Outline of biochemistry

See also: Index of biochemistry articles

The following outline is provided as an overview of and topical guide to biochemistry:

Biochemistry – study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes.

Essence of biochemistry

Main article: Biochemistry

Biochemistry is the science dealing with the chemical composition and chemical reactions happening within, and between the living cells of all organisms (the mammals, the vertebrates, the plants, etc.)

Applications of biochemistry

Ames Test

The Ames test is a test that is used to determine whether a substance will affect (mutate) the structure of DNA. In this test salmonella bacteria is exposed to the chemical under question (food additives, for example), and changes in the way the bacteria grows are measured. Many substances that cause mutations in these bacteria also cause cancer in animals and humans. Indeed, this test is used today to screen chemicals for their potential ability to cause cancer in humans.

Pregnancy Testing

There are two types of pregnancy tests – one uses a urine sample and the other a blood sample. Both detect the presence of the hormone human chorionic gonadotropin (hCG). This hormone is produced by the placenta shortly after implantation of the embryo into the uterine walls and accumulates.

Breast Cancer Screening

Main article: Breast cancer screening

Most breast cancer is not hereditary, but in 5-10 percent of cases, there is a heredity linkage. The vast majority of these cases is due to mutations in two genes: Breast Cancer-1 gene (BRCA1) and the Breast Cancer-2 gene (BRCA2), which were discovered in 1994 and 1995, respectively. Females who inherit a mutation in either one of these genes have a greatly increased chance of developing breast cancer over their lifetime. Positive tests for these mutations allow the individual to schedule increased screening tests at a more frequent rate than the general population.

Prenatal Genetic Testing

Main article: Prenatal diagnosis

Prenatal genetic testing refers to testing the fetus for potential genetic defects. Tests commonly are performed on blood or tissue samples from the fetus. This may involve amniocentesis – collection of a sample of amniotic fluid that contains cells from the fetus—or collection of blood from the umbilical cord. Tests such as these are used ot detect chromosomal abnormalities such as Down syndrome or birth defects such as spina bifida.

PKU Screening

Main article: Phenylketonuria#Screening and presentation

Phenylketonuria (PKU) is a metabolic disorder in which the individual is missing an enzyme called phenylalanine hydroxylase. Absence of this enzyme allows the buildup of phenylalanine, which can lead to mental retardation.

Genetic Engineering

Genetic engineering involves taking a gene from one organism and placing it into another. The recipient may be bacteria or a plant or an animal. One of the most well-known examples of genetic engineering involves the hormone insulin. Diabetes use to be treated with insulin derived from pigs or cows, and although very similar to human insulin, these animal-derived insulin’s were not identical and caused problems for some individuals. Biochemists solved this problem by inserting the gene for human insulin into bacteria. The bacteria, through the process of translation, created human insulin.

Cloning

Main article: Cloning

In 1996, Dolly the sheep was cloned—the first mammal ever cloned from adult animal cells. The cloned sheep was, of course, genetically identical to the original adult sheep. This clone was created by taking cells from the udder of a 6-year-old ewe and growing them in the lab. They then took unfertilized eggs and stripped the genetic material from them. Finally, they inserted the genetic material grown in the lab into these cells and implanted them into the uterus of another sheep. And Dolly was born. Since Dolly, many other animals have been successfully cloned. However, there is worldwide debate on the idea of cloning a human, which will surely continue for decades.

Gene Replacement Therapy

Main article: Gene therapy

In gene-replacement therapy, a modified or healthy gene is inserted into the organism to replace a disease-causing gene. Commonly a virus that has been altered to carry human DNA is used to deliver the healthy gene to the targeted cells of the patient. This process was first used successfully in 1990 on a 4-year old patient who lacked an immune system due to a rare genetic disease called severe combined immunodeficiency (SCID). Individuals with SCID were prone to life-threatening infections. They lead isolated lives, avoiding people and commonly taking massive doses of antibiotics. Scientists removed white blood cells from the patient, grew them in the lab, and inserted the missing gene into the cells. They then inserted this genetically altered blood back into the patient. The process allowed the child to develop normally and even attend school, but the treatment must be repeated every few months.

Branches of biochemistry

Main Branches

• Animal Biochemistry
• Plant Biochemistry
• Molecular Biology
• Cell Biology
• Metabolism
• Immunology
• Genetics
• Enzymology

Other branches

Biotechnology, Bioluminescence, Molecular chemistry, Enzymatic Chemistry, Genetic engineering, Pharmaceuticals, Endocrinology, Cytology, Hematology, Nutrition and Photosynthesis

History of biochemistry

Main article: History of biochemistry

General biochemistry concepts

• Major categories of bio-compounds:
  • Carbohydrates : sugar -- disaccharide -- polysaccharide -- starch -- glycogen
  • Lipids : fatty acid -- fats -- essential oils -- oils -- waxes -- cholesterol
  • Nucleic acids : DNA -- RNA -- mRNA -- tRNA -- rRNA -- codon -- adenosine -- cytosine -- guanine -- thymine -- uracil
  • Proteins :
    • amino acid -- glycine -- arginine -- lysine
    • peptide -- primary structure -- secondary structure -- tertiary structure -- conformation -- protein folding
• Chemical properties:
  • molecular bond -- covalent bond -- ionic bond -- hydrogen bond -- ester -- ethyl
  • molecular charge -- hydrophilic -- hydrophobic -- polar
  • pH -- acid -- alkaline -- base
  • oxidation -- reduction -- hydrolysis
• Structural compounds:
  • In cells: flagellin -- peptidoglycan -- myelin -- actin -- myosin
  • In animals: chitin -- keratin -- collagen -- silk
  • In plants: cellulose -- lignin -- cell wall
• Enzymes and enzyme activity:
  • enzyme kinetics -- enzyme inhibition
  • proteolysis -- ubiquitin -- proteasome
  • kinase -- dehydrogenase
• Membranes : fluid mosaic model -- diffusion -- osmosis
  • phospholipids -- glycolipid -- glycocalyx -- antigen -- isoprene
  • ion channel -- proton pump -- electron transport -- ion gradient -- antiporter -- symporter -- quinone -- riboflavin
• Energy pathways :
  • pigments : chlorophyll -- carotenoids -- xanthophyll -- cytochrome -- phycobilin -- bacteriorhodopsin -- hemoglobin -- myoglobin -- absorption spectrum -- action spectrum -- fluorescence
  • Photosynthesis : light reaction -- dark reaction
  • Fermentation : Acetyl-CoA -- lactic acid
  • Cellular respiration : Adenosine triphosphate (ATP) -- NADH -- pyruvate -- oxalate -- citrate
  • Chemosynthesis
• Regulation
  • hormones : auxin
  • signal transduction -- growth factor -- transcription factor -- protein kinase -- SH3 domain
  • Malfunctions : tumor -- oncogene -- tumor suppressor gene
  • Receptors : Integrin -- transmembrane receptor -- ion channel
• Techniques : electrophoresis -- chromatography -- mass spectrometry -- x-ray diffraction -- Southern blot -- fractionation -- Gram stain -- Surface Plasmon Resonance -- Microscale Thermophoresis

External links

• The Virtual Library of Biochemistry and Cell Biology
• Biochemistry, 5th ed. Full text of Berg, Tymoczko, and Stryer, courtesy of NCBI.
• Biochemistry, 2nd ed. Full text of Garrett and Grisham.
• Costa Rican Biotechnology Society
• Cell Biochemistry
• Biochemistry (the scientific journal)