Biology H Unit 3 - Organic Chem

Carbon

All living things are made up of carbon-based molecules. Carbon enters the biosphere through photosynthesis. Carbon can make up to 4 covalent bonds (as it has 4 valence electrons); it may form almost limitless numbers of carbon skeletons as it readily bonds with other atoms as well as itself. Its bonds may be single, double, or triple and its chains may be straight, ringed, or branched.

Organic Compounds

- made up of carbon and hydrogen atoms

Inorganic Compounds -

do NOT contain carbon and hydrogen atoms

Functional Group

Hydrocarbon - an organic molecule with ONLY carbon and hydrogen

Substituted Hydrocarbon - hydrocarbon with 1+ hydrogen atoms substituted by another atom/group of atoms also known as a functional group.

Substituted Hydrocarbon = Functional Group

Function groups are specific configurations of atoms which are usually attached to carbon skeletons

• They always behave the same

• They give molecules unique properties

• Typically cause chemical reactions

Hydroxyl (-OH)

• Compound Name: Alcohol

• Names usually end in: -ol

• Polar

• Attracts water molecules

• Helps dissolve organic compounds

• Singled-bonded

  • Examples: Ethanol, Methanol

Carbonyl (-CO)

• Compound Names: Aldehyde and Ketone

• Aldehyde - When the functional group is at the END of a carbon change; its characteristics depend on the rest of the molecule. Names usually end in -al

  • Methanal

    

• Ketone - When the functional group is somewhere WITHIN the carbon change; characteristics also depend on the rest of the molecule. Names usually end in -one

  • Testosterone

Carboxyl (-COOH)

• Compound Name: Carboxyl/Organic Acid

• Names usually end in -oic

• Acidic —> H+ donor (pH lab, less hydrogen = more acidic, more hydrogen = more basic)

• Strong Odor

  • Ethanoic Acid

  • Butanoic Acid

Amino (-NH2)

• Compound Name: Amines

• Names usually end in: -amine

• Alkaline (basic)

• Smell like rotten fish

Sulfhydryl (-SH)

• Compound Name: Thiols

• Names usually end in: -thiol

• Stabilize protein structures

• Some have a stinky odor

Phosphate (-PO4)

• Compound Name: Phosphates

• No set name ending

• Transfers energy

• the Anion in energy transfer (negative)

Macromolecules

Necessary substances to all living things, a macromolecule is a huge molecule that is formed when smaller molecules are linked together; macromolecles are polymers. The 4 main classes are Carbohydrates, Lipids, Proteins, and Nucleic Acids.

• ex. Amino acids combine to make proteins (quizizz)

Monomer - a SINGLE sub-unit which serves as a building block for polymers

Polymer - a long chain of similar or identical monomers linked together (Monomer+Monomer = Polymer)

Dehydration Synthesis:

A process that joins monomers together by removing water, (occasionally called condensation reaction)

Hydrolysis -

Any chemical reaction where a water molecule breaks 1+ chemical bonds (seperation)

Carbohydrates

• Carbohydrates are divided into 3 classes: Monosaccharides, Disaccharides, and Polysaccharides (sugars)

• Water soluble (can dissolve)

  
  Monosaccharides:

• Monomer for larger carbs

• Has carbonyl and hydroxyl groups

• Chemical Structure: carbon, hydrogen, oxygen (CnH2nOn) (CHO)

• Found in simple carbohydrates (honey, apples, cheese)

• Quick energy

• Building blocks (especially in plants)

• Ends in -ose

• Hexagon/Pentagon shaped

  Isomer - molecules with the same molecular formula but differ in the arrangement of atoms

• 2:1 Hydrogen:Oxygen

• (Glucose, Ribose)

  

• Disaccharides:

• Forms when 2 monosaccharides are joined by a -

• • glycosidic linkage (which is their covalent bond) through dehydration synthesis

    

  • Polysaccharides:

• Composed of long chains of monosaccharides

• Polymer of carbohydrates

• Found in complex carbohydrates (breads, pastas, potatoes)

• Provide longer-term energy/Energy storage

• Structural

  Types of Polysaccharides

• Glycogen (Animal) - Storage of excess sugars (in liver and muscles), muscle contraction, breaks down glucose for quick energy

• Starch (Plant) - Stored excess sugar in plants

• Cellulose (Plant) - Gives plants rigidity, component of the cell well

  

Lipids

• Fats, oils and waxes (ex. animal fats, butter, shortening)

• Long-term storage of energy (double of carbs)

• Insulation and cushioning

• Absorption of some vitamins

• Component of cell membranes

• Chemical Structure: Carbon, Hydrogen, Oxygen (CHO)

• Hydrophobic - insoluble in water

• Monomer - Glycerol and fatty acid

  

• Polymer - Triglycerides (Glycerol + 3 fatty acids tails, linked by ESTER linkages)

  • Fatty Acids have Carboxyl function groups

  • 1 Glycerol + 3 Fatty Acids = Triglyceride + 3H2O

• Saturated Fatty Acid -

  • Single-bonds,

  • straight,

  • solid at room temp,

  • found in animal fat

• Unsaturated Fatty Acid -

  • some are Double-bonded,

  • not-saturated,

  • kinks in chains,

  • liquid at room temp,

  • better for health,

  • found in plants

    

    Trans Fat:

• Hydrogenation - Industrial process that converts unsaturated fats into trans fats by adding hydrogen (bad for body)

• can lead to cardiovascular disease and clogged arteries

• found in shortening and margarine

  

  Phospholipid Bilayer:

• Phospholipids make up a bilary that surrounds cells

• Bilary protects cells and regulates the movement of molecules across it

Proteins

• NOT used for energy

• Storage

• Transport

• Regulation - hormones

• Movement - muscles

• Structure - hair, nails

• Disease Protection - antibodies

• Enzymes

• Chemical Structure: Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur (CHON)

  Ends in:

• Structural proteins: - in

• Enzymes: -ase

• Monomer = Amino Acid

  • Amino Acid = 1 Amino Group + 1 R-Group + 1 Carboxyl Group

• R-Groups are different for each amino acids; they determine the acid’s property —>

• 20 different acids (9 which are essential and from food, 11 which are non essential and already made by the human body)

  

• Polypeptide = Polymer of Proteins = Protein

  • Straight chains of amino acids assembled through dehydration synthesis, held together by Peptide Bonds

  Protein Structure

• Folded — structure determines function

• Protein Folding - a process that takes a polypeptide chain and turns it into a functional 3D shape

• Four stages:

  1. Primary (Polypeptide Chain) —>

  2. Secondary (Alpha Helix, Beta Pleat) —>

  3. Tertiary (Combines Helices and Pleats) —>

  4. Quaternary (Multiple Tertiary Structures); not all proteins become quaternary

• Denature - occurs when a protein loses shape due to its environment (ex. temperature, salt concentration, pH changes)

  • renature is possible

  • why high fevers are fatal

Nucleic Acids

• Found in DNA, RNA, and ATP

• Stores genetic (hereditary) info

• Assists with protein synthesis (carrying instructions for building proteins)

• Chemical Structure: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus (CHONP)

• Nitrogen Base

• 5-Carbon Sugar

• Contains Phosphate functional groups

• Monomer: Nucleotide

  • Phosphate

  • 5- Carbon Sugar (BASE)
    Nitrogen Base

    

• Polymer:

  • Polynucleotide (Formed by bonding alternate phosphate groups and sugars with phosphodiester bond

ATP - Adenosine Triphosphate

• Storage of energy in high energy bonds

• between phosphate groups (phosphate gives ATP charge)

Chemical Reactions & Enzymes

• Chemical reactions must occur in organisms so they survive

• Enzymes help speed up these reactions

• Reactants - molecules that start a chemical reaction

• Products- molecules that end a chemical reaction

Exergonic Reaction/Exothermic Reaction

• When the change in energy is negative

• Energy is released when bonds are broken

• Products have less energy

• Spontaneous

Endergonic Reaction/Endothermic Reaction

• Needs energy to react

• Energy is absorbed when bonds are created

• Products have higher energy

• Change in energy is positive

• Slow to start; requires assistance — needs constant energy

  

Enzymes

• Specialized, Reusable Proteins that speed up chemical reactions in cells

• Catalyst - speeds up reactions

• Structure determines function

• Unchanged by reactions

• Activation Energy - the amount of energy required to start a reaction

• lowered activation energy = working enzyme

How Enzymes Work -

• Lock & Key Model - Each enzyme only fits the shape of its corresponding reactant molecule(s)

  • (therefore each reaction requires a different enzyme)

• Lock = Substrate (what is acted on by an enzyme, the reactant)

  Enzymes are typically named after their substrate

• Key + Enzyme’s Active Site (region of an enzyme in which a substrate fits in

• Steps:

1. Substrate bonds to enzyme’s active site

2. Water is needed for hydrolysis; removed for dehydration synthesis

3. Enzyme catalyzes reaction by lowering activation energy to form/break bonds

4. New product(s) form and are released

5. Enzyme is reused again

Factors that Affect Enzymes

• Environmental Conditions (temperature, pH)

• Adding Substrate —> Increases Reaction Speed

  • (only up to Saturation Point)

• Cofactors -a non-protein compound or ion that is necessary for an enzyme’s function

• Coenzyme - an organic molecule that assists the enzyme’s reaction by binding onto its active sites

• Enzyme Inhibitors -

  • Prevents Substrate from Binding

  • Competitive Inhibitors - molecule that prevents substrate from binding by binding to the active site

  • Noncompetitive Inhibitor - molecule that prevents substrate from binding by binding to an enzyme’s non-active site and changing its shape

• pH

  • drastically different pH will cancel each other out