BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah

Amino Acids:

The building blocks of proteins

 amino acids because of the  carboxylic and  amino groups pK₁ and pK₂ respectively pKR is for R group pK’s

pK₁  2.2 while pK₂  9.4

pK₁ pK₂

Amino acids are Ampholytes

They can act as either an acid or a base

They are Zwitterions or molecules that have both a positive and a negative charge

Amino acids can form peptide

bonds

Amino acid residue peptide units

dipeptides tripeptides oligopeptides polypeptides

Proteins are molecules that consist of one or more

polypeptide chains

Peptides are linear polymers that range from 8 to 4000 amino acid residues

Linear arrays of amino acids can

make a huge number of molecules

Consider a peptide with two amino acids

AA1 AA2

20 x 20 = 400 different molecules

AA1 AA2 AA3

20 x 20 x 20 = 8000 different molecules For 100 amino acid protein the # of possibilities are:

130 100

₁

_.

₂₇

₁₀

20



x

Characteristics of Amino Acids

Characteristics of Amino Acids

Amino Acids

You must know:

Their names

Their structure

Their three letter code

Their one letter code

H2N CH C

CH2

OH O

OH

Acid - Base properties of amino acids

Isoelectric point: the pH where a protein carries no net

electrical charge

The tetra peptide Ala-Tyr-Asp-Gly or AYDG

Optical activity ­  The ability to rotate plane ­ polarized  definition only cannot predict

One or many chiral centers

N chiral centers 2N possible stereoisomers and 2N­1 are 

The Fischer Convention

Absolute configuration about an asymmetric carbon

related to glyceraldehyde

(+) = D-Glyceraldehyde

In the Fischer projection all bonds in the horizontal direction is coming out of the plane if the paper, while the vertical bonds project behind the plane of the paper

All naturally occurring amino acids that make up

proteins are in the L conformation

The CORN method for L isomers: put the hydrogen towards you and read off CO R N clockwise

around the C This works

An example of an amino acid with two

asymmetric carbons

Cahn ­ Ingold ­ Prelog system

Can give absolute configuration nomenclature to multiple  chiral centers.

Priority

Atoms of higher atomic number bonded to a chiral center  are ranked above those of lower atomic number with 

lowest priority away from you R highest to lowest = 

clockwise, S _{highest to lowest = counterclockwise}

The major advantage of the CIP or RS system is that the chiralities of compounds with multiple asymmetric centers can be unambiguously

Prochiral substituents are

distinguishable

Two chemically identical substituents to an

Planar objects with no rotational symmetry also

have prochariality

Flat trigonal molecules such as aldehydes can be prochiral With the flat side facing the viewer if the priority is

Lecture 6 Monday Feb 3

• Protein Geometry

• Primary sequence