...
 * Digestion and absorption
 * Kidney
 * Nerve impulse, transmission, neuromuscular junction and modulators.
 * The origin of life on Earth
 * 1) The possible origin of life outside Earth (Astrobiology)
 * Iron, Heme
 * Coagulation
 * 1) Voluntary Muscle (item) metabolic peculiarities (item, item, item) and the neuromuscular junction
 * Connective tissue (collagen, elastin, 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 ? Is there a life force that drives the processes of the emergence of life on Earth, growth, tissue differentiation, morphogenesis and of tissue repair? Something like the egyptians Ka  ? 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
 * 1) The International System of Units, item
 * 2) Nomenclature of organic chemistry,item,
 * 3) Logarithms
 * 4) Nuclides
 * 5) Radioactive decay
 * 6) gas laws, Gases and Gas Laws
 * 7) Partial pressure and mole fraction
 * 8) Osmosis
 * 9) Diffusion
 * 10) pH (needs a little more)
 * 11) Buffers
 * Biomolecules -- Structures, classification and properties of:
 * 1) Nucleic acids
 * 2) Amino acids
 * 3) Protein
 * 4) Carbohydrate
 * 5) Lipid
 * 6) Organic Chemistry – Carbon Chemistry and Macromolecules
 * Laboratory and Analytical Methods
 * 1) Simple (glass) laboratory equipment and how to use it
 * 2) Laboratory safety
 * 3) Size exclusion chromatography
 * 4) UV-VIS Spectrometry
 * 5) IR spectrometry
 * 6) Centrifugation and Ultracentrifugation
 * 7) Electrophoresis
 * 8) Chromatography
 * 9) Gas chromatography and mass spectrometry
 * 10) Gamma counting
 * 11) Beta counting
 * 12) Enzyme assays
 * 13) PCR
 * Metabolic pathways
 * Proteins
 * 1) In vivo nucleic acids synthesis
 * 2) Nucleic acid degradation, pyrimidine and purine catabolism
 * 3) Peptide bond
 * 4) In vivo protein synthesis
 * 5) Micronutrients and Vitamins
 * 6) Enzymes
 * 7) Regulation of metabolic pathways
 * 8) Associated: Hemoglobin, gas transportation


 * Amino acids
 * 1) Decarboxylation
 * 2) Transamination
 * 3) General amino acid synthesis
 * 4) General amino acid catabolism
 * 5) Special amino acid metabolism
 * 6) Amino acid interconversion
 * 7) Urea cycle, item
 * 8) Gamma-glutamyl cycle
 * 9) Associated: Gout,Maple syrup disease
 * Carbohydrates
 * 1) Glycolysis
 * 2) Krebs' cycle
 * 3) Pyruvate decarboxylation
 * 4) The ATP cycle
 * 5) Oxidative phosphorilation
 * 6) C4 carbon fixation
 * 7) Photosynthesis
 * 8) Calvin Cycle
 * 9) Dickens-Horecker cycle
 * 10) Hexose interconversions
 * 11) Neoglucogenesis
 * 12) Glycogenesis
 * 13) Glycogenolysis
 * 14) Cori cycle
 * 15) Carbohydrate regulation mechanism: glucagon and insulin
 * 16) Associated: ...
 * Lipids
 * 1) fatty acids
 * 2) Essential fatty acids, item, poly-unsaturated fatty acids (PUFA); eicosanoids: prostaglandins, thromboxanes, prostacyclin and leukotrienes.
 * 3) The lipid bilayer, item, and transport across it
 * 4) Lipid peroxidation
 * 5) Acylglycerols
 * 6) Triacylglycerols
 * 7) Sn system
 * 8) Carnitine and membrane transport of fatty acids
 * 9) Fatty acid oxidations
 * 10) Beta oxidation
 * 11) Ketogenesis
 * 12) Lipid synthesis (lipogenesis)
 * 13) Arachidonic acid cascade and the eicosanoids (above)
 * 14) Associated: ...
 * 15) Lipoproteins and cholesterol
 * 16) The serum lipoprotein transport system
 * 17) Cholesterol metabolism, regulation and transport
 * 18) Lipoprotein metabolism
 * 19) Chylomicra and VLDL
 * 20) LDL and HDL
 * 21) Regulation of lipoprotein metabolism
 * 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 9781572591677.


 * Biochemistry Wikibook


 * The more general Entrez


 * Online Biology Book or


 * Exercises

Other resources
UH tutorial

Interactives