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Common Functional Groups

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Common Functional Groups

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common functional groups in biochemistry

These functional groups define common molecules, compounds, and reactions in biochemistry, including biochemical polymers such as proteins, DNA and carbohydrates.

FOUR GROUPS

Individual molecules affiliated with each of these groups

Carbon-oxygen groups

These functional groups are so ubiquitous that they are responsible for almost all biochemical reactions.

  • Alcohols
  • Aldehydes
  • Ketones
  • Carboxylic Acids
  • Ethers
  • Acid Anhydrides

Carbon-nitrogen groups

Amines are most notably involved in primary protein structure, which is the most basic structure of proteins.

  • Amino groups (primary amines)
  • Quaternary amines

Carbon-sulfur groups

Carbon-sulfur linkages are integral to the complex structure of proteins and are necessary for proper protein folding.

  • Sulfhydryl groups
  • Disulfides

Esters & Amides

These functional groups comprise many of the bonds that make up complex molecules within us, including fats, nucleic acids, and proteins.

  • Esters
  • Thioesters
  • Phosphoesters
  • Amides

Carbon-oxygen groups

Alcohols

  • The alcohol functional group is the simplest of the carbon-oxygen functional groups.
  • "R" represents carbon chains attached to the functional group. We connect an R to an OH.

Alcohol groups are found on sugars and take part in both ring-forming reactions and the condensation reactions that create biological polymers such as proteins, carbohydrates, and nucleic acids.

Aldehydes

  • We draw a carbon double-bonded to an oxygen and single bonded to a hydrogen. And we add an R as the fourth bond on this carbon atom.

Aldehyde groups are commonly found on monosaccharides and because they are highly reactive, participate in their ring-forming reactions. Many fragrances are aldehydes, as such they are found in many essential oils and other scents.

Ketones

  • We draw a carbon double-bonded to an oxygen atom and single-bonded to R groups on either side.

-Ketone groups are also found on simple sugars and participate in their ring-forming reaction because they are reactive.

-As a clinical correlate, ketosis occurs when ketone bodies are present in the blood, and may be caused by fasting, hypoglycemia, congenital disorders of metabolism, or a ketogenic diet like the Atkins diet. Ketoacidosis is an extreme version of ketosis and may be toxic because it lowers the pH of the blood significantly.

Carboxylic acids

  • We draw a carbon double-bonded to an oxygen and single bonded to an OH group. R is the fourth bond on the carbon atom.

Carboxylic acids are an important part of amino acid structure and participate in the formation of peptide bonds, which create primary protein structure, the most basic protein structure.

Ethers

  • We draw an R connected to an oxygen atom, which is connected to another R group, for the general formula R-O-R.

Ether bonds connect sugars to each other to form more complex carbohydrates such as starch, glycogen and cellulose, all of which are complex energy stores for the body.

Acid anhydride

  • We draw a carbon, double-bonded to an oxygen and single bonded to another oxygen atom.
  • To the single-bonded oxygen atom, we add another carbon double-bonded to an oxygen.
  • We add R groups on either side so that each carbon has four bonds.

Acid anhydrides are quite reactive. Notable acid anhydrides include ATP, the energy currency of the cell ands 1,3 bisphosphoglycerate, an intermediate formed in glycolysis, which is commonly known for its role in energy release but also has significant roles in numerous other biochemical processes.

Carbon-nitrogen functional groups

We include two types of amines: the simplest and the most complex.

Amino group (the simplest form of amine)

  • We draw an R connected to an NH2 group.
    -This is also called a primary amine, because it is a nitrogen atom with a single R group attached.

-Amino groups are an important part of amino acid structure and participate in the formation of peptide bonds. Many neurotransmitters, including epinephrine, dopamine, serotonin and histamine are also amines.

-As a clinical correlate, many pharmaceutical drugs and illicit drugs are actually amines that interfere with natural neurotransmitters, such as ephedrine and amphetamine. In addition, amines can be relatively easily converted from one amine to another, and for this reason, Sudafed, which contains pseudoephedrine (one of the key components of the illicit drug "crystal meth") is now a regulated pharmaceutical.

Quaternary amine (the most complex amine)

  • We draw a nitrogen with four R groups bound to it.
  • We show that the nitrogen atom has a positive charge.
    -This type of functional group is called a quaternary ammonium compound because the nitrogen atom has four attachments.

-Quaternary amines are commonly used as antimicrobials.

  • Primary amines have one R group and quaternary amines have four.
    -Keeping with this convention, secondary amines have two R groups (and one hydrogen atom) and tertiary amines have three R groups (and no hydrogen atoms).

Carbon-sulfur functional groups

Sulfhydryl group (Thiols)

  • We connect an R to an SH.
    Sulhydryls are also known as thiols, and are the sulfur analogs of alcohols.

Sulfhydrl groups are integral to enzyme function; they are in enzyme active sites and contribute to catalytic activity.

They are part of many cofactors, including coenzyme A, which is important in fatty acid biosynthesis and the Krebs cycle.

Disulfides

  • Two sulfhydryl groups may react to form disulfide linkages.
  • We connect an R to a sulfur, which itself is connected to a sulfur, which is connected to an R.

Disulfides are important in both the tertiary and quaternary structure of proteins, which give them their 3-dimensional structure and functional ability. Heavy metals, such as zinc, cadmium, lead and mercury have a high affinity for sulfhydryls and disulphides; thus, they can disrupt disulfide bonds and deform proteins, which results in heavy metal poisoning: a potentially life-threatening condition.

Esters (& Amides)

Comprise many of the types of bonds found in the body.

Ester

  • We draw C double-bond O, with an R group and another oxygen attached to the carbon and another R group attached to that oxygen atom.
    Esters are formed when carboxylic acids and alcohols react, and include glycerides and fats.

Esters are also major components of many scents and odors (as are aldehydes).

Variations of esters: thioesters, phosphoesters, and amides.

Thioester

  • The sulfur variant of an ester
    It is an ester with a sulfur atom in place of the single-bonded oxygen.

Thioesters are intermediates in a number of biosynthetic reactions, including the formation and degradation of fatty acids and steroids. The most commonly known thioester is acetyl CoA, the ester form of coenzyme A, which plays a major role in the Krebs cycle (as does coenzyme A, described previously).

Phosphoester

  • The phosphorus variant of ester
    It includes a phosphorous atom instead of carbon. We draw a phosphorus (P) with four attachments: a double-bonded oxygen, two alcohol groups, and an oxygen. We add an R group as the second bond of the oxygen atom.

Phosphoesters are most commonly found in the body as phosphodiesters meaning that instead of one of the alcohol groups, there is another O-R bond. Phosphodiesters are the bonds that link bases together to form nucleic acids (DNA and RNA).

Amides

  • The nitrogen variant of an ester.
    Draw a C double-bond O. Add an N bound to the carbon and an R bound to the N. As the third bond on nitrogen, add a hydrogen, and as the fourth bond on carbon add another R group.

Amide bonds are also called peptide bonds, because they are the bonds that join amino acids together in primary protein structure, the most basic structure of proteins. They are formed by the reaction of amines and carboxylic acids.

Full-Length Text

  • Here we will learn the common functional groups in biochemistry and some of their functional roles.
  • Denote that these functional groups define common molecules, compounds, and reactions in biochemistry, including biochemical polymers such as proteins, DNA and carbohydrates.
  • Denote that we will learn the following four groups:
    • Carbon-oxygen groups.
    • Carbon-nitrogen groups.
    • Carbon-sulfur groups.
    • Esters & amides.

Next, let's list the individual molecules that are affiliated with each of these groups.

  • Within the Carbon-oxygen group are:
    • Alcohols
    • Aldehydes
    • Ketones
    • Carboxylic Acids
    • Ethers and
    • Acid Anhydrides

These functional groups are so ubiquitous that they are responsible for almost all biochemical reactions.

  • Our second category of functional group is Carbon-Nitrogen Groups, including
    • Amino groups (primary amines) and
    • Quaternary Amines
    • Amines are most notably involved in primary protein structure, which is the most basic structure of proteins.
  • The next set of functional groups is Carbon-Sulfur Groups
    • Sulfhydryl groups and
    • Disulfides
    • Carbon-sulfur linkages are integral to the complex structure of proteins and are necessary for proper protein folding.
  • The fourth category of functional group is Esters & Amides, which are
    • Esters
    • Thioesters
    • Phosphoesters and
    • Amides

These functional groups comprise many of the bonds that make up complex molecules within us, including fats, nucleic acids, and proteins.

Now that we've established the molecules and major functions of these four main groups: carbon-oxygen; carbon-nitrogen; carbon-sulfur; esters & amides, let's draw them out, so we can get a better understanding of their chemistry.

  • Let's start with groups that have carbon-oxygen bonds.
    • Be aware that will use the letter "R" to represent carbon chains attached to the functional group, as needed.
  • First draw the alcohol functional group; it is the simplest of the carbon-oxygen functional groups.
    • Connect an R to an OH.
    • Write that alcohol groups are found on sugars and take part in both ring-forming reactions and the condensation reactions that create biological polymers such as proteins, carbohydrates and nucleic acids.

Next, let's draw the aldehyde functional group.

  • Draw a carbon double-bonded to an oxygen and single bonded to a hydrogen.
    • Add an R as the fourth bond on this carbon atom.
    • Write that aldehyde groups are commonly found on monosaccharides and because they are highly reactive, participate in their ring-forming reactions.
    • Many fragrances are aldehydes, as such they are found in many essential oils and other scents.
  • Next, draw the ketone functional group, a carbon double-bonded to an oxygen atom and single-bonded to R groups on either side.
    • Write that ketone groups are also found on simple sugars and participate in their ring-forming reaction because they are reactive.
    • As a clinical correlate, ketosis occurs when ketone bodies are present in the blood, and may be caused by fasting, hypoglycemia, congenital disorders of metabolism, or a ketogenic diet like the Atkins diet. Ketoacidosis is an extreme version of ketosis and may be toxic because it lowers the pH of the blood significantly.
  • Now draw a carboxylic acid as follows: draw a carbon double-bonded to an oxygen and single bonded to an OH group.
    • R is the fourth bond on the carbon atom.
    • Write that carboxylic acids are an important part of amino acid structure and participate in the formation of peptide bonds, which create primary protein structure, the most basic protein structure.
  • Next, draw an ether functional group, which is an R connected to an oxygen atom, which is connected to another R group, for the general formula R-O-R.
    • Write that ether bonds connect sugars to each other to form more complex carbohydrates such as starch, glycogen and cellulose, all of which are complex energy stores for the body.

Finally, draw our last carbon-oxygen functional group: acid anhydride.

  • Draw a carbon, double-bonded to an oxygen and single bonded to another oxygen atom.
  • Now, to the single-bonded oxygen atom, add another carbon double-bonded to an oxygen.
    • Add R groups on either side so that each carbon has four bonds.
    • Write that acid anhydrides are quite reactive.
    • Notable acid anhydrides include ATP, the energy currency of the cell ands 1,3 bisphosphoglycerate, an intermediate formed in glycolysis, which is commonly known for its role in energy release but also has significant roles in numerous other biochemical processes.
    • We will learn more about this elsewhere.

Now, let's draw our carbon-nitrogen functional groups. We will draw two types of amines: the simplest and the most complex.

Begin with the simplest: an amino group.

  • Draw an R connected to an NH2 group.
    • This is also called a primary amine, because it is a nitrogen atom with a single R group attached.
    • Write that amino groups are an important part of amino acid structure and participate in the formation of peptide bonds.
    • Many neurotransmitters, including epinephrine, dopamine, serotonin and histamine are also amines.
    • As a clinical correlate, many pharmaceutical drugs and illicit drugs are actually amines that interfere with natural neurotransmitters, such as ephedrine and amphetamine.
    • In addition, amines can be relatively easily converted from one amine to another, and for this reason, Sudafed, which contains pseudoephedrine (one of the key components of the illicit drug "crystal meth") is now a regulated pharmaceutical.

Now, let's draw the most complex amine: a quaternary amine.

  • Draw a nitrogen with four R groups bound to it.
  • Show that the nitrogen atom has a positive charge.
    • This type of functional group is called a quaternary ammonium compound because the nitrogen atom has four attachments.
    • Write that quaternary amines are commonly used as antimicrobials.
    • Primary amines have one R group and quaternary amines have four.
    • Keeping with this convention, secondary amines have two R groups (and one hydrogen atom) and tertiary amines have three R groups (and no hydrogen atoms).

Next, we will draw carbon-sulfur functional groups, including sulfhydryl and disulfide groups.

Let's begin with the sulfhydryl group.

  • Connect an R to an SH.
    • Write that sulhydryls are also known as thiols, and are the sulfur analogs of alcohols.
    • Sulfhydrl groups are integral to enzyme function; they are in enzyme active sites and contribute to catalytic activity.
    • Thiols are part of many cofactors, including coenzyme A, which is important in fatty acid biosynthesis and the Krebs cycle.
    • Two sulfhydryl groups may react to form disulfide linkages, which we will draw next.
  • Connect an R to a sulfur, which itself is connected to a sulfur, which is connected to an R.
    • Write that disulfides are important in both the tertiary and quaternary structure of proteins, which give them their 3-dimensional structure and functional ability.
    • As a clinical correlate, write that heavy metals, such as zinc, cadmium, lead and mercury have a high affinity for sulfhydryls and disulphides; thus, they can disrupt disulfide bonds and deform proteins, which results in heavy metal poisoning: a potentially life-threatening condition.

Now, let's draw our last set of functional groups: esters and amides, which comprise many of the types of bonds found in the body.

  • Draw the general form of an ester as: C double-bond O, with an R group and another oxygen attached to the carbon and another R group attached to that oxygen atom.
    • Write that esters are formed when carboxylic acids and alcohols react, and include glycerides and fats.
    • Interestingly, esters are also major components of many scents and odors (as are aldehydes).

Next, let's draw some variations of esters: thioesters, phosphoesters, and amides.

  • First, draw a thioester, which is the sulfur variant of an ester; it is an ester with a sulfur atom in place of the single-bonded oxygen.
    • Write that thioesters are intermediates in a number of biosynthetic reactions, including the formation and degradation of fatty acids and steroids.
    • The most commonly known thioester is acetyl CoA, the ester form of coenzyme A ,which plays a major role in the Krebs cycle (as does coenzyme A, described previously).

Next, draw a phosphoester, which is the phosphorus variant of ester; it includes a phosphorous atom instead of carbon.

  • Draw a phosphorus (P) with four attachments: a double-bonded oxygen, two alcohol groups, and an oxygen.
  • Add an R group as the second bond of the oxygen atom.
    • Write that phosphoesters are most commonly found in the body as phosphodiesters meaning that instead of one of the alcohol groups, there is another O-R bond.
    • Phosphodiesters are the bonds that link bases together to form nucleic acids (DNA and RNA).

Finally, let's draw the amide functional group, the nitrogen variant of an ester.

  • Once again, draw a C double-bond O.
  • Add an N bound to the carbon and an R bound to the N.
  • As the third bond on nitrogen, add a hydrogen, and as the fourth bond on carbon add another R group.
    • Write that amide bonds are also called peptide bonds, because they are the bonds that join amino acids together in primary protein structure, the most basic structure of proteins.
    • They are formed by the reaction of amines and carboxylic acids.