Water Chemistry and Hydrogen Bonding

Chemistry of Life Overview

• This unit explores the chemical foundations of life, focusing on biological macromolecules like proteins and nucleic acids.
• Aims to provide a better understanding of the chemical properties that make life possible.

Structure of Water and Hydrogen Bonding

• Water's essential role in life is emphasized due to its unique and complex properties.
• Topics covered include hydrogen bonding, capillary action, surface tension, cohesion, adhesion, solvent properties, specific heat, heat of vaporization, and density.
• Importance of water for life is discussed.

Hydrogen Bonding in Water

• Hydrogen bonds are relatively weak bonds that form between water molecules due to their polarity.
• These bonds are responsible for many of water's unique properties.

Hydrogen Bonds in Water

• Water is a polar molecule with a partial positive charge on hydrogen atoms and a partial negative charge on the oxygen atom.
• Positive areas of one water molecule are attracted to negative areas of another, forming a hydrogen bond.
• Each water molecule can form hydrogen bonds with up to four other water molecules.

Capillary Action and Meniscus

• Capillary action is the movement of water within a narrow space due to cohesion and adhesion.
• A meniscus is the curved surface of water in a tube, resulting from adhesion to the tube walls and cohesion among water molecules.

Surface Tension

• Surface tension is the property of a liquid that allows it to resist an external force, due to the cohesive nature of its molecules.
• Water has a high surface tension, allowing small insects to walk on it

Cohesion and Adhesion of Water

• Cohesion is the attraction between water molecules, allowing for high surface tension.
• Adhesion is the attraction between water molecules and other surfaces, aiding capillary action.

Water as a Solvent

• Water's polarity makes it an excellent solvent, capable of dissolving many ionic and polar substances.
• Hydrophilic substances dissolve in water, while hydrophobic substances do not.

Specific Heat, Heat of Vaporization, and Density of Water

• Water has a high specific heat, meaning it requires a lot of energy to change its temperature.
• Water has a high heat of vaporization, requiring a lot of energy to evaporate.
• Water's density is unique because it is less dense as a solid (ice) than as a liquid, allowing ice to float.

Importance of Water for Life

• Water's properties are essential for various biological processes.
• These include temperature regulation, transportation of nutrients, and as a medium for chemical reactions.

Elements of Life

• Focuses on the elements crucial for life, particularly carbon.
• Key concepts include: elements, atoms, carbon's role as a building block, hydrocarbons, functional groups, and elemental building blocks of biological molecules.

Elements and Atoms

• Elements are substances that cannot be broken down into simpler substances by chemical means, composed of atoms.
• Atoms are the smallest unit of matter that retains the chemical properties of an element.

Matter, Elements, and Atoms

• Matter is anything that has mass and takes up space, composed of elements.
• Elements are made of atoms, which consist of protons, neutrons, and electrons.

Carbon as a Building Block of Life

• Carbon is fundamental to life due to its ability to form stable bonds with many other atoms, including itself.
• This allows for the creation of large, complex molecules.

Carbon and Hydrocarbons

• Carbon atoms can form diverse structures, including chains, rings, and branched structures.
• Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, serving as a primary source of energy.

Functional Groups

• Functional groups are specific groups of atoms attached to carbon skeletons that determine the properties and reactivity of organic molecules.
• Examples include hydroxyl (-OH), carbonyl (C=O), carboxyl (-COOH), amino (-NH2), and phosphate (-PO4).

Elemental Building Blocks of Biological Molecules

• Key elements such as carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur are essential for building biological molecules.
• These elements combine to form monomers, which then polymerize into larger macromolecules.

Introduction to Biological Macromolecules

• This section covers the basics of chemical bonds (ionic and covalent) and the introduction to macromolecules.
• Also covered are dehydration synthesis and hydrolysis.

Ionic Bonds

• Ionic bonds are formed through the transfer of electrons between atoms, creating ions (charged particles)
• These bonds occur due to attraction between positive and negative ions.

Covalent Bonds

• Covalent bonds involve the sharing of electrons between atoms.
• They result in a strong bond that holds atoms together in a molecule.

Chemical Bonds

• Chemical bonds are attractive forces that hold atoms together.
• These include ionic bonds, covalent bonds (polar and nonpolar), and hydrogen bonds.

Introduction to Macromolecules

• Macromolecules are large organic molecules necessary for life, including carbohydrates, lipids, proteins, and nucleic acids.
• They are polymers assembled from smaller monomer subunits.

Dehydration Synthesis

• Dehydration synthesis (or condensation reaction) is a chemical reaction where monomers combine to form a polymer by releasing a water molecule.
• This process builds larger molecules from smaller ones.

Hydrolysis

• Hydrolysis is a chemical reaction where a polymer is broken down into monomers by adding a water molecule.
• This process breaks down larger molecules into smaller ones.

Properties, Structure, and Function of Biological Macromolecules

• Focuses on the detailed structure and functions of DNA, RNA, amino acids, proteins, carbohydrates, and lipids (triglycerides).
• Includes saturated, unsaturated, and trans fats.

Molecular Structure of DNA

• DNA is a double-stranded helix composed of nucleotide monomers.
• Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine, guanine, cytosine, or thymine).

Antiparallel Structure of DNA Strands

• DNA strands run antiparallel, meaning they are oriented in opposite directions (5' to 3' and 3' to 5').
• This arrangement is crucial for DNA replication and transcription.

Molecular Structure of RNA

• RNA is typically single-stranded and composed of nucleotide monomers.
• Each nucleotide consists of a ribose sugar, a phosphate group, and a nitrogenous base (adenine, guanine, cytosine, or uracil).

Introduction to Amino Acids

• Amino acids are the building blocks of proteins.
• Each amino acid has an amino group, a carboxyl group, a hydrogen atom, and a unique R-group (side chain) attached to a central carbon atom.

Overview of Protein Structure

• Proteins have four levels of structure: primary (amino acid sequence), secondary (local folding patterns like alpha-helices and beta-sheets), tertiary (overall 3D shape), and quaternary (arrangement of multiple polypeptide chains).

Introduction to Carbohydrates

• Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen in a ratio of 1:2:1.
• They include monosaccharides, disaccharides, and polysaccharides.

Carbohydrates

• Carbohydrates serve as a primary source of energy and provide structural support in cells.
• Monosaccharides (e.g., glucose, fructose) are simple sugars, disaccharides (e.g., sucrose, lactose) are composed of two monosaccharides, and polysaccharides (e.g., starch, cellulose) are complex carbohydrates.

Molecular Structure of Triglycerides (Fats)

• Triglycerides are lipids composed of a glycerol molecule and three fatty acid molecules.
• Fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds).

Saturated Fats, Unsaturated Fats, and Trans Fats

• Saturated fats are solid at room temperature and have no double bonds between carbon atoms.
• Unsaturated fats are liquid at room temperature and have one or more double bonds.
• Trans fats are a type of unsaturated fat with a specific configuration around the double bond, often produced industrially and associated with health risks.

Biological Macromolecules Review

• Macromolecules are large organic molecules essential for life.
• Carbohydrates, lipids, proteins, and nucleic acids and their respective functions and structures are important.

Nucleic Acids

• Focuses on DNA and RNA molecular structures, and antiparallel structure of DNA strands.

DNA

• DNA (deoxyribonucleic acid) is a nucleic acid carrying genetic instructions for all known living organisms and many viruses.
• DNA consists of two strands that coil around each other to form a double helix.
• The DNA carries genetic information.

Molecular Structure of DNA

• DNA is composed of nucleotide monomers, each consisting of a deoxyribose sugar, a phosphate group, and a nitrogenous base (A, T, C, or G).
• The bases pair specifically: adenine (A) with thymine (T), and guanine (G) with cytosine (C).

Antiparallel Structure of DNA Strands

• DNA strands run antiparallel, meaning they are oriented in opposite directions (5' to 3' and 3' to 5').
• This arrangement allows for proper base pairing and DNA replication.

Molecular Structure of RNA

• RNA (ribonucleic acid) is typically single-stranded and composed of nucleotide monomers.
• Each nucleotide consists of a ribose sugar, a phosphate group, and a nitrogenous base (A, U, C, or G).

Nucleic acids

• Nucleic acids are polymers made of nucleotide monomers.
• DNA and RNA are essential for storing and expressing genetic information.