lipid3.htm:
The glycerol and fatty acids are oriented such that the hydroxyl and acid groups are close to each
other.
In an enzyme-catalyzed reaction, the hydroxyl oxygens of glycerol form a bond to the carboxyl
carbons of the fatty acids, releasing water in the process.
Ester bonds are left between glycerol and the fatty acids.
dna13.htm:
The 5' group of a nucleotide triphosphate is held close to the free 3' hydroxyl group of a
nucleotide chain.
The 3' hydroxyl group forms a bond to the phosphorus atom of the free nucleotide closest to the
5' oxygen atom. Meanwhile, the bond between the first phosphorus atom and the oxygen atom
linking it to the next phosphate group breaks.
A new phosphodiester bond joins the two nucleotides. A pyrophosphate group has been
liberated.
The pyrophosphate group is hydrolyzed, releasing energy and driving the reaction forward to
completion.
dna24.htm:
Methionine
Glutamate
Arginine
Phenylalanine
Stop
dna26.htm:
mRNA binds to the ribosome. The start codon resides in the P site of the ribosome and binds a
tRNA with methionine bound to it. The second codon resides in the A site and binds a tRNA
with bound glutamate.
The ribosome catalyzes the formation of a peptide bond between the amino acids in the P and A
sites.
The dipeptide moves to the P site and another tRNA brings the next amino acid into the A site.
Another peptide bond is formed between the second and third amino acids.
This process continues until a stop codon on the mRNA enters the A site. Then the mRNA and
the new protein are released from the ribosome and the protein is free to fold into its native
structure.
prot15.htm:
Two amino acids are brought together. The acid group of the first is close to the amine group of
the second.
A water molecule is eliminated, leaving a bond between the acid carbon of the first amino acid
and the amine nitrogen of the second.
The peptide bond is left between the two amino acids.
prot26.htm:
Hydrophobic groups must be kept away from water, while polar groups must be exposed to it as
much as possible. Thus the interior of the protein is almost entirely hydrophobic while the
exterior is more polar.
The polar main-chain carbonyl and amine groups present in both polar and hydrophobic amino
acids are kept happy by secondary structure elements such as  helices or  sheets.
There is almost no free space in the interior of the protein. The various sizes and shapes of the
hydrophobic amino acids ensure that every space is filled.
As in the interiors of water-soluble proteins, the polar hydrogen-bonding main-chain carbonyl
and amine groups have to be kept satisfied by the formation of either  helices or  sheets.
Side chains facing the lipids are usually hydrophobic; side chains facing other membrane spans
or the aqueous space on either side of the membrane can be polar.
enzyme9.htm:
The hydrated magnesium ion has two functions. First, one of its waters of hydration binds to one
of the oxygen atoms of the phosphate group, holding it in the proper orientation. Second, the
environment of the active site lowers the pKa of another water of hydration enough that it can
lose a proton.
The negatively charged hydroxyl group removes a proton from the 2' hydroxyl group of cytosine
17. This oxygen then starts to form a bond to the phosphorus atom of the phosphate group.
This is the transition state. Five oxygen atoms are arranged in a triangular bipyramid around the
phosphorus atom. A bond is being formed between the 2' oxygen of cytosine 17 and the
phosphorus atom. At the same time a bond is being broken between the phosphorus atom and the
hydroxyl oxygen of the next nucleotide, adenine 1.1.
Cytosine 17 is left with a 2'-3' cyclic phosphate group. The 5' nucleotide recovers a proton from
the aqueous environment, completing a hydroxyl group. The reaction products diffuse away from
the active site, leaving the ribozyme free to bind its substrate and complete another reaction
cycle.