Organic and Inorganic Molecules

• Organic and inorganic molecules are fundamental to life.

Inorganic Molecules

• Typically not derived from living organisms.
• Usually lack both carbon and hydrogen in the same molecule.
• In normal conditions, they return to their original state.
• Examples include water, ammonia, hydrogen, sulfide, metals, and calcium.

Organic Molecules

• Previously thought to only come from living organisms
• Must contain both carbon and hydrogen, though they don't need to be adjacent.
• Most can now be synthesized in a lab.
• Can be irreversibly altered if energy is added or taken away beyond a certain threshold
• Examples include carbohydrates, fats, proteins, and nucleic acids.

Comparing Water and Organic Molecules

• Water is liquid at room temperature and can change to ice, steam, and back to liquid which makes it inorganic.
• Organic molecules cannot return to their original state.
• Cooking an egg is an example of the irreversible change to an organic molecule.

Classifying Molecules as Organic or Inorganic

• CH4 (methane) is organic.
• CO2 (carbon dioxide) is inorganic.
• NaCl (salt) is inorganic.
• C6H12O6 (glucose/fructose) is organic.

Carbon's Special Properties

• Carbon's atomic number is 6.
• Carbon has 4 valence electrons in its outer shell.
• Carbon tends to share electrons rather than donate or receive them.
• Carbon is "friendly" and readily shares electrons to achieve a full outer shell of 8 electrons.
• Carbon can form bonds with many other molecules in various configurations.
• Carbon's versatility makes it a versatile molecule and a foundation for complex structures.
• Carbon forms covalent bonds, sharing electrons, with up to four other atoms.
• A Lewis dot structure shows methane with carbon covalently bonded to four hydrogens.

Representing molecules

• Molecules can be shown by using stick diagrams
• A stick diagram of methane illustrates carbon forming covalent bonds with four hydrogens.
• Carbon always has four sticks around it, representing its tendency to form four bonds because it needs to get 8 electrons in its valence shell.
• Each stick in the diagram is a shared pair of electrons.

Double and Triple Bonds

• Atoms can share two or three pairs of electrons, known as double or triple bonds.
• Carbon often forms double bonds with other elements or another carbon atom.
• A doulbe bond is represented by =
• In carbon dioxide (CO2), carbon shares a double bond with each oxygen atom.
• Each bond represents two electrons, totaling eight valence electrons.
• Carbon can be double-bonded to two molecules instead of singly bonded to four.

Carbon Skeletons

• Carbon skeletons can form diverse molecular shapes.
• Carbon backbone provides the internal structure of molecules.
• A chain of carbons forms the core of many molecular structures.
• Molecules containing only carbon and hydrogen are hydrocarbons.

Functional Groups

• Most organic molecules have a carbon backbone.
• The characteristics and function of a molecule depends on which atom groups are connected to this carbon backbone.
• A functional group is an atom combination attached to the carbon backbone that reacts consistently.
• Functional groups impact the molecule's function and characteristics.
• Estradiol and testosterone have the same carbon backbone but different functional groups, leading to different effects in the body.
• Estradiol has a hydroxyl functional group therefore female traits
• Testosterone has a carbonyl functional group therefore male traits
• Carboxyl and animo groups are in amino acids (a type of biomolecule)

Common Functional Groups

• Hydroxyl Group: -OH, alcohol properties to hydrocarbon chains, polar, attracts water easily.
• Carboxyl Group: -COOH, gives acid properties to hydrocarbons, donates H+ to decrease pH.
• Amino Group: -NH2, gives amine characteristics to hydrocarbons to form amino acids.

Isomers

• Isomers are molecules that share a chemical formula but differ in structure.
• Molecules with the same number of atoms of each type but arranged differently are isomers.
• If molecules have a different number of atoms of each type, they are two completely different molecules.
• Glucose and fructose (C6H12O6) are isomers with the same formula but different atom arrangements.
• Atom rearrangement changes the sugar's taste.

Organic Molecule Vocabulary

• Monomer: A small molecule that links with others to form larger molecules.
• Dimer: Two monomers joined together.
• Polymer: A large molecule composed of repeating monomer subunits.
• Macromolecule: Large and complex molecules made of multiple polymers.

Dehydration Synthesis

• Polymers are assembled the same way: removing a hydroxyl group (OH) from one subunit and a hydrogen (H) from another to form a covalent bond.
• Water (H2O) removal connects two subunits.
• Dehydration synthesis requires energy.
• Dehydration synthesis removes water to build polymters

Hydrolysis

• This is breaking down polymers
• It is the opposite of dehydration synthesis, water is added
• Hydrolysis releases energy
• Adding water to split a polymter into monomers

Enzymes

• Enzymes are required to perform dehydration synthesis or hydrolysis
• Speical proteins bing monomers close together and helps facilitate the reaction
• Cell use enzymes reactions and enabling cells to obtain available energy sources
• Reactants or substrates bind to one or more specific molecules
• Binding happens in a site called the active site
• The substrates bind to the active site, forming an enzyme-substrate complex
• As a result, chemical bonds weaken to link together
• Eventually a chemical reaction occurs and leads to the formation of a different molecule called the product

Building Blocks of Life

• Organic molecules can be found in living organisms in four forms
• CHO for Carbohydrates equal a 1:2:1 ration.
• Lipids (fats) are CHO with fewer O and more H.
• Proteins are CHONR.
• Nucleic acids are CHONP.
• “R” represents a particular functional group that determines protein function.
• "P" represents a phosphorus group

Carbohydrates

• Biomolecules contain carbon, hydrogen, and oxygen at a 1:2:1 ratio.
• Can represent the elements' proportion inside carbohydrate molecules with the CH20 formula
• Most carbohydrates are characterized as monosaccharides, disaccharides, or polysaccharides

Monosaccharide

• Monosaccharide is another word for term "saccharide"
• The prefixes mono, di and poly refer to how many sugars are in the molecules
• A one-unit of sugar carbohydrate
• The building block (monomers) of all carbohydrates
• Examples are glucose, fructose, galactose, ribose, deoxyribose
• Glucose is abundant, water-soluble, easily transported through the body and a cellular respiration energy source and ATP production
• Fructose is the primary monosaccharide in fruit and plants
• Galactose is the primary monosaccharide in milk
• C6H12O6 is the chemical formula of all monosaccharides which have 6 carbon sugars

Dissacharides

• Carbohydrates with two units of sugar
• When monosaccharides join, dehydration reactions create glycosidic linkages
• Maltose (malt-sugar) = two glucose molecules
• Sucrose (table sugar) = glucose + fructose.
• Lactose (milk sugar) = glucose + galactose.

Polysaccharides

• Carbohydrates with multiple sugar units bonded
• Glucose monomers linking together form long chains.
• Long glucose unit chains ideal to store energy
• Chains can have straight or branched formation
• Plants store energy as straight amylose or branched amylopectin,
• Animals store energy as glycogen, a highly branched polysaccaride
• Cellulose, chitin, and peptidoglycan are structural molecules
• Most abundant polysaccharide = cellulose = glucose polymer with different bonds between the glucose units, therefore most organisms cannot break these bonds
• In animals and fungi, chitin is a structural polysaccaride and makes up the exoskeleton (in insects and crustaceans)
• Peptidoglycans have are complex polysaccharides which are found in bacteria cell walls

Carbohydrates vs Sugars

• Carbohydrates are frequently referred to as either basic sugars or complex carbohydrates.
• Simple sugars are monosaccharides and disaccharides
• Polysaccharides are complex carbohydrates
• Sugars end often end in -ose

Lipids

• Lipids are insoluble, nonpolar (hydrophobic) molecules that are insoluble with water molecules
• Lipids are used for protection insulation and lubrication and also for storing energy

Lipid Groups

• Trigylcerides
• Phospholipids
• Steriods
• Waxes
• Lipids and water don't mix because lipids are hydrophobic

Triglycerides

• Includes both fats and oils
• Fats (ie lard and butter are solid in room temperature and are used by animals for isolation and protection.
• Oils (ie corn oil and olive oil) are liquid in room temperature and are used by plants for long-term energy storage.
• A triglyceride contains by two subunit molecules: Glycerol and Fatty acids

Fatty Acids

• A fatty acid has 3 main parts: A carbon and hydrogen atom chains = hydrocarbon chain. A methyl group at one end and an acid group at the other end.
• Can either be saturated or un-saturated: A saturated fatty acid has a single carbon to carbon bond because the carbon chain is "saturated with all the hydrogen atoms it can hold. Unsaturated fatty acids have one double bond and a bend in the molecule. Animal fats are stable at room temperature, vegetable oils liquid.
• Trans-fat; hydrogen atoms are on opposite sides of the double-bond/ increase shelf life and melting point

Triglyceride Synthesis

• 3 separate fatty acids have to bond with a glycerol molecule though dehydration synthesis

Phospholipids

• Like, triglycerides, they contain glycerol and two fatty acids
• Unlike triglycerides, they have a phosphate group rather than a acid group

Phospholipids and Water

• Phospholipids have water in regards to their properties
• Phosphate's head mix well with water
• Hydrophilic tails do not mix with water and therefore phospholipids only have hydrophilic tails interact with a watery environment.
• This is a major component of plasma membranes

Steriod Rings

• steriods have 4 fused carbon rings, their different functions groups are attached
• Cholesterol is the steriod molecule which steriods use such as testosterone, estrogen, vitamin D, and cortisone to synthesis
• Cholesterol can stabilise the membrane when present,
• Testosterone/ estrogen have minor function groups, but large differences on their effects on an organism

Wax

• Is non-polar
• Repels water
• Used for protection for leaves, animals, and in ears and produce honeycombs

Proteins

• Proteins are made of long amino acid chains
• They all have a similar structure (carboxyl and amino function groups)

Amino Acids

• What makes the amino acid unique is a R group which gives each amino acid its chemical properties
• Linked together by peptide bonds.
• Polypeptide develops multiple levels of structure which all determine its shape
• These includes primary, secondary, tertiary, and quaternary structures

Protein - Primary Structure

• It is the order of amino acids in the polypeptide chain
• Amino acids are likened to letters in the alphabet, like how words are arranged, proteins are arranged too.

Protein - Secondary Structure

• Refers to the pleated sheet and alpha helix that a protein chain can form due to hydrogen bonding
• The overall shape of a polypeptide is its tertiary structure

Protein - Tertiary Structure

• Created when the secondary structure folds and twists upon itself
• A variety of bonds form between the R groups of amino acids on the chain
• Polypeptides have a tertiary structure become proteins.

Quaternary Structure

• Proteins create proteins with multiple proteins (interactions form protein complexes)
• Proteins that have quaternary structures: Hemoglobin; the sodium channels

Levels on Protein Structure and Folding

• Primary Sequence have amino acids held together by peptide bonds
• In protein synthesis, amino acids produce from polypeptide protein chains and are made of 1 or more of these polypeptide chains
• Genes (made of DNA determine) dictate a protein's structure and its function
• Each amino acid had a carboxyl group, an amino group, and R group
• Secondary amino acids can be folded different ways
• Ways in which a protein depends on its arrangement
• Hydrogen bonds can occur on amino acids' proteins such as backbones
• Tertiary structure can occur due to R groups that behave diffirently
• Ex. some R groups are hydrophilic and some are hydrophobic
• There are interactions besides hydophobic interactions
• Interactions (Ionic bonds/Vanderwall/disulfide groups) influence folding that occurs in tertiary structure
• Can also be not in all proteins
• Made of polypeptide chains
• Needs bonding

Protein Folding

• Proteins use chaperonins or proteins that help with its process in the cell
• The barrel helps with the proteins folding
• Can result in many misfoldings of diseases
• Interactions are paramount for a nature protein so it can have a correct shape/can depend on its function
• Have diseases related to protein misfoldings (Huntington's/Parkison's)

Ideal Protein

• Each one has an ideal environment to include a temperature and pH range
• If the protein is exposed, the interactions can be distrusted

Protein Interference

• Some proteins can denature which intereferes with levels or are irreverisble

Protein Functions

• Structure: Supports cells

• Contractile: For movement

• Transport: moves cells/organisms

• Enzymes: catalyst for reactions Ensuring Correct Protein Folding

• In the cell proteins are "chaperone" to folding correct

• They edit misfoldong

• Diseases are by a chaperone protein/ callied pirons

Diseases

• Individuals with sickle cell have a mutation in DNA code
• DNA is the recipe so mutation = bad amino acid
• Patients which create hemoglobin dont fold correctly

Protein Function

• Protein functions depends on:
• Temperature
• pH
• Salt concentration

Protein encounters

• Denatured= 3D breaks

Proteins - Denatured

• Function alters and causes temp/ph can ruin denaturing proteins
• Proteins in eggs become liquid from heat (hard or nonexistant funtion)

Nucleic Acids

• Storge genetic information
• The monomers for nucleic acids are nucleotides
• Made of 3 components
• 5 sugar carbon Present if DNA

Phosphate/ Nitogen

• Group 4 bases for adensine, guamine, etc. By dehydration A sugar-phosphate

DNA Composision

• Two strands form the double helix
• Held by hydrogen bonds/ oriented opposite ways or antiparallel (adensine, guamine)
• Hydrogen/ pairs complement what parts replicate

RNA

• Different with dioxibrise + uracil instead
• Not stable
• Regulates what happens when the consturct is completed
• Not always in cell.