• Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate (ATP), the
  primary energy-carrier molecule found in all living organisms.

• One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind.

• By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.

• It is this “R” group that made each amino acid different, and the properties of the side-chains greatly influence the overall three-dimensional conformation of a protein.

• [46] Examples of protein structures from the Protein Data Bank Members of a protein family, as represented by the structures of the isomerase domains Ingested proteins are
  usually broken up into single amino acids or dipeptides in the small intestine and then absorbed.

• Just six elements—carbon, hydrogen, nitrogen, oxygen, calcium and phosphorus—make up almost 99% of the mass of living cells, including those in the human body (see composition
  of the human body for a complete list).

• The amino acids may then be linked together to form a protein.

• While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino
  acids.

• A similar process is used to break down proteins.

• These forms are called furanoses and pyranoses, respectively—by analogy with furan and pyran, the simplest compounds with the same carbon-oxygen ring (although they lack the
  carbon-carbon double bonds of these two molecules).

• [2] Biochemistry focuses on understanding the chemical basis which allows biological molecules to give rise to the processes that occur within living cells and between cells,[3]
  in turn relating greatly to the understanding of tissues and organs, as well as organism structure and function.

• [8] The mechanisms used by cells to harness energy from their environment via chemical reactions are known as metabolism.

• There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell
  to cell interactions and communications.

• Lipids are usually made from one molecule of glycerol combined with other molecules.

• [7] The chemistry of the cell also depends upon the reactions of small molecules and ions.

• These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid
  cycle), and led to an understanding of biochemistry on a molecular level.

• Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

• This is shown in the following schematic that depicts one possible view of the relationships between the fields: • Biochemistry is the study of the chemical substances and
  vital processes occurring in live organisms.

• [49] It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought
  to be the reason why complex life appeared only after Earth’s atmosphere accumulated large amounts of oxygen.

• For example, the aldohexose glucose may form a hemiacetal linkage between the hydroxyl on carbon 1 and the oxygen on carbon 4, yielding a molecule with a 5-membered ring,
  called glucofuranose.

• These can be inorganic (for example, water and metal ions) or organic (for example, the amino acids, which are used to synthesize proteins).

• Cellulose is an important structural component of plant’s cell walls and glycogen is used as a form of energy storage in animals.

• Antibodies are an example of proteins that attach to one specific type of molecule.

• When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis.

• The study of “mutants” – organisms that lack one or more functional components with respect to the so-called “wild type” or normal phenotype.

• The central dogma of molecular biology, where genetic material is transcribed into RNA and then translated into protein, despite being oversimplified, still provides a good
  starting point for understanding the field.

• [37] Many biological molecules are polymers: in this terminology, monomers are relatively small macromolecules that are linked together to create large macromolecules known
  as polymers.

• The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two molecules of ATP, six more NADH molecules and two reduced (ubi)quinones
  (via FADH2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide.

• [45] The enzyme itself is not used up in the process and is free to catalyze the same reaction with a new set of substrates.

• Finally, quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits.

• They are complex, high-molecular-weight biochemical macromolecules that can convey genetic information in all living cells and viruses.

• Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver
  gene therapy or drug molecules).

• [13] The structure of proteins is traditionally described in a hierarchy of four levels.

• Metabolism Carbohydrates as energy source[edit] Main articles: Carbohydrate metabolism and Carbon cycle Glucose is an energy source in most life forms.

• Virtually every reaction in a living cell requires an enzyme to lower the activation energy of the reaction.

• The resulting molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than thirty) are called peptides or polypeptides.

• The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin
  so much that it results in sickle-cell disease.

• The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula
  CnH2nOn, where n is at least 3).

• This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton,
  and then an amino group is added, often via transamination.

• Some amino acids have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter.

• The side chain “R” is different for each amino acid of which there are 20 standard ones.

• [6] They provide the structure of cells and perform many of the functions associated with life.

• In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid’s amino group to the carbon of the other’s carboxylic
  acid group.

• [25] DNA structure (1D65)[26] It was once generally believed that life and its materials had some essential property or substance (often referred to as the “vital principle”)
  distinct from any found in non-living matter, and it was thought that only living beings could produce the molecules of life.

• The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to
  oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes).

• The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of protein families.

• In addition to the six major elements that compose most of the human body, humans require smaller amounts of possibly 18 more.

• Different macromolecules can assemble in larger complexes, often needed for biological activity.

• Probably the most important proteins, however, are the enzymes.

• • ‘Chemical biology’ seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their
  function.

• This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e.g., in
  humans) or to ethanol plus carbon dioxide (e.g., in yeast).

• An amino acid consists of an alpha carbon atom attached to an amino group, –NH2, a carboxylic acid group, –COOH (although these exist as –NH3+ and –COO− under physiologic
  conditions), a simple hydrogen atom, and a side chain commonly denoted as “–R”.

• By lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more;[13] a reaction that would normally take over 3,000 years to complete spontaneously
  might take less than a second with an enzyme.

• Some argued that the beginning of biochemistry may have been the discovery of the first enzyme, diastase (now called amylase), in 1833 by Anselme Payen,[12] while others considered
  Eduard Buchner’s first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts in 1897 to be the birth of biochemistry.

• In order to determine whether two proteins are related, or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods.

• Gluconeogenesis[edit] Main article: Gluconeogenesis In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive
  enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate.

• Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid).

• The same reaction can take place between carbons 1 and 5 to form a molecule with a 6-membered ring, called glucopyranose.

• These molecules tend to be used as markers and signals, as well as having some other uses.

• Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).

• Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids.

 

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