Chemical Organization of the Cell: Lipids, Proteins, & Nucleic Acids

Chemical Organization of the Cell

Part II: Lipids, Proteins, & Nucleic Acids

Chapter 2

Lipids

• Lipids contain Carbon (C), Hydrogen (H), and Oxygen (O), similar to carbohydrates, but not in a 1:2:1 ratio.
• There is significantly less oxygen in lipids than in sugars.

Major Functions of Lipids

• Protection: Lipids cushion the body.
• Insulation: They help in thermoregulation.
• Energy Storage: Lipids are a major energy storage form.
• Cell Membrane Component: Essential for forming plasma membranes.

Major Characteristics of Lipids

1. Insolubility in Water: Lipids are water insoluble but soluble in nonpolar solvents such as ether, alcohol, and chloroform.
2. High Proportion of C-H Bonds: Lipids have a greater proportion of C-H bonds than other organic compounds, allowing them to store more than twice the energy than an equivalent amount of carbohydrates or protein.
   • Fats provide approximately 9000 calories/gram.
   • Carbohydrates and Proteins provide approximately 4000 calories/gram.
   • Thus, lipids are vital energy sources.

• Lipids are stored primarily as triglycerides in cells, synthesized from sugars.
  • Products labeled "fat-free" often become converted to lipids if ingested, thus are truly "fat-free" only if they remain packaged.

Types of Lipids

1. Simple Lipids
   • Include fatty acids, triglycerides, waxes, and oils.
   • Triglycerides are composed of three fatty acids bonded to a glycerol molecule and constitute the major storage form of fat, present in adipose tissue and utilized for energy metabolism.
2. Phospholipids
   • Comprise a lipid portion and a non-lipid portion attached to a glycerol backbone; main components of cell membranes.
3. Steroids
   • Exhibit a structure differing greatly from triglycerides but are nonpolar, fat-soluble molecules composed of four fused rings of carbon atoms.
   • Examples include cholesterol, sex hormones, cortisol, bile salts, and vitamin D.

Simple Lipids Deep Dive

• Fatty Acids: Can be classified into saturated and unsaturated.
  • Saturated Fatty Acids: Every carbon in the hydrocarbon tail has the maximum number of hydrogens (i.e., single bonds).
  • Examples: Animal fats like lard, palm oil, and coconut oil.
  • Saturated fats typically have higher energy content compared to unsaturated fats.
  • Linked in diet studies to atherosclerosis and generally more solid at room temperature.
  • Unsaturated Fatty Acids: Contain double or triple bonds between two or more carbons in the chain, resulting in fewer hydrogens.
  • Can be polyunsaturated (more than one double bond).
  • Examples: Corn oil, safflower oil, and canola oil.
  • Typically, animal fats are saturated while most vegetable fats are unsaturated.
• Dietary Implications: The composition of fats affects health and dietary choices.

Saturated vs. Unsaturated Triglycerides

• Fat molecules (triacylglycerols) consist of glycerol and fatty acids.
  • Saturated fats have single bonds between all carbon pairs; hence, they appear more solid.
  • Unsaturated fats contain double bonds between one or more pairs of carbon atoms, leading to a liquid state.

Phospholipids

• Defined as lipids with both a lipid and a non-lipid portion attached to a glycerol backbone.
• They serve as the principal component in cell membranes.

Steroids

• Steroids, including sterols, are characterized by their four-ring carbon structure.
• Examples include cholesterol, which is crucial for synthesizing sex hormones, vitamin D, and bile salts.
• Cholesterol can be produced by the liver or obtained through diet and is involved in atherosclerosis by clumping in blood vessels.
• Cholesterol crystals can obstruct blood flow, contributing to certain heart diseases.

Fat Digestion

• Bile salts, generated in the liver from cholesterol, emulsify fats into small droplets for digestion and absorption.
• Emulsification: Increases the surface area of lipids for interaction with water-soluble digestive enzymes, which only act on outer triglyceride molecules.

Proteins

• Proteins are composed of Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and Sulfur (S) and are considered macromolecules due to their large size and complexity.
• Comprised of long chains of amino acids, proteins exhibit a diverse range of functions in biological systems.

Functions of Proteins

1. Structural: Serve as structural elements within cells (e.g., collagen in bone, keratin in skin, hair, and nails).
2. Regulatory: Act as hormones and neurotransmitters that regulate physiological processes (e.g., Insulin regulates blood glucose).
3. Contractile: Facilitate muscle tissue contraction and movement (e.g., Myosin and actin in muscle).
4. Immunological: Provide responses to protect against pathogens (e.g., Antibodies).
5. Transport: Carry vital substances (e.g., Hemoglobin carries oxygen).
6. Enzymatic: Serve as catalysts in biochemical reactions, with all enzymes being proteins (e.g., Amylase, Lipase, Lactase).

• Mnemonic for Functions: SECRIT - Structural, Enzymes, Contractile, Regulatory, Immunological, Transport.

Building Blocks of Proteins

• The basic units of proteins are amino acids, with 20 different types available for protein synthesis.
• Amino acids combine to form polymers, which are specific protein types.
• The sequence of amino acids dictates the biological characteristics of the protein, with small variations potentially being catastrophic (e.g., Sickle-cell disease arises from a single amino acid substitution in hemoglobin, altering its structure and function).

Amino Acids

• Each amino acid comprises a hydrogen atom and three functional groups attached to a central carbon atom:
  • Amino group (-NH2)
  • Carboxyl group (-COOH)
  • R group (side chain) that varies among different amino acids and determines individual chemical properties.

Formation of Polypeptides

• Amino acids are covalently linked through peptide bonds via dehydration synthesis, forming dipeptides or polypeptides (long chains constructed from many amino acids).

Levels of Protein Structure

1. Primary Structure: Unique amino acid sequence.
2. Secondary Structure: Patterns such as alpha helices or beta-pleated sheets formed through hydrogen bonding.
3. Tertiary Structure: The 3D shape of the polypeptide due to various interactions (bonds).
4. Quaternary Structure: Involves multiple polypeptide subunits (e.g., Hemoglobin with 2 alpha and 2 beta chains).

Classification of Proteins

1. Fibrous Proteins:
   • Insoluble in water; have structural function.
   • Examples: collagen, keratin, elastin.
2. Globular Proteins:
   • Soluble in water; have metabolic functions.
   • Examples: hemoglobin, enzymes, antibodies.

Denaturation

• The process where proteins lose their functional shape, caused by temperature, pH, or ionic concentration changes.

Enzyme Function

• Enzymes are highly specific catalysts that can accelerate reactions significantly (up to 10 billion times).
• Enzyme names typically end in -ase (e.g., Lipases, Proteases).

Nucleic Acids

• First discovered in cell nuclei.
• Composed of Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and Phosphorus (P).
• Two primary types are:
  1. DNA (Deoxyribonucleic Acid):
  • Contains genetic information and is the material inherited through generations.
  1. RNA (Ribonucleic Acid):
  • Functions mainly to carry instructions from DNA to ribosomes for protein synthesis.

Building Blocks of Nucleic Acids: Nucleotides

• Basic unit of nucleic acids; composed of:
  1. Phosphate group
  2. Pentose Sugar: deoxyribose in DNA, ribose in RNA.
  3. Nitrogenous Base: Varies per nucleotide and distinguishes different nucleotides.
• DNA comprises thousands of nucleotides, considerably larger than most proteins.

DNA Structure

• The structure resembles a twisted ladder (double helix):
  • The backbone consists of sugar and phosphate.
  • The rungs comprise paired nitrogenous bases bonded through hydrogen bonds.

Chargaff’s Rules

• Base pairing is systematic:

1. Purines pair with pyrimidines.
   • Purines: Adenine (A) and Guanine (G).
   • Pyrimidines: Cytosine (C) and Thymine (T).
   • A pairs with T; G pairs with C.

DNA Base Pairing Practice

• If the sequence in one strand of DNA is known, the complementary strand can be predicted.
  • Example: For strand 1 (T - A - C - G - T - A), the complementary strand would be (A - T - G - C - A - T).

DNA Replication

• Essential for cell division; DNA strands separate allowing the synthesis of new strands.
• Mutations during this process can lead to cell death, cancer, or genetic disorders and are further elaborated in Topic #8.

DNA vs RNA

• Pentose Sugars:
  • DNA: Deoxyribose.
  • RNA: Ribose.
• Nitrogenous Bases:
  • DNA: A, G, C, T.
  • RNA: A, G, C, U.

Types of RNA

1. Messenger RNA (mRNA):
   • Carries genetic instructions from DNA for protein synthesis.
2. Ribosomal RNA (rRNA):
   • Essential structural component of ribosomes, the sites of protein synthesis.
3. Transfer RNA (tRNA):
   • Transfers specific amino acids to ribosomes for polypeptide formation.

Comparison Between DNA and RNA (Table 2.9)

• *Differences emphasized in blue.

Preparation for Topic #3 Quiz

• Review lecture notes and outline materials.
• Focus on key questions and concepts for comprehensive understanding.