D. Compounds

• Compound occurs as result of 2 or more individual elements combining in a fixed ratio 

  • Different properties of individual elements

  • Formed by chemical reaction

• Bonds that hold compounds together

  • Ionic bonds TRANSFERRED

    • nonmetal+metal

    • One or more electrons is transferred from one atom to another

    • One atom loses electrons (becomes positively charged) while the other gains electrons (becomes negatively charged)

    • Results from attraction of two oppositely charged ions

    • Cation has a positive charge

    • Anion has a negative charge

    • Cation and anion form to create ionic bond

  • Covalent bonds SHARED

    • nonmetal+nonmetal

    • Molecule consists of 2 or more atoms held together by covalent bonds

    • Formed when electrons are shared between atoms

    • In nonpolar covalent bond, electrons are shared equally

    • In polar covalent bond, electrons are shared unequally

    • In a single covalent bond, one pair of electrons is shared

      • Double covalent when 2 pairs are shared, etc. 

    • Structural formula used to represent atoms and bonding

      • Ex. H-H

    • Molecular formula abbreviates structural formula

      • Ex. H₂

      • Electronegativity is an atom’s attraction for the atoms in a covalent bond

        • The more electronegative an atom, the more strongly it pulls shared electrons toward itself

  • Hydrogen bonds 

    • Hydrogen atom covalently bonds to one electronegative ato is also attracted to another electronegative atom

    • In living cells, hydrogen bonds are usually oxygen or other nitrogen atoms

  • Van der Waals Interactions

    • Weakest

    • If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge

    • Attractions between molecules that are close together as a result of these charges

      • How geckos climb

E. Water: The Versatile Molecule

• In water, electrons are not shared equally in the bonds between hydrogen and oxygen

  • Hydrogen atoms have a partial positive charge while oxygen atoms has a partial negative charge

    • Water is polar

• Hydrogen bonds

  • Weak attractions that result of water’s polarity

    • Positive end of another polar molecule attracted to oxygen negative charge, and vice versa with the hydrogen end

    • Hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

    • Weak Individually, but strong on a larger scale

hydrogen bond= water + water

• Lends watermany special properties

  • Cohesion

    • Tendency for water to stick to water

    • Important during transpiration

      • Water evaporates, pulls other water molecules with it, pulling all the way down from leaves to roots

  • Adhesion

    • Tendency of water to stick to other substances

    • Cohesion + Adhesion = capillary action

      • Allows water to flow up roots/trunks/branches of trees in thin vessels

  • Surface tension

    • Results from cohesion of water molecules

    • Ex. water striders can sit on top of water without sinking

  • High heat capacity

    • Heat CApacity=ability of a substance to resist temperature changes

    • Keeps ocean temperatures stable

    • Allows organisms to keep constant body temperature, since most life forms are mostly made up of water

    • Heat is absorbed  when hydrogen bonds break, released when hydrogen bonds form

  • High heat of vaporization

    • Heat a liquid must absorb for 1g to be converted to gas

    • Evaporative cooling

      • As a liquid evaporates, its remaining surface cools

        • How sweat works to cool body down

  • Expansion on freezing

    • Lattice structure of ice causes water to expand on freezing

    • Allows ice to float on top of lakes in winter

      • Animal life can live beneath ice

  • Versatility as a solvent

    • Solution is a liquid that is a homogenous mix of substances

    • Solvent is the dissolving agent of a solution

    • Solute is the substance that is dissolved

    • Aqueous solution is one where water is the solvent

    • Polarity of water allows it to be a versatile solvent

      • Can form hydrogen bonds easily

      Hydrophobic substances do not dissolve in water, but hydrophilic ones will

• Carbohydrates

  • Contain carbon,  hydrogen, and oxygen in a 1:2:1 ratio

  • Monosaccharides

    • Most common are glucose and fructose

      • Glucose

        • Most abundant

        • Part of food humans eat

        • Made by plants during photosynthesis

          • Broken down to release energy

      • Fructose

        • Common sugar in fruits

      • Can be depicted as either straight or rings

• 6 carbon-sugars

  • Formula: C₆H₁₂O₆

• Disaccharides

  • 1 monosaccharide+1 monosaccharide=1 Disaccharide

  • Formed by dehydration synthesis

    • Aka condensation

    • Hydrogen (-H) from one sugar combines with hydroxyl group (-OH) of another sugar molecule to create water as byproduct

• Bond is called glycosidic linkage

• Broken apart by hydrolysis

  • Reverse of dehydration

  • Water is used to break apart glycosidic linkage

• Polysaccharides

  • Repeated units of monosaccharides

  • Most common

    • Starch

      • Stores sugar in plants

      • Made up of alpha-glucose molecules

    • Cellulose

      • Made up of ß-glucose molecules

      • Chitin

        • Structural molecule in walls of fungi/arthropod exoskeletons

        • Used as surgical thread since it breaks down in body

    • Glycogen

      • Stores sugar in animals

• Proteins

  • Amino acids=monomer of proteins

    • 20 kinds of naturally occurring amino acids

  • Contain:

    • Carbon

    • Hydrogen

    • Oxygen

    • Nitrogen

  • 4 parts of an amino acid centered around a central carbon

    • Amino group (-NH₂)

    • Carboxyl group (-COOH)

    • Hydrogen

    • R group

      • Aka side chain

      • Interchangeable

      • Vary in composition, polarity, charge, shape depending on specific side chain

      • Polar R groups point outward, hydrophobic R groups point inward

  • Polypeptides

    • Amino acid + amino acid= dipeptide

      • Formed by dehydration synthesis

      • Bond is called a peptide bond

      • Multiple amino acids= polypeptide

        • Once a polypeptide chain twists and folds on itself, it forms a 3D structure called a protein

• Higher protein structure (4 levels total)

  • Primary structure

    • Linear sequence of amino acids

    • Covalent (peptide) bonds

  • Secondary structure

    • Protein beings to twist--2 options

      • Forms a coil (alpha-helix)

      • Zigzagging pattern (known as beta-pleated sheets)

    • Shape depends on R-group

    • Formed by amino acids that interact with other amino acids closeby in the primary structure

    • Hydrogen bonds between carbonyl and amino group

    • Interactions between amino and carboxyl groups of protein backbone

    • After secondary structure forms, formerly distant amino acids are now closeby--tertiary structure can form

  • Tertiary structure

    • Can be both alpha and beta helix/sheets within structure

    • Covalent disulfide bridge often stabilizes structure

    • Bonds between R groups

      • Hydrogen bonds

      • Ionic bonds

      • Disulfide bridges

      • Hydrophobic interactions

  • Quaternary structure

    • Several different polypeptide chains sometimes interact with each other

    • Same bonds as above, but between peptide chains rather than between R groups

  • Mistakes in structure can denature a protein

    • Change of shape=change of function

      • Ex. pH or heat can denature protein

  • Protein folding can involve chaperone proteins (chaperonins)

    • Help protein fold properly

    • Make process more efficient

• Lipids

  • Like carbs, consist of carbon, hydrogen and oxygen, but not in a fixed ratio

  • Do not form polymers

  • Little-no affinity for water

    • Hydrophobic due to nonpolar covalent bonds of hydrocarbon

  • Common examples:

    • Triglycerides

      • Glycerol molecule+3 fatty acid chains attached

        • Fatty acid chain is mostly a long chain of carbons where each carbon is covered in hydrogen; One end of the chain has a carboxyl group (-COOH)

          • Vary in length and #/location(s) of double bonds

        • Glycerol is a 3-carbon alcohol with a hydroxyl group attached to each carbon 

      • Fats separate from water because water forms hydrogen bonds with itself while excluding the fats

      • In order to be made, each of the carboxyl groups of the 3 fatty acids must react with one of the 3 hydroxyl groups of the glycerol molecule via dehydration synthesis

        • bond=ester linkage

      • Saturated fatty acid

        • No double bond

        • Carbon chain completely filled (“saturated”) with hydrogen

        • Usually solid at room temp.

      • Unsaturated fatty acid

        • Double bond along carbon chain, causing a bend

          • Bend allows triglyceride to become LESS dense, making it liquid at room temperature

        • Polyunsaturated fatty acid has multiple double bonds within the fatty acid, causing many bends

• Phospholipids

• 2 fatty acid “tails” + 1 negatively charged phosphate “head”

• Tails are hydrophobic, while head is hydrophilic (negative charge on head attracts polar water)

  • Amphipathic molecule (molecule that is both polar and nonpolar)

• In water, phospholipids self-assemble into a “bilayer arrangement” 

  • Hydrophobic tails face towards interior

  • Found in cell membranes

• Steroids

  • Cholesterol

    • 4-ringed molecule dispersed throughout membrane

      • Maintains membrane stability

        • Increases membrane fluidity at lower temperatures by disrupting close packing

        • Decreases fluidity at high temperatures through its constant movement

• Nucleic Acids

  • Contain carbon, hydrogen, oxygen, nitrogen, and phosphorous

  • Structure

    • Nitrogenous base

    • Pentose sugar

    • Phosphate group

    • Portion of nucleotide w/o phosphate group is called nucleoside

  • Store, transmit, and help expres hereditary information

  • monomer=nucleotides

  • Amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

    • Made up of DNA

  • Deoxyribonucleic acid (DNA)

    • sugar=deoxyribose

    • Contains genetic/hereditary information

    • Provides directions for its own replication

    • Directs synthesis of messenger RNA (mRNA), and through mRNA, controls protein synthesis

      • Occurs on ribosomes

  • Ribonucleic acid (RNA)

    • sugar=ribose

    • Essential for protein synthesis

  • 2 families of nitrogenous bases

    • Pyrimidines

      • Single 6-membered ring

      • Ex.

        • Cytosine

        • Thymine (only DNA

        • Uracil (only RNA)

    • Purines

      • 6-membered ring fused to a 5-membered ring

      • Ex.

        • Adenine

        • Guanine

  • Nucleotide Polymers

    • Nucleotide polymers linked together to build a polynucleotide

    • Adjacent nucleotides are joined by covalent bonds that form between the -OH group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon on the next

      • Links create a backbone of sugar-phosphate units with nitrogenous bases as appendages

    • RNA molecules usually exist as single polypeptide chains

    • DNA molecules have 2 polynucleotides spiraling around an imaginary axis, forming a double helix

      • Two backbones run in opposite 5’→3’ directions from each other (antiparallel)

      • One DNA molecule contains many genes

      • Nitrogenous bases pair up and form hydrogen bonds

        • Adenine-Thymine

        • Guanine-Cytosine

        • Complementary base pairing

        • In RNA, thymine is replaced by uracil, so A and U pair

F. Origins of the Earth

• Alexander Oparin and J. B. S. Haldane proposed that the primitive atmosphere contained the following gases:

  • Methane (CH₄)

  • Ammonia (NH₃)

  • Hydrogen (H₂)

  • Water (H₂O)

  • No free oxygen (O₂)

    • No oxidation/reduction

    • Rocks do not release oxygen through weathering

  • Gases collided, producing chemical reactions that eventually led to the organic molecules we know today

  • Substantial support until 1953

• 1953, Stanley Miller and Harold Urey simulated the conditions of primitive Earth in a lab,

  • Put theoried gases into flask, struck them with electrical charges to simulate lightning, and organic compounds similar to amino acids appeared

• Current theory of the origin of life suggests 4 main stages

  • 1. Formation of amino acids

  • 2. Monomers form polymers

  • 3. Enclosure of small organic molecules into larger ones

  • 4. Self-replicating molecules that can direct synthesis of other organic substances

    • Energy sources for early organic synthesis

      • Lightning 

      • Volcanic eruptions

• RNA world hypothesis

  • Original life-forms were simple molecules of RNA

    • RNA not restricted to double helix

    • RNA capable of replicating and passing genes

  • Complex organic compounds must have formed via dehydration synthesis

    • Organic compounds then used as food by cells

      • Simple cells evolved into complex cells