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LECTURE: AMINO ACIDS & PROTEINS

Amino acids structures & properties. Peptides. Proteins primary, secondary, tertiary & quaternary structures. protein folding

What do proteins do in a cell?

Proteins are workhorse of cell processes


Alberts et al

Examples:
Structural functions proteins acting as scaffold of a cell. Enzymes e.g., amylase/digestive enzymes. Transcription factors (participate in reading genetic information & making RNA) Translation factors (participate in making proteins using genetic information) Hormones e.g., insulin.
Antibodies- e.g., IgG, IgM

THERAPEUTIC PROTEIN ECONOMICS


Proteins

Antibodies

Nature Biotechnology 25, 380 - 382 (2007)

Gold - $30 (USD)/g

Erythropoietins - $1,340,000 (USD)/ g!

Mutation in Myostatin protein result in Heavy muscling. Loss of muscle proteins results in muscle wasting

Biomolecules have molecular complex structures


Epogen (anemia, kidney disorder)

Interleukin (cancer, immune disease)

Insulin hexamer (Diabetes M)

Tissue plasminogen activator (acute myocardiac infarction)

Proteins are made up of subunits


Proteins are polymers of amino acids

R
H2N CH

O C OH

R1
O H2N CH C HN

R2
O CH C HN

R3
O CH C

Amino end (N-terminus) Peptide bond

C-terminus (carboxylate end)

Examples of proteins antibodies, enzymes

AMINO ACIDS Building blocks of proteins


All standard amino acids are -amino acids. R group can be different.

Chiral center (because of tetrahedral bonds of carbon)

Fingers/tumb to illustrate asymmetry.

-carbon of most amino acids are chiral centers (except glycine)


R

R H2N H H2N COOH H H NH2 COOH COOH R

Thus, amino acids have stereoisomers In cells, the L-amino acids exist.

20 standard Amino Acids


Depending on the physicochemical properties of the R-group, they can be classified into :

H2N

CH

OH

AMINO ACIDS NON-POLAR POLAR

Aliphatic

Aromatic

Acidic Basic

Uncharged

The comparisons are made between each amino acid.

POLAR uncharged side group

neurotransmitter

Not a good nucleophile (NH2) and do not accept H+ as readily as lysine

NON-POLAR AMINO ACIDS

metabolism

Serotonin

(mood Prozac actions)

POLAR acidic side group

Important excitatory neurotransmitters (epilepsy) chinese restaurant syndrome

POLAR basic side group

Amino acids can also be grouped essential & non-essential.


Starvation in order to generate energy: Carbohydrates Fats Proteins [amino acids are not stored]

We cannot make all amino acids. Plants/microbes make all these.


ESSENTIAL Arginine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine NON-ESSENTIAL Alanine Asparagine Aspartate (Aspartic acid) Cysteine Glutamate (Glutamic acid) Glutamine Glycine Proline Serine Tyrosine

3D Structures of amino acids

Glycine

Alanine

Phenylalanine

Proline cyclic amino acid. Conformational constraints

Illustration - rasmol

ACID BASE PROPERTIES OF AMINO ACIDS

Amphoteric molecules At least 2 pKas, and 3 if R group has dissociable protons (e.g., aspartate, lysine)

Titration of Glycine

pK2 9.6

No net charge pI = 5.9


pK1 2.3

pI = pKa/2 ; pKa of groups that will lose/gain charge of the neutral species.

pI = 9.6 + 2.3 2 = 5.9

Titration of Glutamic Acid

pK3 9.7

pK2 4.2 pK1 2.2

pI = 4.2 + 2.2 2 = 3.2

Titration of Lysine
Note that isoelectric point is more basic than glutamate

pK3 10.8

pK2 9.2 pI = 9.2 + 10.8 pK1 2.2 2 =10

Modified amino acids found in some proteins.


Some amino acids in certain proteins can be modified for special functions. Muscle proteins

Collagen

Formed as a result of post-translational modifications. Specific for only some proteins. Perform important functions in proteins.

Hydroxyproline

Hydroxylated form of proline Found in collagen Provides stability to collagen fibres Insufficient hydroxylation leads to scurvy- due to lack of vitamin C

Modified Amino acid


-Carboxyglutamate Defective carboxylation of the glutamate residues in prothrombin (a clotting protein) can lead to haemorrhage. Prothrombin must bind calcium before activation to thrombin Normal prothrombin contains several residues of -carboxyglutamate

Modified AMINO ACIDS


Phosphoserine/Phosphothreonine/Phosphotyrosine The most common modified amino acids Phosphate groups add negative charges to protein

Present in abundance in casein (milk protein) and hence binds calcium (phosphoserine). Involves in cell signaling and control of enzyme activity. Reversible phosphorylation. Some growth factor receptors switch-on-off by phosphorylation.
OH CH2 H2N CH OH
O

O CH2 OH H2N CH O

PO3O

Phosphoserine
OH

C PO3-

CH2 H2N CH

Phosphotyrosine
O

CH2 OH H2N CH

OH

Cells convey signals from external to internal by exploiting reversible changes in some amino acids e.g., phosphorylation.

PO4- added to tyrosine on receptors

There are some derivatives of amino acids that are Not found in proteins.

Glutamic acid

Histidine

Tryptophan

Metabolism

Nutrasweet sugarfree sweetner

Example of a tetrapeptide

Peptides/polypeptides/proteins are formed by dehydration of amino acids

Condensation

BIOLOGICALLY ACTIVE PEPTIDES

Oxytocin Vassopressin Glucagon

9aa 9aa 29aa

Contraction of uterus Vasoconstrictor Increase sugar in blood

Substance P 11 aa pain transmission (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-amide)

Met-Enkephalin (Tyr-Gly-Gly-Phe-Met)

5aa

suppress pain (morphine mimics)

Can be made synthetically (~20-40 amino acid long) in the laboratory.

How proteins in food are used to make cellular proteins

Food Proteins Use for building cell proteins

Biochemical metabolism

Digestion

Taken up by the cell

Intestine
Absorption

Absorbed as amino acids (building blocks of proteins)

Transcription occurs in the nucleus (from DNA to mRNA) Translation occurs in the cytoplasm (from mRNA to protein)
PROTEINS

MANUFACTURE

mRNA

Translation

Cytoplasm

TRANSLATION OF THE BLUEPRINT

DNA

Proteins
TRANSCRIPTION NUCLEUS

TRANSCRIPTION OF BLUEPRINT

Reading the code How to make Proteins (from RNA to Proteins)


Genetic code
2nd position

3rd position

AUG CCC CUG ACA CCC GGA URNA MetProLeuThr- ProProtein

1st position

20 amino acids.

MOLECULAR MECHANISM workings of the translation machinery

RNA.avi

PROTEIN RECEPTORS ON VIRUS CAN RECOGNIZE & BIND SPECIFICALLY TO CELLS H5N1 virus (blue) infecting cells

Neuraminidase

Virus coat
RNA genome

Cell membrane

HA

Protein receptor binding to cell membrane molecules

Viral membrane

Haemaglutinin (HA) on viral membrane

Russel et al Nature 2006

Active site of enzyme (neuraminidase)

Neuraminidase Required to release newly made viruses from the originally infected cell

Tetramer of Neuraminidase

Release and infect other cells

Human proteins predicted from the genome project

Functions are still unknown. (only know about 50%) enzymes

Proteins are made up of 1 or more polypeptide chains

Protein assembly

Rasmol. ..\..\..\rasmol\r w32b2a.exe

22 (heteromeric) - 141 amino acids - 146 amino acids 12 (homomeric) Each chain 468 amino acid