SFA 2073 Topic II Amino

Acid & Proteins

Nik Norma Nik Mahmood (PhD)

Faculty Science & Technology

Uni.Science Islam Malaysia

NILAI, N.Sembilan

OBJECTIVES

To Classify amino acids according to their structures and properties.

To explain the meaning of pKa and pI of amino acids

To understand the biochemical benefit of amino acids

To describe the importance of some amino acids in the synthesis of important compounds

To understand the biochemical benefit of proteins To Classify proteins according to their structures

and properties. Relate the structure of proteins to their functions

using specific examples. To understand the importance of amino acids &

protein in biochemical efficiency.

Discussion Order: Structure & Function Of: - Amino Acid - Proteins Proteins : - digestion and absorption - metabolism - metabolic disorder disease Amino Acid : - absorption and metabolism - metabolic disorder disease

INTRODUCTION:

Expression of Concentration(the various expressions of concentrations used).

At the end of this lecture, students should be able to: Differentiate molarity and molality Apply the units of concentration used in medicine (g%,

mmol, g/dl, IU/I etc.) Explain dilution, concentrated, saturated and

supersaturated solution Explain biological solution concentration ie hypertonic,

hypotonic and isotonic.

Solution

• I. There are several way to represent concentration of solution:

a) Molarity (M) the number of moles of solute per liter solution.

Unit: or or molar (M)

b) Molality (m) the number of moles of solute per kg of solvent.

Unit: molal (m) or molkg-1

M = moles of solute (mol)

Volume of solution (dm3 or liter)

moldm-3 molL-1

m =moles of solute (mol)

mass of solvent (kg)

4.5

II. Units of concentration used in biological science: a) Percent Composition by Mass (%) Ratio of the mass of solute to the mass of solution multiplyby 100.eg 20g NaCl in 100 g salt solution 20 x 100 = 20 % sodium chloride solution 100

b) mmol: millimol = 1X 10-3 mol or 1 mol= 103 millimol

c) g/dl : gdl-1 = g in 1 deciliter solution 10 dl = 1 L 1 dl = 10-1 L

d) IU/I : International Unit is a unit of measurement for the amount of a substance, based on measured biological activity or effect.

The unit is used for vitamins, hormones, some medications, vaccines, blood products, and similar biologically active substances.

IU is not part of the International System of Units used in physics and chemistry.

IU should not be confused with the enzyme unit, also known as the

International unit of enzyme activity and abbreviated as U.

Mass equivalents of 1 IU Insulin: 1 IU is the biological equivalent of about 45.5 μg pure

crystalline insulin (1/22 mg exactly) Vitamin A: 1 IU is the biological equivalent of 0.3 μg retinol, or of 0.6

μg beta-carotene Vitamin C: 1 IU is 50 μg L-ascorbic acid Vitamin D: 1 IU is the biological equivalent of 0.025 μg cholecalciferol

/ergocalciferol Vitamin E: 1 IU is the biological equivalent of about 0.667 mg d-

alpha-tocopherol (2/3 mg exactly), or of 1 mg of dl-alpha-tocopherol acetate

III. a) Making DilutionsIII. a) Making Dilutionsprocess of adding more solvent to a known

solution. The moles of solute stay the same, moles = M

x L In solution: initial Mole of solute = final Mole of

soluteM1 V1 = M2 V2

III. b) concentrated solutionhas less amount of water and more amount of the substance. Forexample concentrated H2SO4 has 2% water and 98% H2SO4 anddilute has less amount of substance and more amount of water

c) saturated solution contains the maximum amount of a solute that will dissolve in a

given solvent at a specific temperature.

d) supersaturated solution contains more solute than is present in a saturated solution at

a specific temperature.

e) biological solution: concentration is described as hypertonic or hypotonic

Hypertonic solution contain a high concentration of solute relative to another solution on the other side of the membrane. Water from the other side will flow to this solution.

solution

Few notes for weak acid: pH is a direct measure of the H+ concentration. Ka: is acid dissociation/extent of ionisation constant, acidity constant. pKa:The negative logarithm of Ka pKb:The negative logarithm of the base protonation constant

Kb

the extent of ionization of a weak acid (the pKa) influences the final concentration of H+ ions (the pH) of the solution. For a weak acid there is a relationship between pH and its pKa. This relationship is given by the Henderson–Hasselbalch equation:

pKa = pH + log [HA] / [A-] OR pH= pKa + log [A-] / [HA] can be CH3CO2

-

CH3

CZRCO2-

Derivation of Henderson–Hasselbalch equation

Ka = [H3O+] [CH3COO-] [CH3COOH]

[H3O+] = Ka [CH3COOH]

[CH3COO-] X each by (- log) …… – log [H3O+] = – log Ka – log [CH3COOH]

[CH3COO-]

pH = pKa – log [CH3COOH] [CH3COO-]

pH = pKa + log [CH3COO-] [CH3COOH]

Henderson–Hasselbalch equation.

Determination of pKa Titration of 100 mL 0.1 M CH3CO2H with 50 mL 0.1M NaOH

CH3CO2H + NaOH CH3CO2‾+Na +H2O

stoichiometric coefficient 1:1 Initial mole CH3CO2H = 0.01

Final mole CH3CO2ˉ =0.005

Unreacted CH3CO2H = 0.01- 0.005 = 0.005

pH value can be determined by using pH meterSubstituting all the values in the equation, can get pKa

By varying the volume of 0.1M NaOH in each titration can get the corresponding pH and pKa values

Relationship between amino acids and protein:

Amino acids are building units of protein

Peptide bonds

Different coloured balls & box => Amino Acids

Protein

n

Amino Acid: Structure & FunctionAmino Acid: Structure & Function

Amino acid (a.a) 20 altogether = std aa

- all aa share a general formula R-CH-NH2

- 1 aa differ from the other by the feature of –R- Classified based on : i) structure ii) side chain

• aliphatic aa • non-polar

• dicarboxylic aa • uncharge or non- ionic polar • diamino aa • charge or ionic • aromatic aa polar • heterocyclic aa

COOH

Aliphatic Non-polar Amino Acid

hydrophobicity

Properties: - glycine and alanine are also found in the free form.

Aromatic Amino Acid

Properties: tryptophane phenylalanine

-Are non polar - absorb ultraviolet light (to different degree) - tyrosine has ionizable side chain

Basic Amino Acid

Properties:

- Are polar

- Are positively charged at pH values below their pKa’s

-Are very hydrophilic

- imidazole of histidine, at pH 7 exist predominantly in the neutral form.

Histidine lysine arginine

Acidic Amino Acid

Properties:

-are polar

- are negatively charge at physiological pH - the –COOH of side chain can form amide with an amino group.

Essential Nonessential

Isoleucine Alanine

Leucine Asparagine

Lysine Aspartate

Methionine Cysteine*

Phenylalanine Glutamate

Threonine Glutamine*

Tryptophan Glycine*

Valine Proline*

Serine*

Tyrosine*

Arginine*

Histidine*

* Essential in certain cases. Eg arginine & histidine are growth promoting factor there fore become essential in growing children

- iii) Nutritional Requirement • essential aa (8/9). Cannot be synthesized by the body • non-essential aa (12/11). Can be synthesized by the body

- Amino acid is a derivative of organic (weak) acid.- Has 2 functional groups, carboxylic group (-COOH) and amino

group (-NH2).

Carboxylic (-COOH) and amine (-NH2) groups are capable of ionization:

―COOH ―COO‾ + H+ (2< pKa1< 2.5) ―N+H3 ―NH2 + H+ (9< pKa2< 9.5)

( ―N+H3 is a weaker acid ) - All aa is affected by pH: The net charge on the molecule in solution is affected by pH of

their surrounding and can become more positively or negatively charged due to gain or the loss of protons (H+) respectively.

eg. At pH~2.0 the amino group will be as –NH3+, the carboxylic

group will remain as –COOH (aa will migrate towards the cathode).

As pH is increased, –COOH (from some fraction of aa) ionises. When the pH is equal to the pKa1 the amino acid exists as a 50:50 mixture of the cationic and zwitter ionic forms.

As pH is further increased more cationic form converts to the zwitterionic

Can donate & accept H+ i.e amphoteric nature therefore aa are ampholytes

- Adding more base results in continued ionization of the carboxylic acid group until the zwitter ionic form is the predominant form of the amino acid in solution. By the addition of more base, the pKa of the amino group is reached and at this point the amino acid exists as a 50:50 mixture of the zwitter ionic form and the anionic form. As the pH is increased further the amino group continues loses its proton and ultimately, at high pH (pH ~ 12.0), the anionic form is the predominant form in solution.

At pH>~9.6 the amino group will be as –NH2, the carboxylicgroup will remain as -COOˉ (aa will migrate towards the anode).

- So at physiological pH 6.8 - 7.4, the –COOH group exist as COO¯,

and the –NH2 as –NH3

+. Therefore all aa are double-charged structure or zwitterion in this pH region. The pH at which they exist as “whole” zwitterion i.e the molecule carries no

electrical charge, or the negative and positive charges are equal is called Isoelectric point (Ip) or Isoelectric pH .

- Each aa has its Ip value. At Ip: i) aa is double-charge (zewtterionic) i.e +ve & -ve, amount of

positive charge exactly balances the amount of negative charge so net charge is 0 (electrically neutral).

ii) it does not move/migrate in electric current iii) the molecule has minimum solubility. iv) Ip of all aa lie in the range of pH 6.8 - 7.4Isoelectric pH of an aa solution is given by: pH = ½ (pK1 + pK2)

CH3-CHCOOH

CH3CH COO¯

Neutral un-charged NOT THIS

NH2 N+H3

Zwitterion. Neutral but charge

aa Actual structure

Low pH region

High pH region

The pH profile of an acidic solution of alanine when the solution is titrated with a strong base, NaOH.

E.g

50% as cationic 50% as zwitterion 50% as anionic

50% as zwitterion

For aliphatic aa

Physical properties: - colourless crystalline; soluble in water/polar solvents.

Tyrosine is soluble in hot H2O - have high m.pt >200oC - have high dielectric constant and high dipole moment - molecules have minimum solubility in water or salt solutions

at the Ip pH and often precipitate out of solution.Why? At Ip aa is in zwitterionic form therefore non-polar. Hence no interaction with polar water molecules

Chemical properties: involve –COOH & involve –NH2

i) involve –COOH

• decarboxylation or formation of amine & CO2

eg. histadine histamine + CO2

tyrosine tyromine + CO2

tryptophan tryptamine + CO2

lysine cadaverine CO2

Glutamic gamma amino butyric acid (GABA) + CO2

• Amide formation : α-COOH of 1 aa reacts with α-NH2 of aa behind to form a peptide

bond or CO—NH bridge eg in peptides and proteins

Amide formation (at 2nd —COOH) aspartic + NH3 asparagine glutamic + NH3 glutamine (than N donated for N.A synthesis) ii) involve –NH2: ● formation of carbamino compound

–NH2 + CO2 –NH-CO2H

eg transport of CO2 by hemoglobin from tissue to lung

Hb–NH2 Hb–NH-CO2H (carbamino-Hb) ● Transamination eg in metabolism pathway RCHCOOH + R’CCOOH RCCOOH + R’CCOOH NH2 O O NH2

● oxidative Deamination eg. in metabolism pathway RCHCOOH RCCOOH + NH3

NH2 O

‼ ‼

‼

Contributing properties from R groups When R group is plain hydrocarbon (gly, ala, leu, isoleo, val)

the a.a interact poorly with water. * When R group have functional groups capable of hydrogen

bonding e.g -OH ( Ser, thr, tyr) ; -COOH (asp and glu), these a.a are Hydrophilic or ‘water-loving’ so easily interact with water.

Ester Formation by –OH of serine

-OH + H3PO4 phosphoproteins -OH + polysaccharide O-glycoprotein * When R group have functional group –COOH ( asp , glu)

the a.a can exist as –ve molecule physiological pH and can form ionic bonds with basic amino acids.

When R group have functional group –NH2/ -NH (lys and hist) , these a.a are +ve charged at physiological pH and can form ionic bonds with acidic amino acids.

The sulfhydryl group of cysteine is highly reactive.

-Oxidation of two molecules of cysteine forms cystine. The 2 molecules is linked by a disulfide bond/bridge. The reaction is reversible oxidation

Transmethylation methyl group of methionine may be transferred to an

acceptor to become intermediates in metabolic pathway Formation of S-S bridge. sulfhydryl (-SH) group of cysteine can form the S-S bondwith another cysteine residue intrachain or interchain 2 cysteines cystine

Function of R groups is also very significant in function of peptides and Proteins.

Few examples:a) The hydrophobic aa will generally be found in the interior

of proteins shielded from direct contact with waterb) The hydrophilic aa will generally be found in the exterior

& active centre of enzyme.c) The imidazole ring of histidine acts as proton donor or

acceptor at physiological pH hence it is normally found in active site of enzyme, in hemoglobin (RBC).

Few aa are origin/starting molecules for important compounds or amino acid derived molecules:

Glutamic acid Gammaaminobutyric acid (GABA) Tyrosine dopamine. these are neurotransmitters. Histidine histamine, a mediator of allergic

reactions Tyrosine thyroxine, a thyroid hormone Serine cycloserine an anti-tuberculous; azaserine, an anti-cancer molecule Arginine ornithine and citrulline, intermediates in

urea cycle

2. Structure and function of proteins

To enable to:

Describe the formation of peptide bonds Describe the four levels of protein organization with

reference to primary, secondary, tertiary and quaternary structure of proteins using haemoglobin as example

Explain how structure of protein determines its function by looking at examples

Differentiate between globular and structural proteins with examples eg immunoglobulin, hemoglobin, collagen, keratin etc

Describe the functions of protein Relationship between structural protein and its function in

health and disease.

Proteins: Biological Functions as biological catalysts of the chemical reactions that occur

within the cell examples:

i- starch maltose + shorter chain starch

ii- protein amino acids + peptide chain

iii- triglyceride f f a + mono + di

iv- ATP ADP +Pi

glycerides

phosphatase

α-amylase

trypsin

lipase

As regulatory proteins. These proteins regulate the activities of the cell and the ability of other proteins to carry out their cellular function in regulating overall metabolism, growth, development, and maintenance of the organism

eg peptide and protein hormones; allosteric enzyme; gene inducers & repressors.

As transporter molecules eg. hemoglobin; GLUT,SGLUT i- hemoglobin transport O2 from tissue to lungs; myoglobin

transport O2 intracellular

ii- GLUT transport glucose/galactose from intestinal to blood, iii- SGLUT transport glucose from intestinal to blood.

As storage proteins eg myoglobin, stores O2 in muscle tissue

A peptide bond (amide bond): - feature bonds between amino acids (aa) in polypeptides

and proteins. - is formed when the carboxyl group of one aa molecule

reacts with the amine group of the other aa molecule in front of it, thereby releasing a molecule of water (H2O).

- this is a dehydration synthesis reaction or condensation reaction,

- the resulting CO-NH bond is called a peptide bond, and the resulting molecule is an amide. The four-atom functional group -C(=O)NH- is called an amide group or (in the context of proteins) a peptide group.

- living organisms employ enzymes to form peptide bonds. eg. during translation process. - When two amino acids are linked together, the product is

called a dipeptide and when the product is of three amino acids then it is tripeptide

Peptide bond ―C―N O H feature bonds between amino acids (aa) in polypeptides

and proteins. is a bond formed when a carboxylic group reacts with an

amino group instantaneously eliminating a molecule of H2O this is a dehydration synthesis reaction or condensation

reaction, the resulting CO-NH bond is called a peptide bond, and the

resulting molecule is an amide. The four-atom functional group -C(=O)NH- is called an

amide group or (in the context of proteins) a peptide group. living organisms employ enzymes to form peptide bonds. eg. during translation process. When two amino acids are linked together, the product is

called a dipeptide and when the product is of three amino acids then it is tripeptide

Structure organization in proteins

Primary Structure (or primary level of organization)

Definition. Is "The sequence of amino acids in the polypeptide chain.",

The N-terminal on the left and C terminal on the right.

chain has 50 to 2000 amino acid residues so it is a polypeptide

The residues are joined by peptide bonds

Changes in the primary structure can alter the proper functioning of the protein.eg offcoded of 2 amino acid in the protein of the glycoprotein in RBC results in MN blood group

N-terminal C-terminal

In actual chain these R groups will be the various side chains

Peptide bond

At neutral pH

Protein with basic aa will have overall positive charge.

And

that with acidic aa will have overall negative charge

Effect of surrounding pH on the structure

cont

Effect of surrounding pH on the structure

Secondary structure: There are two types : the α -helix and the β-pleated sheet.

The attraction between the R groups can occur within the same chain (case I) or between chains lying next to one another (case II). Case I leads to formation of weak bonds eg hydrogen bonds ; R-R attraction etc. The hydrogen bonds is "Intrachain Hydrogen Bonding" which is between the hydrogen and oxygen atoms of the amino acid backbone. These intrachain weak bondings can cause the chain to twist into a "right handed" coil or α-helix.

Case II leads to formation of β-pleated sheet.

Such “secondary structure α -helix ” often predominate in "globular proteins“ and β-pleated sheet predominate in fibrous proteins.

Globular proteins are (i) compactly folded and coiled somewhat spherical. The molecule’s

apolar a.a bound towards the molecule interior and the polar a.a bound towards the molecule exterior allowing dipole-dipole interaction with the solvent.

(ii) Soluble in aqueous medium giving colloidal solution(iii) Play numerous functions, as: i) enzymes eg esterases ii) messengers/hormones eg.

Insuliniii) transporter of molecules across membran iv) storage eg

myoglobin ** α-helix: "alpha" means, looking down the length of the spring,

the coiling is happening in a clockwise direction β- pleated sheets: the chains are folded so they lie alongside

each other

β-pleated , anti-parallel (arrows running in opposite direction

H2 bond

Myoglobin - first globular protein whose structure was

analysed by X-ray diffraction by protein crystals. The periodic repeats characteristic of alpha helix were recognised, and the structure shown to have 70% of the polypeptide is alpha-helical.

- it is O2 storage site in muscle tissue.

- It is also intracellular transporter of O2.

- Its tertiary (3-D) structure consists of a 8 α-helices which fold to make a compact globular protein.

- - the side facing the interior having amino acids with hydrophobic side-chains ie. hydrophobic groups are on the inside of the protein. The side facing to outside having polar side-chains ie. hydrophillic groups are on the outside of the protein, facing the aqueous environment.

Reference: J.Mol. Biol. 142, 531-554.

Myoglobin Structure

Heme with Fe2+/3+

A representation of the 3D structure of the myoglobin protein. Alpha helices are shown in colour, and random coil in white,

β-pleated sheet - the β-pleated sheet forms when the hydrogen atoms of the

amino group and the oxygen atoms of the carboxyl group of amino acids on two chains (or more) lying side-by-side forms hydrogen bond.

- Closely associate to structural/fibrous proteins- the protein chains are in associate to form long fibers- elongated or needle shaped- possess minimum solubility- resist digestion

- The β-pleated sheet structure is often found in many structural proteins, eg "Fibroin", the protein in spider webs; Keratin- a structural protein found in hair and nails, skin, and tortoise shells

Fibrous proteins are more filamentous or elongated, play only structural funtions. Also known as scleroproteins. Found only in animals. Are water-insoluble. Used to construct connective tissues, tendons, bone matrix, muscle fibers. Examples are keratin (hair; tough and hard bud not mineralized structure as in reptiles) , collagen ( long chains, tied into bundles, has great tensile strength). Its degradation leads to wrinkles that accompanying aging.

"Tertiary" Structure: a 3 dimensional chain arrangement,

the way the whole chain (including the secondary structures) folds itself into its final 3-dimensional shape

is held together by interactions between the side chains - the "R" groups. . Interactions such as: ionic; van der Waals (hydrophobic-hydrophobic); H-bonds; S-S bridge OR

When "proline", an oddly shaped amino acid occurs in the polypeptide chain a "kink" in the a-helix develops. Kinks can also be caused by repulsive forces between adjacent charged R groups. These kinks create a 3 dimensional chain arrangement

This 3 dimensional shape is also held together by weak hydrogen bonds "disulfide" bonds between two amino acids of cystine ("covalent") disulfide "bridges" (linkages) cystine -- s -- s – cystine. .

These strong covalent bonds hold the protein in its specific 3D shape. The 3D shape creates "pockets" or "holes' in the surface of the protein which are very important in enzyme function

pleated sheets

random coilsα-helix

Cystinyl

Quaternary Structure of ProteinsQuaternary Structure of Proteins 2 or more 3 dimensional tertiary proteins and sticking them together to form

a larger protein. Many enzymes and transport proteins are made of two or more parts. only exists, if there is more than one polypeptide chain present in a complex

protein Hemoglobin: an oxygen carrying protein in red blood cells which is made of

4 parts.

Structural Level of Proteins

Denaturation or Loss of 3-D shape

denaturing agents: Temperature> 40oC; mineral acids; salts. eg. when heated, protein can unfold or "Denature". This loss of three dimensional shape will usually be accompanied by a loss of the proteins function. If the denatured protein is allowed to cool it will usually refold back into it’s original conformation.

Protein metabolismProtein metabolism denotes the various processes responsible for thedenotes the various processes responsible for the (i) (i) biosynthesis biosynthesis of proteins from amino acids.of proteins from amino acids. (ii)(ii) catabolismcatabolism the breakdown of proteins by the breakdown of proteins by

/proteolysis liberating of amino acids. /proteolysis liberating of amino acids.

That is, comprises ofThat is, comprises ofI- Protein metabolism (synthesis and breakdown)I- Protein metabolism (synthesis and breakdown)II-Amino Acid metabolism (synthesis and II-Amino Acid metabolism (synthesis and

breakdown)breakdown)

WILL PROCEED WITH WILL PROCEED WITH Protein metabolism (synthesis and breakdown)Protein metabolism (synthesis and breakdown)

PROTEIN SYNTHESISPROTEIN SYNTHESIS

proteins of one organ are similar but differ from proteins of one organ are similar but differ from that of another organ. That is, each chain is that of another organ. That is, each chain is characterized by a specific sequence of a.a. How characterized by a specific sequence of a.a. How is this special feature achieved?is this special feature achieved?

The sequence of a.a in a particular chain is The sequence of a.a in a particular chain is ensured through the following units and process:ensured through the following units and process:

translation; Codons; transciption tRNA; mRNA; translation; Codons; transciption tRNA; mRNA;

Translation is “process of protein synthesis”. It is Translation is “process of protein synthesis”. It is translating genetic messages into the primary translating genetic messages into the primary sequence of a polypeptidesequence of a polypeptide. . tRNA carries a specific tRNA carries a specific amino acid to the matching position along the amino acid to the matching position along the mRNA template.mRNA template. It can be divided into 4 stages: It can be divided into 4 stages: Activation, Initiation, Elongation and Termination, Activation, Initiation, Elongation and Termination, each regulated by a large number of proteins and each regulated by a large number of proteins and coactivators. It occurs in cytoplasm.coactivators. It occurs in cytoplasm.

Codon: a sequence of 3 nucleotide in DNA that Codon: a sequence of 3 nucleotide in DNA that codes a single a.acodes a single a.a

transcription : synthesis of a single strand transcription : synthesis of a single strand messenger RNA (mRNA) by transcribing the messenger RNA (mRNA) by transcribing the sequence of the nucleotide in the template sequence of the nucleotide in the template DNA/genom. The reaction is catalyzed by RNA DNA/genom. The reaction is catalyzed by RNA polymerase . The template DNA is “unzipped” by polymerase . The template DNA is “unzipped” by enzyme helicase prior to the transcription.enzyme helicase prior to the transcription.

tRNA is transfer RNA that carries an a.a to the tRNA is transfer RNA that carries an a.a to the mRNA to be incorporated into the peptide chain.mRNA to be incorporated into the peptide chain.

mRNA is a type of RNA that encoding the mRNA is a type of RNA that encoding the sequence of the protein in the form of asequence of the protein in the form of a trinucleotide code . trinucleotide code . The specific sequence of the The specific sequence of the nucleotide is accomplished through transcription.nucleotide is accomplished through transcription.

Activation: the correct amino acid (AA) is joined Activation: the correct amino acid (AA) is joined to the correct tRNA. The AA is joined by its to the correct tRNA. The AA is joined by its carboxyl group to the 3' OH of the tRNA by an carboxyl group to the 3' OH of the tRNA by an ester bond. The anti-codon determines the ester bond. The anti-codon determines the correct AA.correct AA.

Initiation: involves the small subunit of the Initiation: involves the small subunit of the ribosome binding to 5' end of mRNA with the help ribosome binding to 5' end of mRNA with the help of initiation factor (IF), of initiation factor (IF),

Elongation occurs when the next aminoacyl-tRNA Elongation occurs when the next aminoacyl-tRNA (charged tRNA) in line binds to the ribosome (charged tRNA) in line binds to the ribosome along with GTP and an elongation factor.along with GTP and an elongation factor.

Termination of the polypeptide happens when the Termination of the polypeptide happens when the A site of the ribosome faces a stop codon (UAA, A site of the ribosome faces a stop codon (UAA, UAG, or UGA).This activates release factor which UAG, or UGA).This activates release factor which then causes the release of the polypeptide chain. then causes the release of the polypeptide chain.

The synthesis process/translationThe synthesis process/translation

TRANSLATION in diagrame :LOADED tRNA

RIBOSOME

mRNA

COMPONENTS PRESENT IN THE PROCESS

anticodon

Aminoacid carried

codon

TRANSLATIONTRANSLATIONThe newly made mRNA (transcription) leaves the nuceus and binds with the ribosome in the cytoplasm.

ONE codon is exposed at site P and another codon at site A

A tRNA with a complementary codon in its anticodon site will bind with the codon at site P, bringing an aminoacid.

1º AMINOACID:Methionine (AUG) in site P.

TRANSLATIONTRANSLATION

Even though every protein begins with the Methionine amino acid, not all

proteins will ultimately have methionine at one end. If the "start"

methionine is not needed, it is removed before the new protein goes to

work (either inside the cell or outside the cell, depending on the type of

protein synthesized)

TRANSLATIONTRANSLATION

A

2º AMINOACID: Glycine (only in this case) in site A.

PEPTIDIC BOND IS FORMED

TRANSLATIONTRANSLATION

STOP codon NO aminoacid is added. Its the END of the polypeptide!

Growing polypeptide

PROTEIN CATABOLISMPROTEIN CATABOLISM

Has various indication: Comprises of Digestion and Absorption Is carried out via proteolysis is the directed degradation (digestion) of proteins

by cellular enzymes called proteases (various kinds) releasing peptide/A.A

The digestion of proteins from foods as a source of amino acids (aas)

The aas constituting “aa pool” are metabolized further ( aa catabolism)

Digestion:Source of proteins that come in the diet: - animal eg milk, dairy products, meat, fish, eggs, liver - vegetable sources eg cereals, pulses, peas, nuts and beans In mouth: no proteolytic enzyme so the proteins are

unchanged but the size(food) becomes smaller due to mastication and chewing. Food bolus travels down and reaches stomach and meet gastric juice

In stomach ( pH 1-2 maintains by HCl) : attack by pepsin, renin, gelatinase and gastricin ( enzymes in the gastric juice).

All these enzymes attack internal peptide bonds. - Pepsin( a endoproteinase) acts on : Proteins proteoses + peptones Casein(milk) paracasein + proteos (whey proteins) paracasein + Ca 2+ calcium paracasein

(insoluble)

- gastricin ( a proteinase) - gelatinase: gelatine polypeptide

DIGESTION & ABSORPTION

In small intestine : duodenum, jejunum, ileum - Duodenum: Food bolus meet pancreatic juices. Enzymes in pancreatic juices : Trypsin ( a proteolytic enzyme) Chymortypsin Carboxy peptidases ( 2 types: A and B) are exopeptidases; splits one amino acid at a time fr free end. Elastases : a serine protease Collagenases act on protein present in collagen/connective

tissue yielding peptide

- Jejunum-ileum Food remnant meet intestinal juice. Enzymes in intestinal juices: Amino peptidase: peptides tripeptides Enteropeptidase/Enterokinase Prolidase: acts at terminal proline Di and tri-peptidase: Di and tri-peptide amino acids

Absorption Of Amino Acids Absorption is by active transport Site of absorption is - ileum and distal jejunum: amino acids - duodenum and proximal jejunum: di and tri-peptides After absorption, amino acids and di and tri-peptides

(if any) are carried by portal blood to liver, partly : i- are taken up by liver cells ii- enter the systemic circulation (made up part of aa

pool), diffusing throughout body fluid & taken up by tissue cells.

( ( The body's circulatory system has three distinct parts: pulmonary (the lungs) circulation, coronary (the heart) circulation, and systemic (the rest of the system) circulation. Each part works independently in order for them to all work together)

The aa will be used to synthesize: tissue proteins; enzyme; hormones3 states relates to aa pool -cell : i- dynamic equilibrium amnt of aa taken-up =

amnt of aa loss ii- cell waste amnt of aa taken-up < amnt of

aa loss iii- cell grows amnt of aa taken-up > amnt of

aa loss

Regulatory of Amino AcidRegulatory of Amino Acid

If amino acids are in excess of the body's biological requirements, they are metabolized to glycogen or fat and subsequently used for energy metabolism.

If amino acids are to be used for energy their carbon skeletons are converted to acetyl CoA, which enters the Krebs cycle for oxidation, producing ATP

Summary: Digestion & AbsorptionSummary: Digestion & Absorption

Aas available for use in metabolic processes come from dietary protein and breakdown of tissue protein by proteolysis.

Digestion (dietary protein) occurs in stomach as well as intestine.

In stomach, digested by pepsin, in intestine and duodenum by a group of enzymes, protease (trypsin. Chymotrypsin and carboxypeptidase)

These liberated aas are absorbed into cells and are collectively referred as “aa pool”

## Amino acids are transported into cell by various transport mechanisms involving membrane-bound transport proteins.

Ingested protein→ digested → aa → absorbed (aa pool)

Dietary proteinTissue protein

enzymic proteolysis

e.g trypsin/pepsin

A A pool

─NH2

─ C skeleton

Excreted as urea & uric acid

protein

energy Precursors for other molecules

synthesis

New AAN containing molecules

Healthy & in young subject >> aa breakdown

INSIDE CELL

OUTSIDE CELL

Assimilation of Amino Acids

Amino acid synthesisAmino acid synthesis is the set of metabolic pathways /processes by which the

various amino acids are produced from direct incorporation/ combination

(I) of –NH2 group OR (II) of ammonium ion NH4

+ with other compounds found in the organism’s diet or growth media

I –NH2 group is incorporated into α-keto acid through 2 types of reactions:

i- non-reductive transamination i) glutamate/aspartate as –NH2 donor ii) glutamine/asparagine as –NH2 donor iii) branch chain aa as –NH2 donor ii- reductive transamination

II- ammonium ion NH4+ is incorporated α-keto acid. through

- Reductive amination - non-reductive amination

Non-reductive Non-reductive transamination characteristics:-transamination characteristics:-Reaction of Glutamate (or Aspartate) and an α-keto acid or BCAA. -NH2 is transferred from Glutamate/ Aspartate to an α-keto acid. ( Glutamate/ Aspartate/asparagine is -NH2 group donor; α-keto acid supplies C-skeleton) ** glutamate as -NH2 group donor is more regular Reaction is catalysed by i) enzyme aminotransferase or

transaminase ; ii) required co-enzyme pyridoxal-5’-phosphate (PLP)

R1—C—C--O‾ + R1—CH—C--O‾ + α-ketoglutarate

O O +NH3New AAAcceptor α-ketoacid

referred as pair

O

i) Glutamate i) Glutamate and an α-keto acidand an α-keto acid (pyruvate)(pyruvate)

ii) Aspartate and an α-keto acid ii) Aspartate and an α-keto acid (pyruvate)

NH2 CH3 CH3

OOC-CH2-CH2- CH + C=O HC─NH2 + OOC-CH2-CH2C=O

COOH COOH COOH COOH

Glutamate pyruvate alanine Glutamate pyruvate alanine αα-ketoglutarate-ketoglutarate

NH2 CH3 CH3

OOC-CH2-- CH + C=O HC─NH2 + OOC--CH2C=O

COOH COOH COOH COOH aspartate pyruvate alanine oxaloacetateaspartate pyruvate alanine oxaloacetate

pair

Non-reductive transamination: Examples

iii- asparagine iii- asparagine and an α-keto acid (pyruvate)

CO-CHCO-CH22-CH + C=O-CH + C=O

NHNH2 2 NHNH33+ + COOCOO

COOˉCOOˉ CHCH33

COO-CHCOO-CH22-CH-CH

NHNH33++

COOˉCOOˉ

AsparagineAsparagine PyruvatePyruvate

CHCH33

+ CH-NH+ CH-NH22

COOˉCOOˉAspatateAspatate AlanineAlanine

TransaminaseTransaminase

** Aspartate transaminase** Aspartate transaminase or or aspartate aspartate aminotransferaseaminotransferase is an enzyme is an enzyme associated with liver parenchymal cells. associated with liver parenchymal cells.

Non-reductive Non-reductive transamination (in skeletal muscle)transamination (in skeletal muscle).. enzyme: glutamine synthase (GS)enzyme: glutamine synthase (GS)

Glutamate + BCAA → glutamine + Glutamate + BCAA → glutamine + αα-keto acid-keto acid

( BCAAs are comprised of valine, leucine, and isoleucine)( BCAAs are comprised of valine, leucine, and isoleucine)

OOC-CH2-CH2-CH + (CH3)2CH-CH O=C-CH2-CH2-CH + (CH3)2-CH-C

NH2 NH2 NH2 NH2 O

COO COO COO COO

Glutamate valine glutamine BC α-oxoacid

Enzyme Enzyme Transaminase/AminotransferaseTransaminase/Aminotransferase

requires co-enzyme pyridoxal-5’-POrequires co-enzyme pyridoxal-5’-PO4 4 , ,

abbreviated (PLP).abbreviated (PLP).

a derivative of vitamin Ba derivative of vitamin B66

R of LysineR of Lysine

PLP attaches to the active site of enzyme by noncovalent interaction and a Schiff base aldimine ( condensation of ε-amino of lysine residue and aldehyde group of PLP) is formed.

amino acid substrate becomes bound to PLP via the α-amino group in an imine exchange reaction.

bond 1 breaks leaving –NH2 on the co-enzyme to be

transferred to an α-keto acid,[ Vitamin B6 is involved in the metabolism (especially

catabolism) of amino acids, as a cofactor in transamination reactions. This is the last step in the synthesis of nonessential amino acids and the first step in amino acid catabolism.

Vitamin B6 is a mixture of pyridoxin derivatives. PLP is 1 of them].

GGlutamate in transamination: lutamate in transamination: ((pyruvate/alanine pair)pyruvate/alanine pair)

((oxaloacetate/aspartate)oxaloacetate/aspartate)

NH2 CH3 CH3

OOC-CH2-CH2- CH + C=O HC─NH2 + OOC-CH2-CH2C=O

COOH COOH COOH COOH Glutamate pyruvate alanine Glutamate pyruvate alanine αα-ketoglutarate-ketoglutarate

NH2 CH2 COO CH2COO

OOC-CH2-CH2- CH + C=O HC─NH2 + OOC-CH2-CH2C=O

COOH COOH COOH COOH Glutamate oxaloacetate aspartate Glutamate oxaloacetate aspartate αα-ketoglutarate-ketoglutarate

**(in skeletal muscle) Glutamate + BCAA → glutamine + α-keto acid BCAAs are comprised of valine, leucine, and isoleucine

GS

Reductive TransaminationReductive Transamination Glutamine, asparagine transfer the amide

nitrogen to oxo (or keto) acid to form a new amino acid.

2-oxoglutarate is –NH2 receptor and glutamine is –NH2 donor

The enzyme GOGAT is NADPH dependent

glutamine + 2-oxoglutarate + NADPH + H+ ---> 2 glutamate + NADP+

GOGAT: enzyme glutamine oxoglutarate amidotransferaseGOGAT: enzyme glutamine oxoglutarate amidotransferase

GOGATGOGAT

i) i) Reductive aminationReductive amination reaction of α-ketoglutarate with NHreaction of α-ketoglutarate with NH44

+ + leading leading to to formation of glutamateformation of glutamate (in mitochondria & (in mitochondria & cytoplasm)cytoplasm). .

α-ketoglutarate is –NHα-ketoglutarate is –NH22 acceptor acceptor catalysed by glutamate dehydrogenase, the catalysed by glutamate dehydrogenase, the

enzyme is enzyme is NADH dependentNADH dependent reaction is reversiblereaction is reversible i.e the reverse pathway is i.e the reverse pathway is

a primary means of producing NHa primary means of producing NH44++ for N for N

excretionexcretion.. The enzyme is driven toward right when excess The enzyme is driven toward right when excess

NHNH44++ is present is present

NHNH44++ is from oxidative deamination of glutamate is from oxidative deamination of glutamate

(in extrahepatic tissue)(in extrahepatic tissue)

II- Incoporation ofII- Incoporation of NHNH44+ + ion:ion:

+ NH4+ + NADH + H+

Enzyme: Glutamate Dehydrogenase + NAD+ + H2O

Reductive Amination : left - right

(Oxidative Deamination : right left)

GDGD

NH3 + H+

ii) Non-reductive amination or amidationii) Non-reductive amination or amidation Glutamate or aspartate react with NHGlutamate or aspartate react with NH44

+ + to form to form glutamine, (asparagine) glutamine, (asparagine)

catalyze by glutamine/ asparagine synthetase catalyze by glutamine/ asparagine synthetase respectively. respectively.

Sites : liver, brain , kidney, muscles & intestineSites : liver, brain , kidney, muscles & intestine This rxn forms the path by which cell rid off This rxn forms the path by which cell rid off

excess NHexcess NH44++. .

** ** NHNH44+ + at high conc may be toxic to certain cell at high conc may be toxic to certain cell

e.g brain cell. Glutamine is non toxic.e.g brain cell. Glutamine is non toxic.

COO-CH2-CH2- CH

NH3+

COO-

+ ATP + NH4+

CO-CH2-CH2- CH

NH2 NH3+

COO-

Glutamine

+ ADP

Glutamine Synthetase (GS)

+ Pi

Glutamate

COO-CH2- CH

From excess aa poolFrom excess aa pool

COO-

NH3+

+ ATP + NH4+

Asparagine Synthetase

CO-CHCO-CH22-CH-CH

NHNH2 2 NHNH33++

COO-

AsparagineAsparagine

+ ADP

+ Pi

AspartateAspartate

Non-reductive amination or amidation

www.rcsb.org/pdb/explore/pubmedwww.rcsb.org/pdb/explore/pubmed Glutamine synthetase (GS) catalyzes the ligation of

glutamate and ammonia to form glutamine, with concomitant hydrolysis of ATP. In mammals, the activity eliminates cytotoxic ammonia, at the same time converting neurotoxic glutamate to harmless glutamine; there are a number of links between changes in GS activity and neurodegenerative disorders, such as Alzheimer`s disease.

glutamate

α-ketoglutarateNH4

+

GD

NADH

glutamate

Oxidative deamination

Reductive amination

α-keto acid

transamination

New aa

C skeleton of all non-essential aa are derivatives of:C skeleton of all non-essential aa are derivatives of: Glycerate -3-phosphateGlycerate -3-phosphate PyruvatePyruvate ΑΑ-ketogluterate-ketogluterate OxaloacetateOxaloacetate

But Tyrosine from essential aa phenylalanineBut Tyrosine from essential aa phenylalanine

On basis of common precursor On basis of common precursor ΞΞ similarities in their synthetic similarities in their synthetic

Pathway, aa can be grouped into 5 families.Pathway, aa can be grouped into 5 families.

glutamate familyglutamate family= synthesis of glutamate, = synthesis of glutamate, glutamine, arg, pro.glutamine, arg, pro.

- C skeleton derive fr - C skeleton derive fr αα-ketoglutarate-ketoglutarate serine familyserine family = synthesis of serine, glycine, = synthesis of serine, glycine,

cysteincystein

- C skeleton derive fr glycerate-3-phosphate - C skeleton derive fr glycerate-3-phosphate aspartate familyaspartate family = synthesis of aspartate, = synthesis of aspartate,

lysine, methionine, asparagine, threoninelysine, methionine, asparagine, threonine

- C skeleton derive fr oxaloacetate- C skeleton derive fr oxaloacetate pyruvate family pyruvate family = synthesis of alanine, valine, = synthesis of alanine, valine,

leucine, isoleucineleucine, isoleucine

- C skeleton derive fr pyruvate- C skeleton derive fr pyruvate aromatic family = synthesis of *phenylalanine, aromatic family = synthesis of *phenylalanine,

tyrosine, *tryptophan *EAAtyrosine, *tryptophan *EAA

Glutamate family - key substrate is α-ketoglutarate fr TCA-Glutamate is produced by GD and is the principle rxn of fixation of NH3 in bactria- glutamine is produced by ATP-requiring +n of NH3 to glu and the rxn fnc as a major means of assimilating of NH3 fr environment-Regulation of this family is controlled by repression of mRNA and feedback inhibition: by prolin and arg

Regulatory of Amino AcidRegulatory of Amino Acid

If amino acids are in excess of the body's If amino acids are in excess of the body's biological requirements, they are metabolized biological requirements, they are metabolized to glycogen or fat.to glycogen or fat.

If amino acids are to be used for energy their If amino acids are to be used for energy their carbon skeletons are converted to acetyl CoA, carbon skeletons are converted to acetyl CoA, or other metabolites intermediates (pyruvate, or other metabolites intermediates (pyruvate, oxaloacetate, Succinyl-coAoxaloacetate, Succinyl-coA ) which then ) which then enters the Krebs cycle for oxidation, enters the Krebs cycle for oxidation, producing ATP. producing ATP.

Catabolism of AACatabolism of AA

Generally involves :Generally involves :- Removal of amino groupRemoval of amino group- Disposal of amino group to final compounds Disposal of amino group to final compounds

urea([NHurea([NH22]]22CO) and ammonia (NHCO) and ammonia (NH33); also ); also incoporated into other molecules incoporated into other molecules

- Utilization of C skeleton by channeling into TCA Utilization of C skeleton by channeling into TCA through which they are converted to final through which they are converted to final products carbon dioxide (COproducts carbon dioxide (CO22), water (H), water (H22O), ATP,O), ATP,

or degraded into a variety of metabolite or degraded into a variety of metabolite intermediates which then enter synthesis intermediates which then enter synthesis pathway of other compounds pathway of other compounds

- DecarboxylationDecarboxylation- one carbon metabolism - one carbon metabolism

Removal of amino groupRemoval of amino group Occurs by Occurs by - transamination- transamination - oxidative deamination (only happens with glutamate ) - oxidative deamination (only happens with glutamate )

catalyses by glutamate dehydrogenasecatalyses by glutamate dehydrogenase

glutamate + NADglutamate + NAD+ + −−−− NH NH++44 + + αα-ketoglutarate-ketoglutarate

Transamination ( largely occurs in cytosol of liver cells)Transamination ( largely occurs in cytosol of liver cells)is the transfer of the nitrogen (the amino) group of an is the transfer of the nitrogen (the amino) group of an

L-a.a to L-a.a to αα-ketoglutarate forming L-glutamate. The -ketoglutarate forming L-glutamate. The reaction is catalysed by transaminase and it reaction is catalysed by transaminase and it requires co-enzyme pyridoxal-5’-POrequires co-enzyme pyridoxal-5’-PO44(see earlier (see earlier section for detail mechanism). Glutamate may section for detail mechanism). Glutamate may undergo another transamination, transfering –NHundergo another transamination, transfering –NH2 2

to another to another αα-ketoacid-ketoacid i.e glutamate becomes -NHi.e glutamate becomes -NH2 2

carriercarrier

Oxidative DeaminationOxidative Deamination

Oxidative Deamination (O.xdn)

reaction is prevalent when proteinintake> proteinsynthesis

=> aa from“aa pool” undergoes degradation. The N- in aa is removed by deamination rxn and converted to ammonia which is toxic, therefore need to be detoxified and excreted.

Is :L-glutamate + NAD+ −− NH+4 + α-ketoglutarate

happens only with glutamate catalyses by glutamate dehydrogenase GD. It occurs in liver & in most extrahepatic tissue.

* N of amino group made available for excretion by rxn .

In muscle cell ( no GD) any excess aa transfer its -NH2 to α-ketoglutarate to form L-glutamate (transamination). L-glutamate undergoes transamination with pyruvate catalyse by alanine transaminase to give alanine + α-ketoglutarate. Alanine carries by blood to liver, (alanine cycle) . In liver, alanine + α-ketoglutarate react catalysed by alanine transaminase reforming L-glutamate + pyruvate as alanine transaminase rxn is reversible. Then L-glutamate undergoes Oxidative deamination.

Pyruvate can be diverted to gluconeogenesis. This process is refered to as the glucose-alanine cycle and NH+

4 moves onto urea cycle which is also known as ornithine cycle, be converted to urea.

Urea is transferred through the blood to the kidneys and excreted in the form of urine.

glutamate

α-ketoglutarate

NH4+

Alanine transamination H2O + NAD+

Transported to liver for Oxidative deamination

Alanine transamination

New α-keto acid

transamination

excess aapyruvate

alanine

-NH2 in Muscle NH4+ (liver)

Liver

alanine

α-ketoglutarate

glutamate

pyruvate

GD

α-ketoglutarate

+ NADH

Alanine Cycle

To urea cycle

•Deamination is also an oxidative reaction •occurs under aerobic conditions in all tissues but especially the liver. During oxidative deamination, an amino acid is converted into the corresponding keto acid by the removal of the amine functional group as ammonia and the amine functional group is replaced by the ketone group. • The reaction is catalysed by glutamate dehydrogenase which is allosterically controlled by ATP and ADP. ATP acts as an inhibitor whereas ADP is an activator.

The ammonia eventually goes into the urea cycle.Oxidative deamination occurs primarily on glutamic acid because glutamic acid was the end product of many transamination reactions.

The glutamate dehydrogenase (GD) is allosterically controlled by ATP and ADP. ATP acts as an inhibitor whereas ADP is an activator.

GD

Summary of Urea Cycle Summary of Urea Cycle Occurs in liver cellsOccurs in liver cells Is a 5 steps cycle: 1 step in mitochondria 4 steps Is a 5 steps cycle: 1 step in mitochondria 4 steps

in cytosolin cytosol Main substrates: NHMain substrates: NH33, CO, CO22 and Aspartate. and Aspartate. In the matrix of mitochondria occurs CPS I and In the matrix of mitochondria occurs CPS I and

OTC catalysed rxn, OTC catalysed rxn, CPS rxn uses 2ATP and reaction is irreversibleCPS rxn uses 2ATP and reaction is irreversible Citrulline Citrulline Ornithine occur in cytosol, in 4 steps Ornithine occur in cytosol, in 4 steps -Citrulline is tranported across the inner membrane-Citrulline is tranported across the inner membraneby a carrier neutral aa.by a carrier neutral aa. - enzymes are arginosuccinate synthase, - enzymes are arginosuccinate synthase,

arginosuccinate lyase and arginasearginosuccinate lyase and arginase Urea transferred to kidney through blood and Urea transferred to kidney through blood and

excreted as urineexcreted as urine

Fate of A.A NitrogenFate of A.A Nitrogen

Excreted in the form of urea (urine) Transferred to specific α-keto acids (of the TCA

intermediates) to form new a.a. This can be represented in the form of α-keto acids / aa pair eg:

α-ketoglutarate/glutamate; pyruvate/alanine; aspartate/oxaloacetate pair.

Incorporated into skeleton of non amino acid molecules => aa derived compound

Derived AA Compounds

What are derived amino acid compounds? They are compounds that contain N- atom, S- atom or

part of aa structure as part of their molecular structure .Can be divided into 2 groups: alkaloids (in plants) & animal related.

Animal related and specific parent aa eg. Glutathione (GSH), Serotonin and Histamine, Heme, GABA , DNA bases

Why the synthesis occurs? These molecules are synthesized because they are

important to the body. The synthesis process

Parent aaParent aa derived compdderived compd Parent aaParent aa derived compdderived compd

glutamateglutamate Glutathione(GSH)Glutathione(GSH) tyrosinetyrosine DopamineDopamine

melaninemelanine

GABAGABA tyroxinetyroxine

Epinephrine/Epinephrine/

norepinephrinenorepinephrine

SerineSerine ethanolamineethanolamine

CholineCholine LeucineLeucine ββ-OH--OH-ββ-methylglutaryl--methylglutaryl-CoACoA

BetaineBetaine

LysineLysine carnithinecarnithine

tryptophantryptophan Serotonine, Serotonine, melatoninemelatonine

HistidineHistidine Histamine,Histamine,

Carnosine,Carnosine,

anserineanserine

serotoninserotonin

Fncn to influence the functioning of the cardiovascular, Fncn to influence the functioning of the cardiovascular, renal, immune, and gastrointestinal systems renal, immune, and gastrointestinal systems

Any disruption in the synthesis, metabolism or uptake of Any disruption in the synthesis, metabolism or uptake of this neurotransmitter has been found to be partly this neurotransmitter has been found to be partly responsible for certain manifestations of responsible for certain manifestations of schizophreniaschizophrenia, , depressiondepression, compulsive disorders and learning problems., compulsive disorders and learning problems.

Synthesis:Synthesis:

Function of some AA derived compoundsFunction of some AA derived compounds As neurotransmitter : GABA, dopamine, serotonin, As neurotransmitter : GABA, dopamine, serotonin, Sleep inducing : melatoninSleep inducing : melatonin Carrier : carnithineCarrier : carnithine As hormone: tyroxine, As hormone: tyroxine, Dilating/constriction of blood vessel: histamine Dilating/constriction of blood vessel: histamine Exhibit multifunctions: GSHExhibit multifunctions: GSH

- acts as reducing agent in NA and eicosanoids synthesis- acts as reducing agent in NA and eicosanoids synthesis

- maintain the sulfahydryl grp of enzymes & other - maintain the sulfahydryl grp of enzymes & other molecules in reduced statemolecules in reduced state

- promotes aa transport- promotes aa transport

- protect cells fr radiation, O- protect cells fr radiation, O22 toxicity and environmental toxicity and environmental

toxinstoxins

Utilization of the C-skeletonUtilization of the C-skeleton

The C-skeleton of the standard amino acids are The C-skeleton of the standard amino acids are degraded to seven common metabolic degraded to seven common metabolic intermediates such as Acetyl-coA; Acetoacetyl-CoA; intermediates such as Acetyl-coA; Acetoacetyl-CoA; pyruvate; Oxaloacetate, pyruvate; Oxaloacetate, αα-ketoglutarate, -ketoglutarate,

Succinyl-CoA and fumerate. Succinyl-CoA and fumerate.

Those aa are referred to different names depending Those aa are referred to different names depending to the class to which the final product are classified: to the class to which the final product are classified:

i) degraded to acetyl-CoA and AceAcetyl-CoA are i) degraded to acetyl-CoA and AceAcetyl-CoA are referred to as KETOGENIC because the referred to as KETOGENIC because the intermediates lead to either fatty acids or ketone intermediates lead to either fatty acids or ketone bodies.eg Lys and Leubodies.eg Lys and Leu

ii) degraded to pyruvate; ii) degraded to pyruvate; αα-ketoglutarate, Succinyl--ketoglutarate, Succinyl-

CoA, Oxaloacetate, and fumerate are referred to CoA, Oxaloacetate, and fumerate are referred to

as GLUCOGENIC because they are intermediates as GLUCOGENIC because they are intermediates

of gluconeogenesis. All except Lys and Leu are of gluconeogenesis. All except Lys and Leu are

pure or partly glucogenicpure or partly glucogenic

Those that yield acetyl-CoA are divided into 2 Those that yield acetyl-CoA are divided into 2

groups.groups.

a) Those that yield pyruvate as intermediate: Ala, a) Those that yield pyruvate as intermediate: Ala,

Cys, Gly, Ser and ThrCys, Gly, Ser and Thr

b) Those that do not yield pyruvate as b) Those that do not yield pyruvate as

intermediate: Phe, Lys, Leu Trp and Tyrintermediate: Phe, Lys, Leu Trp and Tyr

utilization of the C-skeleton utilization of the C-skeleton

Decarboxylation of amino acid

•is effected by decarboxylase enzyme, PLP dependent

•Products are alkylamine + CO2 . The alkylamine are neurotransmitters

•There are 4 aa decarboxylase enzymes:

Aromatic L-amono acid decarboxylase (is a group of enzymes); L-glutamate decarboxylase (GAD); lysine decarboxylase (LDC); histidine decarboxylase (HDC)

HDC

HOOC-CH2-CH2-CH(NH2)-COOH ───→ CO2 + HOOC-CH2-CH2-CH2NH2

GABA is a neurotransmitter in brain GAD

(GABA)

Aromatic L-aa decarboxylase synonyms to DOPA decarboxylase, tryptophan decarboxylase, 5-hydroxytryptophan decarboxylase, AAAD.

tryptophan ───→ tryptamine + CO2Tryp D

A.As Metabolic Disorder DiseasesA.As Metabolic Disorder Diseases

- Are diseases resulted from disorders of a.as Are diseases resulted from disorders of a.as processing/metabolism due toprocessing/metabolism due to

Inherited/genetic defectsInherited/genetic defects that cause deficiency that cause deficiency of certain enzymes forof certain enzymes for

i) the breakdown of amino acids or i) the breakdown of amino acids or

ii) the body's ability to get the amino acids into ii) the body's ability to get the amino acids into cells or cells or

iii) Amino acid Transport iii) Amino acid Transport - Symptoms of disease appear early in life Symptoms of disease appear early in life

- Generally are autosomal recessive that is why only - Generally are autosomal recessive that is why only small number of man suffers.small number of man suffers.

Inherited metabolic disorder ( I.M.D) : Inherited metabolic disorder ( I.M.D) : Oculocutaneous albinism Oculocutaneous albinism Tyrosinemia Tyrosinemia of of tyrosinetyrosine AlkaptonuriaAlkaptonuria

PhenylketonuriaPhenylketonuria of phenylalanine of phenylalanine HyperalaninemiaHyperalaninemia

Leucinosis or maple syrup urine disease – of Leucinosis or maple syrup urine disease – of branched-chain a.a branched-chain a.a

homocystinuria – of methioninehomocystinuria – of methionine

Nonketotic hyperglycinemia – of glycineNonketotic hyperglycinemia – of glycine

PROTEIN CATABOLISMPROTEIN CATABOLISM

Has various indication:Has various indication: Is carried out via proteolysisIs carried out via proteolysis is the directed degradation (is the directed degradation (digestiondigestion) of proteins ) of proteins

by cellular enzymes called proteases (various by cellular enzymes called proteases (various kinds) releasing peptide/A.A kinds) releasing peptide/A.A

The digestion of proteins from foods as a source The digestion of proteins from foods as a source of amino acids (aas)of amino acids (aas)

The aas constituting “aa pool” are metabolized The aas constituting “aa pool” are metabolized further (refer to aa catabolism) further (refer to aa catabolism)

aa1

Muscle-cell

+ α-ketoglu

glutamate

Aa aminotransferase

blood

liver

+ pyrv

alanine

+ α-ketoglu

glutamate

Oxidatv deamintn/GD

NH+4 + α-ketoglu

Ala.aminotransferase

Ala.aminotransferase

Glutamate +ATP

Glutmine synthetase

Non-redtv amination

glutamine

Non-liver cell

glutaminase

NH+4

glutamine

glutamate

Oxidatv deamintn/GD

NH+4 + α-ketoglu

One Carbon MetabolismOne Carbon Metabolism..

http://seqcore.brcf.med.umich.edu/mcb500/folmetov.html

source of Diagram on next slide