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Amino acids, peptides, and proteins
Mar. 4th, 2015 09:51 pmamine
amino acid
residue
preotein
hydrolysis
alpha-amino acid
carboxyl
amino group
alpha-carbon
R-groups
additional carbons
heterocyclic
glyceraldehyde
racemic
aliphatic
zwitterion
peptide bond
amide linkage
dehydration
alpha-carboxyl group
alpha-amino group
amino-terminal (N-terminal)
isoelectric
multisubunit
oligomeric
protomer
conjugated proteins
prosthetic group
lipoproteins
glycoproteins
metalloproteins
An amine is a functional group characterized by three R groups (perhaps identical, perhaps not) and a nitrogen atom.
This means N-terminal and amine/amino terminal are the same.
Amine: R-NH2
Amide: R-CO-NH2
An amino acid is a carbon atom (called the alpha carbon) bonded to 4 different groups: an amine group, an R group (also called a side group), a carboxylic acid (COOH) group, and a hydrogen atom.
The fact that there are 4 distinct groups means it's chiral. The amino acids found in real life are L-stereoisomers.
When amino acids are combined, they lose the elements of water. This is a condensation reaction.
To break them up, add water (hydrolyze them). Because they lose the elements of water, they're not pure amino acids. They're amino acid residues.
They join up end to end, carboxyl to amino. This is called peptide bonding. Each peptide chain has a C-terminal end and an N-terminal end.
The amine group in most cases is H3N. Carboxyl and the hydrogen atom are the same. That means it's the R group of the amino acid that makes the difference.
The R group thus determines the properties of each amino acid. They can be broken up into these categories:
Nonpolar, aliphatic
Aromatic
Polar, uncharged
Positively charged
Negatively charged
Aromatic amino acids have a characteristic hydrocarbon ring. Aliphatic do not.
Polar are more hydrophilic. Nonpolar are more hydrophobic. Aromatic are relatively nonpolar.
Positively charged groups have a NHx group that tends to be positive. Histidine has a tendency to lose electrons, such that a significant number of histidine amino acids tend to be ionized.
Negatively charged groups have a second carboxyl group. The alpha-carboxyl group of all the amino acids is negatively charged.
Imino acid is any molecule that contains both imino (>C=NH) and carboxyl (-C(= O)-OH) functional groups. Imino acids are related to amino acids, which contain both amino (-NH2) and carboxyl (-COOH) functional groups, differing in the bonding to the nitrogen.
Proteins can also contain less common amino acid residues. These are caused by modifying one of the 20 common amino acid residues, mostly post-synthetic. Sometimes during synthesis, though.
An amino acid residue has a carboxyl group (COO-) and an amine group (NH3+). The carboxyl residue can accept a hydrogen atom, making it a proton acceptor (base). The amine group can donate a hydrogen atom, making it a proton donor (acid). This can be called a zwitterion, an amphoteric electrolyte, or an ampholyte for short. It is a diprotic acid when fully protonated, and can yield 2 protons.
The titration curve of a diprotic acid looks like two regular titration curves attached at the end. At very low pH, the amino acid is fully protonated. Then COOH loses its proton. Then NH33+ loses its proton. This means it has two regions of buffering power.
This also means there's a relationship between the net electric charge of the amino acid and the pH of the solution. The characteristic pH at which the net electric charge is zero is called the isoelectric point or isoelectric pH, designated pI.
All amino acids with a single alpha-amino group, a single alpha-carboxyl group, and an R group that does not ionize have titration curves resembling that of glycine. Amino acids with an ionizable R group have more complex titration curves, with three stages corresponding to the three possible ionization steps.
Only histidine has an R group (pKa = 6.0) providing significant buffering power near the neutral pH usually found in the intracellular and extracellular fluids of most animals and bacteria.
Most proteins have a single polypeptide chain. Some have multiple chains with noncovalent links. These are called multisubunit proteins. Even fewer have polypeptides linked covalently through disulfide bonds. If at least two of the polypeptide chains are identical, then the protein is called oligomeric.
Most proteins are composed entirely of amino acid residues. Conjugate proteins have non-amino components, like lipids, sugars, or metals.
Lipids are small hydrophobic or amphipathic biological molecules.
Structurally, we define carbohydrates as polyhydroxy aldehydes or ketones.
Polyhydroxy: containing more than one OH group.
Aldehyde: RCHO
Ketone: RCOR
Monosaccharides are the simplest carbohydrates. They contain between 3 and 8 carbon atoms and have only one aldehyde or ketone group.
Polymorphic: a protein that can carry out the same function with substitutions in its primary structure.
Enzymes called proteases catalyze the hydrolytic cleavage of peptide bonds. Some proteases cleave only the peptide bond adjacent to particular amino acid residues.
We compare the sequences of amino acids in proteins and the gene sequences to figure out how far 2 organisms are evolutionarily. But substitutions of amino acids are not random. Amino acids on which the function of the protein depends are less likely to be substituted, and are likely to tolerate substitution, if any, by a limited number of amino acids.
If you're going to compare proteins, best to start with families of proteins that were necessary for early viable life, to reduce the chances that they were introduced later by lateral gene transfer (and thus do not reflect vertical evolutionary mechanisms).
Related proteins that perform related functions in different organisms are called homologs. Orthologs are in different species. Paralogs are in the same species.
When you're comparing amino acids, and trying to come up with a model, substitutions with similar chemical properties get better scores.
amino acid
residue
preotein
hydrolysis
alpha-amino acid
carboxyl
amino group
alpha-carbon
R-groups
additional carbons
heterocyclic
glyceraldehyde
racemic
aliphatic
zwitterion
peptide bond
amide linkage
dehydration
alpha-carboxyl group
alpha-amino group
amino-terminal (N-terminal)
isoelectric
multisubunit
oligomeric
protomer
conjugated proteins
prosthetic group
lipoproteins
glycoproteins
metalloproteins
An amine is a functional group characterized by three R groups (perhaps identical, perhaps not) and a nitrogen atom.
This means N-terminal and amine/amino terminal are the same.
Amine: R-NH2
Amide: R-CO-NH2
An amino acid is a carbon atom (called the alpha carbon) bonded to 4 different groups: an amine group, an R group (also called a side group), a carboxylic acid (COOH) group, and a hydrogen atom.
The fact that there are 4 distinct groups means it's chiral. The amino acids found in real life are L-stereoisomers.
When amino acids are combined, they lose the elements of water. This is a condensation reaction.
To break them up, add water (hydrolyze them). Because they lose the elements of water, they're not pure amino acids. They're amino acid residues.
They join up end to end, carboxyl to amino. This is called peptide bonding. Each peptide chain has a C-terminal end and an N-terminal end.
The amine group in most cases is H3N. Carboxyl and the hydrogen atom are the same. That means it's the R group of the amino acid that makes the difference.
The R group thus determines the properties of each amino acid. They can be broken up into these categories:
Nonpolar, aliphatic
Aromatic
Polar, uncharged
Positively charged
Negatively charged
Aromatic amino acids have a characteristic hydrocarbon ring. Aliphatic do not.
Polar are more hydrophilic. Nonpolar are more hydrophobic. Aromatic are relatively nonpolar.
Positively charged groups have a NHx group that tends to be positive. Histidine has a tendency to lose electrons, such that a significant number of histidine amino acids tend to be ionized.
Negatively charged groups have a second carboxyl group. The alpha-carboxyl group of all the amino acids is negatively charged.
Imino acid is any molecule that contains both imino (>C=NH) and carboxyl (-C(= O)-OH) functional groups. Imino acids are related to amino acids, which contain both amino (-NH2) and carboxyl (-COOH) functional groups, differing in the bonding to the nitrogen.
Proteins can also contain less common amino acid residues. These are caused by modifying one of the 20 common amino acid residues, mostly post-synthetic. Sometimes during synthesis, though.
An amino acid residue has a carboxyl group (COO-) and an amine group (NH3+). The carboxyl residue can accept a hydrogen atom, making it a proton acceptor (base). The amine group can donate a hydrogen atom, making it a proton donor (acid). This can be called a zwitterion, an amphoteric electrolyte, or an ampholyte for short. It is a diprotic acid when fully protonated, and can yield 2 protons.
The titration curve of a diprotic acid looks like two regular titration curves attached at the end. At very low pH, the amino acid is fully protonated. Then COOH loses its proton. Then NH33+ loses its proton. This means it has two regions of buffering power.
This also means there's a relationship between the net electric charge of the amino acid and the pH of the solution. The characteristic pH at which the net electric charge is zero is called the isoelectric point or isoelectric pH, designated pI.
All amino acids with a single alpha-amino group, a single alpha-carboxyl group, and an R group that does not ionize have titration curves resembling that of glycine. Amino acids with an ionizable R group have more complex titration curves, with three stages corresponding to the three possible ionization steps.
Only histidine has an R group (pKa = 6.0) providing significant buffering power near the neutral pH usually found in the intracellular and extracellular fluids of most animals and bacteria.
Most proteins have a single polypeptide chain. Some have multiple chains with noncovalent links. These are called multisubunit proteins. Even fewer have polypeptides linked covalently through disulfide bonds. If at least two of the polypeptide chains are identical, then the protein is called oligomeric.
Most proteins are composed entirely of amino acid residues. Conjugate proteins have non-amino components, like lipids, sugars, or metals.
Lipids are small hydrophobic or amphipathic biological molecules.
Structurally, we define carbohydrates as polyhydroxy aldehydes or ketones.
Polyhydroxy: containing more than one OH group.
Aldehyde: RCHO
Ketone: RCOR
Monosaccharides are the simplest carbohydrates. They contain between 3 and 8 carbon atoms and have only one aldehyde or ketone group.
Polymorphic: a protein that can carry out the same function with substitutions in its primary structure.
Enzymes called proteases catalyze the hydrolytic cleavage of peptide bonds. Some proteases cleave only the peptide bond adjacent to particular amino acid residues.
We compare the sequences of amino acids in proteins and the gene sequences to figure out how far 2 organisms are evolutionarily. But substitutions of amino acids are not random. Amino acids on which the function of the protein depends are less likely to be substituted, and are likely to tolerate substitution, if any, by a limited number of amino acids.
If you're going to compare proteins, best to start with families of proteins that were necessary for early viable life, to reduce the chances that they were introduced later by lateral gene transfer (and thus do not reflect vertical evolutionary mechanisms).
Related proteins that perform related functions in different organisms are called homologs. Orthologs are in different species. Paralogs are in the same species.
When you're comparing amino acids, and trying to come up with a model, substitutions with similar chemical properties get better scores.
