Biochemistry: Glycolipids and Mixtures

General Chemistry - Physical Chemistry - Matter

• Matter is anything that has mass and volume.
• Examples of matter include cups, pens, and erasers.
• Matter is composed of atoms and molecules.
• Atoms are made of protons, neutrons, and electrons.
• Protons have a positive charge.
• Neutrons have no charge.
• Electrons have a negative charge and orbit the nucleus.
• Atoms are constantly moving.
• The nucleus is the positively charged center of an atom.
• The combination of atoms leads to materials with a variety of properties.
• Atoms are the building blocks of matter.
• Atoms' sizes are on the order of 10⁻⁸ cm.
• Nuclei's typical size is about 10⁻¹² cm.
• Quarks' typical size is about 10⁻¹⁶ cm.
• Electrons' typical size is about 10⁻¹⁶ cm.

General Chemistry - Physical Chemistry - States of Matter

• Matter exists in four states: solid, liquid, gas, and plasma.
• Solids have a definite mass, volume, and shape.
• Liquid has a definite mass and volume but not a definite shape.
• Gases have no definite mass, volume, or shape.
• Particles in solids are tightly packed, vibrating about fixed positions.
• Particles in liquids are tightly packed but can slide past each other.
• Particles in gases are very far apart and move freely.
• Plasma is an ionized gas, a good conductor of electricity, and affected by magnetic fields.
• Examples of plasma include lightning, auroras, and neon.
• Matter changes state as more energy is added.

General Chemistry - Physical Chemistry - Phase Changes

• Melting: a solid changes to a liquid when heat is applied. This happens at a set temperature called the melting point for pure substances.
• Freezing: a liquid turns to a solid when its temperature is below the freezing point.
• Vaporization: a liquid turns to a vapor (gas) -- This includes evaporation (liquid to vapor at temperatures below the boiling point) and boiling (transition to vapor at the boiling point).
• Condensation: a vapor (gas) turns to a liquid.
• Sublimation: a solid turns directly to a vapor (gas).

General Chemistry - Physical Chemistry - Intermolecular Forces

• Intermolecular forces (van der Waals forces) are attractive forces between individual particles (atoms, molecules, or ions) of a substance.
• These forces are much weaker than intramolecular forces (covalent, ionic bonds).
• Molecular shape influences the strength of intermolecular attraction.
• Linear molecules have a larger surface area, enhancing intermolecular contact, and thus a stronger dispersion force compared to spherical molecules.

General Chemistry - Physical Chemistry - Kinetic Energy

• Kinetic energy is the energy an object or particle possesses due to its motion.
• The kinetic molecular theory of gases describes the behavior of gases reasonably accurately, focusing on the relationship between kinetic energy and intermolecular forces.
• The state of a substance depends on the balance between the kinetic energy of the individual particles and the intermolecular forces.

General Chemistry - Physical Chemistry - Properties of Gases, Liquids and Solids

• Gases are composed of widely spread molecules.
• Liquids have molecules that flow easily around each other.
• Solids have tightly packed molecules vibrating around fixed positions.
• Gases expand to fill their containers.
• Liquids take the shape of their containers.
• Solids maintain a fixed shape.
• Liquids and solids have a definite volume.
• Gases are less dense than liquids or solids.
• Unlike gases, liquids and solids are far less compressible.

General Chemistry - Physical Chemistry - Solutions

• A solution is a homogeneous mixture of two or more substances.
• It is composed of a solute (substance that dissolves) and a solvent (substance that does the dissolving).
• Solutions differ in the concentration of the dissolved solute.
• Solute concentration is expressed as the amount of solute in a certain amount of solvent at a particular temperature.

General Chemistry - Physical Chemistry - Solubility

• Solubility is the amount of a substance that will dissolve in a given amount of solvent under certain conditions (temperature and pressure).
• Factors affecting the rate at which solids dissolve in a liquid include temperature, particle size, and stirring/shaking.
• Generally, the solubility of solid solutes in liquid solvents increases with increasing temperature.

General Chemistry - Physical Chemistry - Types of Liquid Solutions

• Miscible solutions mean that liquids can easily dissolve into one another.
• Examples include water and ethanol, or water and acetone.
• Semi-miscible solutions can dissolve into one another under specific conditions.
• Examples include water and phenol, or water and ether.
• Immiscible solutions mean that liquids are not able to dissolve into one another.
• Examples include water and benzene or water and chloroform.

General Chemistry - Physical Chemistry - Solubility and Concentration

• Unsaturated solutions have a low concentration of solute dissolved under particular conditions.
• Saturated solutions have dissolved as much solute as possible under current conditions; they have the maximum concentration possible.
• Supersaturated solutions contain more solute than normally possible; they are unstable and can precipitate solute as conditions change.

General Chemistry - Physical Chemistry - Osmosis and Diffusion

• Osmosis is the diffusion of water through a semi-permeable membrane from an area of high water concentration to an area of low water concentration.
• Solutions can be classified into isotonic (same solute concentration as the cell), hypotonic (lower solute concentration than cell), and hypertonic (higher solute concentration than cell).
• Diffusion is the random movement of substances from an area of high concentration to an area of low concentration.
• Kidney dialysis is an example of diffusion.

General Chemistry - Physical Chemistry - Colloids

• A colloid is a heterogeneous mixture where particles are spread throughout a dispersion medium (liquid, solid, or gas).
• Examples of colloids include milk, fog, and smoke.
• Colloids have properties that differ from suspensions or solutions, including not separating into layers over time and not separating through filtration.
• Light scattering (Tyndall effect) can be used to distinguish colloids.
• Types of colloids include gels, sols, emulsions, and aerosols.

General Chemistry - Physical Chemistry - Applications of Colloids

• There are many applications for colloids in everyday life. For instance, colloids act as thickening agents in products such as lubricants, lotions, and toothpaste.
• Colloidal particles are involved in water purification.
• Colloidal solutions of silver bromide in gelatin are used in photography, while paints and inks in ballpoint pens use gel-based colloids.
• Colloidal dispersions are used for smoke screens in warfare.
• Colloidal materials' ability to adhere to the surfaces makes them useful in certain types of medications.

General Chemistry - Physical Chemistry - Properties of Colloids

• Colloids are heterogeneous mixtures with particles that are intermediate in size (smaller than suspensions, larger than solutions).
• They do not separate in layers over time.
• They do not separate through filtration.
• Light scattering (Tyndall effect) is used to distinguish them from other mixtures.

General Chemistry - Properties of Matter

• Matter is any substance that has mass and occupies space.
• Matter can exist in solid, liquid, or gaseous phases, depending on temperature and pressure.
• Matter is composed of basic building blocks called atoms and/or molecules.
• The properties of matter are determined by its composition and structure: Chemical properties describe how substances react with others. Physical properties describe the substance's appearance, state, and behavior.

Carbohydrate Chemistry

• Carbohydrates are polyhydroxy aldehydes or ketones.
• They are represented by the general formula Cₙ(H₂O)ₙ.
• They are the primary source of energy for humans.
• Carbohydrates are classified into monosaccharides (1 basic sugar unit), disaccharides (2 units), oligosaccharides (3-10 units), and polysaccharides (>10 units).
• Examples of carbohydrates include glucose, sucrose, amylose, and fructose.
• Naming often depends on the presence/absence of aldehyde or ketone groups in the molecule.

Carbohydrate Chemistry - Monosaccharides

• Nomenclature of monosaccharide names depends on the presence or absence of an aldehyde or ketone group, along with the number of carbon atoms present in the molecule.
• Trioses are monosaccharides containing 3 carbon atoms.
• Tetroses are monosaccharides containing 4 carbon atoms.
• Pentoses are monosaccharides containing 5 carbon atoms.
• Hexoses are monosaccharides containing 6 carbons.
• Monosaccharides can have a cyclic or a linear structure.
• α and β forms of sugars have slight differences in the arrangement of atoms around the anomeric carbon.

Carbohydrate Chemistry - Ring Structure of Sugars

• Open chain formulas of sugars fail to explain certain properties or reactions of specific sugars.
• Cyclic forms can mask or combine aldehyde/ketone groups to give better explanations of properties in sugar reactions.
• Sugars can exist in α or β configurations.

Carbohydrate Chemistry - Properties of Monosaccharides

• Most monosaccharides are highly soluble in water.
• They have properties related to optical activity.
• Monosaccharides can exist in a or ẞ forms.
• Monosaccharides undergo mutarotation.

Carbohydrate Chemistry - Isomerism

• Optical isomers differ in their spatial arrangement.
• A single asymmetric carbon atom leads to two possible forms (enantiomers).
• Monosaccharides with multiple asymmetric carbons have more possible forms.
• Isomerism is one of the ways to classify these types of molecules.

Carbohydrate Chemistry - Epimeric Carbon

• Epimers are isomers that differ in the configuration around only one specific carbon atom.

Carbohydrate Chemistry - Anomeric Carbon and Anomers

• The anomeric carbon is the carbon that undergoes change from the carbonyl group in the linear form to a hydroxyl group in the cyclic form.
• The cyclic isomers (α and β forms) of glucose are examples of anomers.

Carbohydrate Chemistry - Mutarotation

• Mutarotation is a gradual change in optical rotation observed in some monosaccharides in solution.
• The change in optical rotation occurs due to the interchanging of α and β forms in solution, leading to an equilibrium between these two forms.

Carbohydrate Chemistry - Aldose-Ketoses Isomerism

• Fructose and glucose have the same molecular formula but differ in their structural formula (one contains a keto group and the other an aldehyde).

Carbohydrate Chemistry - Chemical Properties

• Monosaccharides can be oxidized to form aldonic acids, uronic acids, or saccharic acids.
• They can also be reduced to form sugar alcohols.
• They can react with phenylhydrazine to form osazones, allowing different sugars to be identified by the structure of the resultant crystals.
• They can react with alkalis to form polymers or isomerize.
• They can react with acids.
• They can undergo fermentation.

Carbohydrate Chemistry - Monosaccharide Derivatives

• Sugar acids: are oxidized derivative of monosaccharides from aldehyde or hydroxyl group in position C1 and /or C6.
• Sugar alcohols: are the reduced derivatives of monosaccharides (lacks aldehyde or ketone groups).
• Deoxy sugars: have a hydroxyl group replaced by hydrogen.
• Amino sugars: have a hydroxyl group substituted by an amino group often acetylated.
• Amino sugar acids: condense amino sugars and some acids to make the building unit of structural polysaccharides.
• Glycosides: are formed by combining monosaccharides with other molecules with a bond from the hydroxyl group of the anomeric carbon.

Carbohydrate Chemistry - Disaccharides

• Maltose is composed of two α glucose molecules.
• Isomaltose is composed of two α glucose molecules.
• Lactose is composed of β galactose and β glucose.
• Sucrose is composed of α glucose and β fructose.
• Cellobiose is composed of two β glucose molecules.
• Trehalose is composed of two α glucose molecules.

Carbohydrate Chemistry - Polysaccharides

• Polysaccharides are polymers containing more than 10 monosaccharide monomers.
• They are classified as homopolysaccharides (same monomer) or heteropolysaccharides (different monomers).
• Examples of homopolysaccharides include starch (amylose and amylopectin), glycogen, and cellulose.
• Examples of heteropolysaccharides include hyaluronic acid, chondroitin sulfates, and keratin sulfate.

Lipid Chemistry

• Lipids are a diverse group of organic compounds, mostly composed of hydrocarbons and insoluble in water but soluble in nonpolar organic solvents.
• They play key roles in energy storage, cell membrane structure, and signaling.
• Lipids are classified as simple, compound, or derived lipids, along with miscellanous lipids.

Lipid Chemistry - Simple Lipids

• These are esters of fatty acids and alcohols.
• Examples include TAGs (triacylglycerols) and waxes.
• TAGs are the primary storage form of fat, while waxes have various functions including waterproofing and lubrication.

Lipid Chemistry - Compound Lipids

• These contain fatty acids, alcohols, and other components (e.g., phosphoric acid, nitrogenous bases, carbohydrates).
• They include phospholipids (glycerophospholipids -glycerol as alcohol- and sphingophospholipids -sphingosine as alcohol- ), glycolipids (neutral and acidic gangliosides), and lipoproteins (lipids combined with proteins).

Lipid Chemistry - Derived Lipids

• These are formed from simple or compound lipids when they are modified or broken down (e.g., through hydrolysis or oxidation).
• Examples include fatty acids, sterols (e.g., cholesterol), and eicosanoids.
• Sterols and steroids are cyclic compounds (e.g., cholesterol, ergosterol, vitamin D, bile acids).

Lipid Chemistry - Waxes

• Waxes are simple lipids with long-chain fatty acids esterified with long-chain alcohols.
• They are solids at room temperature.
• They have hydrophobic properties and are used for waterproofing, lubrication, and protection in various biological systems.

Lipid Chemistry - Fatty Acids - Classification

• Fatty acids are long-chain hydrocarbon molecules with a carboxyl group (-COOH) at one end.
• Fatty acids are classified based on their saturation (saturated vs. unsaturated), the presence of sulfur or hydroxy groups, or their chain branching (branched vs. unbranched) or cyclic nature.
• Saturated fatty acids have no double bonds between carbon atoms in the hydrocarbon chain.
• Unsaturated fatty acids contain one or more double bonds between carbon atoms in the hydrocarbon chain.
• Additional classification divides these unsaturated fatty acids into mono- and polyunsaturated forms based on the number of double bonds.

Lipid Chemistry - Fatty Acids - Properties

• Saturated fatty acids are typically solid at room temperature, while unsaturated fatty acids are usually liquid.
• The degree of unsaturation of a fatty acid influences its melting point.
• The presence of double bonds in unsaturated fatty acids creates bends in the molecules, preventing close packing.

Lipid Chemistry - Fat Constants

• Some key constants (e.g., saponification value, acid value, iodine value, acetyl value) are determined for fats and oils to assess purity, quality, and potential adulteration.

Protein Chemistry

• Proteins are complex organic compounds that are composed of long chains of amino acid residues joined together by peptide bonds.
• Proteins have vital functions in biological systems, including structural support, catalysis, transport, and signaling.
• Proteins are often classified based on their composition, shape, or biological function.

Protein Chemistry - Amino Acids - General Structure

• Structurally, amino acids have an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom (H), and a variable side chain (R group) connected to the central carbon (α-carbon).
• Amino acids are classified according to their R group chemical properties, and/or whether they are essential nutrients (must be consumed) or nonessential (body produces them).
• The R group differences create significant variations in the specific properties and functions of individual amino acids.

Protein Chemistry - Amino Acid - Classification

• Amino acids are classified into several groups:
  • Aliphatic (neutral).
  • Aromatic.
  • Basic.
  • Acidic.
  • Hydroxy containing.
  • Sulfur containing.
• Classification by nutritional value (essential/non-essential), the way they are broken down in metabolism (ketogenic/glucogenic).

Protein Chemistry - Amino Acids - Properties

Protein Chemistry - Derivation of Amino Acids

• Some amino acids undergo modifications after being incorporated into proteins.
  • 4-hydroxyproline
  • 5-hydroxylysine
  • Cystine

Protein Chemistry - Non-Protein and Non-α-Amino Acids

• These are amino acids that are not found in proteins but play vital roles in metabolic processes.
  • Alanine,
  • Glutathione, and others.

Protein Chemistry - Peptide Bonds

• Peptides are short chains of amino acids.
• Larger peptides, polypeptides, and proteins are chains of more amino acids.

Protein Chemistry - Protein Structure

• Proteins have four levels of structure:

1. Primary: simple linear sequence of amino acids.
2. Secondary: folding patterns (α-helix, β-sheet).
3. Tertiary: overall 3-D shape of the polypeptide chain.
4. Quaternary: 3-D assembly of multiple polypeptide chains.

Protein Chemistry - Protein Denaturation

• Denaturation is the unfolding of a protein's 3-D structure.
• This occurs under certain conditions (e.g., high temperatures, non-polar solvents, changes in pH), and often results in decreased function.
• The structure disruption leads to changes in the protein’s physical or chemical properties.

Protein Chemistry - Protein Properties

Protein Chemistry - Protein Classification