Biochemistry
Carbohydrates, lipids, proteins, and the nucleic acids
All built from simple precursorsHow they are put together is the
key to their activity
Carbohydrates
Glucose – most common•Assembled one way = starch – our
main E source
•Assembled a different way = cellulose – main ingredient in wood and most plentiful organic substance on earth!
Proteins
Constructed from 20 different kinds of amino acids• Great structural
and functional variability
Types of Proteins
Collagen – major component of tendons, skin, and bones
Hemoglobin – transports O2 in the blood stream
Enzymes – catalyst that speeds up rxn’s in all living organisims
Biochem History Until early 19th century, it was thought that
living things had something called “vital forces” that was unique to only living things.
1828 – German Scientist Freidrich Wöhler synthesized Urea from ammonium cyanate (a mineral)• Urea is a waste product of animal metabolism
• NH4OCH H2NCONH2
Current Realizations
Any compound that exists in a living organism can be synthesized in a lab
Rxn’s of biomolecules depend on the functional groups
Functional Groups
Table of functional groupsAlso, carbon containing
derivatives of phosphoric acid [esters and anhydrides of phosphoric acid ADP, ATP
Amino Acids
20 A.A’s - usually found in proteinsGeneral structure in common with
variations in side chainsAmino acids contins amino groups
(RNH2, R2NH, R3N) and a carbonyl group (RCOOH)
Amino Acids
Both groups are bonded to the same carbon atom and labeled α carbon = the one next to the carbonyl group
Amino Acids
Carbon atoms in the R group are labeled using the Greek alphabet starting w/the C adjacent to the carbonyl group
α β γ δ ε
Alpha beta gama delta epsilon
MonosaccharidesCarbohydrates have the general formula
Cn(H2O)n
• All carbohydrates are not just hydrates of water
Simple sugars (monosaccharides) are cmpds that contain a single carbonyl group & 2 or more hydroxyl groups• Either polyhydroxyaldehydes or
polyhydroxyketones
MonosaccharidesThe ones that contain aldehydes=aldasesThe ones that conatin ketones = ketoses6 Carbon sugars are most abundant in
nature but 2, 5 carbon sugars (ribose and deoxyribose) occur in the structures of RNA and DNA
The Structure of Nucleic Acid Monomers
The 2 kinds of nucleic acids are DNA and RNA
There are diffs and sims b/t the twoThey are macromolecules (very large
molecules) formed by polymerizing monomer units (nucleotides = monomer units of nucleic acids)
The Structure of Nucleic Acid Monomers
Nucleotides have a base, a sugar, and a phosphoric acid residue covalently bonded together Nucleic acids can be hydrolyzed to
their constituent nucleotides by acids, bases, or enzymes
The Structure of Nucleic Acid Monomers
The main distinction between the nucleotide monomers of DNA and RNA is the sugar portionDNA = deoxyribose
RNA = ribose
The Structure of Nucleic Acid Monomers
Nucleic acid bases (aka nucleobases) = nitrogen-containing aromatic compounds that fall into 2 categories
1. Pyrimidines – cytosine (in RNA&DNA)/thymine (DNA in rarely in RNA)/uracil (only in RNA)
2. Purines adenine (RNA/DNA)/guanine (RNA/DNA)
Lipid Examples
Insoluble in H2O and soluble in organic solvents
Glycerol esters of fatty acids (long chain carbox.acids) & derivatives of these esters are imoportant examples of lipids
Another example = steroids
Amino AcidsWe know that proteins are long chain of
amino acids linked together by peptide bonds between a + charged N (amino) group at one end and a – charged carbonyl group at the other end.• Along the chain is a series of side chains
that are different for each of the 20 amino acids
Amino AcidsDipeptide = 2 amino acidsTripeptide = 3The sequence of the amino acids is
most important• There are 8,000 ways to arrange them
• In a protein chain of 100 amino acids, there are more ways to arrange them than there are atoms in the universe
Of all the possible AA’s, only 20 are usually found in proteins!
General structure of an AA involves an amino group, a carboxyl group & both are bonded to the α C• The α C is also bonded to a H
and an R group (side chain)
• The R group determines the
identity of the AA
Amino AcidsOne of the most important
properties of a AA is its 3-d shape (stereochemistry)• Mirror images that are superimposable = achiral
• Mirror images that aren’t superimposable = chiral
• Many important molecules are chiral
• Frequently, chiral center is a C atoms bonded to 4 different groups
Amino AcidsGlycine is the only AA that doesn’t have
a chiral center (it’s R group is a single H, giving it 2H’s out of 4 groups)
All other AA have
2 stereoisomers
Amino AcidsIn biochemistry, we don’t use R&S
designations, instead D & L are usedL (laevus) and D (dexter) meaning left
and rightFor AA, D=amino group on right side,
L = amino group on the Left side
Structures and Properties of the Individual AA’s
R group (thus the amino acids) are classified according to several criteria (two very important)
Polar or nonpolar nature of the side chain
Presence of an acidic or basic group in the side chain
Group 1 – AA Nonpolar side chainsAlanine, valine, leucine, isoleucine,
proline, phenylalanine, tryptophan, methionine
Group 2 - AA
With electrically neutral polar side chains (neutral pH)
Serine, threonine, tyrosine, cysteine
Group 3 – AA - carboxyl groups in their side chains
Glutamic acid and aspartic acidCarbonyl group can lose H+ (forming
carboxylate ion) so they are – charged at neutral pH
They frequently bond to –NH2 to form side chain amide groups yielding analogous AA glutamine & asparagine
Others
Some other AA’s are known to occur in some, but not all proteins
Derived from common AA and are produced by the modification of the parent AA after the protein is synthesized by the organism
OthersHydroxyproline and hydroxylysine have
extra –OH groups on the side chainThyroxine (from tyrosine) has an extra
Iodine containing aromatic group on the side chain (found only in thyroglobuin, a protein in the thyroid)
The Peptide Bond AA are linked by covalent bonds joining
the α – carboxyl group with the α-amino group) splitting out an H2O
After the H2O elimination, the groups are linked amino acids residues
A bond formed this way is called a peptide bond (aka: amide bond)