Biochemistry Notes

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.! AMINO/ACIDS/
/
8! These! are! organic! carboxylic! acids! that! has! at! least! one! amino! group! replacing! a! hydrogen! atom! of! the!
hydrocarbon!chain.!!
8! 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.!!
8! Sulfur!containing!
o! Cysteine!and!Methionine!
8! Glycine!
o! Acts!as!an!inhibitory!neurotransmitter;!antagonized!by!strychnine!
8! 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)!

,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! The!major!cell!components!that!play!a!big!role!in!all!biological!processes!
8! 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/
!
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!
!