2.3 Organic Compounds: Carbohydrates, Lipids, Proteins, and Nucleic Acids

Carbohydrates

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Monosaccharides and Polysaccharides

Carbohydrates consist of carbon, hydrogen, and oxygen atoms, typically in a 1:2:1 ratio, represented by the general formula $(CH_2O)_n$. This ratio is worth remembering because it shows up on exams constantly.

Monosaccharides are simple sugars and the building blocks of all carbohydrates. The three you need to know are glucose, fructose, and galactose. All three share the same molecular formula ($C_6H_{12}O_6$), but their atoms are arranged differently, making them structural isomers with distinct properties.

Monosaccharides link together through glycosidic bonds (a type of covalent bond formed via dehydration synthesis) to build larger carbohydrates:

• Disaccharides are two monosaccharides joined together. Sucrose (table sugar) = glucose + fructose. Lactose (milk sugar) = glucose + galactose. Maltose = glucose + glucose.
• Polysaccharides are long chains of many monosaccharides. Their function depends on their structure:
  • Energy storage: Starch (in plants) and glycogen (in animals) are both made of glucose chains but differ in branching. Glycogen is more heavily branched, which allows animals to break it down quickly for fast energy.
  • Structural support: Cellulose forms rigid plant cell walls, and chitin strengthens insect exoskeletons and fungal cell walls. Humans can't digest cellulose because we lack the enzyme to break its specific glycosidic bonds.

Functions and Importance of Carbohydrates

Carbohydrates are the primary energy source for living organisms. Glucose is the most commonly used monosaccharide, broken down during cellular respiration to produce ATP.

Beyond energy, carbohydrates also play roles in:

• Cell signaling and recognition: Carbohydrate chains attached to proteins on the cell surface (glycoproteins) help cells identify each other, which is critical for immune function and tissue organization.
• Nucleic acid structure: The sugars deoxyribose and ribose are monosaccharides that form part of the backbone of DNA and RNA, respectively. You'll see these again in the nucleic acids section below.

Lipids

Structure and Types of Lipids

Lipids are a chemically diverse group of hydrophobic (water-fearing) molecules. What unites them isn't a single structure but the fact that they're largely nonpolar and therefore insoluble in water.

Fatty acids are long hydrocarbon chains with a carboxyl group ($-COOH$) at one end. They come in two main varieties:

• Saturated fatty acids have only single bonds between carbon atoms. The chains pack tightly together, which is why saturated fats (like butter) tend to be solid at room temperature.
• Unsaturated fatty acids have one or more double bonds, creating kinks in the chain. These kinks prevent tight packing, so unsaturated fats (like olive oil) tend to be liquid at room temperature.

The major types of lipids you need to know:

• Triglycerides are the most common lipids, made of three fatty acid chains attached to a glycerol backbone. They function as long-term energy storage in both animals (stored as fat) and plants (stored as oils).
• Phospholipids have two fatty acid chains and a phosphate group attached to glycerol. The phosphate "head" is hydrophilic (water-loving) while the fatty acid "tails" are hydrophobic. This dual nature is what allows phospholipids to spontaneously form the bilayer structure of cell membranes, with tails facing inward (away from water) and heads facing outward (toward water).
• Steroids share a four-ring carbon structure. Cholesterol is the most well-known example and serves as a precursor for steroid hormones like testosterone and estrogen.

Functions and Importance of Lipids

• Energy storage: Lipids store about 9 kcal/g of energy, more than double the 4 kcal/g stored by carbohydrates or proteins. This makes fat an extremely efficient way to store energy.
• Cell membrane structure: Phospholipid bilayers form the foundation of every cell membrane, controlling what enters and exits the cell.
• Signaling: Steroid hormones (testosterone, estrogen, cortisol) and eicosanoids regulate processes like inflammation, blood clotting, and immune responses.
• Insulation and protection: Fat deposits cushion organs and provide thermal insulation.

Proteins

Amino Acids and Peptide Bonds

Proteins are the most functionally diverse macromolecules in living organisms. They're built from amino acids, and every amino acid has the same core structure: a central carbon (called the $\alpha$-carbon) bonded to four things:

1. An amino group ($-NH_2$)
2. A carboxyl group ($-COOH$)
3. A hydrogen atom
4. A variable R group (side chain)

The R group is what makes each amino acid unique. There are 20 different amino acids used in proteins, and their R groups range from small and nonpolar to large and charged. The R group determines how each amino acid interacts with water, other amino acids, and its environment.

Amino acids connect through peptide bonds, which are covalent bonds formed by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the next. A chain of amino acids linked by peptide bonds is called a polypeptide.

Protein Structure and Function

Protein shape determines protein function. If a protein loses its shape (a process called denaturation, caused by changes in pH, temperature, or other conditions), it loses its ability to work. There are four levels of protein structure:

1. Primary structure: The specific sequence of amino acids in the polypeptide chain. Even changing a single amino acid can alter the protein's function (as seen in sickle cell disease, where one amino acid substitution in hemoglobin changes the shape of red blood cells).
2. Secondary structure: Local folding patterns caused by hydrogen bonds along the backbone. The two main patterns are $\alpha$-helices (coils) and $\beta$-sheets (pleated, zigzag folds).
3. Tertiary structure: The overall 3D shape of a single polypeptide, determined by interactions between R groups (hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions).
4. Quaternary structure: The arrangement of multiple polypeptide chains into a single functional protein. Not all proteins have this level. Hemoglobin is a classic example, with four polypeptide subunits.

Proteins perform a huge range of functions:

• Enzymes catalyze (speed up) biochemical reactions. Without enzymes, most reactions in your body would be far too slow to sustain life.
• Structural proteins like collagen (in connective tissue) and keratin (in hair and nails) provide physical support.
• Transport proteins like hemoglobin (carries $O_2$ in blood) and membrane channel proteins move molecules where they need to go.
• Signaling proteins like insulin and other protein hormones transmit messages between cells.
• Defensive proteins like antibodies recognize and help neutralize pathogens.

Nucleic Acids

Nucleotides and Nucleic Acid Structure

Nucleic acids store and transmit genetic information. Their monomers are nucleotides, and each nucleotide has three parts:

1. A nitrogenous base (the part that encodes information)
2. A pentose sugar (deoxyribose in DNA, ribose in RNA)
3. A phosphate group

There are five nitrogenous bases split into two categories:

• Purines (two-ring structure): Adenine (A) and Guanine (G)
• Pyrimidines (one-ring structure): Cytosine (C), Thymine (T, DNA only), and Uracil (U, RNA only)

A quick way to remember: pYrimidines = C, T, U (the word "pyrimidine" has a "y," and so does "cytosine," "thymine," and "uracil"). Purines are the bigger molecules (two rings), and their names are also longer: adenine, guanine.

Nucleotides link together through phosphodiester bonds between the phosphate group of one nucleotide and the sugar of the next, forming a sugar-phosphate backbone. The sequence of bases along this backbone is what encodes genetic information.

DNA and RNA Structure and Function

DNA (deoxyribonucleic acid) is double-stranded, forming the famous double helix. The two strands are held together by hydrogen bonds between complementary base pairs:

• A pairs with T (2 hydrogen bonds)
• G pairs with C (3 hydrogen bonds)

This complementary base pairing is what makes DNA replication possible. During cell division, each strand serves as a template to build a new complementary strand, so both daughter cells receive identical genetic information.

RNA (ribonucleic acid) is typically single-stranded and uses uracil (U) instead of thymine (T). The three main types of RNA work together during protein synthesis:

• mRNA (messenger RNA) carries the genetic instructions from DNA in the nucleus to the ribosomes in the cytoplasm.
• tRNA (transfer RNA) reads the mRNA codons and delivers the matching amino acids to the ribosome during translation.
• rRNA (ribosomal RNA) is a structural and catalytic component of ribosomes themselves, the molecular machines that assemble proteins.

The flow of genetic information follows what's called the central dogma of molecular biology: DNA → (transcription) → RNA → (translation) → Protein. This concept ties together everything in this section and will come up repeatedly throughout the course.