Podcast
Questions and Answers
What are organohalogen compounds?
What are organohalogen compounds?
Organic compounds that contain one or more halogen atoms
What are haloalkanes also known as?
What are haloalkanes also known as?
The generic formula of an alkyl halide is R-X, where R is a generic ______ group and X is a generic halide.
The generic formula of an alkyl halide is R-X, where R is a generic ______ group and X is a generic halide.
alkyl
Alcohols are strong bases.
Alcohols are strong bases.
Signup and view all the answers
Match the following functional groups and their generic formulas:
Match the following functional groups and their generic formulas:
Signup and view all the answers
What are the two parts of organic molecules?
What are the two parts of organic molecules?
Signup and view all the answers
Functional groups define the chemical and physical properties of organic compounds.
Functional groups define the chemical and physical properties of organic compounds.
Signup and view all the answers
What is the simplest alkane?
What is the simplest alkane?
Signup and view all the answers
Alkanes are hydrocarbons with a carbon-carbon ______ bond.
Alkanes are hydrocarbons with a carbon-carbon ______ bond.
Signup and view all the answers
Match the following components with their meanings:
Match the following components with their meanings:
Signup and view all the answers
Which oxidation state indicates that iron has lost two electrons?
Which oxidation state indicates that iron has lost two electrons?
Signup and view all the answers
What is the responsible atom for reversible binding of O2 in heme?
What is the responsible atom for reversible binding of O2 in heme?
Signup and view all the answers
Hemoglobin can bind oxygen reversibly when iron is in the ferric (Fe3+) state.
Hemoglobin can bind oxygen reversibly when iron is in the ferric (Fe3+) state.
Signup and view all the answers
Life-threatening and painful disease caused by sickled erythrocytes is known as ____________.
Life-threatening and painful disease caused by sickled erythrocytes is known as ____________.
Signup and view all the answers
Match the following nitrogenous bases with their corresponding nucleic acid category:
Match the following nitrogenous bases with their corresponding nucleic acid category:
Signup and view all the answers
What is the IUPAC suffix used for naming carboxylic acids?
What is the IUPAC suffix used for naming carboxylic acids?
Signup and view all the answers
What is the functional group in carboxylic acids?
What is the functional group in carboxylic acids?
Signup and view all the answers
Carboxylic acids are generally soluble in water.
Carboxylic acids are generally soluble in water.
Signup and view all the answers
Carboxylic acids can react with alcohols to form ______ and water.
Carboxylic acids can react with alcohols to form ______ and water.
Signup and view all the answers
Match the following with their IUPAC naming:
Match the following with their IUPAC naming:
Signup and view all the answers
Which category of biomolecules are largely composed of nonpolar hydrocarbon functional groups?
Which category of biomolecules are largely composed of nonpolar hydrocarbon functional groups?
Signup and view all the answers
What functional groups are present in proteins?
What functional groups are present in proteins?
Signup and view all the answers
Proteins are polymers of nucleic acids.
Proteins are polymers of nucleic acids.
Signup and view all the answers
A molecule is chiral if it is different from its __________ image.
A molecule is chiral if it is different from its __________ image.
Signup and view all the answers
Match the following terms with their descriptions:
Match the following terms with their descriptions:
Signup and view all the answers
What is the term used for molecules composed of over 50 amino acids?
What is the term used for molecules composed of over 50 amino acids?
Signup and view all the answers
Which sequence of adjacent nucleotides constituting the genetic code determines the insertion of a specific amino acid in a polypeptide chain during protein synthesis?
Which sequence of adjacent nucleotides constituting the genetic code determines the insertion of a specific amino acid in a polypeptide chain during protein synthesis?
Signup and view all the answers
Glycine is the only amino acid among the common amino acids that exhibits optical isomerism.
Glycine is the only amino acid among the common amino acids that exhibits optical isomerism.
Signup and view all the answers
The hydrophobicity of amino acid side chains is critical for the folding of a protein to its native __________.
The hydrophobicity of amino acid side chains is critical for the folding of a protein to its native __________.
Signup and view all the answers
Match the secondary structure of proteins to their corresponding descriptions:
Match the secondary structure of proteins to their corresponding descriptions:
Signup and view all the answers
Study Notes
Organic Compounds and Biochemistry
- Organic molecules have two parts: a carbon backbone that is relatively inert, and one or more functional groups that define the chemical and physical properties of the compound.
- Functional groups are a set of atoms bonded together in a specific way, and molecules with similar functional groups tend to have similar physical and chemical properties.
Functional Groups
- Hydrocarbon functional groups:
- Alkanes: simplest of organic compounds, characterized by carbon-carbon single bonds, and are the carbon backbone for other functional groups.
- Alkenes: unsaturated hydrocarbons with a carbon-carbon double bond, named by adding the suffix "ene" to the parent alkane.
- Alkynes: unsaturated hydrocarbons with a carbon-carbon triple bond, named by adding the suffix "yne" to the parent alkane.
- Aromatic hydrocarbons: contain a benzene ring (C6H6) as part of their structure.
- Functional groups based on water:
- Alcohols: have a generic formula of R-O-H, and are polar at the end with the -OH group.
- Ethers: have a generic formula of R-O-R', and are often used as solvents and protecting groups.
- Phenols: have an -OH attached to one of the carbons of a benzene ring, and are acidic.
- Amines (ammonias):
- Functional groups derived from ammonia (NH3), with a generic formula of R3N3.
- Can form hydrogen bonds and tend to be more soluble in water than many other functional classes.
- Can form salts in which the amine group has a positive charge (is ionic) and can form compounds with negative ions.
- Carbonyl functional groups:
- Aldehydes: have an alkyl group and a hydrogen atom bonded to a carbonyl group, and are relatively rare among naturally occurring compounds.
- Ketones: have two alkyl groups bonded to a carbonyl group, and are very common in nature.
Nomenclature and IUPAC Rules
- Hydrocarbon nomenclature:
- Alkanes: named by citing the number of carbons, and are ending with the suffix "-ane".
- Alkenes: named by adding the suffix "ene" to the parent alkane.
- Alkynes: named by adding the suffix "yne" to the parent alkane.
- Functional groups based on water:
- Alcohols: named by adding the suffix "ol" to the name of the parent, and indicate the position of the hydroxyl group with a locant number.
- Ethers: named by citing the two alkyl groups and then adding "ether".
- Phenols: named by citing the benzene ring and the -OH group.
- Amines (ammonias):
- Named by citing the alkyl groups and then adding "amine".
- In the IUPAC system, substituent groups on a nitrogen atom are given a locant N.
- Carbonyl functional groups:
- Aldehydes: named by appending the suffix "al" to the parent name.
- Ketones: named by appending the suffix "one" to the parent name.
Physical Properties and Solubility
- Alkanes: not polar or charged, and are not water-soluble, but are oil or lipid soluble.
- Alkenes: unsaturated hydrocarbons, and are insoluble in water and soluble in oil and fat.
- Alkynes: unsaturated hydrocarbons, and are insoluble in water and soluble in oil and fat.
- Functional groups based on water:
- Alcohols: tend to be more soluble in water than many other functional classes.
- Ethers: often used as solvents and protecting groups.
- Phenols: tend to be more soluble in water than many other functional classes.
- Amines (ammonias):
- Can form hydrogen bonds and tend to be more soluble in water than many other functional classes.
- Carbonyl functional groups:
- Aldehydes and ketones: the carbonyl bond is very polar, and tend to be soluble in water depending on the other parts of the molecule.### Oxidation and Reduction
- Oxidation is the loss of electrons, while reduction is the gain of electrons.
- Oxidation involves increasing the number of bonds to oxygen, which accompanies decreasing the number of bonds to hydrogen.
- Reduction is the opposite of oxidation, where the number of bonds to oxygen decreases or the number of bonds to hydrogen increases.
- The oxidizing power of oxygen makes many oxidation reactions exothermic and thermodynamically favorable processes.
Formation of Acetals and Ketals
- Aldehydes react with alcohols to form hemiacetals and then acetals.
- Ketones react with alcohols to form hemiketals and then ketals.
- Acetal/ketal formation and hydrolysis occur under very mild chemical conditions and do not require large amounts of energy to drive either the forward process or the reverse process.
Oxidation and Reduction: A “reductionist” view
- Oxidation = addition of oxygen or loss of hydrogen or loss of electrons (valence becomes more positive).
- Reduction = addition of hydrogen or loss of oxygen or gain of electrons (valence becomes more negative).
- Reduction of aldehydes/ketones to alcohols is a frequent biochemical reaction, especially in carbohydrate chemistry.
Carboxylic Acids
- The functional group is the carboxyl group, which is a carbonyl group with a hydroxyl group bonded to the carbonyl carbon.
- Carboxylic acids are important intermediates in metabolism, and fatty acids are long-chained carboxylic acids that are used as the principal long-term energy storage molecules.
- The IUPAC rules for naming carboxylic acids append the suffix “oic acid” to the parent name.
- Simplest is methanoic acid, commonly known as formic acid.
- One important reaction of carboxylic acids is their ability to act as acids, with pKa values typically between 4 and 5.
- Conjugate bases of carboxylic acids are named by adding the suffix “oate” to the parent name.
Carboxylic Acids (continued)
- The carboxyl group is intrinsically polar, with partial positive charges on the hydrogen and the carbon and partial negative charges on the oxygens.
- Depending on the rest of the molecule, carboxylic acids are soluble in water.
- Carboxylic acids can easily donate the hydrogen atom attached to the oxygen and are therefore acidic.
- Carboxylic acids can participate in neutralization reactions with inorganic bases, such as NaOH, to form carboxylate salts and water.
- Carboxylic acids can react with alcohols in a neutralization reaction that forms esters and water.
Esters
- Esters are condensation products between acids and alcohols.
- Many esters have a pleasant, fruity odor.
- The functional group binds three fatty acid molecules to a glycerin backbone, forming a triglyceride.
- The IUPAC rules name esters as alkyl alkanoates.
- The portion of the ester derived from the alcohol is named as an alkyl group.
- The portion of the ester derived from the carboxylic acid is named as the conjugate base of that acid.
- Esters have the general formula RCOOR'.
Amides
- Amides are condensation products between carboxylic acids and amines.
- Proteins are the most biologically important example of amides.
- The IUPAC rules name amides by appending the suffix “amide” to the parent name of the carboxylic acid from which the amide is derived.
- If there are substituents on the amide nitrogen, they are given the locant N.
- Carboxylic acids react with amines to form amides.
- This reaction is also a reversible process, so an amide can be torn apart by water back into a carboxylic acid and an amine.
Amides (continued)
- The hydrolysis of amides requires harsher reaction conditions than the hydrolysis of esters.
- Esters in triglycerides bind fatty acids to glycerin as an energy-dense storage molecule called a triglyceride.
- We need to be able to tear the triglycerides back apart to access the chemical energy stored in the fatty acids.
- Proteins are polymers held together by amide bonds.
Review of Isomerism
- Structural isomerism: more than one structure is possible from the same atoms rearranged in a different way.
- Stereoisomerism: configuration differences with the same connections between atoms.
- Optical isomers: present when a molecule has a chiral carbon.
- A chiral carbon is a carbon with 4 different substituents.
- Enantiomers: two molecules that are mirror images of each other.
- Diastereomers: non-mirror image stereoisomers.
Stereoisomers
- If there is a chiral carbon, there are two molecules possible that are mirror images of each other, called enantiomers.
- Enantiomers have the same connections, but they are not superimposable upon each other.
- Two systems of nomenclature for optical isomers – R & S and D & L.
- Biochemists use the D & L nomenclature.
- D stands for dextro – to the right, and L stands for levo – to the left.
- R stands for Rectus meaning Right handed in Latin, and S stands for Sinister meaning Left handed in Latin.
D & L Nomenclature for Optical Isomers
- Biochemical molecules are written with the chiral carbons arranged similarly to glyceraldehyde.
- D-glyceraldehyde rotates polarized light to the right (+), and L-glyceraldehyde rotates polarized light to the left (-).
- Compounds that have the same arrangement as D-glyceraldehyde are called D, and those that have the same arrangement as L-glyceraldehyde are called L.
- Although D and L forms of other biomolecules correspond to the configuration of D- or L- glyceraldehydes, they do not necessarily rotate polarized light in the same direction.
- The direction of rotation of polarized light is designated by a (+) for right and (-) for left.
- Some compounds may have more than one chiral carbon and will have 2 enantiomers per chiral carbon.
- Enantiomers are identical with respect to their chemical properties in ordinary chemical reactions.
- However, binding of enantiomers to enzymes or receptors in the case of drugs may be (or may not be) stereospecific.### Biomolecules
- Organic molecules that are the building blocks of living organisms
- Roughly fall into four categories:
- Carbohydrates or sugars
- Proteins
- Nucleic acids
- Lipids
Carbohydrates
- Polyalcohol aldehydes or ketones
- Names are largely based on trivial names rather than systematic names generated by IUPAC rules
- Most carbohydrate names end in "ose"
- Categorized based on the number of carbon atoms they contain:
- Trioses (3 carbon atoms)
- Tetroses (4 carbon atoms)
- Pentoses (5 carbon atoms)
- Hexoses (6 carbon atoms)
- Sugars that contain an aldehyde functional group are called aldoses
- Sugars that contain a ketone functional group are classified as ketoses
Fischer Projections
- Used to depict the three-dimensional structure of sugars
- Most carbon atoms in sugars have a tetrahedral geometry
- In a Fischer projection, the main carbon skeleton is vertical with carbon-carbon single bonds rotated so that the carbon chain is curved out toward you
Chirality
- Topological property of an object, an object is chiral if it is different from its mirror image
- A molecule is chiral if there is a "right-handed" form of the molecule that is different from the "left-handed" form
- Enantiomers are different compounds, even though they have identical formulas and identical atom connectivity
- They have identical chemical and physical properties, except for how they interact with other chiral molecules and how they interact with plane-polarized light
- In order for a molecule to be chiral, it must contain one or more stereocenters
- The IUPAC system names the configuration around a stereocenter as R (for right-handed; rectus) or S (for left-handed; sinister)
Optical Activity
- Phenomenon in which the enantiomers of a chiral molecule interact with polarized light, but one enantiomer tilts the polarization in one direction, while the other tilts it in the opposite direction
- The enantiomer that rotates polarized light in a clockwise direction is called the dextrorotatory isomer and labeled as the (+) enantiomer
- The enantiomer that rotates polarized light in a counterclockwise direction is called the levorotatory isomer and is labeled as the (–) enantiomer
- A racemic mixture contains equal amounts of the (+) and (–) enantiomers and has the designation (±)
D-Sugars and L-Sugars
- When glyceraldehyde is drawn as a Fischer projection, the OH group on the stereocenter points to the right—this is called the D-isomer
- All naturally occurring sugars belong to the D-family
- To decide which family a sugar belongs to, draw the molecule as a Fischer projection with the aldehyde or ketone functionality at the top of the structure, then look at the OH group on the next-to-bottom carbon
The D-Aldohexoses
- Have six carbon atoms and an aldehyde functional group
- The OH group on C5 points to the right
- Glucose is the most common
Fructose
- Most common ketohexose
- Structure is very similar to that of glucose—the functional groups on C1 and C2 are simply reversed
Polysaccharides
- Chains of starch molecules can branch by forming [1↔6] glycoside bonds, which leads to more compact forms of starch, such as glycogen and amylopectin
- Cellulose is poly [1↔4] β-glucose with beta glycoside bonds
- Starch is poly [1↔4] α-glucose with alpha glycoside bonds
Lipids
- Glycerides
- Esters composed of glycerin (1, 2, 3-propantriol) and fatty acids
- Triglycerides have three fatty acid residues esterified to the glycerin backbone and are also known as triacyl glycerols
- Fatty Acids
- Long-chained carboxylic acids
- Naturally occurring fatty acids always have an even number of carbon atoms
- Saturated fatty acids have carbon chains that contain only carbon-carbon single bonds
- Unsaturated fatty acids have carbon chains that contain at least one carbon-carbon double bond
- Phospholipids
- Similar in structure to glycerides, except that one of the fatty acid residues has been replaced by a phosphate ester group
- Common in cellular membranes because of their surfactant properties
- Steroids
- Characterized by the cyclopentanoperhydrophenanthrene ring system
- Common steroids include cholesterol, estrogen, and testosterone
- Prostaglandins
- Powerful, but short-lived, hormones in mammalian systems
- Synthesized in vivo from an unsaturated fatty acid called arachidonic acid
Proteins and Amino Acids
- Proteins
- Polymers of amino acids joined by peptide bonds
- Amino Acids
- Contain two organic functional groups: an amine group, and a carboxylic acid group
- Each amino acid has a unique side chain that gives it its characteristic physical and chemical properties
- Stereochemistry of Amino Acids
- Naturally occurring amino acids belong to the L-family
- Proteins are chiral, thus their inherent hardness enables them to differentiate between two enantiomeric isomers
Functional Role of Proteins
- Perform a surprising variety of essential functions in mammalian organisms
- Dynamic functions include catalysis of chemical transformations, transport, metabolic control, and contraction
- Structural functions include proteins that provide the matrix for bone and connective tissue, giving structure and form to the human organism
Amino Acid Side Chains
- Non-polar, aliphatic side chains: glycine, alanine, valine, leucine, and isoleucine
- Aromatic side chains: phenylalanine, tyrosine, and tryptophan
- Polar uncharged side chains: serine, threonine, cysteine, asparagine, and glutamine
- Acidic side chains: aspartate and glutamate
- Basic side chains: histidine, lysine, and arginine
Studying That Suits You
Use AI to generate personalized quizzes and flashcards to suit your learning preferences.
Description
Learn about the structure and properties of organic molecules, including carbon backbones and functional groups. Understand how functional groups define the chemical and physical properties of compounds.
