Carbon and Organic Chemistry

Carbon: The Backbone of Life

• Living organisms are mainly composed of carbon-based compounds
• Sunlight helps producers change atmospheric CO2 to carbon-based molecules through photosynthesis
• Consumers then ingest these molecules
• Carbon can make diverse molecules with large complex structures
• Carbon's 4 bonding locations allows it to form large complex molecules

Organic Chemistry

• Organic chemistry studies carbon compounds
• Organic compounds range in size and complexity
• Hydrogen atoms are present in most organic compounds, in addition to carbon atoms
• Living matter consists of carbon compounds bonded to other elements including proteins, DNA and carbohydrates

Chemical Groups in Biological Processes

• Functional groups are crucial for organic molecules because they participate in chemical reactions
• The number, arrangement and variety of functional groups attached to a carbon skeleton determine an organic molecule's properties
• 7 key functional groups are important in biological processes

Overview: The Molecules of Life

• Carbohydrates, lipids, proteins, and nucleic acids comprise all living things
• Macromolecules consist of thousands of covalently connected atoms
• Molecular structure and function are inseparable

Macromolecules

• Polymers are large covalently bonded molecules with similar building blocks
• The Greek roots polys (many) and meros (part) describe polymers
• Monomers are the small building blocks of polymers
• Carbohydrates, proteins, and nucleic acids represent the 3 of 4 classes of life's organic molecules are polymers

Synthesis and Breakdown of Polymers

• Dehydration reactions occur when two monomers join, releasing a water molecule
• Hydrolysis breaks down polymers into monomers, reversing dehydration

Carbohydrates

• Carbohydrates include sugars and sugar polymers
• Monosaccharides, or simple sugars, are the most basic carbohydrates
• Disaccharides consist of two monosaccharides linked via covalent bond
• Polysaccharides are carbohydrate polymers made of multiple sugar building blocks

Sugars

• The name "monosaccharide" refers to a single sugar
• Monosaccharides typically have molecular formulas that are multiples of CH2O (with a C:H:O ratio of 1:2:1)
• Glucose (C6 H12 O6) is the most common monosaccharide
• A carbonyl group, and multiple hydroxyl groups are present in the glucose molecule

Classification of Monosaccharides

• The location of the carbonyl group is one way to classify monosaccharides
• Aldose sugars have an aldehyde carbonyl group
• Ketose sugars have a ketone carbonyl group
• The number of carbons in the carbon skeleton is another way to classify sugars
• Hexoses have 6 carbons
• Pentoses have 5 carbons
• Tetroses have 4 carbons
• Trioses have 3 carbons
• Spatial arrangement around asymmetric carbons provides an additional means of monosaccharide classification
• Glucose and galactose are both six-carbon aldoses

Structure and Classification of Monosaccharides

• In aqueous (water-based) solutions, monosaccharides usually form rings instead of linear chains

Disaccharides

• A disaccharide consists of two monosaccharides that are linked together by a glycosidic linkage via dehydration reaction
• Maltose (malt sugar) forms from two glucose molecules
• Sucrose (table sugar) is from glucose and fructose
• Lactose (milk sugar) consists of glucose and galactose

Polysaccharides

• Polymers containing hundreds or thousands of monosaccharides joined by glycosidic linkages are polysaccharides
• Polysaccharides function as storage and structural molecules
• The characteristics of the sugar monomers and the positions of glycosidic linkages determine the structure and function of polysaccharides

Starch and Glycogen

• Plants store glucose monomers in starch, a polysaccharide
• Animals store glucose as glycogen

Structural Polysaccharides

• Plant cell walls contain cellulose, a structural polysaccharide
• Arthropod exoskeletons contain the structural polysaccharide chitin

Lipids

• Lipids are a class of large biological molecules that do not form polymers
• Lipids share the property of having very little or no affinity for water
• Lipids consists mostly of hydrocarbons with nonpolar covalent bonds, the reason they are hydrophobic
• The most notable types of lipids are fats, phospholipids and steroids

Fats

• Fats are the product of smaller molecules; glycerol and fatty acids
• A fatty acid has a carboxyl group connected to a long carbon skeleton
• Glycerol is an alcohol whose 3 carbons each have a hydroxyl
• 3 fatty acids join glycerol by an ester linkage, forming a triacylglycerol or triglyceride
• Storage of energy represents the main purpose of fat

Different Attributes of Fat

• Fatty acids can vary in length (number of carbons) and in the number and location(s) of double bonds
• Saturated fatty acids contain the maximum possible number of hydrogen atoms are joined by single bonds only
• Unsaturated fatty acids have one or moreover double bonds

Phospholipids

• A phospholipid has 2 fatty acids and a phosphate group attached to glycerol, instead of 3 fatty acids like in normal fats
• The fatty acid tails are hydrophobic and the phosphate group/attachments create a hydrophilic head.

Steroids

• Steroids consist of a carbon skeleton with four fused rings
• The steroid, cholesterol, is an important component of animal cell membranes and a precursor for vertebrate sex hormones and other molecules
• High cholesterol levels in animals might lead to cardiovascular disease, though cholesterol is essential for their existence

Proteins: Diversity in Structure

• Proteins are responsible for a diverse array of functions within organisms
• The name “protein” comes from the Greek word proteios, which means “first”
• Cells contain over 50% protein in their dry mass
• Proteins perform a wide variety of functions including catalysis (enzymes), defense (antibodies), storage (casein), transport (hemoglobin), cellular communication (hormones), movement (actin and myosin) and structural support (keratin)
• Polypeptides are polymers that use the same 20 amino acids
• Amino acids are connected by peptide bonds in polypeptides
• Proteins are molecules possessing a distinct biological function that are composed of one or more polypeptides

Amino Acid Monomers

• Basic components of an amino acid include:
  • An amino group
  • A carboxyl group
  • A hydrogen atom
  • A variable group (R)
• The R group, or side chain, is unique to each amino acid

Polypeptides

• Peptide bonds link together amino acids
• Polypeptides can range anywhere from a few amino acids to thousands
• Each unique polypeptide has a specific sequence of amino acids with a carboxyl end (C-terminus) and an amino end (N-terminus)

Nucleic Acids

• Store transmit and help express hereditary information
• Monomers called nucleotides make up nucleic acids
• Nucleic acids come in 2 types
  • Deoxyribonucleic acid (DNA)
  • Ribonucleic acid (RNA)

Nucleic Acid Roles

• DNA is the genetic material passed down from parents
• DNA provides directions for its own replication
• DNA leads to RNA synthesis
• DNA controls protein synthesis through RNA in what is called gene expression

Nucleic Acid Components

• Polynucleotides are polymers made of nucleotide monomers
• A nucleotide is made up of Nitrogenous base + sugar + phosphate group
• A nucleoside is made up of Nitrogenous base + sugar

Nitrogenous Bases

• There are two families of nitrogenous bases
• Pyrimidines are nitrogenous bases (cytosine, thymine, and uracil) that have a single six-membered ring
• Purines are nitrogenous bases (adenine and guanine) that have a six-membered ring fused to a five-membered ring

Deoxyribose, Ribose

• Sugars are deoxyribose in DNA, and ribose in RNA

Nucleotide Polymers

• A phosphodiester linkage is when adjacent nucleotides are joined together, its phosphate group links the sugars of nucleotides
• Sugar-phosphate units with nitrogenous bases stemming from them form a nucleotide polymer backbone

DNA and RNA Structures

• RNAmolecules are usually single-stranded polynucleotides
• DNA molecules form a double helix with two polynucleotide strands
• In DNA, nitrogenous bases pair via hydrogen bonds:
  • Adenine (a) with thymine (t)
  • Guanine (g) with cytosine (c)
• Complementary pairing also takes place between two RNA molecules or in separate parts of the same molecule
• Uracil (U) replaces thymine in RNA and pairs with adenine