Core Chemical Principles in Biology

Chemical Bonds and Interactions

Understanding the types and properties of chemical bonds is fundamental to biology, as these interactions determine the structure and function of molecules in living systems.

• Chemical Bonds: Include hydrogen bonds, nonpolar covalent bonds, polar covalent bonds, and ionic bonds.

• Bond Strength: Determined by the nature of the atoms involved and their electronegativity.

• Atomic Structure: The arrangement of electrons around an atom influences bond formation and strength.

• Electronegativity: The tendency of an atom to attract electrons in a bond; differences in electronegativity lead to polar or nonpolar bonds.

• Example: Water (H2O) has polar covalent bonds due to the high electronegativity of oxygen compared to hydrogen.

Types of Bonds in Water

Water molecules exhibit both intramolecular and intermolecular bonding, which are crucial for its unique properties.

• Intramolecular Bonds: Polar covalent bonds between hydrogen and oxygen within a water molecule.

• Intermolecular Bonds: Hydrogen bonds between different water molecules, resulting from partial charges.

• Electronegativity: Oxygen is more electronegative than hydrogen, creating a dipole.

Properties of Water

Hydrogen bonding and hydrophobic interactions give water its unique characteristics, which are essential for life.

• Cohesion and Adhesion: Water molecules stick to each other (cohesion) and to other surfaces (adhesion).

• Surface Tension: The cohesive forces at the surface of water create a 'skin' that resists external force.

• Moderation of Temperature: Water's high specific heat helps buffer temperature changes.

• Global Phenomena: Water's properties influence climate, such as moderating coastal temperatures and affecting ocean currents.

Acids, Bases, and pH

The concepts of acids, bases, and pH are central to understanding biological systems and their chemical environments.

• Acid: A substance that donates protons (H+).

• Base: A substance that accepts protons.

• pH Scale: Measures the concentration of H+ ions; ranges from 0 (strong acid) to 14 (strong base), with 7 being neutral (pure water).

• Equation:

Chemical Properties of Carbon

Carbon's unique bonding properties allow it to form the backbone of biologically important molecules.

• Tetravalency: Carbon can form four covalent bonds, enabling complex structures.

• Diversity: Carbon's ability to bond with many elements leads to a variety of molecular shapes and functions.

Chemical Functional Groups

Functional groups are specific groups of atoms within molecules that confer distinct chemical properties.

• Common Functional Groups: Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl.

• Properties: Influence molecule polarity, acidity/basicity, and reactivity.

• Example: Carboxyl groups act as acids; amino groups act as bases.

Polymers and Monomers

Biological macromolecules are polymers built from monomer subunits through specific chemical reactions.

• Dehydration (Condensation) Reaction: Joins monomers by removing water.

• Hydrolysis Reaction: Breaks polymers into monomers by adding water.

• Role: Essential for the synthesis and breakdown of proteins, nucleic acids, and polysaccharides.

Proteins: Structure and Function

Protein Monomers and Polymerization

Proteins are polymers of amino acids linked by peptide bonds.

• Amino Acids: Contain an amino group, carboxyl group, hydrogen atom, and R group attached to a central carbon.

• Peptide Bond: Covalent bond formed between the carboxyl group of one amino acid and the amino group of another via dehydration.

Amino Acid Structure and Properties

The structure and chemical properties of amino acids determine protein function.

• Core Components: Amino group, carboxyl group, hydrogen, and R group (side chain).

• R Group: Determines polarity, charge, and whether the amino acid is hydrophobic or hydrophilic.

Levels of Protein Structure

Proteins have four levels of structure, each stabilized by specific bonds and interactions.

• Primary Structure: Sequence of amino acids (peptide bonds).

• Secondary Structure: Local folding (α-helices and β-sheets) stabilized by hydrogen bonds.

• Tertiary Structure: 3D shape formed by interactions among R groups (hydrophobic interactions, disulfide bridges, ionic bonds).

• Quaternary Structure: Association of multiple polypeptide chains.

Protein Folding and Function

Proper protein folding is essential for function; misfolding can lead to disease.

• Folding: Determines the protein's shape and function.

• Disruption: Environmental changes or mutations can disrupt folding, leading to loss of function or disease (e.g., prion diseases).

Nucleic Acids: DNA and RNA

Nucleotide Structure and Polymerization

Nucleic acids are polymers of nucleotides, which consist of a sugar, phosphate group, and nitrogenous base.

• Phosphodiester Bond: Covalent bond linking nucleotides in a strand.

• Primary Structure: Linear sequence of nucleotides.

Base Pairing and Double Helix

Complementary base pairing enables the double-helix structure of DNA.

• Base Pairs: Adenine (A) pairs with Thymine (T); Guanine (G) pairs with Cytosine (C).

• Hydrogen Bonds: Hold the two DNA strands together.

• Antiparallel Strands: DNA strands run in opposite directions (5' to 3' and 3' to 5').

Lipids and Membranes

Types of Lipids

Lipids include fats, phospholipids, and steroids, each with distinct structures and functions.

• Fats: Glycerol + 3 fatty acids; energy storage.

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; major component of cell membranes.

• Steroids: Four fused carbon rings; hormones and membrane components (e.g., cholesterol).

Phospholipid Bilayer

Phospholipids spontaneously form bilayers in water, creating the basic structure of cell membranes.

• Hydrophilic Head: Interacts with water.

• Hydrophobic Tails: Avoid water, face inward.

• Bilayer Formation: Driven by hydrophobic interactions.

Membrane Fluidity and Permeability

Membrane composition affects its properties.

• Cholesterol: Modulates membrane fluidity.

• Saturated vs. Unsaturated Fatty Acids: Unsaturated fatty acids increase fluidity; saturated decrease it.

Membrane Transport

Diffusion, Osmosis, and Facilitated Diffusion

Cells regulate the movement of substances across membranes through various transport mechanisms.

• Diffusion: Movement of molecules from high to low concentration.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Facilitated Diffusion: Passive transport via membrane proteins.

Passive and Active Transport

Transport can be passive (no energy required) or active (requires energy, usually ATP).

• Channels and Carriers: Facilitate movement of specific molecules.

• Pumps: Move substances against their concentration gradient using energy.

Membrane Proteins

Integral and peripheral proteins play key roles in membrane structure and function.

• Integral Proteins: Span the membrane; involved in transport and signaling.

• Peripheral Proteins: Attached to membrane surface; support and signaling.

Carbohydrates: Structure and Function

Monomers and Polymerization

Carbohydrates are polymers of monosaccharides linked by glycosidic bonds.

• Monosaccharides: Simple sugars (e.g., glucose).

• Glycosidic Bond: Covalent bond formed via dehydration reaction.

Roles of Carbohydrates

Carbohydrates serve structural and functional roles in cells.

• Energy Storage: Starch (plants), glycogen (animals).

• Structure: Cellulose (plants), chitin (fungi, arthropods).

Comparison of Biological Macromolecules

Biological macromolecules differ in their monomer subunits, bonds, and functions.

Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells

Cells are classified as prokaryotic or eukaryotic based on structural features.

• Prokaryotes: No nucleus, no membrane-bound organelles (e.g., bacteria, archaea).

• Eukaryotes: Nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

Plant vs. Animal Cells

Plant and animal cells share many features but also have key differences.

• Plant Cells: Have cell walls, chloroplasts, and large central vacuoles.

• Animal Cells: Lack cell walls and chloroplasts; have centrioles.

Endomembrane System

The endomembrane system is responsible for the synthesis, modification, and transport of proteins and lipids.

• Components: Nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles.

• Function: Coordinates the production and distribution of cellular materials.

Cytoskeleton

The cytoskeleton provides structural support and facilitates movement.

• Microtubules: Hollow tubes; cell shape, chromosome movement.

• Actin Filaments: Thin fibers; cell movement, muscle contraction.

• Intermediate Filaments: Rope-like; mechanical strength.

Cell Division and the Cell Cycle

Chromosome Structure

Understanding chromosome structure is essential for studying cell division.

• Chromosomes: DNA-protein complexes carrying genetic information.

• Chromatids: Identical halves of a duplicated chromosome.

• Homologous Chromosomes: Chromosome pairs with the same genes.

Mitosis and the Cell Cycle

Mitosis ensures equal distribution of genetic material to daughter cells.

• Stages: Prophase, metaphase, anaphase, telophase.

• Cell Cycle Phases: M (mitosis), G1, S (DNA synthesis), G2.

• Checkpoints: Control progression and prevent abnormalities.

DNA Replication and Repair

DNA Structure and Replication

DNA replication is semiconservative, producing two identical DNA molecules.

• Key Enzymes: Helicase, topoisomerase, DNA polymerase, ligase, primase.

• Replication Bubble: Region where DNA is unwound for replication.

• Leading and Lagging Strands: Synthesized continuously and discontinuously, respectively.

DNA Repair

Cells have mechanisms to detect and repair DNA damage and mismatches.

• Mismatch Repair: Corrects errors missed during replication.

• Excision Repair: Removes damaged DNA segments.

Gene Expression and the Genetic Code

DNA vs. RNA

DNA and RNA differ in structure, function, and cellular location.

• DNA: Double-stranded, deoxyribose sugar, stores genetic information.

• RNA: Single-stranded, ribose sugar, involved in protein synthesis.

Central Dogma and Genetic Code

The flow of genetic information follows the central dogma: DNA → RNA → Protein.

• Transcription: DNA is transcribed to mRNA.

• Translation: mRNA is translated to a polypeptide chain.

• Genetic Code: Triplet codons specify amino acids; code is nearly universal and redundant.

Transcription and RNA Processing

Transcription Initiation and Elongation

Transcription is the process of synthesizing RNA from a DNA template.

• Key Components: Template and coding strands, promoter, RNA polymerase, ribonucleotides.

• Direction: RNA is synthesized 5' to 3'.

RNA Processing

In eukaryotes, mRNA is modified after transcription.

• Splicing: Removal of introns.

• 5' Cap and 3' Poly-A Tail: Added for stability and export from the nucleus.