1.

1​ ​-​ ​Molecules
Isotopes
Isotope:​ ​SAME​ ​element​ ​but​ ​different​ ​#​ ​of​ ​neutrons
Radioisotope:​ ​unstable​ ​isotope​ ​that​ ​decays​ ​over​ ​time​ ​by​ ​emitting​ ​radiation
➢ As​ ​a​ ​result​ ​they​ ​may​ ​ ​convert​ ​from​ ​one​ ​element​ ​to​ ​another
Half-life:​ ​half​ ​the​ ​time​ ​it​ ​takes​ ​for​ ​a​ ​radioactive​ ​sample​ ​to​ ​reach​ ​its​ ​initial​ ​amount
➢ Eg.​ ​iodine-131​ ​(20g)​ ​has​ ​a​ ​half​ ​life​ ​of​ ​8​ ​days.​ ​What​ ​mass​ ​remains​ ​after​ ​24​ ​days?
○ ​ ​=​ ​2.5g
Radioisotope​ ​tracing:​ ​radioactive​ ​material​ ​is​ ​injected​ ​into​ ​patient​ ​and​ ​it’s​ ​movements​ ​are
traced​ ​using​ ​a​ ​PET​ ​scan
➢ Eg.​ ​injecting​ ​a​ ​radioactive​ ​glucose​ ​can​ ​be​ ​used​ ​to​ ​find​ ​a​ ​tumor​ ​bc​ ​cancerous​ ​cells​ ​will
break​ ​the​ ​glucose​ ​down​ ​faster​ ​than​ ​regular​ ​cells
Radiometric​ ​Dating:​ ​dating​ ​rocks​ ​and​ ​fossils​ ​by​ ​seeing​ ​how​ ​much​ ​of​ ​a​ ​naturally​ ​occurring
isotope​ ​is​ ​abundant​ ​in​ ​the​ ​object​ ​(how​ ​much​ ​the​ ​isotope​ ​has​ ​decayed)

Molecule:​ ​a​ ​compound​ ​of​ ​at​ ​least​ ​2​ ​non-metal​ ​atoms

➢ 2​ ​building​ ​blocks​ ​of​ ​biological​ ​molecules:
○ Hydrogen
○ ​ ​Carbon
➢ Nitrogen,​ ​oxygen,​ ​phosphorous,​ ​and​ ​sulfur​ ​work​ ​with​ ​the​ ​H​ ​and​ ​C​ ​to​ ​give​ ​biological
molecules​ ​their​ ​specific​ ​chemical​ ​properties

intramolecular​ ​forces
➢ Ionic​ ​bonds
○ ​ ​occur​ ​b/w​ ​a​ ​cation​ ​(metal)​ ​and​ ​anion​ ​(non-metal)
○ Their​ ​charges​ ​allow​ ​them​ ​to​ ​form​ ​STRONG​ ​bonds​ ​w​ ​other​ ​atoms
○ Their​ ​charges​ ​allow​ ​ions​ ​to​ ​be​ ​polar
➢ Covalent​ ​bonds
○ Occur​ ​b/w​ ​2​ ​non-metal​ ​atoms
○ Valence​ ​electrons​ ​are​ ​shared
○ Level​ ​of​ ​attraction​ ​b/w​ ​2​ ​atoms​ ​depends​ ​on​ ​their​ ​electronegativity
■ If​ ​the​ ​2​ ​atoms​ ​have​ ​similar​ ​electronegativities,​ ​their​ ​electrons​ ​are
dispersed/shared​ ​equally​ ​so​ ​they​ ​have​ ​no​ ​overall​ ​charge​ ​(non-polar)
■ If​ ​the​ ​2​ ​atoms​ ​have​ ​very​ ​different​ ​electronegativities,​ ​their​ ​electrons​ ​are
shared​ ​unequally​ ​so​ ​the​ ​molecule​ ​forms​ ​dipoles​ ​(polar)
■ A​ ​higher​ ​electronegativity​ ​=​ ​higher​ ​attraction​ ​so​ ​electrons​ ​gravitate
towards​ ​it,​ ​giving​ ​that​ ​atom​ ​the​ ​more​ ​negative​ ​charge
■ High​ ​electronegativity​ ​=​ ​O,​ ​N,​ ​Cl
■ Low​ ​electronegativity​ ​=​ ​H,​ ​C,​ ​P
Intermolecular​ ​forces
➢ 2​ ​types:
○ Hydrogen​ ​Bonding
○ Hydrophobic​ ​Interactions
Hydrogen​ ​Bonding
➢ The​ ​slightly​ ​+​ ​hydrogen​ ​atom​ ​of​ ​one​ ​molecule​ ​attracts​ ​another​ ​slightly​ ​-​ ​atom​ ​of​ ​a
different​ ​molecule
➢ Weaker​ ​than​ ​ionic​ ​and​ ​covalent​ ​bonds​ ​but​ ​together​ ​can​ ​be​ ​very​ ​strong
➢ Represented​ ​by​ ​a​ ​dotted​ ​line​ ​bc​ ​it​ ​is​ ​a​ ​very​ ​weak​ ​type​ ​of​ ​covalent​ ​bond
➢ Help​ ​maintain​ ​proper​ ​structure​ ​and​ ​function​ ​in​ ​molecules
○ Capillary​ ​action​ ​and​ ​surface​ ​tension​ ​of​ ​water
■ Cohesion:​​ ​H-bonds​ ​b/w​ ​water​ ​molecules
■ Adhesion:​​ ​H-bonds​ ​b/w​ ​water​ ​and​ ​other​ ​molecules
○ Secondary,​ ​tertiary,​ ​and​ ​quaternary​ ​structures​ ​of​ ​proteins,​ ​and​ ​nucleic​ ​acids
Hydrophobic​ ​Interaction/Effect
➢ ​ ​Nonpolar​ ​molecules​ ​cannot​ ​form​ ​bonds​ ​with​ ​hydrogen​ ​in​ ​H2O​ ​so​ ​instead​ ​they​ ​clump
together​ ​in​ ​the​ ​presence​ ​of​ ​water
○ Considered​ ​hydrophobic​ (​ “water-fearing”)
○ Polar​ ​molecules​ ​are​ ​hydrophilic​ ​(“water-loving”)

Hydrocarbons
➢ Organic​ ​molecules​ ​made​ ​of​ ​only​ ​C​ ​and​ ​H
➢ Non​ ​polar​ ​(C-C​ ​is​ ​also​ ​non-polar,​ ​but​ ​CO​ ​and​ ​HO​ ​are​ ​polar)
➢ Low​ ​boiling​ ​point
➢ Flammable​ ​(used​ ​in​ ​combustion​ ​reactions)
➢ Their​ ​covalent​ ​bonds​ ​are​ ​energy-rich​ ​and​ ​release​ ​that​ ​energy​ ​when​ ​the​ ​bonds
are​ ​broken​ ​(eg.​ ​combustion)

Functional​ ​Groups
Functional​ ​group:​ ​a​ ​group​ ​of​ ​atoms​ ​that​ ​always​ ​behaves​ ​in​ ​a​ ​certain​ ​way,​ ​thus
determining​ ​the​ ​chemical​ ​and
physical​ ​properties​ ​of​ ​the​ ​organic
molecule​ ​its​ ​attached​ ​to
➢ Functional​ ​groups​ ​form​ ​the
reactive​ ​part​ ​of​ ​molecules

Hydroxyl​ ​Group​ ​-​OH

➢ Low​ ​reactivity
➢ Usually​ ​involved​ ​in​ ​hydrogen
bonding
➢ Increases​ ​molecule’s​ ​solubility​ ​in
water
Carbonyl​ ​Group​ ​-C=O
➢ Increases​ ​molecule’s​ ​solubility​ ​in
water
 ➢ Aldehyde:​ ​C=O​ ​group​ ​is​ ​at​ ​the​ ​end​ ​of​ ​the​ ​molecule​ ​w​ ​an​ ​H​ ​bonded​ ​to​ ​the​ ​C
➢ Ketone:​ ​C=O​ ​group​ ​is​ ​located​ ​w/in​ ​the​ ​molecule
○ When​ ​C​ ​is​ ​located​ ​within​ ​a​ ​molecule​ ​it​ ​is​ ​usually​ ​replaced​ ​by​ ​a​ ​bend​ ​in​ ​the
structural​ ​formula
Carboxyl​ ​Group​ ​-​COOH
➢ Contains​ ​both​ ​carbonyl​ ​and​ ​hydroxyl​ ​group
➢ Weak​ ​acid
➢ Can​ ​ionize​ ​by​ ​releasing​ ​the​ ​H​ ​atom​ ​as​ ​a​ ​free​ ​proton,​ ​thus​ ​becoming​ ​relatively​ ​stable
○ The​ ​negative​ ​charge​ ​flip-flops​ ​between​ ​the​ ​two​ ​O’s
Amino​ ​Group​ ​-NH2
➢ Basic
➢ Solubility​ ​decreases​ ​as​ ​the​ ​#​ ​of​ ​C’s​ ​in​ ​organic​ ​molecule​ ​increases
➢ Can​ ​ionize​ ​by​ ​accepting​ ​H​ ​ion
Sulfhydryl​ ​Group​ ​-SH
➢ Slightly​ ​polar
➢ Strong​ ​odour
➢ Lower​ ​boiling​ ​point​ ​and​ ​solubility​ ​than​ ​alcohol
➢ 2​ ​sulfhydryl​ ​groups​ ​can​ ​bond​ ​to​ ​form​ ​a​ ​disulfide​ ​group
Phosphate​ ​Group​ ​-PO4
➢ Involved​ ​with​ ​biological​ ​energy​ ​storage​ ​and​ ​release​ ​when​ ​phosphate​ ​bonds​ ​are​ ​broken
(phosphate​ ​bonds​ ​are​ ​energy​ ​rich)
➢ Found​ ​in​ ​ATP​ ​(adenine​ ​triphosphate),​ ​DNA​ ​&​ ​RNA​ ​(links​ ​nucleotides​ ​together)

Isomers
Isomer:​ ​same​ ​molecular​ ​formula​ ​but​ ​different​ ​structural​ ​formula
➢ Results​ ​in​ ​different​ ​properties​ ​unless​ ​they​ ​have​ ​the​ ​same​ ​functional​ ​groups
➢ Cells​ ​know​ ​which​ ​isomers​ ​they​ ​can​ ​recognize​ ​and​ ​need​ ​to​ ​synthesize
➢ 2​ ​types:
○ Structural​ ​Isomers
■ Positional
■ Chain
■ Functional
○ Stereoisomers
■ Geometric
■ Enantiomers
Structural​ ​Isomers
➢ Chain​ ​-​ ​C​ ​backbone​ ​is​ ​in​ ​a​ ​different​ ​order
➢ Positional​ ​-​ ​carbon​ ​backbone​ ​stays​ ​the​ ​same​ ​but​ ​but​ ​functional​ ​groups​ ​are​ ​moved
around/connected​ ​in​ ​different​ ​areas
➢ Functional​ ​-​ ​different​ ​functional​ ​groups​ ​are​ ​present
Stereoisomers
Geometric:​ ​same​ ​functional​ ​groups​ ​but​ ​arrangement​ ​of​ ​atoms​ ​on​ ​each​ ​side​ ​of​ ​the​ ​double​ ​C
bond​ ​is​ ​different
 ➢ Cis:​ ​when​ ​like​ ​groups​ ​are​ ​on​ ​the​ ​same​ ​sid/symmetrical​ ​about​ ​the​ ​double​ ​C​ ​bond
➢ Trans:​ ​when​ ​like​ ​groups​ ​are​ ​on​ ​opposite​ ​sides​ ​of​ ​the​ ​double​ ​C​ ​bond
Enantiomers:​ ​same​ ​molecular​ ​and​ ​structural​ ​formula​ ​but​ ​they​ ​cannot​ ​be
overlapped/superimposed​ ​ ​(think​ ​about​ ​right​ ​and​ ​left​ ​hands​ ​overlapping)
➢ Usually​ ​due​ ​to​ ​an​ ​asymmetrical​ ​carbon

1.2​ ​-​ ​Macromolecules

Macromolecules:​ ​large,​ ​complex​ ​molecules​ ​made​ ​up​ ​repeating​ ​smaller​ ​molecules​ ​linked
together​ ​-​ ​in​ ​other​ ​words,​ ​polymers​ ​made​ ​up​ ​of​ ​repeating​ ​monomer​ ​units
➢ 4​ ​types​ ​of​ ​macromolecules:
○ Carbohydrates
○ Proteins
○ Nucleic​ ​Acids
○ Lipids​ ​(the​ ​only​ ​one​ ​that​ ​isn’t​ ​a​ ​polymer)
Carbohydrates
Carbohydrate:​ ​macromolecule​ ​that​ ​always​ ​contains​ ​CHO​ ​usually​ ​in​ ​1:2:1​ ​ratio
➢ Molecular​ ​formula​ ​is​ ​technically​ ​C​m​H​2n​O​n
➢ How​ ​to​ ​identify​ ​-​ ​look​ ​for​ ​ringed​ ​structures​ ​that​ ​have​ ​CHO​ ​(monosaccharides​ ​if​ ​there​ ​are
3-7​ ​carbon​ ​atoms)
➢ Usually​ ​polar​ ​bc​ ​of​ ​hydroxyl​ ​and​ ​carbonyl​ ​groups
➢ Functions:
○ Short​ ​and​ ​Long​ ​term​ ​energy​ ​storage
○ Provide​ ​materials​ ​to​ ​build​ ​cell​ ​membrane
➢ 3​ ​types:
○ Monosaccharides/Simple​ ​Sugars
○ Disaccharides
○ Polysaccharides
➢ 2​ ​types​ ​of​ ​glycosidic​ ​linkages
○ Alpha​ ​-​ ​H​ ​on​ ​carbon​ ​1​ ​is​ ​on​ ​top,​ ​hydroxyl​ ​is​ ​on​ ​bottom​ ​ ​(starch​ ​and​ ​glycogen)
○ Beta​ ​-​ ​H​ ​on​ ​carbon​ ​1​ ​is​ ​on​ ​bottom,​ ​hydroxyl​ ​is​ ​on​ ​top​ ​(cellulose)
Monosaccharides/Simple​ ​Sugars
Monosaccharide:​ ​monomer​ ​that​ ​contains​ ​3-7​ ​carbon​ ​atoms
➢ Mono​ ​=​ ​one,​ ​saccharide​ ​=​ ​sugar
➢ Examples:
○ ​ ​glucose​ ​(found​ ​in​ ​blood)
○ Fructose​ ​(found​ ​in​ ​fruit)
○ Galactose​ ​(found​ ​in​ ​milk)
➢ All​ ​these​ ​examples​ ​have​ ​the​ ​formula​ ​C6​ ​H1​ 2​O6​ ​​ ​but​ ​are​ ​isomers​ ​of​ ​each​ ​other​ ​and
therefore​ ​have​ ​different​ ​properties​ ​(glucose​ ​and​ ​galactose​ ​are​ ​stereoisomers)
➢ Always​ ​have​ ​carbonyl​ ​group
Disaccharides
Disaccharide:​ ​2​ ​monosaccharides​ ​that​ ​join​ ​together​ ​through​ ​a​ ​covalent​ ​bond​ ​called​ ​a
glycosidic​ ​linkage​​ ​during​ ​a​ ​condensation​ ​reaction
 ➢ Glycosidic​ ​linkages​ ​form​ ​b/w​ ​specific​ ​hydroxyl​ ​groups
➢ Examples:
○ Sucrose​ ​(table​ ​sugar):​ ​glucose​ ​+​ ​fructose​ ​(broken​ ​down​ ​by​ ​enzyme​ ​sucrase)
○ Lactose​ ​(found​ ​in​ ​milk):​ ​glucose​ ​+​ ​galactose​ ​(broken​ ​down​ ​by​ ​enzyme​ ​lactase)
○ Maltose​ ​(formed​ ​when​ ​starch​ ​digests):​ ​glucose​ ​+​ ​glucose
➢ Enzymes​ ​use​ ​hydrolysis​ ​to​ ​help​ ​break​ ​these​ ​macromolecules​ ​down​ ​into​ ​their
monosaccharides
Oligosaccharide
Oligosaccharide:​ ​short​ ​chain​ ​of​ ​monosaccharides
➢ 3-10​ ​sugar​​ ​molecules
➢ Eg.​ ​disaccharides
➢ Help​ ​with​ ​production​ ​of​ ​glycoprotein​ ​and​ ​glycolipids​ ​in​ ​cell​ ​membranes
○ Functions​ ​-​ ​cell​ ​identification​ ​&​ ​attaching​ ​the​ ​cell​ ​to​ ​the​ ​extracellular​ ​matrix
Polysaccharides
➢ Polymers​ ​that​ ​are​ ​made​ ​up​ ​of​ ​monosaccharides​ ​joined​ ​by​ ​glycosidic​ ​linkages
➢ Eg.​ ​starch,​ ​glycogen,​ ​cellulose
Starch
➢ Form/way​ ​of​ ​storing​ ​of​ ​glucose/energy​ ​in​ ​plants​ ​(grains​ ​can​ ​be​ ​seen​ ​in​ ​chloroplasts)
➢ Short​ ​term​ ​energy​ ​storage​ ​bc​ ​it​ ​can​ ​easily​ ​be​ ​broken​ ​down​ ​into​ ​glucose
➢ Mixture​ ​of​ ​2​ ​types​ ​of​ ​polysaccharides
○ Amylose​ ​-​ ​unbranched​ ​alpha​ ​glucose​ ​polymer​ ​held​ ​together​ ​by
1-4​ ​glycosidic​ ​linkages
○ Amylopectin​ ​-​ ​branched​ ​alpha​ ​glucose​ ​polymer​ ​held​ ​by​ ​1-4
glycosidic​ ​linkages​ ​ ​and​ ​branches​ ​off​ ​at​ ​1-6​ ​glycosidic​ ​linkages
Glycogen
➢ Form​ ​of​ ​storing​ ​glucose​ ​in​ ​animals​ ​(found​ ​in​ ​liver​ ​of​ ​humans)
➢ Granules​ ​Can​ ​be​ ​seen​ ​in​ ​cytoplasm
➢ Short​ ​term​ ​energy​ ​storage​ ​bc​ ​it​ ​can​ ​easily​ ​be​ ​broken​ ​down​ ​into​ ​glucose
➢ Has​ ​multiple​ ​branches​ ​so​ ​it​ ​can​ ​be​ ​broken​ ​down​ ​very​ ​fast​ ​for​ ​energy
➢ Similar​ ​structure​ ​to​ ​amylopectin​ ​(1-4​ ​glycosidic​ ​linkages​ ​b/w​ ​alpha​ ​glucose​ ​monomers​ ​in
the​ ​main​ ​chain​ ​and​ ​1-6​ ​linkages​ ​at​ ​the​ ​branch​ ​points)
○ Glycogen​ ​is​ ​more​ ​highly​ ​branched​ ​than​ ​amylopectin
Cellulose
➢ Provides​ ​structural​ ​support​ ​in​ ​plant​ ​cell​ ​walls
➢ found​ ​in​ ​fruits,​ ​veggies,​ ​and​ ​grains
➢ cellulose​ ​fibres​ ​(called​ ​roughage​)​ ​are​ ​made​ ​of​ ​many​ ​intertwined,​ ​tight​ ​bundles​ ​called
microfibrils​​ ​-​ ​each​ ​microfibril​ ​is​ ​made​ ​of​ ​cellulose​ ​molecules​ ​held​ ​together​ ​by​ ​H-bonds
at​ ​beta​ ​1-4​ ​linkages
➢ Indigestible​ ​bc​ ​we​ ​lack​ ​the​ ​enzyme​ ​that​ ​can​ ​break​ ​down​ ​the​ ​structure​ ​of​ ​cellulose​ ​-beta
1-4​ ​glycosidic​ ​linkages
○ Pass​ ​through​ ​system​ ​undigested
○ Scrape​ ​large​ ​intestine​ ​walls​ ​which​ ​stimulates​ ​mucus​ ​secretion,​ ​lubrication​ ​feces
and​ ​helps​ ​in​ ​elimination​ ​of​ ​solid​ ​waste
Chitin:​ ​modified​ ​polysaccharide​ ​of​ ​glucose​ ​molecules​ ​with​ ​nitrogen
➢ After​ ​cellulose,​ ​chitin​ ​is​ ​the​ ​second​ ​most​ ​abundant​ ​carbohydrate
➢ Found​ ​in​ ​fungi​ ​cell​ ​walls​ ​and​ ​main​ ​component​ ​of​ ​arthropod​ ​exoskeletons

Lipids
➢ Composed​ ​of​ ​CHO,​ ​but​ ​there​ ​are​ ​a​ ​lot​ ​less​ ​oxygens​ ​than​ ​CH’s
➢ Non​ ​polar/hydrophobic
➢ Compared​ t​ o​ ​carbohydrates,​ ​lipids:
○ ​ ​Store​ ​more​ ​energy
■ Yield​ ​more​ ​than​ ​double​ ​energy/gram
○ Since​ ​energy​ ​is​ ​stored​ ​in​ ​hydrocarbons,​ ​their​ ​energy​ ​is​ ​less​ ​accessible​ ​to​ ​cells
than​ ​that​ ​of​ ​carbs
■ This​ ​therefore​ ​provides​ ​longer-term​ ​energy​ ​and​ ​are​ ​broken​ ​down​ ​after
carbs​ ​are​ ​used​ ​up
➢ Other​ ​functions:
○ Insulate​ ​against​ ​heat​ ​lost​ ​(recall​ ​that​ ​lipids​ ​are​ ​fats)
○ Protective​ ​cushion​ ​around​ ​organs
○ Major​ ​component​ ​of​ ​cell​ ​membranes
○ Water-repelling​ ​coatings​ ​for​ ​fur,​ ​feathers,​ ​and​ ​leaves
○ Steroid​ ​hormones​ ​(estrogen,​ ​progesterone,​ ​testosterone)
○ Electrical​ ​insulation​ ​of​ ​nerves
➢ 4​ ​types:
○ Triglycerides
○ Fatty​ ​acids
○ Steroids
○ waxes
Triglycerides
➢ Glycerol​ ​molecule​ ​+​ ​3​ ​fatty​ ​acid​ ​chains
➢ Join​ ​together​ ​through​ ​dehydration​ ​synthesis
➢ Hydroxyl​ ​on​ ​glycerol​ ​and​ ​carboxyl​ ​on​ ​fatty​ ​acid​ ​bond​ ​through​ ​an​ e ​ ster​ ​linkage
○ Forms​ ​3​ ​H2O’s​ ​bc​ ​there​ ​are​ ​3​ ​tails
Fatty​ ​acid:​ ​a​ ​hydrocarbon​ ​chain​ ​that​ ​ends​ ​with​ ​an​​ ​acidic​ ​carboxyl​ ​group
➢ Can​ ​either​ ​be​ ​saturated​ ​or​ ​unsaturated
 Properties Saturated Unsaturated

Double​ ​bonds? no Monounsaturated:​ ​one

double​ ​bond
Polyunsaturated:​ ​2+
double​ ​bonds

Straight​ ​or​ ​Bent​ ​tails? straight Bent​ ​bc​ ​of​ ​double​ ​bond

State​ ​@​ ​room​ ​temp Solid​ ​bc​ ​they​ ​are​ ​easily Liquid​ ​bc​ ​kinks​ ​push​ ​tails
stackable apart

Examples Lard,​ ​butter oil

Hydrogenation
➢ ​ ​bubbling​ ​hydrogen​ ​through​ ​bent​ ​tails​ ​(unsaturated)​ ​to​ ​make​ ​them​ ​saturated​ ​and​ ​straight
➢ Unsaturated​ ​fatty​ ​acids​ ​are​ ​normally​ ​cis​ ​but​ ​get​ ​converted​ ​to​ ​a​ ​trans​ ​configuration,
making​ ​them​ ​structurally​ ​similar​ ​to​ ​a​ ​saturated​ ​fatty​ ​acid
➢ Companies​ ​use​ ​them​ ​bc​ ​they​ ​are​ ​cheap​ ​and​ ​last​ ​long​ ​but
are​ ​harmful​ ​to​ ​your​ ​health
Phospholipids
➢ R​ ​group​ ​+​ ​phosphate​ ​group​ ​+​ ​glycerol​ ​+​ ​2​ ​fatty​ ​acids
➢ Main​ ​component​ ​of​ ​cell​ ​membrane
➢ Phospholipid​ ​head​ ​=​ ​polar,​ ​fatty​ ​acid​ ​tail​ ​=​ ​non-polar
Phospholipid​ ​bilayer
➢ In​ ​aqueous,​ ​extracellular​ ​environments​ ​phospholipids
naturally​ ​form​ ​a​ ​bilayer
➢ ​ ​phospholipids​ ​arrange​ ​themselves​ ​so​ ​the​ ​polar​ ​head​ ​faces​ ​the​ ​outward​ ​environment
and​ ​the​ ​tails​ ​form​ ​hydrophobic​ ​interiors
➢ Cholesterol​ ​molecules​ ​help​ ​maintain​ ​fluidity
○ Grab​ ​onto​ ​fatty​ ​acid​ ​tails​ ​and​ ​hold​ ​them​ ​together
when​ ​they​ ​get​ ​too​ ​warm​ ​and​ ​pull​ ​them​ ​apart
when​ ​they​ ​get​ ​too​ ​cold
Steroids
Steroid:​ ​lipid​ ​composed​ ​of​ ​4​ ​carbon​ ​based​ ​rings
➢ Different​ ​steroids​ ​have​ ​different​ ​arrangements​ ​and​ ​functions
➢ General​ ​functions:
○ Reduces​ ​inflammation
○ Anabolic​ ​steroids​ ​mimic​ ​male​ ​sex​ ​hormones​ ​-​ ​used​ ​for​ ​cancer​ ​and​ ​aids
treatment,​ ​and​ ​to​ ​build​ ​muscle​ ​mass
➢ Examples:
○ Cholesterol
■ Found​ ​in​ ​cell​ ​membrane​ ​&​ ​blood​ ​of​ ​animals
■ Precursor​ ​to​ ​other​ ​steroids
 ○ Testosterone
■ Regulates​ ​sexual​ ​function
■ Helps​ ​build​ ​bone​ ​and​ ​muscle​ ​mass
○ Estrogen
■ Regulates​ ​FEMALE​ ​sexual​ ​function
■ Increases​ ​fat​ ​storage
Waxes
waxes:​ ​lipids​ ​made​ ​of​ ​long​ ​carbon-based​ ​chains​ ​that​ ​are​ ​solid​ ​at​ ​room​ ​temp
➢ Produced​ ​in​ ​both​ ​animals​ ​and​ ​plants
➢ Functions:
○ Coats​ ​leaf​ ​surfaces
■ Prevents​ ​water​ ​and​ ​solutes​ ​from​ ​escaping
○ Repels​ ​insects
○ Coats​ ​skin,​ ​fur,​ ​leather,​ ​exoskeleton​ ​to​ ​keep​ ​surface​ ​dry
○ Forms​ ​barrier​ ​from​ ​infection
Proteins
Protein:​ ​polypeptides​ ​(polymer)​ ​made​ ​of​ ​repeating​ ​amino​ ​acid​ ​units​ ​(monomers)​ ​linked​ ​by
peptide​ ​bonds​ ​(covalent)
➢ Peptide​ ​bond​ ​forms​ ​b/w​ ​carboxyl​ ​and​ ​amino​ ​group
➢ Function​ ​depends​ ​on​ ​structure/shape
➢ Classified​ ​into​ ​groups​ ​based​ ​on​ ​function:
○ Catalyzing​ ​chemical​ ​reactions​ ​(eg.​ ​enzymes)
○ Structural​ ​support
○ Transport
○ Enabling​ ​organisms​ ​to​ ​move
○ Regulating​ ​cellular​ ​process
○ Providing​ ​defense​ ​against​ ​disease​ ​(eg.​ ​antibodies)
Amino​ ​Acids
➢ Central​ ​carbon​ ​bonded​ ​to:
○ Hydrogen​ ​(H)
○ Amino​ ​group​ ​(NH4)​ ​(basic)
○ Carboxyl​ ​group​ ​(COOH)​ ​(acidic)
○ R​ ​group
➢ N-C-C​ ​Backbone
➢ Somewhat​ ​polar​ ​bc​ ​of​ ​carboxyl​ ​and​ ​amino​ ​group
➢ Synthesized​ ​in​ ​ribosomes
➢ 20​ ​amino​ ​acids​ ​exist,​ ​8​ ​are​ ​essential​ ​(must​ ​be​ ​obtained​ ​through​ ​diet)
○ Combinations​ ​of​ ​the​ ​20​ ​amino​ ​acids​ ​are​ ​infinite
Levels​ ​of​ ​protein​ ​organization
➢ 4​ ​levels
○ Primary​ ​structure
■ Linear​​ ​order​ ​of​ ​amino​ ​acids​ ​bonded​ ​together​ ​through​ ​peptide​ ​bonds
■ Only​ ​one​ ​that​ ​does​ ​not​ ​involve​ ​protein​ ​folding/3d​ ​shape
 ○ Secondary​ ​structure
■ 2​ ​shapes
● Alpha​ ​helix​ ​-​ ​coil
● Beta-pleated​ ​sheet​ ​-​ ​folded
■ Occur​ ​due​ ​to​ ​H-bonds​ ​b/w​ ​polar​ ​groups
○ Tertiary​ ​structure
■ Responsible​ ​for​ ​folding​ ​of​ ​proteins,​ ​affected​ ​by:
● How​ ​different​ ​r-groups​ ​interact
● Mostly​ ​affected​ ​by​ ​hydrophobic​ ​effect
● Also​ ​affected​ ​by​ ​H-bonding
● ​ ​ionic/electrostatic​ ​bonding​ ​b/w​ ​different​ ​r-groups
○ Quaternary​ ​structure
■ How​ ​multiple​ ​polypeptides​ ​fold​ ​together​ ​to​ ​form
a​ ​protein
■ Also​ ​affected​ ​by​ ​H-bonds
Protein​ ​Denaturation
➢ Occurs​ ​when​ ​r-group​ ​bonds​ ​are​ ​disturbed​ ​(intermolecular
forces​ ​break),​ ​so​ ​the​ ​protein​ ​starts​ ​to​ ​unfold
➢ Affects​ ​2,​ ​3,​ ​and​ ​4,​ ​structures
➢ Can​ ​cause​ ​protein​ ​to​ ​lose​ ​function​ ​and​ ​can​ ​be​ ​irreversible
➢ Caused​ ​by:
○ Extreme​ ​temps
○ Exposure​ ​to​ ​chemicals
○ extreme​ ​pH
○ Agitation

Nucleic​ ​Acids
Nucleic​ ​acid:​ ​macromolecule​ ​composed​ ​of​ ​repeating​ ​nucleotides
(monomer)
➢ 2​ ​types​ ​of​ ​nucleic​ ​acids:
○ DNA​ ​(deoxyribonucleic​ ​acid)
■ More​ ​stable​ ​than​ ​RNA
○ RNA​ ​(ribonucleic​ ​acid)

DNA RNA

function -​ ​Contains​ ​genetic​ ​info -​ ​Converting​ ​the​ ​info

that​ ​codes​ ​for​ ​the stored​ ​stored​ ​in​ ​DNA​ ​to
synthesis​ ​of​ ​particular synthesize​ ​proteins​ ​in
amino​ ​acid​ ​sequences the​ ​ribosomes
-​ ​only​ ​found​ ​in​ ​nucleus -​ ​found​ ​in​ ​various​ ​parts
of​ ​the​ ​cell
 Type​ ​of​ ​pentose​ ​sugar deoxyribose ribose

Nitrogenous​ ​bases Adenine​ ​&​ ​thymine, Thymine​ ​is​ ​replaced​ ​with

guanine​ ​&​ ​cytosine uracil

How​ ​many​ ​strands? 2 1

➢ Nucleotide​ ​is​ ​made​ ​up​ ​of​ ​3​ ​components​ ​(covalently​ ​bonded)

○ Phosphate​ ​group
○ Pentose​ ​Sugar​ ​w/​ ​5​ ​carbon​ ​atoms
○ Nitrogenous​ ​base
➢ A​ ​polymer​ ​of​ ​nucleotides​ ​is​ ​called​ ​a​ ​strand​ ​or​ p
​ olynucleotide
➢ Nucleic​ ​acid​ ​strands​ ​have​ ​a​ ​backbone​ ​of​ ​alternating​ ​phosphates​ ​and​ ​sugars
○ Phosphate​ ​group​ ​on​ ​one​ ​nucleotide​ ​form​ ​a​ ​phosphodiester​ ​bond
○ With​ ​the​ ​hydroxyl​ ​group​ ​on​ ​the​ ​other​ ​nucleotide’s​ ​sugar
➢ Nitrogenous​ ​bases​ ​in​ ​DNA​ ​are​ ​held​ ​together​ ​by​ ​H-bonds
➢ Purines:​ ​A​ ​&​ ​G​ ​(2​ ​rings,​ ​bigger)
➢ Pyrimidines:​ ​C,​ ​T,​ ​U​ ​(single​ ​ringed,​ ​smaller)
Testing​ ​for​ ​macromolecules
➢ monosaccharides/glucose​ ​-​ ​Benedict's​ ​solution​ ​w/​ ​heat​ ​turns​ ​from​ ​blue​ ​to​ ​yellow-orange
➢ Starch​ ​-​ ​iodine​ ​turns​ ​from​ ​red-brown​ ​to​ ​blueish-black
➢ Triglycerides/Lipids​ ​-​ ​leave​ ​a​ ​translucent​ ​spot​ ​on​ ​brown​ ​paper
➢ Proteins​ ​-​ ​Biuret​ ​reagent​ ​turns​ ​from​ ​blue​ ​to​ ​purple
Molecular​ ​Model​ ​Legend
Hydrogen​ ​-​ ​white
Oxygen​ ​-​ ​red
Carbon​ ​-​ ​black
Nitrogen​ ​-​ ​blue
1.3​ ​-​ ​Biochemical​ ​Reactions​ ​&​ ​Enzymes
Acid:​ ​a​ ​substance​ ​that​ ​releases​ ​H​ ​ions​ ​when​ ​dissolved​ ​in​ ​water,​ ​increasing​ ​[H]​ ​in​ ​water
Base:​ ​a​ ​substance​ ​that​ ​releases​ ​an​ ​[OH]/​ ​accepts​ ​an​ ​[H]​ ​when​ ​dissolved​ ​in​ ​water,​ ​increasing
[OH]​ ​in​ ​water
pH
➢ pH​ ​is​ ​a​ ​measure​ ​of​ ​hydrogen​ ​ion​ ​concentration
○ >7​ ​=​ ​acidic
 ○ <7​ ​=​ ​basic
➢ Optimal​ ​pH​ ​of​ ​human​ ​blood​ ​is​ ​7.35​ ​-​ ​7.45
➢ pH​ ​below​ ​7​ ​or​ ​above​ ​7.8​ ​can​ ​be​ ​fatal
➢ Alkalosis:​ ​increase​ ​of​ ​blood​ ​pH​ ​to​ ​7.5​ ​-​ ​7.8​ ​due​ ​to:
○ ​ ​anxiety,​ ​hyperventilation,​ ​or​ ​over​ ​consumption​ ​of​ ​antacids
○ ​ ​causes​ ​dizziness​ ​and​ ​agitation
➢ Acidosis:​ ​blood​ ​pH​ ​falls​ ​to​ ​range​ ​of​ ​7.1​ ​-​ ​7.3​ ​due​ ​to:
○ ​ ​hypoventilation,​ ​severe​ ​vomiting,​ ​brain​ ​damage,​ ​kidney​ ​disease
○ causes​ ​disorientation​ ​and​ ​fatigue
Acid-Base​ ​Buffer​ ​System
Buffers:​ ​substances​ ​that​ ​minimize/resist​ ​pH​ ​changes​ ​by​ ​donating​ ​or​ ​accepting​ ​H​ ​ions​ ​as
needed
➢ When​ ​a​ ​fluid​ ​is​ ​too​ ​basic​ ​a​ ​weak​ ​acid​ ​will​ ​release​ ​its​ ​H​ ​ions​ ​and​ ​is​ ​now​ ​called​ ​a
conjugate​ ​base
➢ When​ ​a​ ​fluid​ ​is​ ​too​ ​acidic,​ ​the​ ​CB​ ​will​ ​take​ ​the​ ​H​ ​ions​ ​back​ ​up​ ​to​ ​become​ ​the​ ​weak​ ​acid
again
Bicarbonate​ ​Ion​ ​Buffer​ ​System
➢ Buffer​ ​system​ ​in​ ​humans
➢ Blood​ ​is​ ​too​ ​basic
○ water​ ​and​ ​carbon​ ​dioxide​ ​react​ ​to​ ​form​ ​carbonic​ ​acid​ ​(H​2​CO​3​)
○ Carbonic​ ​acid​ ​breaks​ ​down/dissociates​ ​into​ ​a​ ​bicarbonate​ ​ion​ ​(HCO​3​-​)+​ ​H
○ [H]​ ​increases,​ ​therefore​ ​increasing​ ​acidity
➢ Blood​ ​is​ ​too​ ​acidic
○ HCO​3​-​ w
​ ill​ ​take​ ​the​ ​H​ ​back​ ​up​ ​to​ ​create​ ​carbonic​ ​acid​ ​which​ ​becomes​ ​water​ ​and
carbon​ ​dioxide
○ CO2​ ​is​ ​breathed​ ​out
➢ For​ ​instance,​ ​hyperventilating​ ​people​ ​are​ ​told​ ​to​ ​breath​ ​in/out​ ​of​ ​a​ ​bag​ ​so​ ​[CO2]​ ​in​ ​the
bag​ ​increases,​ ​allowing​ ​more​ ​of​ ​it​ ​to​ ​be​ ​breathed​ ​in​ ​and​ ​being​ ​able​ ​to​ ​get​ ​turned​ ​into
bicarbonate​ ​ion

➢ 4​ ​main​ ​types​ ​of​ ​reactions

○ Neutralization
○ oxidation-reduction/redox
○ Dehydration​ ​synthesis/condensation
○ Hydrolysis
Neutralization
➢ When​ ​an​ ​acid​ ​and​ ​a​ ​base​ ​react​ ​they​ ​automatically​ ​undergo​ ​neutralization
○ the​ ​acid​ ​loses​ ​its​ ​acidic​ ​properties​ ​and​ ​the​ ​base​ ​loses​ ​its​ ​basic
○ Properties​ ​(i.e.​ ​properties​ ​get​ ​ca
○ ncelled​ ​out/neutralized)
➢ Acid​ ​+​ ​Base​ ​->​ ​salt​ ​(no​ ​charge)​ ​+​ ​water
➢ Eg.​ ​HCl​ ​+​ ​NaOH​ ​->​ ​NaCl​ ​+​ ​H2​ ​O
Oxidation-Reduction​ ​Reactions
➢ Processes​ ​where​ ​electrons​ ​are​ ​lost​ ​(oxidation)​ ​or
gained​ ​(reduction)
○ Redox​ ​happens​ ​bc​ ​the​ ​electrons​ ​want​ ​to​ ​move
from​ ​where​ ​they​ ​are​ ​weakly​ ​held​ ​to​ ​where​ ​they
are​ ​more​ ​strongly​ ​held
○ Oxidation​ ​and​ ​reduction​ ​happen​ ​simultaneously
➢ Reducing​ ​agent​:​ ​compound​ ​that​ ​undergoes​ ​oxidation/loses​ ​electrons
➢ Oxidizing​ ​agent​:​ ​compound​ ​that​ ​undergoes​ ​reduction/gains​ ​electrons
➢ Abbreviation​ ​-​ ​OIL​ ​RIG​ ​(oxidation​ ​is​ ​loss,​ ​reduction​ ​is​ ​gain)
➢ Eg.​ ​combustion​ ​reactions​ ​and​ ​cellular​ ​respiration
Condensation/Dehydration​ ​Synthesis
➢ Joining​ ​two​ ​molecules​ ​(eg.​ ​monomers)​ ​together​ ​to​ ​form​ ​a​ ​bigger​ ​molecule​ ​(eg.​ ​polymers)
through​ ​a​ ​covalent​ ​bond
➢ H​ ​atom​ ​on​ ​one​ ​functional​ ​group​ ​reacts​ ​with​ ​an​ ​OH​ ​on​ ​another​ ​functional​ ​group​ ​to​ ​form
H​2​O​ ​as​ ​a​ ​byproduct
Hydrolysis
➢ Opposite​ ​of​ ​condensation
➢ Adding​ ​H2O​ ​to​ ​break​ ​the​ ​two​ ​molecules​ ​apart
➢ H​ ​and​ ​OH​ ​attach​ ​back​ ​to​ ​their​ ​respective​ ​molecules
➢ Eg.​ ​breaking​ ​down​ ​macromolecules​ ​during​ ​digestion
*Look​ ​at​ ​table​ ​1.27​ ​in​ ​textbook​ ​(pg.35)
Enzymes
Activation​ ​energy​ ​(E​A​):​ ​the​ ​amount​ ​of​ ​energy​ ​that​ ​it​ ​would​ ​regularly​ ​take​ ​to​ ​complete​ ​a​ ​reaction
➢ Factors​ ​that​ ​speed​ ​up​ ​reactions
○ Increasing​ ​temp
○ Increasing​ ​SA
○ Increasing​ ​agitation
○ catalyst
➢ The​ ​higher​ ​the​ ​activation​ ​energy,​ ​the​ ​longer​ ​the​ ​reaction​ ​will​ ​take
➢ Catalysts​ ​lower​ ​the​ ​EA​ ​​ ​of​ ​a​ ​reaction
Catalyst:​​ ​a​ ​protein​​ ​that​ ​speeds​ ​up​ ​a​ ​chemical​ ​reaction​ ​without​ ​being​ ​consumed​ ​in​ ​the​ ​reaction
➢ In​ ​biological​ ​systems,​ ​these​ ​catalysts​ ​are​ ​called​ e ​ nzymes
○ Enzymes​ ​have​ ​a​ ​highly​ ​specific​ ​shape/size
○ Made​ ​of​ ​folded​ ​amino​ ​acid​ ​chains
○ Name:​ ​substrate​ ​+​ ​-ase
Enzyme-Substrate​ ​Complex
Substrate:​ ​the​ ​reactant​ ​in​ ​the​ ​reaction​ ​that​ ​the​ ​enzyme​ ​reacts​ ​with
Active​ ​site:​ ​pocket/indentation​ ​in​ ​enzyme​ ​where​ ​the​ ​substrate​ ​will​ ​bind​ ​to/where​ ​the
catalyzation​ ​takes​ ​place
Induced​ ​fit:​ ​once​ ​the​ ​substrate​ ​fits​ ​into​ ​the​ ​active​ ​site,​ ​the​ ​enzyme​ ​can
slightly​ ​adjust​ ​their​ ​shape​ ​to​ ​accommodate​ ​the​ ​substrate
➢ ​ ​Use​ ​intermolecular​ ​bonds​ ​and​ ​H-bonds​ ​(R-group​ ​of​ ​the​ ​enzyme​ ​w/
substrate)​ ​to​ ​achieve​ ​this
➢ Combined​ ​shape​ ​is​ ​called​ ​an​ ​enzyme-substrate​ ​complex
➢ Synthesis:​ ​when​ ​2​ ​substrates​ ​are​ ​combined​ ​in​ ​one​ ​enzyme​ ​to
produce​ ​a​ ​combined​ ​product
➢ degradation/decomposition:​ ​the​ ​substrate​ ​is​ ​broken​ ​down​ ​into​ ​2​ ​products​ ​after​ ​it
comes​ ​out​ ​of​ ​the​ ​enzyme
How​ ​enzymes​ ​work​ ​to​ ​lower​ ​E​A
➢ R​ ​groups​ ​in​ ​active​ ​sited​ ​bend/stretch​ ​the​ ​substrate’s​ ​bonds​ ​therefore​ ​weakening
the​ ​bond
○ Weak​ ​substrate​ ​bonds​ ​allow​ ​for​ ​it​ ​to​ ​react​ ​with​ ​other​ ​compounds​ ​more
easily
➢ Positioning​ ​2​ ​substrates​ ​in​ ​a​ ​certain​ ​way​ ​that​ ​allows​ ​them​ ​to​ ​react​ ​more​ ​easily
with​ ​other​ ​compounds
➢ Transferring​ ​electrons​ ​to/from​ ​the​ ​substrate​ ​(redox​ ​reaction)​ ​to​ ​make​ ​the
substrate​ ​unstable
○ Unstable​ ​substrates​ ​are​ ​more​ ​likely​ ​to​ ​undergo​ ​reactions
➢ Acting​ ​as​ ​an​ ​acid​ ​or​ ​base​ ​to​ ​add/remove​ ​H​ ​ions​ ​from​ ​the​ ​substrate​ ​to​ ​make​ ​it
more​ ​unstable,​ ​therefore​ ​more​ ​likely​ ​to​ ​react
➢ Once​ ​the​ ​reaction​ ​is​ ​complete​ ​and​ ​the​ ​substrate​ ​is​ ​released,​ ​the​ ​enzyme​ ​is​ ​ready​ ​to
accept​ ​another​ ​substrate​ ​and​ ​begin​ ​the​ ​process​ ​again
○ Called​ ​the​ ​catalytic​ ​cycle
Enzyme​ ​Helpers
 ➢ Some​ ​enzymes​ ​cannot​ ​catalyze​ ​a​ ​reaction​ ​unless​ ​one​ ​of​ ​the​ ​following​ ​is​ ​present:
○ ​ ​Coenzyme
■ Organic​ ​molecules​ ​that​ ​assists​ ​the​ ​enzyme
○ ​ ​cofactor
■ Metal​ ​ions​ ​(such​ ​as​ ​Fe​ ​or​ ​Zn)​ ​that​ ​assists​ ​the​ ​enzyme
■ The​ ​enzyme​ ​is​ ​inactive​ ​until​ ​the​ ​c​ofactor​ ​(activator)​ ​gets​ ​binded​ ​to​ ​it
● Sometimes​ ​the​ ​substrate​ ​cannot​ ​even​ ​fit​ ​unless​ ​the​ ​substrate​ ​is
connected​ ​to​ ​it
➢ Vitamins​ ​and​ ​minerals​ ​are​ ​vital​ ​bc​ ​one​ ​of​ ​their​ ​functions​ ​is​ ​helping​ ​in​ ​catalyzations

Factors​ ​that​ ​affect​ ​enzyme​ ​activity

➢ Temp
○ Denaturing​ ​occurs​ ​at​ ​extreme​ ​temps
○ low​ ​temp​ ​-​ ​enzyme​ ​bonds​ ​are​ ​not​ ​flexible​ ​enough​ ​to​ ​fit​ ​substrate​ ​i.e.​ ​poor
induced​ ​fit
○ High​ ​temp​ ​-​ ​shape​ ​starts​ ​to​ ​change​ ​bc​ ​enzyme​ ​bonds​ ​are​ ​too​ ​weak
➢ pH
○ If​ ​enzymes​ ​are​ ​not​ ​functioning​ ​at​ ​their​ ​optimal​ ​temps,​ ​then​ ​they​ ​start​ ​to
denature​ ​therefore​ ​losing​ ​their​ ​function
○ Different​ ​organs​ ​in​ ​the​ ​body​ ​have​ ​different​ ​pH’s,​ ​determining​ ​what​ ​pH
the​ ​enzyme​ ​works​ ​best​ ​at
➢ Substrate​ ​concentration
○ Increase​ ​in​ ​substrate​ ​concentration​ ​=​ ​more​ ​likely​ ​that​ ​enzymes​ ​and
substrates​ ​will​ ​encounter​ ​each​ ​other​ ​=​ ​increase​ ​in​ ​enzymatic​ ​activity/faster
○ However​ ​it​ ​will​ ​eventually​ ​plateau​ ​because​ ​there​ ​is​ ​a​ ​limited​ ​amount​ ​of
enzymes
Enzyme​ ​regulation
Inhibitors:​ ​molecule​ ​that​ ​hinders/reduces​ ​an​ ​enzyme’s​ ​ability​ ​to​ ​catalyze​ ​a​ ​reaction
➢ Prevent​ ​overproduction​ ​of​ ​products
Allosteric​ ​site:​ ​a​ ​site​ ​on​ ​the​ ​enzyme​ ​that​ ​isn’t​ ​the​ ​active​ ​site
➢ 2​ ​types:
○ Competitive​ ​inhibitors
■ Competes​ ​against​ ​the​ ​substrate​ ​by​ ​binding​ ​to​ ​the​ ​active​ ​site​ ​so​ ​the
substrate​ ​cannot​ ​bind​ ​to​ ​it​ ​and​ ​therefore​ ​the​ ​reaction​ ​does​ ​not​ ​occur
○ Non-competitive​ ​inhibitors
 ■ Bind​ ​to​ ​the​ ​allosteric​ ​site​ ​which​ ​changes​ ​the​ ​enzyme’s​ ​shape​ ​so​ ​that​ ​it​ ​is
harder​ ​for​ ​the​ ​substrate​ ​and​ ​enzyme​ ​to​ ​interact
Activators:​ ​molecules​ ​that​ ​bind​ ​to​ ​the​ ​allosteric​ ​site​ ​in​ ​such​ ​a​ ​way​ ​that​ ​it​ ​increases​ ​enzymatic
activity
➢ Activators​ ​and​ ​non-competitive​ ​inhibitors​ ​are​ ​called​ a ​ llosteric​ ​regulation
Feedback​ ​Inhibition
Biochemical​ ​pathways:​ ​pathway​ ​of​ ​enzymes​ ​where​ ​the​ ​product​ ​of​ ​one​ ​reaction​ ​is​ ​the
substrate​ ​of​ ​the​ ​next​ ​enzyme-catalyzed​ ​reaction
➢ The​ ​method​ ​of​ ​regulation​ ​for​ ​biochemical​ ​pathways​ ​is​ ​called​ ​feedback​ ​inhibition
➢ The​ ​last​ ​substrate​ ​in​ ​the​ ​pathway​ ​has​ ​an​ ​end-product​ ​that​ ​acts​ ​as​ ​a​ ​non-competitive
inhibitor​ ​for​ ​the​ ​first​ ​enzyme​ ​in​ ​the​ ​pathway
○ When​ ​it​ ​attaches​ ​to​ ​the​ ​allosteric​ ​site​ ​the​ ​active​ ​site​ ​is​ ​now​ ​changed​ ​so​ ​the
original​ ​substrate​ ​can​ ​no​ ​longer​ ​fit​ ​in​ ​it

2.1​ ​-​ ​Cells

➢ Prokaryotes
○ DNA​ ​is​ ​circular
○ No​ ​nucleus,​ ​mitochondria,​ ​or​ ​any​ ​membrane-bound​ ​organelles
○ Eg.​ ​bacteria
➢ Eukaryotes
○ DNA​ ​is​ ​linear,​ ​bounded​ ​in​ ​membrane
○ Has​ ​mitochondria,​ ​nucleus,​ ​and​ ​membrane-bound​ ​organelles
○ Unicellular​ ​or​ ​multicellular
○ Organelles​ ​are​ ​specialized
➢ 3​ ​features​ ​all​ ​eukaryotic​ ​cells​ ​have​ ​in​ ​common
○ membrane-bound​ ​nucleus​ ​with​ ​DNA
○ phospholipid​ ​bilayer​ ​(double​ ​layer)​ ​as​ ​cell​ ​membrane
○ Filled​ ​with​ ​cytoplasm
Nucleus
➢ Nucleoplasm​ ​-​ ​thick​ ​fluid​ ​that​ ​fills​ ​the​ ​nucleus
➢ Nuclear​ ​matrix
○ structure/support
➢ Nucleolus
○ Contains​ ​RNA,​ ​protein,​ ​&​ ​chromatin
 ➢ Nuclear​ ​envelope
○ Double​ ​membrane​ ​consisting​ ​2​ ​phospholipid​ ​bilayers
■ Space​ ​b/w​ ​2​ ​bilayers​ ​is​ ​called​ ​the​ ​lumen
○ Surrounds​ ​nucleus
○ Covered​ ​in​ ​nuclear​ ​pore​ ​complex
■ Proteins​ ​that​ ​form/control​ ​openings​ ​in​ ​the​ ​nuclear​ ​envelope
■ Small​ ​ions​ ​can​ ​pass​ ​through​ ​freely​ ​but​ ​large​ ​macromolecule​ ​transport​ ​is
controlled
➢ Contains​ ​DNA
○ Stores​ ​genetic​ ​info​ ​of​ ​the​ ​cell
○ DNA​ ​combines​ ​with​ ​protein​ ​to​ ​form​ ​chromosomes​ ​(unfolded​ ​state​ ​is​ ​called
chromatin)

Endomembrane​ ​System
➢ Composed​ ​of​ ​endoplasmic​ ​reticulum,​ ​golgi​ ​apparatus,​ ​vesicles,​ ​and​ ​cell​ ​membrane
➢ All​ ​work​ ​together​ ​to​ ​process​ ​and​ ​transport​ ​proteins
Ribosomes
➢ Composed​ ​of​ ​RNA​ ​and​ ​proteins
➢ Ribosomes​ ​found​ ​in​ ​cytosol​ ​(​free​ ​ribosomes​)​ ​synthesize​ ​polypeptides
Endoplasmic​ ​Reticulum
➢ Membrane-bound​ ​tubules​ ​&​ ​sacs
➢ Connected​ ​to​ ​nuclear​ ​envelope
➢ 2​ ​types:
○ Rough​ ​ER
■ Covered​ ​in​ ​ribosomes
 ● Synthesize​ ​proteins​ ​(eg.​ ​polypeptides)
○ Smooth​ ​ER
■ No​ ​ribosomes
■ synthesizes​ ​lipids​ ​(eg.​ ​phospholipids​ ​in​ ​membranes)
■ Can​ ​also​ ​perform​ ​other​ ​functions​ ​depending​ ​on​ ​cell
1. Ribosomes​ ​on​ ​Rough​ ​ER​ ​surface​ ​produce​ ​proteins​ ​and​ ​then​ ​push​ ​them​ ​to​ ​Smooth​ ​ER
(through​ ​lumen)​ ​where​ ​they​ ​are​ ​stored​ ​and​ ​processed
2. Smooth​ ​ER​ ​forms​ ​vesicles​ ​around​ ​lipids​ ​and​ ​proteins​ ​to​ ​get​ ​sent​ ​to​ ​cis​ ​face​ ​of​ ​golgi
apparatus
Golgi​ ​Apparatus
➢ Stack​ ​of​ ​curved​ ​membrane​ ​sacs
➢ Cis​ ​face​ ​-​ ​longer​ ​tubed​ ​side
➢ Trans​ ​face​ ​-​ ​more​ ​circular​ ​tubed​ ​side
➢ “Post-office”​ ​of​ ​the​ ​cell
○ Packages,​ ​sorts,​ ​and​ ​distributes​ ​substances​ ​to​ ​be​ ​sent​ ​around​ ​the​ ​cell
➢ Produces​ ​lysosomes​ ​and​ ​carbohydrates
3.​ ​Vesicles​ ​release​ ​proteins​ ​and​ ​lipids​ ​into​ ​golgi​ ​apparatus​ ​where​ ​they​ ​are​ ​modified​ ​and​ ​stored,
then​ ​packaged​ ​into​ ​vesicles​ ​to​ ​be​ ​sent​ ​to​ ​their​ ​destination​ ​via​ ​the​ ​trans​ ​face

Other​ ​Parts​ ​of​ ​the​ ​Endomembrane​ ​System

Lysosome
➢ A​ ​type​ ​of​ ​vesicle​ ​that​ ​contains​ ​enzymes​ ​to​ ​catalyze​ ​hydrolysis​ ​reactions
➢ Break​ ​down​ ​foreign​ ​particles​ ​and​ ​worn​ ​out​ ​parts​ ​of​ ​the​ ​cell
Secretory​ ​Vesicle
➢ Fuses​ ​with​ ​plasma​ ​membrane​ ​as​ ​secretion​ ​occurs
Incoming​ ​Vesicle
➢ Brings​ ​substances​ ​into​ ​the​ ​cell​ ​to​ ​the​ ​lysosomes​ ​to​ ​get​ ​digested
Transport​ ​Vesicle
➢ Transports​ ​molecules/substances​ ​to​ ​organelles
*​ ​all​ ​vesicles​ ​are​ ​formed​ ​by​ ​pinching​ ​off​ ​from​ ​membranes
Peroxisomes
➢ Membrane-bound​ ​sac​ ​that​ ​contains​ ​enzyme​ ​catalase​ ​and​ ​enzymes​ ​called​ o ​ xidases
○ These​ ​enzymes​ ​catalyze​ ​redox​ ​reaction
➢ Break​ ​down​ ​toxins,​ ​hydrogen​ ​peroxide,​ ​and​ ​excess​ ​fatty​ ​acids
➢ Help​ ​synthesize​ ​bile​ ​acids​ ​and​ ​cholesterol
Vacuoles
➢ A​ ​type​ ​of​ ​vesicle
➢ Animal​ ​cells​ ​that​ ​many​ ​vesicles​ ​but​ ​plant​ ​cells​ ​only​ ​have​ ​one​ ​large​ ​central​ ​vesicle​ ​called
a​ ​vacuole
➢ stores​ ​water,​ ​ions,​ ​sugars,​ ​amino​ ​acids,​ ​and​ ​macromolecules
➢ Contains​ ​enzymes
➢ Determines​ ​turgor​ ​pressure
Chloroplasts
 ➢ Only​ ​in​ ​plant​ ​cells
➢ Inner​ m ​ embrane​ ​is​ ​surrounded​ ​by​ ​a​ ​thick​ ​liquid​ ​called​ s
​ troma
➢ Filled​ w ​ ith​ ​grana​​ ​(a​ ​stack​ ​of​ ​thylakoids​)
○ Thylakoids​ ​are​ ​flattened​ ​disks​ ​that​ ​contain​ ​chlorophyll
■ Absorbs​ ​energy​ ​for​ ​photosynthesis
Mitochondria
➢ Converts​ ​stored​ ​energy​ ​from​ ​photosynthesis​ ​into​ ​useable​ ​energy​ ​through​ ​a​ ​redox
reaction
➢ Smooth​ ​outer​ ​membrane
➢ folded​ ​inner​ ​membrane
○ Folds​ ​are​ ​called​ ​cristae
○ Inner​ ​membrane​ ​is​ ​filled​ ​with​ ​fluid​ ​called​ ​matrix
Cell​ ​Wall
➢ Not​ ​in​ ​animal​ ​cells
➢ Rigid​ ​layer​ ​surrounding​ ​plant,​ ​bacteria,​ ​algae,​ ​and​ ​some​ ​archaea
cells
➢ Composed​ ​of​ ​carbohydrates​ ​and/or​ ​proteins​ ​(eg.​ ​cellulose)
➢ Gives​ ​cell​ ​structural​ ​support​ ​and​ ​it’s​ ​shape
Cytoskeleton
➢ Network​ ​of​ ​fibres​ ​made​ ​of​ ​protein​ ​that​ ​extend​ ​all​ ​over​ ​the​ ​cytoplasm
➢ Provide​ ​structure​ ​and​ ​support​ ​to​ ​organelles​ ​and​ ​act​ ​as​ ​tracks​ ​that​ ​lead​ ​from​ ​one​ ​part​ ​of
the​ ​cell​ ​to​ ​another​ ​(motility)
➢ 3​ ​types​ ​of​ ​protein​ ​fibres:
○ Microtubles
■ Thickest​ ​fibre
■ Hollow​ ​tube
■ facilitates​ ​movement​ ​of​ ​organelles,​ ​assists​ ​in​ ​cell
division​ ​helps​ ​maintain​ ​cell​ ​shape
○ Intermediate​ ​filaments
■ Second​ ​thickest
■ Coiled​ ​into​ ​a​ ​cable
■ Anchors​ ​organelles,​ ​form​ ​inner​ ​scaffolding​ ​of​ ​nucleus,
helps​ ​maintain​ ​cell​ ​shape
○ Microfilaments
■ Thinnest
■ 2​ ​strands​ ​of​ ​actin​ ​wound​ ​together
■ Involved​ ​in​ ​muscle​ ​contractions,​ ​assists​ ​in​ ​cell​ ​division,​ ​maintains​ ​cell
shape
Cilia​ ​&​ ​Flagella
➢ Enables​ ​the​ ​cell​ ​to​ ​move​ ​or​ ​to​ ​move​ ​substances​ ​over​ ​the​ ​cell
surface
Cilium:​​ ​tiny​ ​hair-like​ ​projections​ ​around​ ​the​ ​cell
Flagellum:​​ ​tail-like​ ​projection​ ​attached​ ​to​ ​the​ ​cell
Fluorescence​ ​Microscopy
Fluorescence​ ​microscopy:​ ​makes​ ​it​ ​possible​ ​to​ ​see​ ​inside​ ​a​ ​cell​ ​by​ ​staining​ ​cells​ ​with
fluorescent​ ​compounds​ ​in​ ​UV​ ​light​ ​-​ ​ ​emits​ ​light​ ​of​ ​various​ ​colours​ ​to​ ​make​ ​it​ ​easy​ ​to​ ​observe
different​ ​organelles
➢ 4​ ​techniques
○ Confocal​ ​microscopy
 ■ 3D​ ​image​ ​is​ ​formed​ ​when​ ​optical​ ​slices​ ​of​ ​a​ ​specimen​ ​are​ ​put​ ​together
○ Fluorescent​ ​in​ ​Situ​ ​Hybridization​ ​(FISH)
■ Dye-tagged​ ​antibodies​ ​that​ ​bind​ ​to​ ​specific​ ​DNA​ ​sequences​ ​are​ ​used​ ​to
stain​ ​chromosomes
○ Indirect​ ​immunofluorescence
■ Specific​ ​cell​ ​parts​ ​are​ ​stained​ ​when​ ​they​ ​are​ ​bound​ ​by​ ​primary​ ​antibodies,
which​ ​in​ ​turn,​ ​are​ ​bound​ ​by​ ​secondary​ ​dye-tagged​ ​antibodies
○ Ion​ ​Staining
■ Fluorescent​ ​probes​ ​are​ ​added​ ​to​ ​cells​ ​and,​ ​if​ ​certain​ ​ions​ ​are​ ​present,​ ​the
cells​ ​will​ ​fluoresce

2.1​ ​-​ ​2.2​ ​-​ ​cell​ ​membrane​ ​and​ ​cellular​ ​transport

➢ 3​ ​methods​ ​of​ ​transports​ ​in​ ​cells
○ Passive​ ​Transport
■ Diffusion
■ Osmosis
■ Facilitated​ ​diffusion
○ Active​ ​transport
■ Primary​ ​active​ ​transport
■ Secondary​ ​active​ ​transport
○ Membrane​ ​assisted​ ​transport
■ Endocytosis
● Phagocytosis
● Pinocytosis
● Receptor-mediated​ ​endocytosis
■ Exocytosis

Cell​ ​Membrane
➢ Acts​ ​as​ ​a​ ​boundary​ ​from​ ​extracellular​ ​fluid​ ​and​ ​the​ ​cell​ ​itself
➢ Regulates​ ​movement​ ​of​ ​ions​ ​and​ ​molecules​ ​into​ ​and​ ​out​ ​of​ ​the​ ​cell
➢ Semi-permeable​ ​(only​ ​allows​ ​some​ ​substances​ ​through)
○ Small​ ​uncharged​ ​polar​ ​and/or​ ​lipid​ ​soluble​ ​(hydrophobic)​ ​molecules​ ​can​ ​pass
thru​ ​the​ ​phospholipid​ ​bilayer​ ​easily
■ water,​ ​oxygen,​ ​carbon​ ​dioxide,​ ​&​ ​small​ ​fatty​ ​acids
○ Ions,​ ​Large​ ​Polar​ ​and/or​ ​water-soluble​ ​molecules​ ​have​ ​a​ ​hard​ ​time​ ​passing
through​ ​bc​ ​of​ ​hydrophobic​ ​interior
■ Have​ ​to​ ​pass​ ​through​ ​protein​ ​channels​ ​that​ ​are​ ​inserted​ ​throughout​ ​the
membrane
■ Eg.​ ​Ions,​ ​amino​ ​acids,​ ​triglycerides,​ ​glucose,​ ​&​ ​nucleic​ ​acids

Fluid​ ​Mosaic​ ​Model

 ➢ Basic​ ​framework​ ​is​ ​a​ ​phospholipid​ ​bilayer​ ​(recall​ ​polar​ ​heads​ ​face​ ​ECF,​ ​hydrophobic
fatty​ ​acid​ ​tails​ ​form​ ​hydrophobic​ ​interior)
➢ Proteins​ ​are​ ​inserted​ ​throughout​ ​the​ ​layer
○ Can​ ​be​ ​binded​ ​to​ ​other​ ​proteins​ ​or​ ​lipids,​ ​including​ ​glycoproteins​ ​and​ ​glycolipids
that​ ​are​ ​polar​ ​and​ ​therefore​ ​protrude​ ​from​ ​the​ ​surface​ ​of​ ​the​ ​membrane
■ glycoprotein:​ ​protein​ ​covalently​ ​bonded​ ​to​ ​carb​ ​chain
■ Glycolipid:​​ ​lipid​ ​covalently​ ​bonded​ ​to​ ​carb​ ​chain
➢ Phospholipids​ ​in​ ​bilayer​ ​have​ ​weak​ ​intermolecular​ ​bonds,​ ​therefore​ ​can​ ​easily​ ​move
around,​ ​exchanging​ ​places​ ​millions​ ​of​ ​times/sec
➢ If​ ​a​ ​tear/puncture​ ​occurs,​ ​phospholipids​ ​will​ ​quickly​ ​rearrange​ ​themselves​ ​to​ ​seal​ ​the
rupture
➢ Flip​ ​flopping​ ​from​ ​head​ ​to​ ​tail​ ​is​ ​rare,​ ​but​ ​may​ ​occur
Fluidity
➢ Fluidity​ ​must​ ​be​ ​regulated​ ​to​ ​prevent​ ​too​ ​little​ ​or​ ​too​ ​many​ ​molecules​ ​from​ ​freely
entering/exiting​ ​the​ ​cell
➢ Recall​ ​that​ ​cholesterol​ ​maintains​ ​cell​ ​fluidity
➢ 3​ ​factors​ ​that​ ​affect​ ​fluidity:
○ Temperature
■ Increase​ ​in​ ​temp​ ​=​ ​increase​ ​in​ ​fluidity
● Cholesterol​ ​will​ ​increase​ ​the​ ​intermolecular​ ​forces​ ​in​ ​the
membrane​ ​and​ ​hold​ ​it​ ​more​ ​tightly​ ​together,​ ​therefore​ ​reducing
fluidity
■ Decrease​ ​in​ ​temp​ ​=​ ​decrease​ ​in​ ​fluidity
● Phospholipids​ ​start​ ​to​ ​solidify​ ​into​ ​a​ ​gel-like​ ​fluidity​ ​but​ ​cholesterol
will​ ​break​ ​up​ ​the​ ​phospholipid​ ​packing,​ ​therefore​ ​increasing​ ​fluidity
○ #​ ​of​ ​double​ ​bonds​ ​in​ ​fatty​ ​acid​ ​tails
■ Increase​ ​in​ ​double​ ​bonds/kinks​ ​cause​ ​fatty​ ​acids​ ​to​ ​be​ ​less​ ​tightly​ ​packed
together,​ ​therefore​ ​increasing​ ​fluidity
○ Length​ ​of​ ​fatty​ ​acid​ ​tails
■ Longer​ ​FA​ ​chains​ ​=​ ​stronger​ ​intermolecular​ ​attractions​ ​=​ ​decrease​ ​in
fluidity
Cell​ ​Membrane​ ​Proteins
➢ 3​ ​types​ ​of​ ​proteins​ ​can​ ​be​ ​found​ ​inserted​ ​in​ ​the
phospholipid​ ​bilayer:
○ Transmembrane​ ​protein
■ Intersects​ ​the​ ​entire​ ​membrane
○ Integral​ ​protein
■ only​ ​integrated​ ​into​ ​one​ ​of​ ​the​ ​bilayers
○ Peripheral​ ​protein
■ Remain​ ​on​ ​the​ ​edge/perimeter​ ​of​ ​the​ ​phospholipid​ ​or​ ​on​ ​other​ ​integral
proteins
➢ Peripheral​ ​and​ ​some​ ​integral​ ​proteins​ ​help​ ​stabilize​ ​membranes​ ​by​ ​linking​ ​them​ ​to​ ​the
cytoskeleton
Possible​ ​Functions​ ​of​ ​membrane​ ​proteins
➢ Transporting​ ​substances​ ​into/out​ ​of​ ​the​ ​cell
➢ Reaction​ ​catalysis
○ Enzymes​ ​found​ ​on​ ​membrane​ ​will​ ​catalyze​ ​reactions
➢ Cell​ ​recognition
○ carb​ ​chains​ ​that​ ​protrude​ ​attached​ ​to​ ​glycoproteins​ ​enable​ ​cells​ ​to​ ​“recognize”
each​ ​other​ ​so​ ​they​ ​know​ ​when​ ​something​ ​is​ ​foreign/harmful
➢ Signal​ ​reception​ ​and​ ​transduction
○ Hormones​ ​bind​ ​to​ ​receptors​ ​on​ ​the​ ​protein
○ Allow​ ​cells​ ​to​ ​receive​ ​and​ ​send​ ​signals​ ​to​ ​the​ ​rest​ ​of​ ​the​ ​body

Passive​ ​Transport​ ​vs​ ​Active​ ​Transport

Passive​ ​transport:​ ​movement​ ​on​ ​substances​ ​along​ ​[​ ​]​ ​gradient​ ​(does​ ​not​ ​require​ ​energy)
➢ Diffusion
➢ Osmosis
➢ Facilitated​ ​diffusion
Active​ ​Transport:​ ​movement​ ​of​ ​substances​ ​against​ ​[​ ​]​ ​gradient​ ​(requires​ ​ATP)
➢ Primary​ ​active​ ​transport
○ Direct​ ​use​ ​of​ ​ATP
➢ Secondary​ ​active​ ​transport
○ Indirect​ ​use​ ​of​ ​ATP
Passive​ ​Transport
Diffusion
➢ Moving​ ​from​ ​an​ ​area​ ​of​ ​low​ ​[​ ​]​ ​to​ ​an​ ​area​ ​of​ ​high​ ​[​ ​]
➢ When​ ​[​ ​]​ ​inside​ ​=​ ​[​ ​]​ ​outside,​ ​dynamic​ ​equilibrium​ ​is​ ​reached
➢ Factors​ ​affecting​ ​diffusion:
○ Increased​ ​Temp​ ​=​ ​higher​ ​rate​ ​of​ ​diffusion
○ smaller​ ​size​ ​=​ ​higher​ ​rate​ ​of​ ​diffusion
○ Charged​ ​molecules​ ​generally​ ​cannot​ ​diffuse​ ​across​ ​cell​ ​membranes
○ Concentration​ ​gradient​ ​and​ ​membrane​ ​SA
○ Hydrophobic​ ​molecules​ ​>​ ​small,​ ​uncharged​ ​polar​ ​molecules​ ​>​ ​large,​ ​uncharged
polar​ ​molecules​ ​>​ ​Ions
Osmosis
➢ Diffusion​ ​of​ ​water
➢ Not​ ​all​ ​solutes​ ​can​ ​pass​ ​through​ ​the​ ​cell​ ​membrane​ ​so​ ​in​ ​osmosis​,​ ​water​ ​is​ ​always​ ​the
substance​ ​that​ ​moves​ ​to​ ​adjust​ ​the​ ​concentration
➢ 3​ ​types​ ​of​ ​osmotic​ ​concentrations
○ When​ ​both​ ​solutions​ ​have​ ​the​ ​same​ ​osmotic​ ​[​ ​]
■ both​ ​considered​ ​isotonic
○ When​ ​there​ ​is​ ​unequal​ ​osmotic​ ​concentrations
■ Hypertonic:​ ​solution​ ​outside​ ​cell​ ​has​ ​higher​ ​solute​ ​[​ ​]
■ Hypotonic:​ ​solution​ ​outside​ ​cell​ ​lower​ ​solute​ ​[​ ​]
*​ ​look​ ​at​ ​red​ ​blood​ ​cell​ ​diagram​ ​in​ ​notes

Facilitated​ ​Diffusion
➢ Since​ ​large​ ​polar​ ​molecules​ ​and​ ​ions​ ​cannot​ ​diffuse​ ​through​ ​the​ ​membrane,​ ​regularly,
they​ ​can​ ​diffuse​ ​using​ ​either​ ​a:
○ transmembrane/channel​ ​protein
○ Carrier​ ​protein
➢ Works​ ​as​ ​long​ ​as​ ​[​ ​]​ ​outside​ ​cell​ ​>​ ​[​ ​]​ ​inside​ ​cell
Channel​ ​proteins/transmembrane
➢ Tubular​ ​shape​ ​made​ ​of​ ​proteins
➢ Exterior​ ​is​ ​made​ ​up​ ​of​ ​amino​ ​acids​ ​with​ ​non-polar​ ​chains
○ non-polar​ ​allows​ ​it​ ​to​ ​interact​ ​with​ ​the​ ​phospholipid’s​ ​non-polar​ ​interior
➢ Tunnel​ ​in​ ​the​ ​channel​ ​protein​ ​is​ ​very​ ​specifically​ ​shaped​ ​so​ ​only​ ​certain​ ​molecules/ions
can​ ​pass​ ​through
○ Generally​ ​passes​ ​smaller​ ​polar​ ​molecules/ions
➢ Some​ ​channels​ ​are​ ​always​ ​open​ ​but​ ​some​ ​can​ ​open/close​ ​in​ ​response​ ​to:
○ Hormones
○ Electric​ ​discharge
○ Pressure
○ Light
Cystic​ ​Fibrosis
➢ Fatal​ ​genetic​ ​disorder​ ​when​ ​channel​ ​proteins​ ​that​ ​move​ ​chloride​ ​ions​ ​is​ ​defective
➢ Causes​ ​improper​ ​water​ ​movement​ ​in​ ​and​ ​out​ ​of​ ​cells​ ​which​ ​builds​ ​up​ ​thick​ ​mucus​ ​in
respiratory​ ​passages​ ​and​ ​organs
Carrier​ ​Proteins
➢ Generally​ ​passes​ ​bigger​ ​polar​ ​molecules/ions
➢ Difference​ ​is​ ​that​ ​carrier​ ​proteins​ ​must​ ​BIND​ ​to​ ​the​ ​molecules/ions​ ​that​ ​pass​ ​through
➢ Carrier​ ​proteins​ ​change​ ​shape​ ​while​ ​they​ ​transport​ ​molecules/ions
 Since​ ​they​ ​can​ ​only​ ​bind​ ​to​ ​a​ ​few​ ​molecules​ ​at​ ​a​ ​time,​ ​this​ ​type​ ​of​ ​transport​ ​takes
○
longer​ ​than​ ​channel​ ​proteins​ ​(i.e.​ ​lower​ ​diffusion​ ​rate)
➢ Exterior​ ​is​ ​also​ ​made​ ​of​ ​amino​ ​acids​ ​with​ ​non-polar​ ​side​ ​chains
○ Non-polar​ ​side​ ​chains​ ​allow​ ​it​ ​to​ ​interact​ ​with​ ​the​ ​phospholipid’s​ ​non-polar​ ​interior
➢ Interior​ ​is​ ​lined​ ​with​ ​amino​ ​acids​ ​that​ ​form​ ​intermolecular​ ​bonds​ ​with​ ​the​ ​molecule​ ​of
transport
Cystinuria
➢ Genetic​ ​disorder
➢ Inability​ ​to​ ​remove​ ​cystine​ ​and​ ​other​ ​amino​ ​acids​ ​from​ ​urine
○ If​ ​cystine​ ​isn’t​ ​removed​ ​then​ ​it​ ​can​ ​cause​ ​them​ ​to​ ​crystalize​ ​into​ ​stones​ ​called
calculi​ ​which​ ​block​ ​the​ ​urinary​ ​tract

Active​ ​Transport
➢ Since​ ​the​ ​molecules​ ​are​ ​going​ ​against​ ​the​ ​[​ ​]​ ​gradient​ ​they​ ​require​ ​energy​ ​called​ ​ATP
○ ATP​ ​(adenosine​ ​triphosphate)​ ​is​ ​made​ ​of​ ​an​ ​adenine​ ​nucleotide​ ​with​ ​3
phosphate​ ​groups)
○ ​ ​goes​ ​through​ ​hydrolysis​ ​to​ ​create​ ​ADP​ ​and​ ​1​ ​phosphate,​ ​with​ ​the​ ​release​ ​of
energy

Primary​ ​Active​ ​Transport

➢ Uses​ ​ATP​ ​directly
➢ The​ ​carrier​ ​protein​ ​needs​ ​to​ ​use​ ​ATP​ ​to​ ​move​ ​the​ ​molecule/ion​ ​against​ ​its​ ​concentration
gradient
Ion​ ​pump:​​ ​a​ ​carrier​ ​protein​ ​that​ ​uses​ ​ATP​ ​to​ ​“pump”​ ​ions​ ​across​ ​the​ ​membrane
 ➢ Eg.​ ​sodium-potassium​ ​pump
○ 3​ ​Na​ ​ions​ ​bind​ ​to​ ​the​ ​pump
○ Phosphate​ ​from​ ​hydrolysis​ ​of​ ​ATP​ ​attaches​ ​to​ ​pump​ ​which​ ​allows​ ​it​ ​to
change​ ​shape/move​ ​into​ ​next​ ​step
○ Shape​ ​changes​ ​and​ ​Na​ ​ions​ ​are​ ​released​ ​outside​ ​the​ ​cell
○ New​ ​configuration/position​ ​allows​ ​2​ ​K​ ​ions​ ​from​ ​the​ ​outside​ ​of​ ​the​ ​cell
bind​ ​to​ ​the​ ​pump​ ​causing​ ​the​ ​phosphate​ ​group​ ​to​ ​detach
○ Detachment​ ​of​ ​P​ ​group​ ​allows​ ​the​ ​protein​ ​to​ ​return​ ​to​ ​it’s​ ​original​ ​shape,
allowing​ ​the​ ​2​ ​K​ ​into​ ​the​ ​cell
➢ The​ ​pump​ ​results​ ​in​ ​one​ ​side​ ​of​ ​the​ ​membrane​ ​being​ ​positively​ ​charged​ ​and​ ​the
other​ ​side​ ​being​ ​negatively​ ​charged​ ​due​ ​to​ ​accumulation​ ​of​ ​negative​ ​or​ ​positive
ions​ ​on​ ​one​ ​side
➢ Electric​ ​potential​ ​difference​ ​+​ ​concentration​ ​gradient​ ​is​ ​called​ ​the
electrochemical​ ​gradient
○ Electrochemical​ ​gradient​ ​is​ ​responsible​ ​for​ ​storing​ ​energy​ ​that​ ​can​ ​be
used​ ​by​ ​the​ ​cell
Secondary​ ​Active​ ​Transport
➢ Using​ ​energy​ ​stored​ ​in​ ​the​ ​electrochemical​ ​gradient​ ​created​ ​by​ ​Primary​ ​active
transport​ ​to​ ​move​ ​ions/molecules​ ​across​ ​membrane
➢ Eg.​ ​Hydrogen-sucrose​ ​pump
○ Hydrogen​ ​ions​ ​go​ ​through​ ​Primary​ ​active​ ​transport​ ​to​ ​come​ ​out​ ​of​ ​the​ ​cell
using​ ​ATP
■ This​ ​creates​ ​an​ ​electrochemical​ ​gradient​ ​which​ ​stores​ ​the​ ​energy
that​ ​secondary​ ​active​ ​transport​ ​will​ ​use
○ Hydrogen​ ​ions​ ​and​ ​Sucrose​ ​molecules​ ​outside​ ​the​ ​cell​ ​bind​ ​to​ ​the
hydrogen-sucrose​ ​pump​ ​and​ ​come​ ​into​ ​the​ ​cell​ ​using​ ​the​ ​energy​ ​from​ ​the
electrochemical​ ​gradient

Membrane​ ​Assisted​ ​Transport

➢ Molecules​ ​that​ ​are​ ​too​ ​big​ ​(eg.​ ​macromolecules)​ ​have​ ​to​ ​use​ ​membrane-assisted
transport​ ​to​ ​get​ ​into​ ​the​ ​cell
➢ Forms​ ​vesicles​ ​to​ ​transport​ ​molecules
➢ Energy​ ​required
➢ 2​ ​methods:
○ Endocytosis​ ​-​ ​Cell​ ​membrane​ ​engulfs​ ​around​ ​cell​ ​and​ ​pinches​ ​off​ ​to​ ​form​ ​vesicle
■ Phagocytosis
● Engulfing​ ​solid/discrete​ ​particles​ ​w/​ ​liquid
■ Pinocytosis
● Engulfing​ ​liquid​ ​particles​ ​w/​ ​solutes
■ Receptor-mediated​ ​endocytosis
● Coated​ ​pit:​ ​a​ ​portion​ ​on​ ​the​ ​cell​ ​membrane​ ​that​ ​is​ ​coated​ ​in​ ​a
layer​ ​of​ ​protein​ ​and​ ​has​ ​receptor​ ​proteins​ ​on​ ​it
● Receptor​ ​proteins​ ​only​ ​bind​ ​to​ ​specific​ ​molecules
● Coated​ ​pit​ ​binds​ ​to​ ​molecule​ ​and​ ​then​ ​pinches​ ​off​ ​to​ ​form​ ​the
vesicle
● Receptor​ ​proteins​ ​can​ ​be​ ​recycled
○ Exocytosis​ ​-​ ​How​ ​excretory​ ​products​ ​leave​ ​the​ ​cell
■ Vesicles​ ​carry​ ​molecules​ ​back​ ​to​ ​the​ ​cell​ ​membrane
● Vesicle​ ​fuses​ ​back​ ​into​ ​the​ ​cell​ ​membrane
● Vesicle​ ​releases​ ​products​ ​into​ ​the​ ​extracellular​ ​fluid
■ In​ ​plant​ ​cells​ ​this​ ​mechanism​ ​is​ ​used​ ​to​ ​export​ ​materials​ ​needed​ ​to​ ​build
the​ ​cell​ ​wall
■ In​ ​animal​ ​cells​ ​this​ ​mechanism​ ​is​ ​used​ ​to​ ​secrete​ ​hormones,
neurotransmitters,​ ​digestive​ ​enzymes,​ ​etc.