Biology Notes: Grade 12

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Organic Chemistry Classification

study of simple/synthetic/complex C-compounds

petroleum products and by-products: organic animal/vegetable, inorganic mineral (produced chemicals but now they are synthesized without having to extract, also carbonate & cyanide compounds)

6 common organic compounds in order of abundance from least to most: S, P, N, O, C, H

Bergelius' Vital Theory: forces produce compounds in living things only

Vohler, German scientist: 1824, produced oxalic acid COOH COOH & 1828 produced urea

other scientists began to synthetically produce acetic acid, benzene lab

Covalent bonds

Catenation: C atoms joined together in chain or ring/cyclo

London forces b/w organic molecules

Isomers: one molecular formula could represent more than one organic compound

Chemical properties determined by the functional groups



Non-polar, hydrophobic most

C bonds covalently with H

Branched, unbranched, rings, shapes, 1x/2x/3x bonds

Aliphatic: open chain, alkane C-C, alkene C=C, alkyne, cyclo, meth/eth/prop/but/pent/hex/hept/non/dec

Aromatic: benzene ring, have aroma (scent) ie. Benzene C6H6, see Kekule Hydrocarbons below

C-H bonds consistent length with C-H bonds of hydrocarbons (C-C > C-_-_-C bond length < C=C)

All C-C have same length/reactivity = structural formula written as I/II/III "Resonance Formula"



soluble in water, hydrophilic (alkanes/parafines)

CO: diatomic (2 atoms of same/different elements)

single H (HCl), OH (C2H5OH), O (OCl), N (NF3)

alcohol (hydroxyl), aldehyde/ketone (carbonyl), carboxylic acid (carboxyl), amine (amino)


insoluble in water, hydrophobic (alkenes/ynes)

all elements Cl2

most C compounds: oil, CO2, CH4


Saturated Hydrocarbons

single C-C bonds, alkanes/parafines

Max # of H atoms


Substitution reaction

Unsaturated Hydrocarbons

Double C=C or triples bonds, alkenes, alkynes, non-polar

Oils, Teflon, Plexiglass (contacts), Synthetic rubber (Cl radical), Natural Rubber (methyl radical), tire rubber, (black since C-S not C-H monomers, smell since Sulphur burns)

Addition reaction


1+ 2x bond


Chain molecules of identical monomer units (held by Van der Waals Forces)

Polysaccharides, plastics


smallest repeating unit of polymer


1 molecule = dimer, 2 molecules = trimer, 3 molecules = polymer

1000s of monosaccharides linked in branched or unbranched (linear) chains

Hydrophilic: water loving

Hydrophobic: water hating (fats, hydrocarbons, oils, waxes)

Amphiliphic: dual nature (phospholipids)



High surface tension/cohesion

leaves pull upward from root

High boiling point

wants to stick together from hydrogen bonds

lot of energy to break H-bonds

liquid into gas state (hard to boil into gas)

Temperature stabilizer

lots of energy

H-bonds absorb heat

H-bonds break and release heat

raise temperature of water (otherwise moderates temperature changes near large bodies of water)

Ice less dense then water

water cools

molecules have less kinetic energy

H-bonds get stronger & hold water molecules in rigid crystalline structure

ice volume more than liquid = ice lower density = ice floats to

gone if lakes froze into ice water


Carbon Compounds

Hydrocarbons largest group, most have carbon-carbon covalent bonds, aliphatic & aromatic

Long chains of atoms that are covalently bonded to hydrogen atoms and other carbon atoms

Non-polar, almost all hydrophobic (water-hating)

Branched/unbranched(linear), chains/cyclic(ring) shapes, 2x/3x bonds, isomers

Bohr-Rutherford Diagram of Carbon: 6p, 2e, 4ve



same #/type of atom but different arrangement


different covalent arrangement b/w atoms

different loc. of double/triple bonds


same covalent arrangement b/w atoms

inflexibility of 2x bond, no rotation possible as with C-C


mirror image, D - amino acids & L - amino acids

inactive/harmful (thalidomide sedative toxic to embryo & fetus)


Structural Formula: H3-C-C-H3 or H3CCH3

Molecular Formula: C2H6

Radical: CH3 (methyl) radical of CH4 (methane) & C5H11 (pentyl) radical of C5H12 (pentane)

Atoma: indivisible



b/w alcohols, R - O - R

polar, but not as polar as alcohols

boiling point lower than alcohols, good solvent

Ester (scent)

b/w alcohols and carboxylic acids R - (C=O) - O - R

found in hydrocarbon chains in phospholipids, mono/triglycerides

esterification, hydrolosis

Organic Acids: R - C=O - OH

Cyanides: R - C -3- N, R - C(=-)N

Sulphonates: R - SH - O3

Anhydrides: b/w acids

Peptides: b/w amine & acids

Pi Bond

Double bond

2 electrons shared by overlapping orbital, tend to arrange so mix overlapping of the orbitals occur

Hybrid orbital: electron from one orbital moves into an empty orbital but on the same energy level =equals= an extended valence =then= can bond with more atoms

Double Bonds: C=C-C-C-C

Conjugated: C=C-C=C-C=C, alternating

Cumulate: C=C=C=C=C=C

Sigma Bond


overlapping of s/p/sp orbitals =makes= bond (where electron density concentrated above/below imaginary rest line)

electron density b/w nuclei of 2 atoms along imaginary rest line




role in carbohydrate formation: precursor for simple sugars, oxidizes readily to form carboxylic acids

oxidation, hydrogenation


general formula: R - CH=O (no isomers)

simplest: CH2O, formaldehyde

"-al" IUPAC ending (International Union of Pure and Applied Chemistry)


general formula: R - (CH=O) - R

simplest: CH3COCH3, acetone/dimethyl ketone

"-one" IUPAC ending (International Union of Pure and Applied Chemistry)

found in fats




general formula:

Primary: R - OH, d.brown

Secondary: R - OH - R, brown

Tertiary: R - OHR - R, purple

simplest: CH3OH, methanol

"-ol" IUPAC ending (International Union of Pure and Applied Chemistry)

Phenol: product when -OH is added to an aromatic ring


Carboxylic Acid


general formula: R - C(OH) =O

simplest: CHOOH, methanoic acid

"-ic" IUPAC ending (International Union of Pure and Applied Chemistry)

in amino acids and fats, highly reactive, produce H+ ions in soln

2 dicarboxylic acids: 1--- COOH COOH, oxalic acid 2---COOH (CH2)3COOH, succinic acid

ionization, neutralization, reacts with metals, esterification



polar, weaker since H has low electro-negativity

general formula: R - C - NH2

simplest: CH3NH2, methyl amine

"-amine" IUPAC ending (International Union of Pure and Applied Chemistry)

in amino acids: enables it to act as base, removes H+ from solution, form OH- ions


general formula: R - (C=O) - NH2

CH3CONH2, ethanamide

"-amide" IUPAC ending (International Union of Pure and Applied Chemistry)



slightly polar

general formula: R--SH

simplest: CH3SH, methathiol

"-thiol" IUPAC ending (International Union of Pure and Applied Chemistry)


Phosphate *not really organic*


General formula: R-O-P-(=O, OH, OH)

Part of DNA & RNA so it is abundant since everything has DNA


Electronegativity (Linus Pauling)

to attract shared electron pairs when forming bonds (like to be stable so pair up & fill outer (valence) shell)

Depends on # of protons and size of atom (distance from valence to the nucleus)

Increases as we go up/across the periodic table (ie. F is most electro (-) element)

Determines type of bond that forms b/w two atoms


Van der Waals forces (strongest >>> weakest)

Hydrogen Bonds: b/w polar (H & F O, N) ~~~ covalent bonds: H very + and others - (H2O, NH3, HF, CH3OH)

Dipole-dipole: b/w polar ~~~ + attracted to - charged (SCl2, PCl3, CH3Cl)

London/Dispersion forces: b/w non-polar molecules (H2, Cl2, CO2, N2O4, CH4) >>>uneven e- distribution in close molecules, more e- = stronger dispersion force

INTRAMOLECULAR FORCES (Van der Waals forces 1 & 2)

Electron cloud size: large = not held tightly = forces stronger

# of atoms: more atoms = more forces = higher temperature

Ionic Bonds

Metals (LS of PT) & Non-metals (RS of PT)

Strongest bond: form b/w atoms w/ different negativities

Na + Cl Na+[Cl]-, unequal sharing of electron pairs: more electromagnetic atom will attract/steal electron pair becoming -ly charged ion, while the other becomes +ly charged

Have high melting points, dissociate (split apart) in aqueous solution

Covalent Bonds

common in organic life forms, bonds b/w atoms of similar/identical electro negativities, high electron similarity/ionization energy

high melting/boiling points, remain liquids over short temp range, don't conduct electricity

Bond Length: Distance of covalent bonds, C--_--_--C length b/w C-C and C=C (gives substitution not addition)

Bond Energy/Enthalpy = bonds broken - bonds formed

2 atoms approach

e- density around each nucleus shifts to the middle

distance decreases, probability of finding either e- near their nucleus until each of H-atoms in molecule reaches a sharing of the two e-

atoms of different elements form compounds (classical naming system: iron + sulfur = iron sulfur)

3 Types of Covalent Bonds (strongest >>> weakest):

Polar Covalent: different electro negativities, H2O

Non-Polar/Pure Covalent Bonds: similar/identical electro negativities, O2

Coordinate Covalent: shared electrons donated by same atom, weak since borrow lone pair, SO2 & H3PO4

Why Some Covalent Compounds Dissolve In H2O?

C + H atoms = polar, small difference in e-negativity level

O + H atoms = polar, ie. H2O + alcohol

(+) dipole + (-) dipole = Hydrogen bond, attracted to each other

INTERMOLECULAR FORCES (Van der Waals forces 1, 2 & 3)

Weaker than covalent bonds: b/w electrostatically attracted molecules


2 important pentose sugars, many phosphate groups

DNA - Deoxyribose: C5H10O4 (missing -OH group)

RNA - Ribose: C5H10O5


in phospholipid cell membrane

consist of hydrocarbons in ester linkage

C, H, more carbohydrates then O's

4 uses: Protect organs (kidneys), Prevent H2O loss in plants, Long term energy, Thermal insulation (bladder)


17 C atoms in 4 rings

testosterone/estrogen (sexual), adrenaline (heart), anabolic (muscular), bile salts (digestive)


Fatty acids + monohydroxy alcohol

Hydrophobic, high melting points

Protective outer covering of fruits, leaves, animals skins


Glycerol: 3C with OH on each (trihydroxy alcohol) + fatty acid's COOH (carboxyl) in synthesis/condensation rxn = ester link

Monoglyceride: 1 fatty acid + glycerol in dehydration rxn = ester linkage

Diglyceride: 2 fatty acid + glycerol in dehydration reactions

Triglyceride: 3 fatty acid + glycerol in dehydration reactions

Oils: unsaturated, liquid, hydrophobic, low melting point, olive oil

Fats: saturated, solid @ room temp, hydrophobic, high melting points, butter fats

Fatty acids: long hydrocarbon chains (unbranched) ending in COOH (monocarboxylic), even #of C (16-24 C)


C6H12O6 (1:2:1) aldohexose (6C)

16 isomers (mainly stereoisomers) + 5 -OH groups + C=O at end

1 isomer of glucose: fructose, C6H12O6 (1:2:1)

1 stereoisomer of glucose: galactose, C6H12O6 (1:2:1)


Chlorophyll A

Participates in light rxns

Head: porphyrin ring w/ Mg center

Tail: hydrocarbons, interacts with hydrophobic proteins in the thylakoid membrane

Carbonyl group: CH3 bonded to porphyrin ring (head)

Chlorophyll B

Methyl group: not CH3 but CHO bonded to porphyrin ring (head)


Yellow to red pigments (as carotenes)

2 small 6C rings, connected by chain of C atoms


Acid-Base Reaction

Involve transfer of protons [H]+ from one molecule to another

Acids donate [H]+, bases accept

Oxidation-Reduction 'Redox' Reactions

Involve transfer of electrons from one molecule to another

Reducing agent stays the same in reactants and products, oxidizing agent is split apart in product

Condensation (dehydration, condensation, synthesis):

Hydrolysis Reaction (reverse of synthesis: hydrolysis, degragation, digestion):

H2O produced/used to break/form new bonds

These bring monomers together to form bond


Carboxylic acid + water carboxylic acid + alcohol

ATP + H2O ADP + Phosphate

Transfer Pi b/w mol, if added endothermic & lost exothermic


COOH removed, releases O2

Catalyst can be NaOH


Substrate into isomer

Oxidative Phosphorylation

Product is pyruvic acid

Pyruvate Oxidation

In mitochondrial matrix

2 pyruvic molecules produced at the end of glycolysis

Get converted into Acetyl CoA by addition of coenzyme A

Oxidative Decarboxylation

Decarboxylation + redox reaction


Lose e- and H atoms

Combustion: Oxygen, water is product


Gain e-/ H atom

NAD, FAD coenzymes accept e- from substrate



Add water to break a bond, such as double bond in alkenes

CH2=CH2 -----> H2O, [+H] ----> CH3-CH2-OH

Ethane -----> H2O, [+H] ----> ethanol


CO2 is released

Thermic Decomposition

Cracking: alkanes to alkenes, T˚C @ 650˚C

Pyrolise: compound is split, T˚C > 1000˚C


Alkanes produces alkenes, water and [H]+

When between 2 monomers makes a condensation reaction

CH3CH2OH2+ CH2=CH2 + H2O + [H]+


Acid is added to water, products are -charged acid radical and +charged H3O

Acetic/ethanoic acid acetate/ethanoate (acid radical), CCOOH + HOH CCOO- + HHOH+


Ethanoic acid + methanol methyl ethanoate, or dimethyl ester + water


Usually occurs with Fe and Br2

Chain Reaction: CH4 + Cl2 CH3Cl + HCl

Alkenes, industrial field

add halogens


Use Markovnikov Rule

Hx(aq) = hydro...ic acid

Wohler Method

(C=-C) both C attached to one Ca water vapour is added Ca(OH)2 + (C=-C)



A - Element hard to separate, 1 atom

B - Binary compound

C - Compound 2+elements chemically united

Mixtures: easy to separate, combination of substances

Metals: form + ions (cations), copper

Non-metals: form - ions (anions), O2

Electrolytes: conduct electricity

Oxides: O2 + element, H20


Element + element = binary compound

A+ A=C

Hydrogen + Chlorine = Hydrogen Chloride


Binary compound = element + element

C = A + A

CH4 + O = CO2 + H2O


A1 + C1 = A2 + C2

Zn + H2SO4 = ZnSO4 + H2

Double Displacement:

C1x + C2y = C1y + C2x

NaCl + NgNO3 = NaNO3 + AgCl

Ag + Cl = AgCl


Thermodynamics: study of Energy in matter

Efree = Etot + Entropy (Entropy is measure of chaos in universe)

∆G= ∆H + Entropy x ∆T

Epot: stored

Ekinetic: E of motion

Eheat: random motion of molecule, wasteful, can't do work with it

Energy neither created/lost, but transferred/transformed

Energy transfer = increase in Entropy

Endothermic (ΔG='+')

heat made

ATP lost, Pi gained

entropy increases

Anabolic: small > large polymers w/ energy

Exothermic (ΔG='-')

heat lost

ATP gained, Pi lost

entropy decreases

Catabolic: large > small



chemical reaction in organisms

Cellular Respiration

glucose 3 molecules of CO2

cytochrome proteins (in mitochondrial membrane) pass electrons to O2 (product of C. Respiration)

molecular oxygen is reduced



Solar energy > saccharides synthesized > inorganic components > potential chemical energy

6CO2 + 6H2O > C6H12O6 + 6O2

Green bacteria: cellular membrane (no organelles)

Plants: chloroplasts

Occurs through two reactions

1. Light-Dependent Reactions:

Within grana

Light + H2O = ATP + NADPH

Require light directly

Solar energy >>> chemical potential energy

Recycle waste products of Calvin Cycle

2. Calvin Cycle/Light-independent reaction

Within in stroma

Require light indirectly

Chemical to ATP + NADPH+ CO2 = sugar (CH2O)

Chemical potential energy used to drive anabolic reactions that create energy-rich sugars

Depends on products of light-dependent reaction to occur

Non-Cyclic Electron Flow

Protons, photons (light) hits thylakoid membrane

Hits antennae complex

Hits light-trapping pigment (Ch. A, Ch.B, Cartenoids)

Trap light and transfer energy from molecule to molecule

Reaches reaction center and absorbs energy

Energy absorbed drives oxidation reaction

Reaction donates excited electron to the primary electron acceptor (redox reaction) through e- carriers

H2O excites & oxidizes (looses 2 electrons)

Result is 2H+ + O2

2H plus picked up by reaction center

Electron replaces ones lost in step 2 to primary receptor

2H plus in cytochrome complex produced (keep H+ high)

2H plus undergoes series of redox reactions (cytochrome proteins)

Cytochrome proteins use energy of electrons to pump H+ into thylakoid compartment (keeps low H in stroma)

Protons diffuse out through ATP synthetase

ATP synthesized

Excited electrons passes through series of enzymes

Used by NADP reductase (enzyme), NADP+ >>> NADPH (chemical potential energy)

NADPH (chemical potential energy) used in Calvin Cycle to take CO2 (non e-rich) and build it into sugar

DNA Structure

Found in nucleus of all dividing cells, carries genetic material

Open structure, 2x stranded helix that twists

Held by H bonds between nitrogenous bases (+ivly charged, hydrophobic)

-ivly charged phosphates like to stay outside and interact with +ivly charged/aqueous/polar/hydrophilic nucleus environment

H2O content high, but when low H2O content then bases tilt and compact

2 Helical Chains/Strands

Sequence of atoms in opposite directions

Follow right-handed helixes, coiled around same axis

Held together by 2 bases perpendicular to fibre axis

On each strand there is a 5' and 3' end

Phosphodiester Bonds

Joins polymer of nucleotides

Between the 3 OH (on the DNA sugar) & the phosphate group (on the adjacent nucleotide)


Joined by hydrogen bonds

Lie side-by-side = z coordinates identical

Specific bonding pairs so spread out evenly = no gaps/kinks/errors in DNA

2 types of bases

A (2x bond) T, purine position 1 + pyrimidine position 1

C (3x bond) G, purine position 6 + pyrimidine position 6


Adenine, guanine

Larger, 2x ring


Thymine, cytosine

Smaller, 1x ring

Acids (produce H+ ions)

taste: sour (acere = Latin "sour")

changes litmus: blue >>> red

*conducts electric current: H2O solns conduct (electrolytes)

react with: bases to form salts + H2O (neutralization reaction)

other: evolve H2 gas when rxn with active metal (Alkali mtls, zinc, aluminium)

examples: citric acid (fruits, veggies), ascorbic acid (vitamin c), vinegar (5% acetic acid), lactic acid (buttermilk), Sulphuric Acid

Bases (remove H+ ions)

taste: bitter

changes litmus: red >>> blue

*conducts electric current: H2O solns conduct (electrolytes)

react with: acids to form salts and H2O (neutralization reaction)

other: feel slippery/soapy

examples: detergents, soaps, lye (NaOH), household ammonia, Sodium hydroxide

Salts (produce non-H+/OH-ions)

taste: salty

examples: Sodium chloride


maintain constant internal environment, steady state

recognize and respond to stress/significant change

External Stress: change in light, temp, food, produce

Internal Stress: metabolic activities, water, substrates disease, aging


stress produced (controlled by feedback mechanisms)

series of reactions

response/feedback: +/- (+ reduces stress, - increa stimulus)

Feedback System

receptors - detect stimulus

regulators - course of action/response

effectors - execute response

Sensory pathway: receptors > regulators

Motor pathway: regulators > effectors

Homeostatic System

1. Limits:

Boundaries, responds to critical amounts of stress, cannot cope with extreme envio. changes)

thermoregulation only effective in 15˚C - 50˚C, beyond range homeostatic system can't cope = hypothermia

2. Energy

energy to activate effectors, effectors activate large amounts of ATP

What is Homeostatically Maintained?

Nutrient Concentration (supply of energy production)

O2 [] (needs for energy production)

CO2 [] (in excess leads to acid formation in blood)

pH (changes outside normal range can affect enzyme activity and nerve cell communication)

Salt/electrolytes [] (maintain proper volume of cells, role in cardiac function/nerve cell communication)

Temperature (nerve cells detect temp 2 low=cell function slow, temp 2 high= structural/enzymatic proteins are impaired)

Volume & pressure (plasma volume-pressure ration to ensure body-wide distribution)


Mammalian Diving Reflex: slight changes in infants can damage enzymes and cause brain damage

Hypothermia: body mimicking sleep heart rate shoots up in cold water because of shock, but then comes down to conserve heat

Achilles Reflex, Knee Jerk: action of walking, used to that motion

Babinski Reflex: toes curl, motor functions, sensitive nerve

Papillary Reflex: pupils dilute and expands with increase/decrease of light

Aldosterone in Osmoregulation:

A steroid hormone (regulates Na+ and K+) secreted by adrenal gland

controls cells of distal tubule: promotes (secretion of K+ from blood>distal tubule) & (absorption of Na+ from distal tubule>blood)

high K+ in blood >>> increased aldosterone secretion >>> secretion of K+ into distal tubule from blood >>> reduced K+ in blood


Diabetes Mellitus

'diabetes' to walk or stand with legs apart & 'mellitus' sweet pee

disorder in which you cannot use the nutrients you digest properly, especially sugar (stays in bloodstream,

goes into urine)


takes sugar out of blood stream and makes energy, diabetics do not have the insulin to extract this energy

HYPOglycaemia: too little sugar, may pass out, not enough energy, may go into coma

HYPERglycemia: too much sugar in blood, thirsty, nap, need to pee, blindness (blood clots in eyes), kidneys shut down, amputation (circulation, cells bounce off in tight space and damage cells)Type I: 10% of cases

body cannot produce insulin

auto-immune disorder/juvenile diabetes: at birth or before birth or at young age body makes mistake, says beta cells are bad and foreign and kills them all off, therefore body cannot make insulin

Treatment: violet cell implants ie. cells that make diabetes, insulin injections

Type II: 90 % of cases, 1 in 4 chance

body does not make enough insulin or is inefficient at using insulin

genetic/environmental/adult-onset diabetes, inactivity and obesity, do not exercise , strain on pancreas, body cannot distribute or create insulin

Treatment: pills and exercise

Diabetes Insipidus:

damage hypothalamus, which makes NADH, which makes nerve cells

urine input increases so drink more water

Kidney Stones

more concentrated urine (minerals, alkaline and acid salts)

abdominal lower back pain, more urine output, tears tissues, causes pain so must be surgically removed

Bright's Disease

inflammation of nephrons and glomerulus lets through larger molecules that should not be there

urine output and urgency increases, thirst so drink water

Kidney/Bladder Cancer

smoking, exposure to cadmium, hereditary (as with all cancers)

pain, fatigue (growth of cells taking nutrients), blood in urine, urine output increases so treat with chemo, amino therapy, kidney transplants

Interstitial Cystitis

'itis' means inflammation

frequent urination, discomfort, blood in urine, so urinalysis, steroids, radiation, cystoscopy