Biomolecules, DNA and RNA

Biomolecules

Definition

  • Biomolecule: Any substance made or found inside a living cell.

Four Main Classes of Biomolecules

  1. Carbohydrates

  2. Lipids

  3. Proteins

  4. Nucleic Acids

Structure of Biomolecules

Macromolecules

  • Polymers: Chain-like sequences of connected molecules linked by covalent bonds.

  • Monomers: Repeating units that form polymers.

Polymer Formation and Breakdown

  • Dehydration Reaction: Monomers connect by losing a water molecule.

  • Hydrolysis: The process by which polymers are broken down, releasing energy.

Carbohydrates

Classification

  1. Monosaccharides

    1. Simplest sugars (e.g., glucose, fructose).

    2. Major nutrients for cells and a source of energy.

    3. Molecular formulas typically follow the pattern of multiples of CH2O.

    4. Glucose (C6H12O6) is the most common monosaccharide.

  2. Disaccharides

    • Formed by the condensation of two monosaccharides.

    • Common example: Sucrose (table sugar), formed from glucose and fructose.

  3. Polysaccharides

    • Composed of hundreds to thousands of monosaccharides.

    • Serve as energy storage and building materials.

    • Starch: Plant storage polysaccharide made entirely of glucose.

    • Glycogen: Animal storage polysaccharide, found in liver and muscle cells.

    • Cellulose: Major component of plant cell walls, most abundant organic compound on Earth.

    • Structurally, cellulose is a straight polymer of glucose.

Functions of Carbohydrates

  • Energy: Provide a readily accessible energy source for cells.

  • Storage: Serve as energy storage macromolecules (starch in plants, glycogen in animals).

  • Structure: Contribute to structural integrity (cellulose in plant cell walls).

Lipids

Characteristics

  • Hydrophobic molecules: Repel water; do not form polymers.

  • Mostly composed of hydrocarbons; dominated by nonpolar covalent bonds.

  • Three major groups of lipids:

    1. Fats

    2. Phospholipids

    3. Steroids

Fats Structure

  • Assembled from glycerol and fatty acids.

  • Glycerol: Three-carbon skeleton with attached hydroxyl groups.

  • Fatty Acids: Consist of a carboxyl group attached to a long carbon chain.

  • Triacylglycerol (Triglyceride)

    • Formed by the combination of 3 fatty acids with 1 glycerol via an ester linkage (connection between a hydroxyl and a carbonyl group).

Saturated vs. Unsaturated Fats

  • Saturated Fats

    • Composition: Fatty acid chains are tightly packed due to no double bonds, solid at room temperature (e.g., butter).

    • Structural Formula: Represented linearly with the carbon atoms in a zigzag pattern.

  • Unsaturated Fats

    • Composition: Contain double bonds that introduce kinks in the fatty acid chains, preventing tight packing; liquid at room temperature (e.g., olive oil).

    • Structural Formula: Shows hydrogens not depicted in molecular diagrams.

    • The presence of cis double bonds results in bending.

Phospholipids

  • Structure

    • Composed of two fatty acid tails and a negatively charged phosphate group.

    • Exhibit hydrophobic (water-hating) tails and hydrophilic (water-loving) heads.

    • Figures 3.15 show phospholipids' arrangement in cell membranes.

  • Cell Membrane Formation

    • Phospholipids arrange in a double layer (bilayer) with hydrophobic tails oriented inward, away from water, providing structure and protection.

Steroids

  • General Structure

    • Steroids are lipid molecules characterized by four fused rings, are hydrophobic, and insoluble in water.

    • Cholesterol

      • A crucial component of cell membranes.

      • Precursor for vital substances such as vitamin D, testosterone, estrogen, and bile salts.

Proteins

  • Roles and Functions

    • Involved in various cellular functions: structural support, storage, transport, signaling, movement, metabolism, defense.

    • Composed of polymers made from 20 amino acids, known as polypeptides.

    • A protein can consist of one or more folded polypeptides, defining its unique function.

  • Protein Structure

    • Conformation refers to the 3D shape of a protein.

    • Simplified diagrams can represent proteins in various ways (e.g., ribbon, space-filling models).

Amino Acids

  • Components

    • Each amino acid contains:

      • Hydrogen atom

      • Carboxyl group

      • Amino group

      • Variable R group (side chain) that distinguishes each of the 20 amino acids.

  • R Groups

    • Range from simple (e.g., a single hydrogen) to complex structures.

    • Determine the unique characteristics of each amino acid, affecting protein function.

    • Basic (positively charged) and acidic (negatively charged) amino acids are examples.

Peptide Bond Formation

  • Dehydration Reaction

    • Two amino acids link through a dehydration reaction, forming a peptide bond between the carboxyl group of one and the amino group of another.

Protein Structure Levels

  • Proteins exhibit:

    • Primary Structure: Linear sequence of amino acids.

    • Secondary Structure: Local folding (e.g., alpha helices and beta sheets).

    • Tertiary Structure: Overall 3D shape of a single polypeptide.

    • Quaternary Structure: Assembly of multiple polypeptides.

Proteins

  • Functioning proteins are composed of one or more polypeptides twisted, folded, or coiled into a unique shape (conformation).

  • Proteins feature three main levels of structure:

    • Primary Structure: The unique sequence of amino acids in a polypeptide.

    • Secondary Structure: Formed from hydrogen bonds between the polypeptide backbone; includes α-helix and β-pleated sheets.

    • Tertiary Structure: Determined by interactions among R groups and between R groups and the backbone.

    • Quaternary Structure: The overall structure from aggregation of multiple polypeptide subunits.

Primary Structure

  • Defined by the unique sequence of amino acids.

  • Example: Lysozyme is an enzyme with a polypeptide chain of 129 amino acids.

  • The primary structure is dictated by genetic information.

  • A small change can significantly impact the protein's conformation and function, as seen in sickle-cell disease.

Secondary Structure

  • Results from hydrogen bonds along the polypeptide backbone.

  • Although individual hydrogen bonds are weak, they collectively shape sections of the protein.

  • Common secondary structures:

    • α-helix

    • β-pleated sheet

Tertiary Structure

  • Determined by various interactions among the R groups or between the R groups and the polypeptide backbone

    • Hydrophobic interactions due to non-polar amino acids.

    • Disulfide bridges between the sulfhydryl groups of cysteine monomers.

    • Ionic bonds.

Quaternary Structure

  • Overall structure from the aggregation of two or more polypeptide subunits.

  • Example: Collagen, a fibrous protein made of three supercoiled polypeptides, provides structural strength in connective tissue.

Protein Structure Overview

  • Proteins function properly by recognizing and binding to other molecules; for example,

    • Normal β subunit of hemoglobin carries oxygen in red blood cells.

    • In sickle-cell disease, abnormal β subunit causes aggregation and reduces oxygen-carrying capacity.

Protein Denaturation

  • Denaturation refers to the unraveling of proteins due to alterations in environmental conditions:

    • Changes in pH, salt concentration, or temperature can lead to loss of structure and function.

Nucleic Acids

Structure of Nucleic Acids

  • Polymers and Monomers:

    • Nucleic acids are polymers known as polynucleotides.

    • Each polynucleotide comprises monomers called nucleotides.

  • Nucleic acids enable the reproduction and inheritance of characteristics.

  • Two types of nucleic acids:

    • Deoxyribonucleic Acid (DNA): Heritable material controlling protein synthesis through RNA.

    • Ribonucleic Acid (RNA): Plays a functional role in the process of protein synthesis.

Composition of Nucleotides

  • Components of a Nucleotide:

    • Nitrogenous base

    • Pentose sugar

    • One or more phosphate groups

  • Nucleosides:

    • Portion of a nucleotide without the phosphate group.

Nitrogenous Bases

  • Two Families of Nitrogenous Bases:

    1. Pyrimidines:

      • Cytosine, Thymine, Uracil

      • Structure: Single six-membered ring

    2. Purines:

      • Adenine, Guanine

      • Structure: Six-membered ring fused to a five-membered ring.

Linkage between Nucleotides

  • Phosphodiester Linkage:

    • Connects nucleotides by linking the phosphate group of one nucleotide to the sugar of the next.

    • Forms the backbone of the nucleic acid, with nitrogenous bases as appendages.

DNA: a double helix molecule, stored inside mucleus cell

  • The backbones run from 5’ → 3’ (antiparallel)

  • Template and complementary base pairing: A ←→ T, G ←→ C

RNA: single-stranded

  • Pentose sugar is ribose

  • RNA molecules are variable in form

  • Complementary pairings can occur between 2 different RNA molecules or parts of the same molecule

Similar to DNA: T ←→ A, G ←→ C EXCEPT: A ←→ U

Transcription: the making of RNA using DNA

  • 1) separate 2 DNA strands

  • 2) read 1 trans (always template strand) → transcribe to RNA

  • 3) only mRNA could then be translated into polypeptides

Translation: making polypeptide using information from mRNA

  • Eukaryotic mRNA travels out of nucleus

  • At ribosomes, mRNA read 3 nucleotides at a time = codon → read from 5’ to 3’

  • Each codon specifies an amino acid to be placed along the chuoi polypeptide

=> Codons must be read in the correct reading frame to produce specific polypeptide

  • There is a start codon

  • There are three stop codons

  • The genetic code is redundant

=> Central Dogma of Biology: explains that DNA is copied into mRNm, then translated to a chain of amino acids using ribosomes