Molecular Polarity and Biological Substances

• Biochemistry is the investigation of chemical structures, functions, and properties of biological molecules involved in common cellular processes and reactions.

Overall expectations of this unit

• Technological applications of enzymes are analyzed in industrial processes and advances evaluated in cellular biology
• The structures, functions, and properties of molecules involved in cellular processes and biochemical reactions are investigated.
• Understandings of the structures and functions of biological molecules and reactions required to maintain normal cellular processes are demonstrated.

Big ideas in biochemistry

• Uses of technological applications that affect biological processes and cellular functions are seen in industries like food, pharmaceutical, etc
• Properties of biological molecules affect biochemical reactions and cellular processes.
• Biochemical compounds have important structural and functional roles in living organism cells.

Focus on STSE: Promoting the good fats

• Omega-3 fatty acids are essential fatty acids that maintain human health
• Humans cannot produce omega-3 fatty acids, so they get them from food consumption
• Sardines, salmon, and mackerel are rich sources of omega-3 fatty acids as well as nuts, oils, and other plant sources.
• Omega-3 fatty acids play a significant role in brain function, cardiovascular health, and the production of healthy skin
• The Heart and Stroke Foundation of Canada recommends eating fish at least twice a week to maintain optimal Omega-3 levels
• A diet rich in Omega-3 reduces the risk of inflammation and may help reduce chronic diseases, such as cancer, heart disease, and arthritis
• Human brain neurons use Omega-3 fatty acids for important cognitive and behavioral functions.
• Babies whose mothers lack omega-3 fatty acids in their diet during pregnancy have a greater risk of developing vision and nerve problems.
• Omega-3 fatty acids can treat number of conditions in adults, such as high cholesterol, depression, diabetes, high blood pressure, skin disorders, and asthma
• People who don't consume enough omega-3’s in their diet may suffer from fatigue, heart problems, dry skin, mood swings, poor memory, and poor circulation.
• It is important to obtain a balance of all nutrients in your diet to ensure the proper functioning of cells

Fundamental concepts of chemistry

• Matter is composed of elements, that cannot be broken down into simpler substances by physical or chemical techniques
• The smallest particle of an element is an atom
• Atoms bind to each other chemically in ratios to form molecules
• A chemical compound is a stable combination of different elements held together by chemical bonds
• All carbon-containing compounds in organisms primarily consist of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).
• The four elements: carbon, hydrogen, oxygen, and nitrogen make up 96% of the weight of a living organism
• 4% of the weight of a living organism consists of seven other elements: chlorine, potassium, phosphorus, calcium, sodium, sulfur, and magnesium
• Organisms require trace elements such as iodine and iron
• Atoms are composed of protons, electrons, and neutrons
• The number of protons determines its elemental identity
• Protons and neutrons are located in the nucleus, while electrons are located in the region surrounding it
• Protons have a positive charge, electrons have a negative charge, and neutrons have no charge.
• Number of protons is equal to the number of electrons, giving the atom no net charge
• The atomic number is equal to the number of protons
• The mass number is the total number of protons and neutrons
• Electrons are not included in the mass number because their mass is negligible
• Isotopes are forms of the same element with different atomic masses and a different number of neutrons
• Isotopes of the same element behave the same way in chemical reactions
• Radioisotopes unstable isotopes that give off particles and energy
• Radiation from decaying isotopes can damage molecules in living cells, harming the organism
• The rate of decay of a radioisotope is independent of environmental conditions and chemical reactions
• Radioactive tracers are radioisotopes used to follow a specific chemical through a reaction.
• A radioisotope gives off a radioactive signal, so they are easily detectable in a cell
• Radioisotopes can be used in biological, medical, and chemical research
• A pioneer of photosynthesis, Melvin Calvin used ¹⁴C-labeled molecules to determine the sequence of reactions in photosynthesis.

Review of Electron Arrangements

• Electron arrangements are the determining factor for the chemical properties of an atom
• The number of electrons is equal to the number of protons in the nucleus in an electrically neutral atom
• Electrons move around the atomic nucleus in orbitals
• An orbital is a region of space that can be occupied by one or two electrons
• The most balanced condition is reached when the orbital contains two electrons.
• Orbitals group into energy levels, or shells, numbered 1, 2, 3, and so on, based on distance from the nucleus
• The innermost shell of an atom can hold a max two electrons.
• The second and third shell can hold up to 8 and 18 electrons, respectively.
• The first electron shell (1s orbital) is a spherical orbital
• Hydrogen contains only one electron that occupies one 1s electron orbital
• Helium has two electrons occupying one 1s electron orbital
• Atoms with greater than two electrons have higher energy levels
• Second energy level consists of a 2s and three 2p orbitals
• The 2p orbitals have three 2p orbitals bisecting the center at right angles
• The orbital an electron occupies determines its energy level
• The farther away the electron is from the nucleus, the greater is energy
• Large atoms consist of some higher energy electrons occupying d and f orbitals with more complex shapes
• Valence electrons are in an atom's outermost energy shell, or valence shell
• Atoms with an incomplete shell tend to be chemically reactive
• Inert atoms have a complete outermost energy level
• In order to complete their outermost shell, atoms can gain, lose, or share electrons.
• All elements in living organisms have unfilled outermost shells and can participate in reactions with other atoms
• Stable charged ions are formed in some atoms when they gain or lose electrons
• Atoms become more stable when they share electrons allowing valence orbitals to be filled
• Sharing of electrons through hybridized electron orbitals produces chemical bonds, underlying most biological molecules

Chemical Bonds

• Atoms of inert elements occur naturally as single-atom forms.
• Atoms of reactive elements form stable attractions to one another called chemical bonds
• Four main types of chemical bonds in bio-molecules include ionic bonds, covalent bonds, and intermolecular forces
• Ionic bonds are formed when atoms have lost electrons and become charged
• Ions of opposite charge are strongly attracted to one another, leading to an ionic bond
• Ions are strongly attracted to water molecules, causing ionic compounds to dissolve in water and form hydrated ions
• Covalent bonds are formed when atoms share one or more pairs of valence electron
• The strength of the bond depends on the electronegativity
• In molecular diagrams, a dash or dots are used to represent pairs of shared electrons in a covalent diagram
• Shared orbitals that form covalent bonds extend between atoms at specific angles (covalently bound molecules have distinct three-dimensional forms)
• Carbon has four electrons in its valence shell so it can bond with four atoms with the tetrahedral molecular shape
• Polarity is influenced by electronegativity (oxygen has a very high electronegativity because additional electrons can occupy valence orbitals close to the nucleus)
• Unequal sharing of electrons produces a polar bond and an unequal distribution of charges on a molecule
• Polar molecules tend to be soluble in water, while non-polar molecules have low solubility

Intermolecular Forces

• Intermolecular forces are forces of attraction between molecules
• Intermolecular forces are also known as Van der Waals forces (influence physical properties of substances and act between similar and different molecules)

Hydrogen Bonds

• The hydrogen atom becomes attracted to a strongly electronegative atom in different molecule or same molecule.
• Hydrogen bonds are stronger and more useful than van der waal forces.
• Cohesion is the staying of water molecules together with help of hydrogen bond lattice
• Hydrogen bonds are weaker and easier to break compared to covalent and ionic bond when there is increase in temperature

Other Van Der Waals Forces

• Attract electrons of one molecule to the nuclei of another molecule.
• Size and shape affects van der Waals forces of attraction
• Hydrogen chloride also attracts between a positive and negative with interactions of molecule

Chemical Reactions

• There are thousands of different chemical reactions that are classified as dehydration, hydrolysis, neutralization, and redox reactions
• Dehydration reactions removal of AH and H from two reactant molecules and bond them (Most common method)
• Hydrolysis reactions are opposite of dehydration reactions (water is a reactant and it splits larger molecules into smaller)
• Neutralization reactions involves acids and bases producing salts.(water is also often produced)
• Redox reactions Named for “reduction” and “oxidation, electrons are lost and gained by another atom. (Oxidation refers to loss of electrons and reducing is gain of electrons)

Water

• Up to 60% of human body weight comes from water
• Up to 90% of lungs, 70% of Brain and 22% of bone tissue is water
• Most substances dissolve in water (excellent solvent)
• Water dissolves in blood and thousands of solutions for life

Properties

• Abundant liquid (the “universal solvent"). Water molecules consist of a polar structure.
• Water can associate with hydrogen bonding. hydrogen bonds form with liquid water and Ice
• Liquid water forms an average of 3.4 hydrogen and the molecules of liquid water allow water molecules to slip and reform the lattice of
• Hydrogen bonds forms with molecules and allow water molecules to slip

Water Lattice

• Rigid for water molecules- Each molecule in ice consist of four hydrogen bonds and space water molecules farther apart than other molecules

• Density is more Unusual

• Water has the properties of being 10% less dense in its solid state

• Water is good with heat capacity- the amount of thermal energy requires and increase of temperature by 1 degree Celsius

• A significant percentage of thermal energy and high temperature is use to break bonds in bodies

• Temperature will rise slowly as thermal energy is added so Hydrogen need high temperature and lot of energy.

• Stabilizing hydrogen bonds will causes water to have high specific heat capacity

• High bonding results with water molecules staying closed ( property Called cohesion)

• Related to definition of how long surface may go before stretching.

The Hydrogen

• Causes molecule to bond with more other polar molecules call Adhesiaon

Aqueous Solutions

• Water molecules consist of small and strong polar, Helps surrounds charged ions and polar molecules of substances ( coat of water , hydration shell)

Solvent vs Solute

• Solvent is water and and Solutes are other substances which dissolve in water for solution
• Substance of sodium chloride and sodium ions break when mixed with H2O
• Electrolyte interaction reduces water molecules around macromolecules like nucleic acid and sugar
• Attracted molecule to water are hydrophilic , and not attracted molecules are hydrophobic
• Autoionization Process in molecules easily separate into ions

Water: Review of Ionization and pH

• Water: Critical properties and bonding to separate into ions
• Sample of water with a sample consist of H2O molecule , Oh- ions. and H3O+ Ions
• two in roughly every550 million h2o , will react to form two hydrogen ions called auto ionization water
• autoionization produces with hydroxide ions or an equal number
• concentration with hydronium ions are higher when a property of an acid is higher and creates sour and conducts electronic as well as turns into a color

Acids:

• Increased amount will cause burn with one ionizing hydrogen
• Strong Acid: 100 % of Acid and hCL releases that in turn relates hydrogen bonds with h20 which in turn related to releases or ions increases and is classified strong
• Strong Base: Relates H20 an 100 oh- increase with hydrogen bonds to h20 which are known as Hydroxide

Base:

• High and enough it will cause burn and Base helps increase oh- for H2O.

Acids and base reactions

• Reaction will create base and h2Os chemical result

• High level water or 7 mean it has base or acidic

• The process is called Neutrailiztion

• Chemicals or Buffers are chemical which balances PH and reduce too big PH and water solution

• Week Acid: reverses H+ ions bond with water molecules since has been in extra molecules

Carbon

• Consist atoms which are mainly base and organic
• Its is unique becacuse bonds that form has branching , change structure molecules bonds and allows form to substances like rings or diamonds.

Carbon chains

• Are mostly hydrogen and oxygen molecules with rings/ chains or a complex with hydrogen structure
• carbon atoms in biological molecules form an carbon molecules. Carbon can be rings or branch which allows form polymers and sugar chains
• With single bonds with double and triple is almost endless however are used in biological molecules. and
• there are 4 groups Carbohydrates lipids fats protein and nucleic acids, carbon is 4 bonding with chains which allows.

Functional GroupS

• Groups allow degradation and synthesis of carbohydrates, lipids fats nucleic and protein
• functional groups groups are mainly ioni or molecules which allows influence the property of water and molecules
• Functional groups act ad " Handles that attract groups strongly and is in order to a chemical group in what chemical react and form a bond.
• Polar groups act as "handles in order to act attraction or get dissolve in the cytosole
• The comparison with ethane give us example which gives polar groups influence physical molecules the ethanol is polar and high and alcohol in alcohol