BIOCHEMISTRY! generally! deals! with! the! physical! and! chemical! properties! of! compounds! that! that! make! up! the!
smallest!unit!of!life!and!how!these!compounds!undergo!processes!and!relate!it!with!how!it!affects!the!daily!function!of!
human!beings.!!
!
I.!
8!
8!
8!
8!
8!
AMINO/ACIDS/
/
These! are! organic! carboxylic! acids! that! has! at! least! one! amino! group! replacing! a! hydrogen! atom! of! the!
hydrocarbon!chain.!!
All!of!the!20!amino!acids,!with!the!exception!of!Glycine,!are!levorotatory!since!glycine!doesn’t!have!an!asymmetric!
carbon,!hence!it!cannot!exhibit!stereoisomerism.!!
Sulfur!containing!
o! Cysteine!and!Methionine!
Glycine!
o! Acts!as!an!inhibitory!neurotransmitter;!antagonized!by!strychnine!
In!a!protein!chain,!the!α!8!carboxyl!group!of!each!amino!acid!is!joined!by!peptide!bonds!covalently!to!the!α!8!amino!
group!of!the!next!amino!acid!
!
NAME/
3/LETTER/
1/LETTER/
CLASSIFICATION/
STRUCTURE/
SYMBOL/
SYMBOL/
Alanine!
Ala!
A!
Aliphatic!
!
(Hydrophobic!Side!
Chain)!
Isoleucine!
Ile!
I!
Aliphatic!
(Hydrophobic!Side!
Chain)!
Leucine!
Leu!
L!
Aliphatic!
!
(Hydrophobic!Side!
Chain)!
Methionine!
Met!
M!
Aliphatic!
(Hydrophobic!Side!
Chain)!
Valine!
Val!
V!
Aliphatic!
(Hydrophobic!Side!
Chain)!
Phenylalanine!
Phe!
F!
Aromatic!
(Hydrophobic!Side!
Chain)!
Tryptophan!
Trp!
W!
Aromatic!
(Hydrophobic!Side!
Chain)!
Tyrosine!
Tyr!
Y!
Aromatic!
(Hydrophobic!Side!
Chain)!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
Asparagine!
Asn!
N!
Polar!Neutral!Side!
Chain!
Cysteine!
Cys!
C!
Polar!Neutral!Side!
Chain!
Glutamine!
Gln!
Q!
Polar!Neutral!Side!
Chain!
Serine!
Ser!
S!
Polar!Neutral!Side!
Chain!
Threonine!
Thr!
T!
Polar!Neutral!Side!
Chain!
Aspartic!Acid!
Asp!
D!
Acidic!
Glutamic!Acid!
Glu!
E!
Acidic!
Arginine!
Arg!
R!
Basic!
Histidine!
His!
H!
Basic!
Lysine!
Lys!
K!
Basic!
Glycine!
Gly!
G!
Unique!
Proline!
Pro!
P!
Unique!
!
!
!
!
!
!
!
!
!
!
!
!
II.!
PROTEINS/
!
8!
8!
The!major!cell!components!that!play!a!big!role!in!all!biological!processes!
These! are! organic! compounds! with! high! –! molecular! weights! that! contain! nitrogen! with! complex! structural!
organization!
8! Contain!amino!acids!linked!by!covalent!peptide!bonds!
8! Amphoteric!in!nature!
!
A.! Protein/Structures/
8! Structurally! organized! into! four! levels! (with! each! level! having! its! proper! specificity):! PRIMARY,! SECONDARY,!
TERTIARY,!and!QUATERNARY!!
!
1.! Primary/Structure/
/
o! The!simplest!level!of!structural!organization!composed!of!the!amino!acid!resides!linked!through!peptide!
bonds!
o! The!sequence!is!written!from!left!to!right!(N8!Terminal!to!C!–!Terminal!amino!acid)!
o! In!an!electric!field:!Positively!charged!proteins!8>!Cathode!(8)!;!Negatively!charged!proteins!8>!Anode!(+)!;!
Proteins!at!the!isoelectric!pH!8>!no!migration!since!net!charge!is!0!
!
2.! Secondary/Structure/
!
8!
8!
!
!
!
!
!
!
o! α!8!Helix!
!! A!helical!configuration!of!the!polypeptide!chain!formed!by!the!Hydrogen!bonding!between!the!
peptide!groups!of!every!first!and!fourth!AA!residues.!
!
o! β!8!Sheets!
!! Pleated!sheet!structure!resembling!an!accordion!
!! Can!be!in!a!form!of!a!parallel!or!an!antiparallel!chain!
!! Examples!are!Keratin,!Collagen,!and!Fibroin!
!! Creutzfeldt!–!Jakob!Disease!
•! Caused!by!the!transmission!of!Prions!(a!proteinaceous!infectious!agent!that!causes!
neurodegenerative!diseases)!that!results!to!the!misfolding!of!the!normal!prion!protein!
found!abundantly!in!the!brain!
o! Prions!causes!Mad!Cow!Disease!
•! Replacement!of!the!normal!α!8!helical!arrangement!of!the!normal!prion!protein!with!β!8!
pleated!sheet!
•! Dementia!and!Involuntary!Jerking!Movements!(Startle!Myoclonus)!
!
3.! Tertiary/Structure/
/
o! Refers!to!the!spatial!arrangement!of!the!polypeptide!chain!
o! Can!either!be!Fibrous!or!Globular!
o! Different!bonds!contribute!to!the!stabilization!of!the!structure!
!! Covalent!bond:!Disulfide!Bond!
!! Polar!bonds:!Hydrogen!bonding,!Ionic!bonding!
!! Non8Polar/!van8der8Waals!
o! Chaperones!
!! Proteins!that!assist!in!the!folding!and!unfolding!of!the!polypeptide!to!correctly!form!the!tertiary!
structure!
!! Example:!Heat!Shock!Proteins!
!
4.! Quaternary/Structure/
!
o! Spatial!arrangement!of!proteins!made!up!of!several!polypeptide!chains,!with!each!peptide!chain!having!
a!tertiary!structure!
o! Referred!to!as!Oligomers!
o! Example:!Hemoglobin!
!
!
Denaturation/(Denativation)!of!proteins!happen!when!certain!agents!such!as!heat!and!urea!destroy!the!higher!
structural!levels!of!protein!without!destroying!the!peptide!bonds!
Renaturation/(Renativation),!on!the!other!hand,!is!the!recovery!of!the!protein!from!its!denatured!state!!
!
B.! Medically/Important/Proteins/
/
1.! Hemoglobin/
o! Globular!Transport!Protein!for!Oxygen/
o! Contains!Heme!which!is!a!complex!of!porphyrin!ring!and!a!Ferrous/
o! Sickle!Cell!Anemia/
!! Caused!by!a!mutation!in!hemoglobin!where!the!Glutamate!at!position!six!in!the!beta!–!chain!of!
hemoglobin!is!replaced!by!Valine/
o! Has!higher!affinity!to!CO!than!CO2/
/
2.! Collagen/
o! Found!mainly!in!the!bones!and!cartilage!
o! Mainly!contains!Glycine,!Proline,!Hydroxyproline!
o! Types:!
!! I!–!Found!in!skin!and!bones!
•! Osteogenesis/Imperfecta!is!a!disorder!in!the!synthesis!of!Type!I!collagen!characterized!
by!a!distinctive!blue!sclera!and!predisposed!multiple!childhood!fracture/
!! II!–!Found!in!the!Cartilage!
!! III!–!Found!in!the!arterial!walls!
!! IV!–!found!in!the!basal!lamina!
!! V!–!Found!in!the!hair!and!placenta!
o! Ehlers!–!Danlos!Syndrome!
!! A!group!of!connective!tissue!disorders!that!are!generally!characterized!by!hyperextensible!skin,!
joint!hypermobility,!and!defects!in!large!blood!vessels!
!
3.! Insulin!
o! A!polypeptide!hormone!produced!by!the!beta!–!cells!of!the!pancreas!
o! Synthesis!of!Preproinsulin!in!the!rough!ER!8>!Proinsulin!is!cleaved!in!the!secretory!granules!8>!C!–!petide!
is!released!8>!the!remaining!molecule!forms!Insulin!
!
C.! Qualitative/Tests/for/Proteins/&/Amino/Acids!
!
!
!
!
!
!
1.! Biuret!Test!
o! Identifies!the!presence!of!proteins!
o! Uses!1%!NaOH!and!a!solution!of!Copper(II)!sulfate!
o! Positive!Result:!Violet!Color!
!
2.! Ninhydrin!Test!
o! Uses!Ninhydrin!to!detect!the!presence!of!amines!
o! Positive!Result:!Purple!(Ruhemann’s!Purple)!=!Amino!Acids!with!a!free!amino!group,!Yellow!=!Imino!
Acids!(Proline!&!Hydroxyproline)!
!
3.! Xanthoproteic!Test!
o! For!Tyrosine,!Tyrptophan!
o! Uses!conc.!HNO3!and!40%!NaOH!
o! Positive!Result:!Yellow!Color!
!
4.! Millon’s!test!
o! Specific!for!Tyrosine!
o! Uses!Mercury!dissolved!in!conc.!HNO3!
o! Positive!Result:!Yellow!Coloration!
5.! Hopkins’s!–!Cole!Test!
o! Specific!for!Tyrosine!(indole!group)!
o! Uses!Glyoxylic!Acid!in!Glacial!Acetic!Acid!and!Sulfuric!Acid!
o! Positive!Result:!Purple!Color!on!the!surface!
!
6.! Nitroprusside!Test!
o! Specific!for!Cysteine!
o! Uses!nitroprusside!in!alkaline!solution!
o! Positive!Result:!Red!Coloration!
7.! Sakaguchi!Test!
o! Specific!for!Arginine!(guanido!group)!
o! Uses!NaOH,!α!8!naphthol,!and!Bromine!solution!
!
III.!
8!
ENZYMES/
/
These!are!biological!catalysts!of!protein!nature!which!catalyzes!energetically!feasible!reaction!without!altering!the!
reaction!route.!Like!other!nonbiological!catalysts,!enzymes!are!not!consumed!during!a!reaction!and!decreases!the!
Ea!of!a!reaction.!
!
8!
Enzymes!are!highly!specific!for!their!substrates!and!products!with!most!enzymes!recognizing!only!1!compound!
as!substrate.!!
8!
The!velocity!of!a!reaction!is!directly!proportional!with!temperature!at!an!optimal!pH!
o! However,!as!the!temperature!goes!higher!than!37!degrees!(Celsius),!enzymes!start!to!degrade!
o! !Changes!in!pH!can!cause!changes!in!reaction!and!may!cause!enzymes!to!denature!
!! Pepsin:!optimal!pH!is!2!
!
Many!enzymes!require!cofactors!or!coenzymes!to!catalyze!reactions.!These!coenzymes!are!commonly!derived!
from!vitamins!and!metal!ions.!
!
8!
!
A.! Nomenclature/
/
!
1.! Oxidoreductases!
o! Catalyzes!REDOX!reactions!
o! Also!called!as!dehydrogenases!or!reductases!
2.! Transferases!
o! Catalyzes!reactions!involving!the!transfer!of!different!groups!from!the!substrate!to!another!
o! Amino!Transferases,!Methyl!Transferases!
3.! Hydrolases!
o! Catalyzes!the!substrate!bond!cleavage!by!adding!water!
o! Amylase,!Saccharase!
4.! Lyases!
o! Catalyze!bond!–!cleaving!reactions!without!oxidation!or!addition!of!water!
o! Pyruvate!decarboxylase!
5.! Isomerases!
o! Catalyzes!structural!rearrangements!
o! Triose!Isomerase!
6.! Ligases!
o! Also!called!as!synthetases!
o! Catalyzes!the!addition!of!2!moleculesusing!ATP!as!energy!source!
o! DNA!–!Ligase!
B.! Inhibition/
8! Inhibitors!are!agents!capable!of!exerting!a!specific!deterrent!action!on!the!activity!of!en!enzyme/
/
/
1.! Competitive!
o! An!inhibitor!that!is!structurally!related!to!the!substrate!binds!to!the!active!center!preventing!the!
formation!of!the!enzyme!–!substrate!complex!
2.! Noncompetitive!
o! An!inhibitor!binds!to!the!enzyme!or!enzyme!–!substrate!complex!which!leaves!the!active!center!free!and!
may!induce!conformational!change!which!hinders!the!formation!of!the!enzyme!–!substrate!complex.!!
3.! Irreversible/
o! An!inactivator!binds!covalently!to!the!enzyme!and!inactivates!it.!/
C.! Isoenzymes/
/
8! Also!known!as!isozymes!
8! These!are!enzymes!that!may!differ!in!amino!acid!sequences!and!physical!properties!but!catalyze!the!same!
reaction!
!
!
IV.!
DNA/&/RNA/
/
A.!
8!
8!
8!
DNA/Structure/
Contains!nucleotides!that!is!made!up!of!a!nitrogenous!base,!deoxyribose,!and!phosphate!
The!nitrogenous!bases!are!classified!into!Purines!and!Pyrimidines!
The!primary!structure!of!DNA!and!RNA!is!a!linear!polynucleotide!chain!made!up!of!mononucleotides!which!are!
linked!by!a!3’,5’!–!phosphodiester!bond!(3’!–!C!of!one!sugar!to!the!5’!–!C!of!the!next!sugar)!
!
/
/
/
/
/
/
/
/
/
/
/
!
/
/
B.! DNA/Double/Helix/
8! Proposed!by!Watson!and!Crick!in!1953/
8! The!secondary!structure!of!DNA!is!formed!by!the!pairing!two!polynucleotide!chains!that!are!antiparallel./
o! One!chain!runs!5’!–!3’!and!the!other!3’!–!5’/
o! The!base!sequences!of!the!two!strands!are!complementary/
!! Adenine!and!Thymine!via!2!hydrogen!bonds!(major!groove)/
!! Guanine!and!Cytosine!via!3!hydrogen!bonds!(minor!groove)/
8! One!full!turn!of!the!DNA!helix!contains!10!nucleotides.!
8! Has!3!different!conformations:!
o! B!Form:!Right!Handed!
o! Z!Form:!Left!Handed!
o! A!Form:!Dehydrated!and!compact;!Right!Handed!
C.! Denaturation/
8! Separation!of!the!DNA!strands!due!to!heat!or!alkali!exposure!without!breaking!the!phosphodiester!bond/
/
D.! Renaturation/
8! Upon!heating,!DNA!strands!separate!and!the!base!pairs!reform!once!the!temperature!is!slowly!decreased!!
!
E.! Hybridization/
8! A!single!strand!of!DNA!or!RNA!pairs!with!a!complementary!base!sequence!on!another!strand!of!DNA!or!RNA!
!
F.! Histones/
8! These!are!small,!basic!proteins!rich!in!Arg!and!Lys;!not!present!in!prokaryotes!
8! Eukaryotic!chromatins!consist!of!a!DNA!complexed!with!histones!
!
G.! RNA/vs./DNA!
8! RNA!contains!ribose!as!sugar!instead!of!deoxyribose!
8! Uracil!replaces!Thymine!!
!
Single!stranded!with!extensive!base!pairing!
RNAs!can!sometimes!act!as!catalysts!and!enzymes!(ribonucleases,!Peptidyl!transferase)!
!
H.! Types/of/RNA/
8!
8!
/
!
!
!
1.! Messenger!(mRNA)!
o! Contains!a!cap!consisting!of!a!methylated!guanine!triphosphate!attached!to!the!hydroxyl!group!on!the!
ribose!at!the!5’!end!
o! The!poly(A)!tail!contains!up!to!200!Adenine!nucleotides!
!
2.! Ribosomal!(rRNA)!
o! Aids!in!the!formation!of!ribosomes!
o! Prokaryotic:!70S!(Large!subunit!=!50S!;!Small!subunit!=!30S)!
o! Eukaryotic:!80S!(Large!subunit!=!60S!;!Small!subunit!=!40S)!
!
3.! Transfer!(tRNA)!
o! Has!a!characteristic!cloverleaf!structure!
!
V.!
DNA/REPLICATION!
!
8!
Known!as!the!transfer!of!genetic!information!within!a!single!class!of!nucleic!acids,!i.e.!from!DNA!to!DNA!or,!as!in!
certain!viruses,!from!RNA!to!RNA.!!
8! DNA!Replication!is:!
o! Bidirectional!
!! Replication!begins!at!a!specific!origin!and!simultaneously!moves!out!in!both!directions!
!! Prokaryotes!have!one!site!of!origin!while!eukaryotes!can!have!multiple!sites!of!origin!
!
o! Semiconservative!
!! The!resulting!daughter!DNA!contains!one!intact!parental!strand!and!one!newly!synthesized!
complementary!strand!
!
A.! Steps/in/Replication/
/
1.! Initiation!
a.! The!parental!DNA!is!separated!and!uncoiled!by!helicases!where!the!uncoiled!DNA!strand!serves!as!the!
template!
b.! As!the!strands!separate,!an!active!site!for!synthesis!known!as!replication!fork!is!formed!where!each!
separated!strand!is!stabilized!by!a!single!–!stranded!binding!protein!
c.! As!the!strands!separate,!supercoiling!happens!which!is!removed!by!DNA!Topoisomerase!
!! Etoposide!inhibits!topoisomerase!
d.! The!Primase!aids!in!the!production!of!the!RNA!primer!in!a!5’!–!3’!direction!!
!
2.! Elongation!&!Termination!
a.! From!the!initiation!site,!DNA!Polymerase!III!adds!deoxyribonucleotides!at!the!3’!OH!end!of!the!
primer!
!! DNA!polymerase!can!only!copy!in!a!3’!–!5’!direction!and!produce!the!daughter!strand!in!a!5’!–!3’!
direction!
!! DNA!polymerase!always!requires!primers!and!cannot!initiate!the!formation!of!new!strands!
b.! DNA!Polymerase!III!forms!continuous!strands!in!a!3’!–!5’!direction!forming!the!leading!strand!
c.! In!the!5’!–!3’!strand,!a!discontinuous!formation!of!DNA!happens!forming!smaller!fragments!known!
as!Okazaki!fragments.!These!fragments!are!joined!together!by!DNA!ligase!
d.! Once!complete,!RNA!primer!is!removed!by!the!exonuclease!acivity!of!DNA!Pol!I!!
e.! Gaps!are!filled!with!the!complementary!bases!
f.! Replication!is!terminated,!forming!2!daughter!DNA!molecules.!
!
VI.!
8!
8!
8!
8!
8!
RNA/TRANSCRIPTION/
/
The!process!of!making!an!RNA!from!a!DNA!template!is!known!as!transcription.!
It!is!the!major!control!point!in!gene!expression!and!protein!production.!!
Catalyzed!by!DNA!–!dependent!RNA!polymerase!
No!primer!is!needed!
Uses!one!strand!of!DNA!as!template!
A.!
8!
8!
8!
RNA/Polymerase/
Can!initiate!synthesis!of!new!chains!without!a!primer!
Copies!the!DNA!template!in!a!3’!–!5’!direction!and!the!resulting!RNA!elongates!in!a!5’!–!3’!!direction!
Precursors:!Ribonucleoside!Triphosphates!(ATP,!UTP,!GTP,!and!CTP)!
/
!
B.! Steps/in/Prokaryotic/Transcription!
/
1.! Initiation!and!Elongation!
!
!
o! Rifampin!inhibits!the!beta!subunit!of!Bacterial!dependent!RNA!Polymerase!
o! Actinomycin!D!binds!to!DNA!and!inhibits!the!elongation!of!RNA!Transcription!by!RNA!Polymerase!
a.! RNA!polymerase!is!directed!by!the!sigma!factor!to!bind!to!the!promoter!!
o! Promoters!contain!a!sequence!TATAAT!known!as!the!Pribnow!box!or!TATA!BOX!
o! In!eukaryotes,!Hogness!box!(TATA!Box)!has!a!sequence!of!TATATAA!
b.! An!RNA!Polymerase!–!closed!promoter!complex!is!formed!
c.! The!DNA!unwinds!at!promoter!and!forms!the!open!promoter!complex!
d.! RNA!polymerase!initiates!the!mRNA!synthesis!with!a!purine!ribonucleoside!triphosphate!
e.! RNA!polymerase!holoenzyme!catalyzes!the!elongation!of!mRNA!by!about!4!more!units!
f.! Upon!reaching!about!10!nucleotides,!the!sigma!–!subunit!dissociates!and!will!bind!to!another!RNA!Polymerase!
!
!
!
!
!
2.! Termination!
!
a.! Intrinsic!(Rho!–!independent!Transcription!Termination)!
o! Controlled!by!specific!sequences!called!termination!sites!wherein!the!sequences!form!a!hairpin!loop!
structure!that!allows!the!RNA!Polymerase!to!detach!from!the!DNA!template!strand!
!
b.! Rho!–!dependent!Transcription!Termination!
o! Involves!the!Rho!–!Protein!
o! The!rho!–!protein!binds!to!the!RNA!and!chases!the!polymerase!until!it!reaches!the!termination!site!to!
facilitate!the!dissociation!of!the!RNA!Polymerase!from!the!DNA!Template!Strand.!
/
C.! Eukaryotic/Transcription!
/
1.! RNA!Polymerases!(Promoters)!
a.! RNA!Pol!I!!
!! Found!in!the!nucleoulus!and!synthesizes!the!precursors!of!ribosomal!RNA!
b.! RNA!Pol!II!
!! Found!in!the!nucleoplasm!and!synthesizes!mRNA!precursors!
!! α!8!Amanitin!(a!toxin!from!the!mushroom!Amanita'phalloides)!binds!and!inhibits!RNA!Pol!II!
which!halts!mRNA!synthesis!resulting!to!severe!GIT!symptoms,!liver!toxicity,!and!death.!!
c.! RNA!Pol!III!
!! Found!in!the!nucleoplasm!and!synthesizes!the!tRNA!precursors!
!
2.! Steps/in/Eukaryotic/Transcription/
/
/
a.! mRNA!Synthesis/
1.! RNA!Polymerase!II!produces!a!heterogenous!nuclear!RNA!(hRnNA)!containing!exons!and!introns/
!! Exons!are!sequences!appearing!in!the!mature!mRNA/
!! Introns!are!the!non8coding!region!and!are!removed!during!splicing/
2.! The!primary!transcript!(hnRNA)!is!capped!at!the!5’!end/
3.! A!poly(A)!tail!with!a!nucleotide!length!range!of!20!–!200!!is!added!at!the!3’!end!of!the!transcript/
4.! The!introns!are!removed!and!the!exons!are!connected!to!form!the!mature!mRNA!through!splicing/
/
3.! Reverse/Transcription/
o! The!process!of!transcribing!the!single!stranded!RNA!into!a!double!–!stranded!DNA!!
o! Enzyme:!Reverse!Transcriptase!(RNA!–!dependent!DNA!polymerase)!!
o! Retroviruses!contain!RNA!as!genetic!material!
VII.! RNA/TRANSLATION/AND/PROTEIN/SYNTHESIS/
/
!
A.! Genetic/Code/
8! A!collection!of!codons!that!specify!all!the!amino!acids!found!in!proteins!
8! Characteristics:!
o! It!is!degenerate!(Redundant;!Many!amino!acods!have!numerous!codons)!
o! It!is!non!–!overlapping!
!! Begins!with!the!start!codon!AUG!(Methionine)!near!the!5’!end!of!the!mRNA!which!determines!
the!reading!frame!
!! Ends!with!a!stop!codon!(UGA,!UAA,!UAG)!near!the!3’!end!
o! The!code!is!commaless!(no!markers!to!differentiate!one!codon!from!one!another)!
o! The!code!is!nearly!universal!
8! Codons!
o! A!sequence!of!3!bases!in!mRNA!that!specifies!a!particular!Amino!Acid!
B.! Mutations!
8! Mutations!in!DNA!are!carried!over!into!the!mRNA!that!causes!changes!in!the!encoded!protein!
!
!
!
!
1.! Point!Mutations!
o! A!base!in!the!DNA!is!replaced!by!another!which!alters!the!codon!in!the!mRNA!
!
a.! Silent!
o! The!codon!containing!the!changed!base!codes!for!the!same!amino!acid!
b.! Missense!
o! The!codon!containing!the!changed!base!codes!for!a!different!amino!acid!
c.! Nonsense!
o! The!codon!containing!the!changed!base!codes!for!a!stop!codon!
!
2.! Insertions!
o! Occur!when!a!base!or!a!number!of!bases!are!added!to!the!DNA!
!
3.! Deletions!
o! Occur!when!a!base!or!a!number!of!bases!are!added!to!the!DNA!
!
4.! Frameshift!
o! Occurs!when!the!number!of!bases!added!or!deleted!is!not!a!multiple!of!3!which!shifts!the!reading!frame!
to!a!completely!different!set!of!codons!
!
C.! Steps/in/Eukaryotic/Translation/
/
1.! Initiation!
!
a.! The!40S!ribosomal!subunit!binds!close!to!the!5’!cap!until!it!recognizes!the!start!codon!(AUG).!
!! The!ribosome!recognizes!the!AUG!in!the!correct!context!known!as!the!Kozak!Sequence!
(ACCAUGG)!
!! In!prokaryotes,!Streptomycin!binds!to!the!30S!subunit!which!hinders!initiation!
b.! A!special!initiator!tRNA!recognizes!the!start!codon!carries!a!non!formylated!Methionine!
c.! The!60S!ribosomal!unit!is!recruited!to!form!the!80S!initiation!complex.!!
!
2.! Elongation!
!
a.! The!ribosome!moves!from!5’!to!3’!direction!
b.! The!amino!acid!containing!tRNA!(aminoacyl8tRNA’s)!forms!a!complex!with!an!elongation!factor!and!
enters!the!empty!A!8!site!
c.! The!anticodon!of!the!aminoacyl8tRNA!is!matched!against!the!mRNA!codon!in!the!A!8!Site!
d.! When!the!correct!aminoacyl8tRNA!enters!the!A8Site,!the!polypeptide!chain!in!the!P!8!site!is!linked!to!
the!new!amino!acid!in!the!A!–!Site!via!a!peptide!bond!
!! The!reaction!is!catalyzed!by!peptidyltransferase!
•! Chloramphenicol!inhibits!prokaryotic!peptidyltransferase!
!! The!new!peptidyl8tRNA!is!left!in!the!A!site!
e.! The!peptidyl8tRNA!is!translocated!from!the!A!–!Site!to!the!P!–!Site!facilitated!by!an!elongation!factor.!
!! Eryhtromycin!binds!to!a!site!on!the!50S!subunit!which!inhibits!translocation!
f.! A!new!aminoacyl!–!tRNA!in!the!A!–!Site!is!made!available!for!the!next!codon!in!the!mRNA!
g.! The!steps!are!repeated!until!the!ribosome!encounters!a!stop!codon.!
!
3.! Termination!
!
a.! The!stop!codon!is!recognized!by!a!release!factor.!
b.! The!newly!synthesized!protein!is!released!and!the!synthesizing!complex!dissociates.!!
!
VIII.! CARBOHYDRATES/
!
8!
8!
8!
8!
8!
The!most!widespread!compounds!involved!in!the!buildup!and!biological!functions!of!the!cell!
Presence!of!a!carbonyl!(Aldo!or!Keto!group)!and!at!least!two!hydroxyl!groups.!
Stereoisomers:!Same!chemical!formula!but!differs!in!the!position!of!hydroxyl!groups!
Enantiomers:!Stereoisomers!that!are!mirror!images!
Epimers:!Stereoisomers!that!differ!in!the!position!of!the!hydroxyl!group!at!only!one!asymmetric!carbon.!!
!
A.! Monosaccharides/
8! These!are!simple!carbohydrates!that!are!named!depending!on!the!number!of!Carbon!atoms!and!the!specific!
carbonyl!group!present.!!
8! They!can!either!be!Dextrorotatory!or!Levorotatory!!
8! Examples;!D!–!Galactose,!L!–!Fructose!
!
!
!
!
B.! Oligosaccharides!
8! Composed!of!2!to!12!monosaccharide!units!linked!by!a!glycosidic!bond!
8! Sucrose!
o! Table!Sugar!
o! Glucose!+!fructose!
8! Lactose!
o! Milk!Sugar!
o! Galactose!–!linked!β81,4!to!glucose!
!
C.! Polysaccharides!
8! These!are!high!–!molecular!carbohydrates!with!more!than!ten!monosaccharide!units!linked!by!glycosidic!bonds!
8! Neutral!Polysaccharides!such!as!Starch!(Plants)!and!Glycogen!(Human!and!Animals)!are!found!inside!the!cell!as!
reserve!material!
8! Acidic!polysaccharides!such!as!Chondroitin!sulfate!and!Hyaluronic!acid!are!found!extracellularly!
!
!
D.! Digestion/of/Carbohydrates!
8! Salivary!α!8!amylase,!which!is!present!in!the!saliva,!!cleaves!starch!by!breaking!the!α!8!1,4!linkage!between!
glucose!residues!
8! Sucrase!converts!sucrose!to!glucose!and!fructose!
8! Lactase!converts!lactose!to!glucose!and!galactose!
8! α!8!glucosidase!inhibitors!work!in!the!intestine!to!slow!down!the!digestion!of!carbohydrates!to!facilitate!better!
postdigestive!blood!glucose!control!
!
!
E.! Qualitative/Tests/for/Carbohydrates/
/
1.! Molisch!Test!
o! General!test!for!Carbohydrates!
o! Monosaccharides!give!the!most!rapid!result!
o! Uses!α!8!naphthol!&!sulfuric!acid!
o! Positive!Result:!purple!ring!
!
2.! Benedict’s!Test!
o! Test!for!the!presence!of!reducing!sugars!
!! All!monosaccharides!give!a!positive!result!
o! Uses!Copper(II)!sulfate,!Sodium!citrate!and!Sodium!carbonate!in!a!mildly!basic!solution!
o! Positive!Result:!red!precipitate!
!
3.! Barfoed’s!Test!
o! Uses!Copper(II)!in!a!slightly!acidic!medium!
o! Used!to!differentiate!a!reducing!monosaccharide!from!a!reducing!disaccharide!
o! Positive!Result:!red!precipitate!(within!3!minutes!=!Monosaccharide,!longer!than!3!minutes!=!
disaccharide)!
!
4.! Bial’s!Test!
o! Test!for!differentiating!pentose!and!hexose!monosaccharides!
o! Uses!conc.!HCl!and!orcinol!+!Ferric!Chloride!
o! Positive!Result:!Pentoses!=!Bluish!to!green,!Hexoses!=!Brownish!to!gray!
!
!
5.! Seliwanoff’s!Test!
o! Test!for!differentiating!aldoses!from!ketoses!
o! Uses!6M!HCl!and!resorcinol!!
o! Positive!Result:!Ketoses!=!Cherry!Red,!Aldoses!=!Bluish!8!green!to!peach!
IX.!
8!
8!
8!
A.!
1.!
2.!
3.!
4.!
5.!
GLYCOLYSIS!
!
Principal!route!of!metabolism!for!glucose!
Takes!place!in!the!cytoplasm;!Can!provide!ATP!anaerobically!
Glucose!enters!the!cells!via!a!transport!protein!(GLUTs)!
!
Steps/in/Glycolysis!
!
Glucose!8>!glucose!6!–!phosphate!
o! Utilizes!ATP!and!produces!ADP!
o! Catalyzed!by!hexokinase!in!all!tissues;!glucokinase!in!the!liver!
o! Hexokinase!is!inhibited!by!Glucose868Phophate!making!it!active!when!G6P!is!depleted!
o! Glucokinase!is!induced!when!insulin!levels!are!high!
Glucose!6!–!phosphate!is!isomerized!to!Fructose!6!–!phosphate!byPhosphoglucose!isomerase!
Fructose!6!–!phosphate!is!phosphorylated!by!ATP!to!form!Fructose!1,6!–!Biphosphate!and!ADP!
o! Catalyzed!by!Phosphofructokinase81!(PFK81)!
o! The!first!committed!step!of!glycolysis!(Irreversible)!
Fructose!1,6!–!Biphasphate!is!cleaved!by!aldolase!to!form!triose!phosphates,!Glyceraldehyde!38phosphate!(G3P)!
and!Dihydroxyacetone!phosphate!(DHAP)!
DHAP!is!isomerized!by!Triose!phosphate!isomerase!(TPI)!to!G3P!
o! 2!moles!of!G3P!are!formed!for!every!mole!of!Glucose!
o! Deficiency!from!TPI!causes!neonatal!onset!hemolytic!anemia!and!progressive!neurologic!involvement!
6.! G3P!is!oxidized!by!NAD+!and!reacts!with!inorganic!phosphate!to!form!1,38biphosphoglycerat!and!NADH!
7.! 1,38Biphosphoglycerate!reacts!with!ADP!to!produce!3!–!Phosphoglycerate!
o! Catalyzed!by!Phosphoglycerate!kinase!
8.! 3!–!Phosphoglycerate!8>!2!–!Phosphoglycerate!
o! Catalyzed!by!Phosphoglyceromutase!
9.! 2!–!Phosphoglycerate!Is!dehydrated!by!enolase!to!form!PEP!
10.!Phosphoenolpyruvate!reacts!with!ADp!8>!Pyruvate!+!ATP!
o! Catalyzed!by!Pyruvate!Kinase!(more!active!in!fed!state)!
o! Lactate!dehydrogenase!converts!pyruvate!to!Lactate!
o! Puyruvate!carboxylase!converts!pyruvate!to!Oxaloacetate!
o! Transamination!of!Pyruvate!forms!Alanine!
!
B.! Shuttles!
1.! Glycerol!Phosphate!Shuttle!:!1!mole!of!glucose!8>!30!moles!of!ATP!
2.! Malate!–!Aspartate!Shuttle:!1!mole!of!glucose!8>!32!moles!of!ATP!
!
!
!
!
!
!
!
!
X.!
THE/TRICARBOXYLIC/ACID/CYCLE/(KREBS/CYCLE)/
!
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8!
8!
8!
!
Involves!the!oxidation!of!Acetyl!CoA!and!reduction!of!coenzymes!which!are!subsequently!reoxidized!to!produce!
ATP!
An!amphibolic!cycle!which!provides!carbon!skeletons!for!other!pathways!
All!enzymes!utilized!by!the!TCA!are!found!in!the!miyochondrial!matrix!except!succinate!dehydrogenase!(inner!
mitochondrial!membrane).!
!
A.! Reactions/of/the/TCA/
!
!
!
1.! Acetyl!CoA!and!Oxaloacetate!condense!to!form!Citrate!
o! Catalyzed!by!Citrate!Synthase!
o! The!reaction!is!inhibited!by!the!product,!Citrate!
2.! Isomerization!of!Citrate!to!Isocitrate!
o! Catalyzed!by!Aconitase!
3.! Isocitrate!undergoes!oxidation!to!form!α!8!ketoglutarate!
o! Catalyzed!by!Isocitrate!Dehydrogenase!
o! CO2!is!produced!!
o! Electrons!are!passed!to!NAD+!to!form!NADH!!
4.! α!8!ketoglutarate!is!converted!to!Succinyl!CoA!
o! Catalyzed!by!α!8!Ketoglutarate!Dehydrogenase!
5.! Succinyl!CoA!is!cleaved!to!Succinate!
o! Catalyzed!by!Succinate!Thiokinase!(Succinyl!CoA!Synthetase)!
6.! Succinate!is!oxidized!to!fumarate!
o! Catalyzed!by!Succinate!Dehydrogenase!
o! Succinate!transfers!two!protons!to!FAD!to!form!FADH2!
7.! Fumarate!is!converted!into!Fumarase!
o! Catalyzed!by!Fumarase!
8.! Malate!is!oxidized!to!regenerate!Oxaloacetate!
o! Catalyzed!by!Malate!Dehydrogenase!
o! Two!protons!and!electrons!are!transferred!to!NAD+!to!produce!NADH!
!
8!
Total!ATP!Produced!for!every!cycle!utilizing!one!mole!of!Acetyl!CoA:!10!moles!of!ATP!
o! For!every!mole!of!NADH!=!2.5!moles!of!ATP!
!! 3!moles!per!cycle!=!7.5!ATPs!
o! For!every!mole!of!FADH2!
!! 1!mole!per!cycle!=!1.5!ATP!
o! 1!ATP!from!the!GTP!produced!upon!cleavage!of!Succinyl!CoA!
XI.!
!
GLYCOGEN/METABOLISM/
/
Glycogen!
o! Composed!of!α81,48!linked!D!glucose!residues!with!branches!that!are!attached!by!α81,68!linkages!
o! Liver!Glycogen!is!used!to!maintain!blood!glucose!during!fasting!and!exercise!
o! Muscle!Glycogen!is!used!to!generate!ATP!for!muscle!contraction!
!
A.! Glycogenisis/
/
1.! Synthesis!of!UDP!–!glucose!
o! UDP!–!glucose!is!the!precursor!to!glycogen!synthesis!
o! Glucose!enters!the!cell!and!converted!to!G6P!by!hexokinase!or!glucokinase!
o! Phosphoglucomutase!converts!G6P!to!G1P!
o! G1P!reacts!with!uridine!triphosphate!to!form!UDP!–!Glucose!
2.! Glycogen!synthase!transfers!glucose!residues!from!UDP!–!glucose!to!the!nonreducing!ends!of!a!glycogen!
primer!
3.! Branch!Formation!
o! When!a!chain!formed!contains!more!than!11!glucose!residues,!6!to!8!residues!in!length!is!removed!from!
the!non!reducing!end!and!is!reattached!via!an!α81,68!linkages!to!a!glucose!residue!within!an!α81,48!
linked!chain!
o! Glucosyl!4:6!transferase!is!a!branching!enzyme!that!breaks!α81,48!bond!and!forms!an!α81,6!bond.!!
4.! Glycogen!synthase!continuously!adds!glucose!residues!to!the!nonreducing!ends!
5.! Additional!branches!are!formed!by!the!branching!enzyme!
!
B.! Glycogenolysis!
8! Glycogen!can!be!degraded!in!the!lysosomes!by!the!enzyme!α8!Glucosidase!
!
1.! Glycogen!Phosphorylase!successively!cleaves!α81,48!bonds!to!produce!glucose!18phosphate!(G1P)!units!until!
four!glucose!units!from!an!α81,68!branch!remains!
2.! The!remaining!four!units!are!removed!by!the!debranching!enzyme!(glucosyl!4:4!transferase!and!an!α81,68!
glucosidase!activity)!
3.! Three!glucose!residues!from!the!remaining!four!units!will!be!removed!as!a!trisaccharide!and!will!be!attached!
to!a!nonreducing!end!of!another!chain!by!a!4:4!transferase!cleaving!the!old!and!forming!a!new!α81,48!bond!
4.! The!remaing!glucose!residue!with!an!α81,6!linkage!will!be!hydrolyzed!by!the!anzyme!α81,68glucosidase!to!
form!a!free!glucose.!!
!
C.! Glycogen/Storage/Diseases/
/
TYPE/
0/
NAME/
GSD/0/
DEFICIENCY/
Glycogen!Synthase!
I/
Von/Gierke/Disease/
Glucose!6!–!Phosphatase!
II/
Pompe/Disease/
Lyosomal!Storage!Disease!
Manifestation/
Results!in!fasting!
hypoglycemia!with!
occasional!muscle!
cramping!
Results!in!ntracellular!
accumulation!of!glucose!6!
phosphate!and!severe!
hypoglycemia!
!
Hepatomegaly,!platelet!
dysfunction!and!growth!
retardation!
Accumulation!of!glycogen!
within!the!lysosome!
!
IIa!–!Infantile!form!that!
presents!with!muscle!
wakness!that!may!cause!
heart!muscle!dysfunction!
!
!
!
III/
Cori/Disease/
Deficiency!from!
Debranching!Enzyme!
IV/
Andersen/Disease/
Glucosyl!4:6!transferase!
V/
McArdle/Disease/
Muscle/Phosphorylase/
VI/
Hers/Disease/
Partial/deficiency/of/Liver/
Phosphorylase/
*IIb!–!Juvenile!Form!
!
*IIc!–!Adult!form!
!
*skeletal!muscle!weakness!
Hepatomegaly,!
Hypoglycemia!during!
fasting,!Myopathy!
Glycogen!has!very!long!
outer!branches!which!leads!
to!death!within!5!years!of!
age!
Exercise!induced!cramps!
secondary!to!
rhabdomyolysis!
Extreme!enlargement!of!
the!liver!resulting!from!
glycogen!accumulation.!
!
XII.! GLUCONEOGENESIS/
/
8!
8!
8!
8!
8!
Main!site!of!reaction:!Liver!
o! Hepatic!gluconeogenesis!is!inhibited!by!biguanides!that!decreases!the!circulating!glucose!concentration!
Synthesis!of!Glucose!from!non!–!carbohydrate!sources!
Major!Precursors:!Lactate,!Amino!Acids,!and!Glycerol!
Insulin!and!Glucagon!mainly!regulates!blood!glucose!
o! Insulin!stimulates!the!transport!of!glucose!into!the!adipose!and!muscle!cells!
o! Type!I!DM:!Insulin!Dependent!;!Type!II!DM:!Non!–!insulin!Dependent!
o! Thiazolidinediones!induce!genes!that!increase!cell!responsiveness!towards!circulating!insulin!
o! Sulfonylureas!stimulate!the!release!of!preformed!insulin!to!prevent!hyperglycemia!
o! Glucagon!level!increases!during!fasting!state!and!stimulates!gluconeogenesis!
Glucagon!is!elevated!in!fasting!state!which!stimulates!Gluconeogenesis!
!
A.! Steps/in/Gluconeogenesis/
!
1.! Pyruvate!is!converted!to!Oxaloacetate!by!the!enzyme!pyruvate!carboxylase!
2.! Oxaloacetate!is!decarboxylated!by!Phosphoenolpyruvate!Carboxykinase!to!form!PEP!
3.! PEP!is!converted!to!Fructose!1,6!–!bisphosphate!
4.! Fructose!1,68Biphosphate!is!converted!to!Fructose!6!–!Phosphate!by!the!enzyme!Fructose!1,68!Biphosphate!
5.! Fructose!68Phosphate!is!converted!into!G6P!
6.! G6P!releases!an!inorganic!phosphate!that!produces!free!glucose!catalyzed!by!Glucose!68Phosphatase!
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XIII.! LIPIDS/AND/FATTY/ACIDS/
!
A.!
8!
8!
8!
!
Fatty/Acids/
Exists!freely!in!the!body!in!their!unesterified!form!and!fatty!acyl!esters!such!as!Triacylglycerol!(TAG)!
Consist!of!a!hydrophobic!hydrocarbon!chain!with!a!terminal!carboxyl!group!
Fatty!acids!present!in!the!human!usually!contains!an!even!number!of!carbon!atoms!(16!820)!that!can!either!be!
saturated!or!unsaturated!(with!double!bond)!
!
1.! Essential!Fatty!Acids!
o! Linoleic!Acid!(18:2!(9,12))!serves!as!the!precursor!of!Arachidonic!Acid!
o! Provided!by!daily!diet!
2.! Fatty!Acid!Synthesis!
!
a.! Glucose!is!converted!into!Acetyl!CoA!to!supply!the!Carbon!needed!for!fatty!acid!synthesis!occurring!in!
the!cytosol!
b.! The!fatty!acid!synthase!(multienzyme!complex)!in!the!cytosol!initiates!the!synthesis!utilizing!2!acetate!
units!from!the!Acetyl!–!CoA!pool!
c.! Addition!of!2!Carbon!Units!
!! Acetyl!CoA!reacts!with!the!phosphopantetheinyl!residue,!transferring!the!ecetyl!group!to!the!
cysteinyl!residue!
!! A!thioester!is!formed!between!a!malonyl!unit!and!the!phosphopantetheinyl!sulhydryl!group!
!! The!acetyl!group!on!the!fatty!acid!synthase!condenses!with!the!malonyl!group!
!! CO2!will!be!released!from!the!malonyl!group!
!! A!β!8!ketoacyl!group!with!four!carbons!is!produced!
d.! Reduction!of!the!β!8!ketoacyl!group!!
!! !Reduced!to!a!β!8!hydroxyl!group!by!NADPH!
!! A!double!bond!is!added!between!Carbons!2!and!3!via!dehydration!
!! NADPH!reduces!the!double!bond!to!form!a!four!8!carbon!acyl!group!
e.! Elongation!of!the!growing!FA!Acyl!Chain!
!! The!acyl!group!is!transferred!to!the!cysteinyl!sulfhydryl!group!
!! Malonyl!CoA!reacts!with!phosphopantetheinyl!group!
!! The!acyl!and!malonyl!groups!release!CO2!via!condensation!
!! Reduction!of!the!β!8!keto!group!!
!! The!reaction!continues!until!a!16!–!Carbon!FA!is!produced!
f.! Palmitate!is!the!final!product!released!via!hydrolysis!
!! Palmitate!can!undergo!further!elongation!and!desturation!to!form!longer!saturated!and!
unsaturated!FAs!
!
3.! β!8!Oxidation!of!Even!–!Numbered!FA’s!
o! FA’s!are!activated!in!the!cytosol!by!ATP!and!CoA!to!form!Fatty!Acyl!CoA!
o! Reaction!happens!in!the!mitochondria!
o! Energy!generating!(ATP!producing)!
o! Computing!for!the!ATPs!produced!(Palmitic!Acid!for!example!(16!Carbons)):!!
!! Compute!for!the!number!of!Acetyl!CoA!formed:!
•! Number!of!Carbons/2!
•! 16/2!
•! 8!moles!of!Acetyl!CoaA!
!! Compute!for!the!number!of!rounds!to!complete!1!cycle:!
•! Number!of!Acetyl!CoA!formed!–!1!
•! 8!81!
•! 7!Rounds!
!! Granting!that!each!NADH!yields!2.5!ATP!and!each!FADH2!yields!1.5!ATP,!multiply!the!number!of!
rounds!by!4!(the!number!of!NADH!and!FADH2!is!equal!to!the!number!of!rounds!to!complete!1!
cycle):!
•! 7!x!4!
•! 28!ATPs!
o! 17.5!ATPs!from!NADH!!
!! 7!moles!of!NADH!x!2.5!
o! 10.5!ATPs!from!FADH2!
!! 7!moles!of!FADH2!x!1.5!
!! Multiply!the!number!of!Acetyl!CoA!formed!by!10:!
•! 8!x!10!
•! 80!ATPs!
!! Subtract!2!from!the!total!since!2!ATPs!were!used!for!the!activation!of!the!FA:!
•! (80!+!28)!–!2!=!106!ATPs!produced!for!Palmitic!Acid!
!
B.! Phospholipids/
8! These!are!polar,!ionic!compounds!made!up!of!alcohol!attached!to!a!sphingosine!or!diacylglycerol!via!a!
phosphodiesterbond/
/
!
1.! Glycerophospholipids!
o! Contains!glycerol!and!are!the!predominant!lipids!in!membranes!
o! Cardiolipins,!Plasmalogens,!Platelet!–!Activating!Factor!
2.! Sphingophospholipids!
8! Contains!ceramide!with!various!groups!attached!to!it!
!
o! Sphingomyelin!
!! Contains!phosphocholine!
o! Cerebrosides!
!! Has!one!sugar!residue!
o! Gangliosides!
!! More!than!1!sugar!residue!
!
XIV.! CHOLESTEROL/
/
A.! Synthesis/
8! Precursor:!Cytosolic!Acetyl!CoA!
!
a.! Cytosolic!Acetyl!CoA!forms!acetoacetyl!CoA!and!condenses!with!another!acetyl!CoA!forming!HMG!–!CoA!
b.! Cytosolic!HMG!–!CoA!is!reduced!to!mevalonic!acid!by!HMG!–!CoA!reductase!
!! Statins!act!as!competitive!inhibitors!of!HMG!–!CoA!reductase!
c.! Mevalonic!Acid!undergoes!phosphorylation!and!decarboxylation!to!form!isopentyl!phyrophosphate!
which!is!a!five!carbon!isoprenoid!
d.! Isopentyl!pyrophosphate!forms!geranyl!pyrophosphate!(C810)!via!condensation!which!reacts!with!
another!C85!unit!to!form!farnesyl!pyrophosphate!(C815)!
e.! Two!units!of!farnesyl!pyrophosphate!combines!to!form!Squalene!
f.! Squalene!undergoes!oxidation!and!cyclization!to!from!lanosterol!
g.! Lanosterol!is!converted!to!Cholesterol!
!! Steroid!hormones!are!synthesized!from!cholesterol!
!
B.! Bile/Salts!
8! Bile!salts!are!synthesized!in!the!liver!from!cholesterol!and!secreted!via!the!bile!through!the!gallbladder!into!the!
intestine!which!aids!in!lipid!digestion!
o! Bile!acid!sequestrants!such!as!cholestyramine!bind!with!bile!acids!present!in!the!intestinal!lumen!!
8! Primary!Bile!Salts:!Cholic!Acid,!Chenocholic!Acid!
!
C.! Blood/Lipoproteins/
o! Chylomicrons!
!! Least!dense!with!the!least!amount!of!protein!but!has!the!highest!amount!of!TAG!
!
o! Very!–low!density!lipoprotein!(VLDL)!
!! More!dense!than!chylomicrons!but!still!has!a!high!amount!of!TAG!
!! Synthesized!in!the!liver!specifically!after!a!high!carbohydrate!meal!
!! Digested!by!lipoprotein!lipase!and!conerted!to!IDL!
•! Fibrates!such!as!gemfibrozil!activates!the!transcription!of!lipoprotein!lipase!by!activating!
the!PPAR!receptors!
!
o! Intermediate!–!low!density!lipoprotein!(IDL)!
!! Denser!than!VLDL!but!Has!less!than!half!of!the!amount!of!TAG!as!compared!to!VLDL!
!
o! Low!density!lipoprotein!(LDL)!
!! Lesser!Tag!content!than!IDL!and!has!more!protein!
!! Has!the!highest!content!of!cholesterol!
!
o! High!density!lipoproteins!(HDL)!
!! The!densest!lipoprotein!with!the!lowest!TAG!content!and!has!the!highest!amount!of!protein!
!
!
!
!
!
!
!
XV.! OTHER/LIPID/DERIVATIVES/
/
A.! Ketone/Bodies!
8! Synthesized!in!the!liver!mitochondria!when!there!is!an!increased!concentration!of!FAs!in!the!blood!which!is!
observed!during!starvation,!fasting,!or!high!fat!diet!
o! During!starvation,!increased!concentration!of!ketone!bodies!in!the!blood!permits!entry!to!the!brain!and!
undergo!oxidation!
8! Taken!up!by!peripheral!tissues:!Muscles!and!Kidney!
8! Oxidation!of!ketone!bodies!produces!energy!
!
B.! Sphingolipids!
8! Derived!from!Serine!
8! Degraded!by!lyosomal!enzymes!where!defiency!of!such!enzymes!causes!mild!to!severe!diseases!
!
Disease/
Niemann!–!Pick!Disease!
Deficient/Enzyme/
Sphingomyelinase!
Acuumulated/Products/
Sphingomyelin!in!both!
brain!and!blood!cells!
Fabry!Disease!
α!8!Galactosidase!A!
Krabbe!Disease!
β!8!Galactosidase!
Glycolipids!in!the!brain,!
heart,!and!kidney!causing!
ischemia!
Glycolipids!which!causes!
destruction!of!myelin!–!
producing!
oligodendrocytes!
Gaucher!Disease!
Glucocerbrosidase!
Glucocerbrosides!in!the!
blood!cells,!liver,!and!
spleen!
Tay!–!Sachs!Disease!
Hexosaminidase!
GM2!gangliosides!in!
neurons!
Manifestation/
Mental!retardation,!
spasticity,!and!ataxi!
resulting!to!death!by!age!3!
Acroparesthesia,!skin!
lesions,!and!hipohidrosis!
Spasticity!and!rapid!
neurodegeneration.!
Hypertonia,!hyperreflexia,!
decerebrate!posturing,!
blindness,!and!deafness!
Hepatosplenomegaly,!
Thrombocytopenia,!
specifically!prevalent!in!
Ashkenazi!Jews!
Progressive!
neurodegeneration,!
developmental!delay!and!
death.!!
!
XVI.! AMINO/ACID/METABOLISM/AND/PRODUCT/FORMATION/
/
A.! Nitrogen//
8! Amino!acids!undergo!reactions!wherein!the!Nitrogen!moiety!is!converted!into!ammonia!or!ammonium!as!
product/
8! Ammonia!is!very!toxic,!specifically!to!the!CNS/
8! Ammonia!enters!the!Urea!cycle!to!form!urea!an!is!excreted!by!the!kidneys/
/
B.! Synthesis/of/Amino/Acids/
/
8!
8!
8!
!
Amino!Acids!derived!from!Glucose:!
o! Serine,!Glycine,!Cysteine,!Alanine,!Glutamic!Acid,!Glutamine,!Aspartic!Acid,!Asparagine,!Proline,!Arginine!
Essential!amino!Acids!(derived!from!daily!diet):!
o! Histidine,!Isoleucine,!Leucine,!Lysine,!Methionine,!Phenylalanine!(from!Tyrosine),!Threonine,!
Tryptophan,!Valine!
Amino!Acids!derived!from!TCA!Cycle!intermediates!
o! Aspartate,!Asparagine,!Glutamate!
C.! Degradation/of/Amino/Acids/
/
8!
8!
8!
!
!
!
Amino!acids!that!form!pyruvate!or!intermediates!of!the!TCA!in!the!liver!are!glucogenic!
o! Provides!carbon!for!glucose!synthesis!
o! Alanine,!Arginine,!Asparagine,!Aspartic!Acid,!Cysteine,!Glutamic!Acid,!Glutamine,!Glycine,!Histidine,!
Methionine,!Proline,!Serine,!Valine!
Amino!Acids!that!form!Acetyl!CoA!are!ketogenic!
o! Forms!ketone!bodies!
o! Leucine!and!Lysine!
Amino!Acids!that!are!both!ketogenic!and!glucogenic!
o! “PITTT”!
o! Phenylalanine,!Isoleucine,!Threonine,!Tryptophan,!Tyrosine!
8!
8!
D.!
8!
E.!
8!
F.!
8!
8!
8!
G.!
8!
Degradation!of!branched!amino!acids!is!catalyzed!by!the!branched!–!chain!α!8!ketoacid!dehydrogenase!complex!
o! A!defect!in!the!enzyme!complex!(α!8!ketoacid!dehydrogenase)!causes!the!accumulation!of!Valine,!
isoleucine,!and!Leucine!in!the!blood.!!
!! Maple!Syrup!Urine!Disease!
!! Urine!has!a!characteristic!Maple!Syrup!odor!
!! Causes!mental!retardation!and!poor!nerve!myelination!
Phenylalanine!is!converted!into!Tyrosine!by!phenylalanine!hydroxylase!
o! A!defect!in!phenylalanine!hydroxylase!prevents!the!conversion!of!Phe!to!Tyr!
!! Phenylketonuria!
!! Characterized!by!a!urine!with!musty!odor!
!! Leads!to!mental!retardation!
Creatine/
from!glycine,!arginine!and!S8adenosylmethionine/
/
Glutathione/
A!tripeptide!formed!from!glutamate,!cysteine,!and!glycine!
/
Decarboxylation/products/
GABA!
o! A!major!inhibitory!neurotransmitter!from!the!decarboxylation!of!glutamate!
Histidine!
o! From!the!decarboxylation!of!Histidine!
o! Causes!vasodilation!and!bronchoconstriction!and!stimulates!the!secretion!of!HCl!in!the!GIT!
!! H1!receptors!are!found!in!the!GIT,!H2!receptors!trigger!allergic!reactions!
Serotonin!
o! From!the!decarboxylation!of!Tryptophan!
o! Stimulatory!neurotransmitter!involved!in!mood!regulation!
!
Melanin/
Produced!from!Tyrosine!upon!the!action!of!Tyrosinase/
o! Albinism!results!to!the!deficiency!of!Tyrosinase/
!! Characterized!by!the!absence!of!pigment!in!the!hair,!skin,!and!eye/
/
H.! Xanthine!is!oxidized!to!Uric!acid!by!xanthine!oxidase!and!is!excreted!by!the!kidneys.!/
/
XVII.! DIET/&/NUTRITION/
/
A.! /Carbohydrates/
8! Sourced!out!from!daily!intake!of!simple!and!refined!sugars,!and!starches!
8! Constitutes!45!–!65!%!of!the!total!daily!caloric!intake!
!
B.! Lipids/
8! Daily!caloric!intake!should!contain!no!more!than!30%!of!Fats/
8! Cholesterol!intake!should!not!exceed!300!mg/day/
/
Number/of/Carbon/Atoms//
Name/of/Fatty/Acid/
Double/Bonds/
4!
Butyric!Acid!(C4:0)!
None!
6!
Caproic!Acid!(C6:0)!
None!
8!
Caprylic!Acid!(C8:0)!
None!
10!
Capric!Acid!(C10:0)!
None!
12!
Lauric!Acid!(C12:0)!
None!
14!
Myrisitic!Acid!(C14:0)!
None!
16!
Palmitic!Acid(C16:0)!!
None!
16!
Palmitoleic!Acid!(C16:1,!Omega!7)!
Carbon!9!
18!
Stearic!Acid!(C18:0)!
None!
18!
Oleic!Acid!(C18:1,!Omega!9)!
Carbon!9!
18!
Linoleic!Acid!(18:2,!Omega!6)!
Carbon!9,!12!
18!
α!8!Linolenic!Acid!(18:3,!Omega!3)!
Carbon!9,12,15!
20!
Arachidic!Acid!(C20:0)!
None!
20!
Arachidonic!Acid!(C20:4)!
Carbon!5,8,11,14!
/
/
/
/
!
C.! Proteins/
8! Recommended!daily!intake!is!0.8g/Kg!body!weight/
8! Kwashiorkor!Disease/
o! Caused!by!a!low!protein!diet!and!characterized!hepatomegaly/
8! Marasmus/
o! Caused!by!a!diet!deficient!from!protein!and!calories/
/
D.! Water/Soluble/Vitamins/
/
1.! Vitamin!B1!(Thiamine)/
o! Acts!as!cofactor!for!pyruvate!and!α8ketoglutarate!dehydrogenase!
o! Beriberi/
!! Characterized!by!high!output!heart!(Wet!type)!failure!and!peripheral!neuropathy!(Dry!Type)/
o! Wernicke!–!Korsakoff!Syndrome/
!! Manifested!by!ataxia,!ophthalmoplegia!and!confabulation/
/
2.! Vitamin!B2!(Riboflavin)/
o! Precursor!to!Flavin!Adenine!Dinucleotide!(FAD)!
o! Common!sources!are!grain!and!cereal!products!fortified!with!riboflavin!
o! Deficiency!is!manifested!by!glossitis!and!cheilosis!
!
3.! Vitamin!B3!(Niacin)/
o! Needed!for!the!production!of!NAD!and!NADP!
o! Pellagra!
!! Characterized!by!diarrhea,!dementia,!and!dermatitis!
o! Deficiency!can!result!from!Isoniazid!intake!
!
4.! Vitamin!B6!(Pyridoxine)/
o! Utilized!in!transamination!and!decarboxylation!reactions/
o! Deficiency!can!result!from!Isoniazid!intake!
/
5.! Vitamin!B12!(Cobalamin)/
o! Required!by!Methmalonyl!CoA!mutase!and!Methionine!synthase!
o! Deficiency!blocks!the!purine!and!thymidine!biosynthesis!resulting!to!megaloblastic!anemia!
!
6.! Biotin!
o! Utilized!in!carboxylation!reactions!
o! Produced!by!gastrointestinal!bacteria!
o! Deficiency!may!be!caused!by!long!term!antibiotic!use!
!
7.! Folate!
o! Reduced!to!Tetrahydrofolate!which!act!as!one!–!carbon!donor!in!different!pathways!
o! Pregnant!women!who!are!deficient!from!folate!causes!the!fetus!to!suffer!from!Spina!Bifida!
o! Can!be!sourced!out!from!dark!leafy!vegetables!
!
8.! Vitamin!C!(Ascorbic!Acid)!
o! Aids!in!the!hydroxylation!of!proline!in!collagen!!
o! Aids!in!iron!absorption!
o! Acts!as!an!antioxidant!
o! Scurvy!
!! Characterized!by!easy!bruising,!muscular!fatigue,!hemorrhage!and!swollen!gums!
!
E.! Fat/–/Soluble/Vitamins/
/
1.! Vitamin!K!!
o! K1!=!exists!as!Phylloquinone!in!plants!
o! K2!=!exists!as!Mendaione!!in!intestinal!bacterial!flora!
o! Vitamin!K!is!highly!involved!in!activating!precursors!of!prothrombin!and!other!clotting!factors!via!the!
carboxylation!of!glutamate!residues!
!
2.! Vitamin!A!(Retinol)!
o! Essential!for!vision,!reproduction,!growth,!and!maintenance!of!epithelial!tissue!
o! Can!refer!to!several!related!active!molecules!
!! Retinol!
!! Retinal!
!! Retinoic!Acid!
•! Retinoic!acids!and!its!derivatives!(Isotretinoin)!can!be!used!for!treating!dermatologic!
diseases!
!! β!8!Carotene!
!
3.! Vitamin!E!
o! Consist!of!8!naturally!occurring!tocopherols!having!the!α!8!tocopherol!as!the!most!active!form.!
o! Acts!as!an!antioxidant!
!
4.! Vitamin!D!
o! Refers!to!a!group!of!sterols!which!act!as!hormones!
o! Highly!present!in!Fatty!fish,!liver,!and!egg!yolk!
o! The!precursor,!7!–!Dehydrocholesterol,!is!converted!into!Cholecalciferol!in!the!dermis!and!epidermis!of!
humans!after!sunlight!exposure!
o! Vitamin!D2!=!Ergocalciferol!!
!! Present!in!plants!
o! D3!=!Cholecalciferol!
!! Present!in!animal!tissues!
o! D2!and!D3!are!converted!to!the!active!form!1,25!–!Dihydrocholecalciferol!
o! Rickets!
!! Deficiency!of!Vitamin!D!in!children!manifested!by!incomplete!mineralization!of!the!forming!bone!
o! Osteomalacia!
!! Deficiency!of!Vitamin!in!adults!manifested!by!increased!risk!of!bone!demineralization!
/
/
XVIII.!GENETICS/
/
A.! Chromosomes/
8! DNA!is!organized!into!chromosomes!in!the!human!body!
8! The!normal!somatic!cells!in!the!body!are!diploid!with:!
o! 46!Chromosomes!
!! 22!pairs!of!autosomes!
!! 1!Pair!of!Sex!chromosomes!
8! Mature!gametes!(sex!cells)!contains!a!haploid!number!of!chromosomes!
o! 22!Autosomes!
o! 1!Sex!chromosome,!either!X!or!Y!chromosome!
8! The!combination!of!DNA!and!protein!forms!a!Chromatin!
8! Sex!Chromosomes!dictate!the!gender!of!the!fetus!
o! XY!(male)!
o! XX!(female)!
o! An!excess,!or!lack!of!these!chromosomes!can!cause!disorders!
!! 45X0:!Turner!Syndrome!
!! 47XXY:!Klinefelter!Syndrome!
!! 47XYY:!XYY!Syndrome!
!
B.! Cell/Cycle!
8! Cells!give!rise!to!two!identical!daughter!cells!
!
1.! Interphase!
8! Divided!into!3!phases!befor!the!cell!undergoes!Mitosis!
a.! G1!
!! Point!of!entry!for!cells!into!the!cell!cycle!
!! Production!of!proteins!needed!for!the!cell!cycle!
b.! S!
!! Synthesis!of!DNA!via!semiconservative!replication!
c.! G2!
!! Preparation!for!Mitosis!with!continuous!protein!and!organelle!synthesis!
!! Resulting!DNA!is!assessed!
2.! Mitosis!
8! The!process!of!nuclear!division!
!
a.! Prophase!
!! Chromatins!condense!!
!! Structural!proteins!(Centrioles)!start!to!move!towards!the!opposite!poles!of!the!cell!
!
b.! Metaphase!
!! The!most!visualized!stage!in!Mitosis!
!! Sister!chromatids!line!up!along!the!equatorial!plane!
!
c.! Anaphase!
!! “Action!Stage”!
!! The!sister!chromatids!separate!into!two!equal!parts,!ensuring!equal!genetic!material!
!
d.! Telophase!
!! Chromosomes!decondense!and!formation!of!a!nuclear!membrane!encapsulates!the!separated!
genetic!material!
!! Cytokinesis!follows!
•! The!plasma!membranes!pinch!–!off!and!forms!two!daughter!cells!
C.! Meiosis/
8! The!reductive!division!of!diploid!chromosomes!to!form!haploid!chromosomes!
8! For!gametes!
8! Involves!Meiosis!I!and!Meiosis!II!
!
/
/
1.! Meiosis!I!
o! Separation!of!a!homologous!chromosome!pairs!that!forms!two!diploid!cells!
!
a.! Prophase!I!
!! Duplicate!chromatin!condenses!with!each!chromosome!containing!two!sister!chromatids!
!! A!tetrad!is!formed!
•! 2!chromosomes,!4!chromatids!held!together!by!a!Chiasmata!
b.! Metaphase!I!
!! The!tetrads!attach!to!the!meiotic!spindle!and!align!
!
c.! Anaphase!I!
!! The!tetrads!divide!and!move!to!the!opposite!poles!composed!of!two!chromatids!each!
!
d.! Telophase!I!
!! Nuclear!membranes!forms!completing!the!division!
•! In!Spermayogenesis,!equal!division!happenes!
•! In!Oogenesis,!unequal!division!happens,!forming!a!larger!primary!oocyte!and!a!polar!
body!
2.! Meiosis!II!
8! The!cell!division!continues!with!the!exemption!of!DNA!synthesis!
8! Goes!through!Prophase!II!until!a!cell!containing!a!haploid!number!of!chromosomes!is!produced!
8! Failure!of!sister!chromatids!to!separate!results!to!daughter!cells!with!an!abnormal!number!of!chromosomes!that!
leads!to!different!disorders!
o! Trisomy!21:!Down!Syndrome!
o! Trisomy!13:!Patau!Syndrome!
o! Trisomy!18:!Edwards!Syndrome!!
XIX.! MISCELLANEOUS/
!
A.! Cancer/
8! Proto8!oncogenes/
o! These!are!normal!proteins!that!regulates!growth!and!development/
8! Oncogenes/
o! Misexpressed!or!mutated!proto!–!oncogenes!become!oncogenes!and!start!to!grow!uncontrollably/
8! Overexpression!of!the!growth!factor!receptor!HER2/neu!is!commonly!associated!to!the!development!of!breast!
CA/
8! The!most!commonly!mutated!oncogene!in!CA!is!the!ras!gene/
8! Human!papilloma!virus!(HPV!–!16!and!HPV!–!18)!are!closely!associated!to!cervical!CA/
8! BRCA'–'1'and'BRCA62!genes!are!associated!with!breast!and!ovarian!CA/
/
B.! Separating/the/DNA/
/
1.! Gel!Blotting!
8! The!molecules!such!as!DNA!are!subjected!to!electrophoresis!allowing!the!migration!of!the!components!within!an!
electric!field.!
8! After!electrophoresis,!separated!molecules!will!be!blotted!using!a!nitrocellulose!filter!and!will!be!visualized!with!
the!aid!of!a!solution!containing!a!probe.!
!
o! Western!Blot!
!! Proteins!are!separated!by!gele!electrophoresis!and!probed!with!antibodies!that!bind!a!specific!
protein!
o! Southern!Blot!
!! A!radioactive!DNA!probe!hybridizes!with!DNA!!
!! Detects!DNA!mutations!
o! Northern!Blot!
!! A!radioactive!DNA!probe!hybridizes!with!RNA!
!
!
Prepared!by:!
!
Martin/Raemond/B./Mallabo,/R.Ph./
!
References:!
!
Biochemistry/(6th/Edition),!Mary!K.!Campbell,!Shawn!O.!Farrell!
Biochemistry,/Molecular/Biology/&/Genetics/(5th/Edition),!Todd!A.!Swanson,!Sandra!I.!Kim,!Marc!J.!Glucksman!
Biochemistry/(6th/Edition),/Denise!R.!Ferrier!
!
!
/
/