Chemical Reactions in Biochemistry

General Chemistry - Physical Chemistry

• Physical chemistry is a branch of general chemistry
• Focuses on the structure and properties of matter

Matter

• Matter is anything that has mass and volume
• Examples of matter are cups, pens, and erasers
• Another definition of matter is anything composed of atoms and molecules
• Matter is ultimately made of protons, neutrons, and electrons

Structure of Matter

• Atoms are the building blocks of matter
• Atoms are constantly in motion
• Combinations of atoms form different materials with varied properties

Atoms

• Atoms are composed of protons, neutrons, and electrons
• Protons have a positive charge
• Neutrons have no charge (neutral)
• Electrons have a negative charge
• The nucleus, at the atom's center, contains protons and neutrons
• Electrons orbit the nucleus

Nucleus

• The nucleus is the positively charged center of an atom
• Protons and neutrons are found in the nucleus
• Protons have a positive charge
• Neutrons have zero charge

Atom

• Electrons orbit the atom's nucleus
• Electrons have a negative charge

Structure of Atom

• Atoms are of the order of 10-8 cm in size
• Nuclei are of the order of 10-12 cm in size
• Electrons are of the order of 10-16 cm in size
• Quarks are smaller than electrons; they compose protons and neutrons

Phases of Matter

• Matter exists in four phases (or states): solid, liquid, gas, and plasma
• Solids have definite mass, volume, and shape
• Liquid have definite mass and volume, but indefinite shape
• Gases have indefinite mass, volume, and shape
• Plasma is an ionized gas, exhibiting indefinite mass and volume, and an indefinite shape

States of Matter

• Matter's states depend on particle arrangement, energy, and distance between particles

Solid

• Solids have definite mass, volume and shape
• Particles of solids are tightly packed, vibrating in a fixed position

Liquid

• Liquids have definite mass and volume but do not have a definite shape
• Particles of liquids are tightly packed but are far enough apart to slide over each other

Gas

• Gases have no definite mass, volume and shape
• Particles of gases are relatively far apart and move freely

Plasma

• Plasma is an ionized gas
• Plasmas are good conductors of electricity and are affected by magnetic fields
• Plasmas have an indefinite shape and volume

Phase Changes

• Melting: solid to liquid
• Freezing: liquid to solid
• Vaporization: liquid to gas
  • Boiling: rapid type of vaporization
  • Evaporation: slow type of vaporization
• Condensation: gas to liquid
• Sublimation: solid to gas

Melting

• Melting is a solid-to-liquid change
• Melting typically occurs at a fixed temperature (melting point)
• In pure crystalline solids, this is a fixed temperature

Freezing

• Freezing is a liquid-to-solid change
• Freezing occurs at a fixed temperature (freezing point)

Vaporization

• Vaporization is liquid-to-gas change, including boiling and evaporation
• Liquids turn into gas when temperature is increased, and kinetic energy of molecules increases.
• Molecules escape into surrounding as vapors

Evaporation

• Evaporation is a type of vaporization
• Evaporation occurs at temperatures below the boiling point

Condensation

• Condensation is the change from gas to liquid
• Condensation results when water vapor cools to below its boiling point

Sublimation

• Solid changing to gas with no liquid phase in between
• Dry ice (solid carbon dioxide) sublimates at ordinary pressure and temperature

Intermolecular Forces

• Intermolecular forces are the forces that occur between individual particles of atoms, molecules or ions of a substance
• These forces relative to intramolecular forces are quite weak; ie covalent or ionic bonds

Kinetic Energy

• Kinetic energy is the energy an entity has because of its motion
• Work done on an object by applying a net force results in a gain of kinetic energy

Properties of Gases

• Gases consist of widely separated molecules
• The kinetic energy of gas molecules is greater than any attractive force
• Gases expand to fill their containers because of the lack of significant attractive forces

Properties of Liquids

• Liquids have strong intermolecular forces to hold molecules close together
• Liquids are less compressible than gases
• Liquids are more dense than gases
• Molecules of liquids are free to flow past one another
• Liquids assume the shape of their container

Properties of Solids

• Solids have strong intermolecular forces to keep their constituent molecules fixed
• Solids are less compressible due to lack of space between molecules
• Highly ordered arrangements of molecules produce solid crystals

Types of Intermolecular Forces

• Permanent dipole-permanent dipole forces (Kessom forces)
• Permanent dipole-induced dipole forces (Debye forces)
• Induced dipole-induced dipole forces (London or dispersion forces)
• Hydrogen bonding

Permanent Dipole-Permanent Dipole Forces

• Dipole-dipole forces exist between polar covalent molecules
• One molecule's (+) charged poles attract the (-) charged poles of other molecules

Permanent Dipole-Induced Dipole Forces

• Polar molecules can induce dipoles into nonpolar molecules
• Polar molecules induce dipoles in surrounding molecules

Induced Dipole-Induced Dipole Forces (London or Dispersion Forces)

• These forces are present between all molecules
• They arise from momentary, asymmetrical electron distributions

Hydrogen Bonding

• Hydrogen bonding is a strong type of dipole-dipole interaction between a hydrogen atom bonded to a highly electronegative atom (F, O, or N) and another highly electronegative atom in a neighboring molecule

Molecular Shape and Intermolecular Attraction

• Molecular shape affects the strength of intermolecular forces
• Linear shape molecules have a larger surface area, increasing intermolecular attraction
• Sphericity decreases dispersion forces

Carbohydrate Chemistry

• Carbohydrates are polyhydroxy aldehydes or ketones
• General formula is Cn(H2O)n
• They are the chief energy source in the human body (50-60%)

Classification of Carbohydrates

• Monosaccharides: contain one basic sugar unit
• Disaccharides: contain 2 monosaccharide units
• Oligosaccharides: contain 3 to 10 monosaccharide units
• Polysaccharides: contain more than 10 monosaccharide units

Monosaccharides Naming

• Named based on the presence of aldehyde or ketone groups, and the number of carbon atoms

Trioses

• Monosaccharides with 3 carbon atoms
• Aldotriose: Glyceraldehyde (parent sugar)
• Ketotriose: Dihydroxyacetone

Tetroses

• Monosaccharides with 4 carbon atoms
• Aldotetrose: Erythrose
• Ketotetrose: Erythrulose

Pentoses

• Monosaccharides with 5 carbons
• Aldopentoses: Ribose, arabinose, xylose and lyxose
• Ketopentoses: Ribulose and xylulose

Hexoses

• Monosaccharides with 6 carbon atoms
• Aldohexoses: Glucose, galactose, and mannose
• Ketohexose: Fructose

Ring (Cyclic) Structure of Sugars

• Open chain formulas of sugars fail to explain all reactions
• This indicates that the -CHO group must be masked or combined somewhat

Haworth and Chair Forms

• Cyclic forms of monosaccharides
• The 1-5 ring form is called pyranose
• The 1-4 ring form is called furanose

Mutarotation

• Mutarotation: change of specific rotation in optically active compounds; usually carbohydrates

Aldose-ketose isomerism

• Isomers with the same molecular formula but which differ in structure
• Glucose is an aldose
• Fructose is a ketose

Epimeric Carbon and Epimers

• Isomers that differ in configuration at only one asymmetric carbon
• D-glucose and D-galactose are epimers

Properties of Monosaccharides

• All monosaccharides are soluble in water
• Monosaccharides are optically active
• Monosaccharides can exist in a and ẞ forms, and exhibit mutarotation

Chemical Properties of Carbohydrates

• Oxidation: converting aldehyde group to aldonic acid; last alcoholic group to uronic acid; aldehyde and last alcoholic groups to saccaric acid
• Reduction: reducing aldehyde or ketone groups into alcohols
• Action of alkalis: isomerization; polymerization (aldol condition)
• Action of acids: phosphate esters; furfural derivatives (Molisch test)
• Fermentation: converting sugars into alcohol and CO2 by bacteria or yeast
• Osazone formation: forming yellow crystals by reacting with phenylhydrazine

Monosaccharide Derivatives

• Sugar acids
• Sugar alcohols
• Deoxy sugars
• Amino sugars
• Amino sugar acids
• Glycosidic bond and glycosides (Glycosides)

Glycosidic Bond and Glycosides (Glycosides)

• The bond between a carbohydrate and another compound; could be another monosaccharide or a noncarbohydrate (aglycone) group
• Glycosides are naturally occurring substances and often extracted as drugs

Disaccharides

• Formed from two monosaccharides bonded by a glycosidic bond
• Maltose (glucose + glucose, α(1→4) glycosidic bond)
• Isomaltose (glucose + glucose, α(1→6) glycosidic bond)
• Lactose (galactose + glucose, β(1→4) galactosidic bond)
• Sucrose (glucose + fructose, α(1→2) glycosidic bond)
• Cellobiose (glucose + glucose, β(1→4) glycosidic bond)
• Trehalose (glucose + glucose, α(1→1) glycosidic bond)

Polysaccharides

• Polymers of more than 10 monosaccharides
• Classified as homopolysaccharides or heteropolysaccharides

Homopolysaccharides

• Contain repeated same sugar units
• Starch (amylose and amylopectin): plants; storage form of glucose
• Glycogen: animals; storage form of glucose
• Cellulose: plant cell walls; fibrous material; ẞ-linkages

Heteropolysaccharides

• Contain two or more different repeated monosaccharide units
• Acidic: containing uronic acid + aminosugar (GAGs); e.g. hyaluronic acid, chondroitin 4,6-sulfate, dermatan sulfate, heparin sulfate
• Neutral: no uronic acid or sulfuric acid; e.g. blood groups, glycoprotein hormones

Specific Properties of TAG, Waxes

• TAG: (triacylglycerol): usually liquid at room temperature (is fats/oils)
• Waxes: typically solid at room temperature

Lipids: Definition and Classification

• Simple lipids: fatty acids + alcohol
• Compound lipids: fatty acids + alcohol + additional group
• Derived lipids: result from the hydrolysis of simple or compound lipids

Simple Lipids

• Neutral fats (triacylglycerols or TAGs): glycerol + fatty acids (storage form for fat)
• Waxes: fatty acids + long chain alcohol (like that used in cosmetics)

Properties of TAG

• TAG are soluble in fat solvents
• TAG rich in unsaturated fatty acids: typically liquid at room temperature
• TAG rich in saturated fatty acids: typically solid or semi-solid at room temperature
• Acrolein Test
• Hydrolysis
• Saponification: cleaved by alkali into glycerol and salts of fatty acids (soaps)
• Halogenation
• Oxidation (rancidification); occurs readily if unsaturated fatty acids are present

Complex (Compound) Lipids

• 1- Phospholipids (fatty acids + alcohol + phosphoric acid residues + nitrogenous base)
  • Glycerophospholipids: alcohol is glycerol
  • Sphingophospholipids: alcohol is sphingosine
• 2- Glycolipids (Fatty acid + sphingosine + carbohydrate)
  • Neutral glycolipids (Cerebrosides) : ceramide + monosaccharide
  • Acidic glycolipids (Gangliosides): ceramide + monosaccharide + one or more sialic acids
• 3- Lipoproteins: lipids conjugated with proteins; facilitates transport between blood and tissues
• 4- Sulfolipids
• 5- Aminolipids

Steroids and Sterols

• Cyclic compounds containing cyclopentanoperhydrophenanthrene ring
• Cholesterol: major sterol; found in cell membranes, precursor to steroid hormones and bile acids

5- Branched Chain Fatty Acids

• Primarily saturated fatty acids with branches in the hydrocarbon chain
• Phytanic acid (18C) is an example; it is formed by bacterial degradation of chlorophyll

6- Cyclic Fatty Acids

• Unusual class of minor fatty acids produced primarily by bacteria
• Cyclopropane and omega-cyclohexyl fatty acids are examples; found in bovine meat and dairy products

Classification of Fatty Acids

• Saturated fatty acids: no double bonds in the hydrocarbon chain
  • Examples include acetic acid (2C), butyric acid (4C), caproic acid(6C), caprylic acid (8C), capric acid (10C), lauric acid (12C), myristic acid (14C), palmitic acid (16C), stearic acid (18C), arachidic acid (20C), behanic acid (22C), and lignoceric acid (24C)
• Unsaturated fatty acids: 1 or more double bonds in the hydrocarbon chain
  • Examples include myristoleic acid, oleic acid, linoleic acid, linolenic acid, and arachidonic acid
• Essential fatty acids
  • Polyunsaturated fatty acids (PUFAs)

Omega-3 Fatty Acids

• Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are examples
• Found predominantly in fish
• Potential roles in disease prevention

Omega-6 Fatty Acids

• Linoleic acid (LA) and arachidonic acid (ARA) are examples
• Found in vegetable oils like corn, soybean, and cottonseed
• Possible roles in inflammation, growth and development

Cis- and Trans Fatty Acids

• Cis isomers: hydrogen atoms(on the same side of the double bond)
• Trans isomers: hydrogen atoms are (on opposite sides of the double bond); more common in processed foods; less healthy

Waxes

• Acetyl alcohols are present
• Long-chain fatty acids are present

Enzymes

• Protein catalysts produced from cells
• Increase the rate of chemical reactions
• Act in all living systems without changing themselves
• Have specific active sites, interacting with particular substrates, and requiring specific substrates, cofactors, etc.
• Nomenclature: -ase suffix to enzyme; also named according to their class and function (e.g. Oxidoreductase, transferases and hydrolases etc)
• Enzyme code (EC) numbers are used; have 4 digits and are an identifier for enzymes
• Factors affecting enzyme activity: substrate concentration, enzyme concentration, end product concentration, temperature, pH, time and activators / inhibitors

Enzyme Specificity

• Absolute specificity: enzymes act on only one substrate
• Relative specificity: enzymes act on one type of bond
• Structural specificity: enzymes act on specific structures of a molecule

Enzyme Classification

• 1 - Oxidoreductase: catalyzes oxidation-reduction reactions
  • Oxidases: form water
  • Hydroperoxidases: act on hydrogen peroxide; e.g. catalase, peroxidase
  • Dehydrogenases
  • Oxygenases
• 2 - Transferase: catalyzes the transfer of a functional group (other than hydrogen) from one substrate to another
• 3 - Hydrolases: catalyzes the hydrolysis of bonds by the addition of water
  • Glycosidases: act on glycosidic bonds
  • Estrases: catalyzes the hydrolysis of ester bonds
  • Lipidase
• 4 - Lyases: catalyze the addition or removal of atoms or molecules from substrates; do not involve water
• 5 - Isomerases: catalyze the interconversion of isomers - two isomer forms of the same molecule
• 6 - Ligases: catalyze the joining of two molecules using energy from ATP

Factors Affecting Enzyme Activity

• 1 - Substrate concentration
• 2 - Enzyme concentration
• 3 - End product concentration
• 4 - Temperature
• 5 - pH
• 6 - Time
• 7 - Activators: increase reaction rate (removing inhibitory peptides, reducing agent)
• 8 - Inhibitors:

Enzyme Inhibitors

• Competitive inhibitors
• Non-competitive inhibitors
• Uncompetitive inhibitors
• Irreversible inhibitors; e.g. lead, cyanide

Protein Structure

• Primary structure: sequence of amino acids
• Secondary structure: local folding of polypeptide chain (e.g. helices and sheets)
• Tertiary structure: complete 3D shape of a polypeptide chain
• Quaternary structure: multiple polypeptide chains

Denaturation of Protein

• Loss of native structure (natural conformation) caused by physical or chemical agents
• Example: heat, violent shaking, chemical agents, etc.

Protein Classifications

• Based on shape: fibrous proteins (long, rod-shaped) and globular proteins (compact, spherical)
• Based on function
  • Dynamic Function: (enzymes, hormones, contractile proteins
  • Structual function
• Based on composition: simple/conjugated proteins
• Based on biological value

Simple Proteins

• Albumins and globulins
• Protamines
• Histones
• Gliadins (prolamines)
• Glutelins
• Scleroproteins (e.g. keratin, collagen, elastin, ossein, reticulin)

Conjugated Proteins

• Phosphoproteins: contain phosphoric acid
• Glycoproteins: contain carbohydrates
• Lipoproteins: contain lipids
• Nucleoproteins: contain nucleic acids
• Chromoproteins: contain colored prosthetic groups
• Metalloproteins: contain metals as prosthetic groups (e.g. iron in hemoglobin)

Derived Proteins

• Hydrolytic by-products of proteins
• E.g. gelatin

Explore key concepts in biochemistry related to the oxidation of sugar aldehyde groups and phase changes in matter. This quiz includes questions about reducing reactions, the effects of temperature on these processes, and specific properties of amino acids. Test your knowledge and understanding of fundamental biochemical reactions and physical chemistry.