Serkan SAYINER, DVM PhD. Assist. Prof.Near East University, Faculty of Veterinary Medicine, Department of Biochemistry
Amino Acids, Peptides
and Proteins
2
Proteins form a very important part of the living
organism.
Protein word means "leading" in Greek.
C, H, O and N are absolutely carried in the
constructions. They are extremely important for life.
Growth, proliferation and self-repair events, which are
the main characteristics of life, are closely related to
proteins and proteins that form very important
compounds.
Overview
3
The plants synthesize proteins from compounds such as
carbon dioxide, water and inorganic nitrogen. Animals
can not do that. Animals need plants for their protein
needs.
Proteins are large molecules.
Shapes can be fibrous, oval or spherical.
Building blocks are amino acids.• Proteins are amino acid polymers. The genetic code that
determines its synthesis.
• 20 amino acids are used in the synthesis of proteins.
Overview
4
While half of the amino acids used in protein synthesis
are synthesized as intermediate metabolic products,
some are required to be taken with nutrients.
Protein molecules than 45-55% C, H 6-8%, 20-25% O, N
can be between 15-17%.• N, It looks like a special element for protein.
◦ It is found in 16% of average molecules. Based on this determination of
the amount of nitrogen calculated the amount of total protein.
There are many different proteins in different tissues.• Each protein synthesized in the body is structurally and
functionally unique.
Overview
5
Cells, tissues, organs and organ systems are involved in
the processes that characterize the individuality
A cell contains thousands of proteins, each with a
different function. For example,◦ Enzymes; Every reaction in living cells requires enzymes...
◦ Transport proteins;. Lipoproteins, transferrin ....
◦ Bilirubin-binding proteins,
◦ Depot proteins; myoglobin...
◦ Defense proteins; Coagulation, immunoglobulins...
◦ Contractile proteins; Actin, myosin, troponin...
◦ Structural proteins;. Collagen, elastin...
Overview
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Food percentage % Food %
Muscles 18 – 20 Lettuce 1,2
Blood plasma 6,5 – 7,5 Cabbage 1,6
Brain 8 Potato 2
Egg yolk 15 Almond 21
Egg white 12 Fruits 0,4 – 1,5
Cow milk 3,3 Haricot bean 18-22
Cheese 14 - 49 Soybean 37
Protein Rates in Some Tissues and Nutrients
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D- and L-Forms, Classification, Essential Amino Acids, Modified Amino Acids, Non-
Protein Amino Acids, Physical and Chemical Properties
Amino Acids
8
Hydrolysis of Proteins
When proteins are hydrolyzed with acids, alkalis, or enzymes, they are cleaved into amino acids.Compounds having amino (-NH2) and carboxyl group (-
COOH) in their molecules are called amino acids. In the structure of amino acids, 4 different groups are
connected to 4 valences of carbon atom. 1. Carboxyl group2. Amine group3. Hydrogen4. Group R
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Hydrolysis of Proteins Amino acids are briefly indicated by a single letter or three letters.
• Glycine, for example; Gly or G
Only the simplest amino acid, glycine, is the R group H.• Glycine is the first isolated amino acid (1820). • The last identified and isolated is Treonine (1935).
The carbon atom nearest to the carboxyl group in the amino acids is called the α-carbon atom.
Since amino acids other than two amino acids are linked to the α-carbon atom of the NH2 group, these amino acids are called α-amino acids.
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Hydrolysis of Proteins
Amino acids connect with each other by peptide bonds
which are acid amide bonds to form peptides and
proteins.
If the protein molecule gives only amino acids, after
hydrolysis, it is called a simple protein. If gives other
molecules together with amino acids, it is called a
conjugated protein or proteid.
12Source: W.H. Freeman and Company 2012. Biochemistry, 7th ed.
13
Amino acids are classified in various forms according to their properties. The most common classification is neutral amino acids, acidic amino acids and basic amino acids.
Another classification refers to the number of amino and carboxyl groups presented. • Mono-amino monocarboxylic acids,
• Mono-amino di-carboxylic acids,
• Di-amino monocarboxylic acids,
• Di-amino di-carboxylic acids.
Classification of Amino Acids
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Amino acids are also classified on the basis of chains
and ring structures in their molecules. Aliphatic amino
acids, aromatic amino acids, heterocyclic amino acids.
In classification of amino acids;• According to the chain and ring structures, they are classified
as aliphatic, aromatic and heterocyclic amino acids. Each class
is then sub-classified as acidic, basic and neutral amino acids,
and whether they contain sulfur or not.
Classification of Amino Acids
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Aliphatic Amino Acids• Neutral amino acids, Glycine, Alanine, Valine, Serine,
Threonine, Leucine, Isoleucine
• Acidic amino acids : Aspartic acid, Asparagine, Glutamic acid, Glutamine
• Basic amino acids : Arginine, Lysine
• Sulfur-bearing amino acids : Cysteine, Methionine
Classification of Amino Acids
Aromatic Amino Acids• Tyrosine
• Phenylalanine
• Tyroptophan
Heterocyclic Amino Acids▫ Proline
▫ Histidine
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In another classification;• Hydrophobic Amino Acids
◦ Aliphatic side chain
◦ Aromatic side chain
◦ Branched-chain amino acids
• Hydrophilic Amino Acid◦ Uncharged side chain
◦ Charged side chain; Basic and Acidic amino acids..
• Neither Hydrophilic nor Hydrophobic Amino Acid
Classification of Amino Acids
17
The side chains of hydrophobic amino acids do not interact well with the water and usually located inside the proteins. They consist largely of hydrocarbons. • Except the sulfur atoms in the structure of methionine and
cysteine and the nitrogen atom in the structure oftryptophan,
-SH group in the cysteine, that allow it to dimerize through the disulfide bond (-S-S-). The amino acid oftenly exists in the oxidized form in protein. This oxidized form is cystine.
Hydrophobic Amino Acids
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The different regions of the cystine polypeptide chains are covalently linked. So it balances proteins and makes denaturation more resistant
Proline is generally considered to be hydrophobic and is found frequently in the regions of folded polypeptide chains and is particularly found in collagen.
Proline can be formed by cyclization of glutamate.
Hydrophobic Amino Acids
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Methionine
(Met or M)
Cysteine
(Cys or C)
Alanine
(Ala or A) Proline
(Pro or P)
(Imino acid)
Hydrophobic, Aliphatic Side
Chain Amino Acids
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Cystine
Cysteine
(Cys or C)
Cysteine
(Cys or C)
21
The aromatic amino acids (AAA) category includes phenylalanine, tyrosine, and tryptophan.
The group R in the,• Phenylalanine contains a benzene ring,
• Tyrosine contains a phenol,
• Tryptophane contains a heterocyclic structure known as an indole.
These three amino acid in the aromatic moieties are linked to α-carbon through a methyl (-CH2-) bridge.
Hydrophobic Amino Acids
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Aromatic amino acids are important hepatic
metabolites.
Although hydrophobic, phenol (-OH) group tyrosine and -
NH group of indole group of tryptophan allows them to
interact with water, thereby rendering a bit uncertain
properties.
Hydrophobic Amino Acids
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Phenylalanine
(Phe) Tyrosine
(Tyr or Y)
Tryptophane
(Trp or W)
Hydrophobic, Aromatic Side
Chain Amino Acids
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Valine, Leucine and Isoleucine are branched chain
amino acids (BCAA).
They carry a aliphatic side chain which includes methyl
group (as a substituent).
They should be taken with diet in highly organizes
animals. In other words they are essential. There are no
enzymes necessary for synthesis in these organisms.
Although present in many tissues, BCAAs are
catabolized by muscle tissue, especially for energy
purposes in the final stage of hunger.
Hydrophobic Amino Acids
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Leucine
(Leu or L)Isoleucine
(Ile or I)
Valine
(Val or V)
Hydrophobic, Branched Side
Chain Amino Acids (BCAA)
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Amino acids with positively charged side chains include
basic amino acids such as histidine, lysine and arginine.
Histidine contains weak charge at only physiological pH.
In contrast, amino acids including negatively charged
side chains are acidic and they are aspartic acid and
glutamic acid (available as glutamate and aspartate).
Hydrophilic Amino Acids
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Glutamate
(Glu or E)
Aspartate
(Asp or D)
Hydrophilic, Charged
Side chain
Acidic Amino Acids
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Histidine
(His or H)Lysine
(Lys or K)Arginine
(Arg or R)
Hydrophilic, Charged
Side chain
Basic Amino Acids
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A hydroxylated version of the alanine which is serine
and threonine contains a non-charged side chain, and a
-OH group. For this reason, strong interactions with
water occur as a result of the formation of hydrogen
bonds.
They are much more hydrophilic compared to other non-
hydroxylated closely related amino acids (alanine and
valine).
Hydrophilic Amino Acids
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The uncharged side chains of asparagine and glutamine
have amide groups with greater hydrogen bonding
capacity.
Nonetheless, asparagine and glutamine are readily
hydrolyzed with acid or base to form non-amides
(aspartic acid and glutamic acid).
All nine of these amino acids are hydrophilic and
therefore interact with water. Side chains are oftenly
found on the surface of the protein to which they are
exposed to an aqueous medium.
Hydrophilic Amino Acids
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Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Serin
(Ser or S)
Treonin
(Thr or T)
Hydrophilic, Amino Acids
with Uncharged
Side chain
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It is neither a hydrophilic nor a hydrophobic amino acid.
Glycine having only one hydrogen atom in the side chain
is known as the simplest amino acid.
Due to the simple structure, it can fit many gaps in the
polypeptide chains of protein molecules and therefore is
located on both the inner side surfaces.
Glycine
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Neither Hydrophilic
nor Hydrophobic
Amino acid
Glycine
(Gly or G)
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Proteins taken into the organism must be broken up into
amino acids in order to be absorbed through the intestines.
Amino acids absorbed from the intestine are transfered to
the tissues through the blood and are used for protein
synthesis.
Plants, microorganisms and fungi are autotrophs. They do
not need amino acids to feed. They can synthesize
themselves.
Advanced organisms are heterotrophic. They have to take
some amino acids from the outside. These organisms can
perform protein synthesis from amino acids.
Essential Amino Acids
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Essential amino acids or exogenous amino acids are
amino acids that are not synthesized by the organism
and are required to be taken externally with foods.
An amino acids which is capable to produce it’s α-
ketoacid are not essential and can be synthesized during
metabolism.
Dry Beans contain more protein than meat, but not as
valuable as meat. Why?• Because; it does not contain essential amino acids as mush as
to meet animals’ need.
Essential Amino Acids
36
If there is an inadequacy of any essential amino acid, the remaining 19 amino acids can not be used for protein synthesis. However, they become catabolized and negative nitrogen balance arises.
Essential amino acids show differences between animals. Amino acids that are essential for some species may not be essential in some species
It also varies with age.
Essential Amino Acids
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Lysine
HUMAN DOG
RAT
PIG CHICKEN
Triptofan
Phenylalanine
Leucine
Isolösin
Treonin
Methionine
Valin
Histidine
Arginine
Glycine
Glutamic acid
Essential Amino Acids
In young
people
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BCAAs are constantly oxidized by muscle tissues.
Phenylalanine is required for tyrosine biosynthesis. It is
necessary to synthesize catecholamines and thyroid
hormones.
Methionine is required for cysteine formation.
Tryptophan is required for serotonin and melatonin
biosynthesis.
The non-essentials are mostly obtained by conversion
with enzymes (aminotransferases) during metabolism.
Essential Amino Acids
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There are some modified amino acids in the protein structure.Methylhistidine and methyllysine are methyl derivative
of histidine and lysine. They are located in the structure of some proteins.Hydroxyproline is a derivative of proline. It is found in
collagen structure in the form of -Proline-Hydroxyproline-Glycine- (tripeptide). • Collagen is a fibrous connective tissue protein.
• It is found in blood vessels, tendons, cartilage and bone.
• It is the most abundant protein in mammalians.
• ~ 30% of total body protein and ~ 6% of body weight is collagen.
Modified Amino Acids
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Methylhistidine Methyllysine Hydroxyproline
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Hydroxylisine is the 5-hydroxy derivative of lysine and
is found in the collagenous structure.
Desmosine and isodesmosine are formed by oxidation
and cross-linking of four lysines.• It is found in the structure of elastin which is a connective
tissue proten.
• It is found in tissues containing smooth muscle (such as blood
vessels) with collagen.
• Elastin has two-way elasticity.
• Arteries contain elastin much more than veins.
Modified Amino Acids
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HydroxylysineDesmosine
Isodesmosine
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Phosphothreonine, phosphotyrosine and
phosphoserine are occured by phosphorylation of the
hydroxyl groups of threonine, tyrosine and serine side
chains.• These three derived amino acids are particularly involved in
the construction of regulatory proteins.
γ-Carboxyglutamate is synthesized by carboxylation of glutamic acid in the liver.• This amino acid is involved in the structure of prothrombin (factor II),
one of the coagulation factors.
• Provides calcium chelating.
Modified Amino Acids
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Phosphothreonine Phosphotyrosine Phosphoserineγ-Carboxyglutamate
(Chelate with Ca++)
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There are amino acids other than the 20 amino acids
involved in the protein structure. These amino acids do not
participate in the protein structure.
They are important intermediate metabolites or
precursor molecules during metabolism.• β-Alanine is the building block of Pantothenic acid (B5 vitamin).
◦ This vitamin is also a building component of coenzyme A.
• Homocysteine and homoserine are important intermediates in
methionine metabolism.
• Ornithine and sitrulin take place in the hepatic urea cycle and
are important intermediates in the synthesis of arginine.
Non-protein Amino Acids
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• Taurine is formed by the oxidation of the sulphydryl group in the cysteine and subsequent carboxylation. ◦ In cats, because they can not synthesize as much as competence, they
have to take it with the diet. It is essential for the cat.
◦ Retinal degeneration, blindness, reproductive disturbances, growth retardation, and skeletal deformities are seen due to taurine failure in the cat.
• γ- Aminobutyric Acid (GABA) is a neurotransmitter inhibitor in the central nervous system (with glycine).◦ It is mainly located in substantia nigra, globus pallidus, and
hypothalamus.
◦ Alcohol, barbiturates, and benzodiazepines increase the GABA effect, especially in postsynaptic areas.
Non-protein Amino Acids
48
Non-protein Amino Acids
Homocysteine
Citrulline
Ornithine
Β-AlanineTaurine Homoserine γ- Aminobutyric
Acid (GABA)
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Solvents Water Acid Alkali Ethanol Ether
Solution States + + + ± -
Melting Points: Melts at 200 °C and sometimes at 300 °C.
Flavors
Tasteless Bitter Sweet
Leucine Isoleucine, Arginine Others
Physical Properties of Amino Acids
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Amino acids are ampholytes.• Since amino acids carry the carboxyl group together with
the amino group, they are both acid and base.
• The α-carbon atom of amino acids is stable at physiologically pH;◦ The group R, H bonds to the unprotonated COO- and protonated NH3+.
◦ There is a difference in the prolin. It contains the imino group (NH2+)
instead of the amino group.
• The COOH group dissociates to the -COO- (carboxylate anion) and H+ ions by giving H ions in the alkaline environment.
• NH2 groups gain H+ in the acidic environment and converted to positively charged NH3
+ group (ammonium cation).
Physical Properties of Amino Acids
51
• At isoelectric points (at physiological
pH), H ions, passes through COOH groups
to NH2 groups. COOH group is a COO-
group carrying a negative charge
because it gives H ion and it is side by
side with the NH3+ group which is
positively charged.
• Ions that carry both positive and
negative charges are called
zwitterions. The substances that can
form zwitterion are also called
amphoteric/ampholyte.
Physical Properties of Amino Acids
Glycine
(Gly or G)
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• Ionisation conditions vary depending on pH.
• In alkaline solutions (pH>7.4), the carboxylic group generally
remains in ionized form (-COO-). In contrast, the amino group
is anionic (-NH2).
• In acidic solutions (pH<7.4), the carboxyl group remains
anionic (-COOH) while the amino group protects its ionized
form (NH3+).
• The pK value of carboxyl or amino group of each amino acid
is different. This difference is related to some factors such as
temperature, ionic strength, and the presence of ionizable
group.
Physical Properties of Amino Acids
53
Cation(Acidic solution)
Anion(Alkali solution)
Zwitterion(Isoelectric point)
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Optical Activities• All amino acids except glycine have α-carbon atoms and are
therefore optically active.
• There are mirror images which are L-isomer and D-isomer
(enantiomer).
• Amino acids similar to D-glyceraldehyde are D-amino acids,
Amino acids similar to L-glyceraldehyde are L-amino acids. It is
indicated by (+) if light turns to right and (-) if light turns to
left.
• While almost all carbohydrates of plants and animals are in
D series, amino acids in proteins are in L series.
Physical Properties of Amino Acids
55
• D-amino acids are usually found on cell walls of bacteria and
some antibiotics (D-glutamic acid etc.)
Physical Properties of Amino Acids
D-Form L-Form
If the functional group
is on the right
If the functional group is
on the left
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D-Glyceraldehyde
C OH
C
CH2OH
OHH
C OH
C
CH2OH
HHO
L-Glyceraldehyde
D-Amino acid
COOH
C
R
H2NH
L-Amino acid
COOH
C
R
HNH2
According to Fischer
projection;
• In D-amino acids - The NH3+
group is on the right side.
These amino acids are rarely
found in nature.
• In L-amino acids - The NH3+
group is on the left side.
These amino acids are
widely found in the nature.
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MIRROR
L-Amino acid D-Amino acid
58
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There are 3 types of functional groups in the amino
acid molecule. 1. Amino groups
2. Carboxyl groups
3. R groups
The chemical properties of amino acids depend on these
3 groups.
Chemical Properties of Amino Acids
60
Inactivation of the amino group with alcohol• In alcoholic environments, amino groups do not change to
ammonium cations (NH3+). This is known as the inactivation of
amino groups by alcohol.
• They are not amphoteric in an alcoholic environment. They are
acids. Thus, they can be titrated
Sörensen Titration• It is a method of determining the carboxyl group in the amino
acid solution. It is utilized to determine the amino acid
content in a solution.
Reactions of Amino Groups
61
Bonding of the amino group with aromatic acids• The incorporation of amino acids into aromatic acids
eventually becomes insoluble.
• This ensures that harmful substances are expelled from the
organism. Ex. Hippuric acid (the most important nitrogenous
substance in urine after it is produced in grass eaters).
Reactions of Amino Groups
Betain Reaction• When the amino acids are in the zwitterion
state, betaines are formed with 3 CH3 groups passing instead of 3 H in the NH3
+ group.◦ Ex. Trimethylglycine is a betaine formed with glycine.
◦ Betaines are biologically involved in methylation reactions and detoxification of homocysteine.
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Carbomino acid reaction• Carbonic acids are formed on the amino groups by CO2
bonding.
• When it is heated, again CO2 and amino acid are decomposed. Hemoglobin brings carbamino acid with CO2 and it is important for transporting CO2 from tissues to the lungs.
Ninhydrin Reaction• All of the free amino groups give this reaction (amino acids,
peptides, proteins).
• Ninhydrin is an important qualitative assay for amino acids.Less than 1 gram is even susceptible. Practical importance is great.
Reactions of Amino Groups
63
Nitric acid reaction• When amino acids react with nitric acid, the nitrogen of the amino
groups passes into the free element, such as nitric acid nitrogen.
• On the other side the amino group is replaced by the -OH group.
• At the reaction, a molecule corresponding to each amino group is
released to nitrogen.
• For this reason, nitric acid reassignment can be used to determine the
amount of free amino groups.
• Nitric acid reaction; Also called Van Slyke method.
Reactions of Amino Groups
64
Uramine Acid Reaction• If a urea molecule is added to the amino groups, the uramine
acids will form.
• It is used in the identification of amino acids.
Diketopiperazine formation• The ethyl esters of amino acids are condensed to form
anhydride ring structures bearing two amino acid groups,
resulting in the formation of diketopiperazine.
Reactions of Amino Groups
65
Chelating amino acids with metal ions• Amino groups form complex chelates with many heavy metal
ions such as Cu++, Co++, Mn++, Fe++.
Reactions of Amino Groups
Kaynak: Ası T. Tablolarla Biyokimya Cilt I
Copper diglycerateCysteine-cobalt complex
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Salt formation• Amino acids can form salts with heavy metals and easily
crystallize.
• Especially the salts formed with Cu are easily crystallized. This
property is used to obtain pure amino acids.
Esterification• If they react with alcohol in the presence of anhydrous
hydrochloric acid, they will bring their esters.
• The esters of amino acids are utilized in their functional
distillation.
Reactions of Carboxyl Groups
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**Decarboxylation of amino acids• It is the name given to the separation of carbon dioxide from
the amino acid molecule. So the amines are occured.
• In the tissues, the amino acids decarboxylate to the amines.
• Ex; histidine to histamine, lysine to cadaverine, ornithine to
putressin, tyrosine to tyramine, tryptophan to tryptamine.◦ They are also converted by anaerobic microorganisms.
◦ That's the spoiled gut. Cadaverine and putressin are amines found in
stinky meats. Poisonous effects are low. The toxins are the poisons of
the microorganisms that constitute them.
Reactions of Carboxyl Groups
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Decarboxylation of amino acids
Source: Ası T. Tablolarla Biyokimya Cilt I
Histidine
Decarboxylase
Histidine Histamine
Amino acid Amine
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Reactions of R groups
The R groups of amino acids are composed of multiple
variable groups.
Due to the differences in the groups, different reactions
occur.
Especially they give their unique color reactions. These
color reactions allow amino acids to be separated and
recognized.
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R-Groups Amino acid Reaction Color CreatedReaction specific
name
PhenylTyrosine,
Phenylalanine
Heating with Hg(NO3)2 and concantrated
HNO3
Red MillonReaction
Phenyl
Imidazole
Tyrosine,
Phenylalanine,
Histidine
In alkaline environment, treatment with
sulfanilic acid and NaClORed Pauly Reaction
Guanidine Argininen an alkaline medium, α-naphthol and
treated with NaClORed Sakaguchi Reaction
Free SH CysteineTreatment with dilute NH4OH solution of
sodium nitroprussideRed
Nitroprussid
Reaction
Indole TryptophanTreatment with H2SO4 solution of p-
dimethylaminobenzaldehydePink Ehrlich Reaction
Cyclic amino
acids
The phenyl
alanine,
tryptophan
Dense with HNO3
When heated
With the addition of alkali
White residue
Yellow
orange
Xanthoproteic
Reaction
Indole TryptophanIf after treatment with glyoxylic acid is
layered with dense sulfuric acidViolet ring
Hopkins Cole
Reaction
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Peptide Bonds, Oligo- and Polypeptides, Some Important Di-, Oligo- and Polypeptides,
Seperation of Amino Acids from Proteins and Quantitative Determinations
Peptides
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Amino acids polymerize with acid amide bond/peptide
bond to form proteins.
The number of amino acids added together by peptide
bonds is important when the peptide is named.• 2 is dipeptide, 3 is tripeptide
• 4-10 is oligopeptide
• Between 10-100, the polypeptide
• >100, the macro peptide
Peptide Bonds and Oligo-Polypeptides
73
When the peptide chain is formed, the COOH group of one of the amino acids joins with the NH2 group of the other amino acid. So that an NH2 group with a COOH group will eventually remain freeterminal ends.• The tips are on paper; NH2 at
the left end. N-terminus or terminal/C-terminus orterminal
The free NH2 group is called the free amino group.
Peptide Bonds and Oligo-Polypeptides
74
Amino acids Features
Carnoline β-alanine histidine Dipetid. It is found in the muscles
Anterin β-alanine N-methyl histidine Dipetid. It is found in the muscles.
Glutathione Glutamyl cysteine glycine
Tripeptide. It is involved in oxidoreduction. It is
found in the structure of some enzymes. Controls the
absorption of Fe.
Ophthalmic acid Glutamyl aminobutyryl glycine Tripeptide. Located in the eye lens.
Non-Ophthalmic acid The glutamyl alanine glycine Tripeptide. Located in the eye lens.
Oxytocin 8 amino acids Octapeptide. It's the hormone of the pituitary gland.
Vasopressin 8 amino acids Octapeptide. It's the hormone of the pituitary gland.
ACTH 39 amino acids Pituitary anterior lobe hormone.
Insulin 51 amino acidsPancreas hormone. It plays a role in glucose
metabolism.
Glucagon 29 amino acids Pancreatic hormone.
Some important di-, oligo-, and polypeptides
75
Insulin It is secreted by the β-cells of
the langerhans islets of the
pancreas.
It is synthesized as proinsulin;
contains A-chain of 21 amino
acids, the B-chain of 30 amino
acids and the C-peptide chain
of 31 amino acids.
There is no C-peptide chain in
the active form.
76
77
Separation of Amino Acids in Proteins and Quantification
Tyrosine• They can be easily crystallized and separated at the isoelectric
point.
Arginine, Lysine, Histidine• Since these amino acids can be precipitated with the
phosphotungstic acid from the protein solution, their total amounts can be easily detected.
Tyrosine, Tryptophan• Since these amino acids can give color reactions, quantities can
easily be detected by colorimetric methods.
Monoamino acids • Since these amino acids can be converted into ethyl esters, they
can be subsequently removed from the reaction mixture by fractional distillation.
78
Methods Principle
Chromatographic
Adsorption Method- Paper chromatography
- Ion exchange chromatography
- Thin layer chromatography
- HPLC
Adsorption of various amino acids by different adsorbents at
different levels. Acid character amino acids are trapped by the
basic adsorbents, basic amino acids are trapped by the acid
adsorbents.
Isotope Dilution Method
It is a phenomenon in which an unknown amino acid mixture is
added to a known amount of a specific amino acid marked with
an isotope atom, and then it is determined from this mixture
how much it is diluted after the same amino acid is obtained in
pure form.
Microbiological Method
It is based on the principle that certain amino acids must be
present in a certain amount in the medium environment for the
reproduction of some microorganisms.
Separation of Amino Acids in Proteins and Quantification
79
Structure, General Properties, Classification (Structural: Simple-Conjugate-Derivative Proteins, Functional: Catalytic Proteins, Transport Proteins, Nutrient and
Depot Proteins, Contractile Proteins, Defense Proteins, Physiological Regulatory Proteins), Nucleoproteins (DNA, RNA, ATP ...), Chromoproteins (Porphyrins, Bile
colored substances), Icterus (Jaundice), Main Proteins in the Liquid and Tissues of the Organism
Proteins
80
Proteins are composed of peptide chains. It is in the
polypeptide structure.
If there are n-amino acids in the protein structure,
there are n-1 number of peptide bonds.
A complete protein molecule represents four
complementary substructures.1. Primary Structure
2. Secondary Structure
3. Tertiary Structure
4. Quaternary Structure
Structure of a Protein Molecule
81
Structure of a Protein Molecule
1. Primary Structure• A certain number of amino acids refers to the sequence of
chains that are ordered by a particular sequence.
2. Secondary Structure• α-Helix: It occurs when the peptide chain is twisted in the
form of a helix around an axis.
• β-Sheet: It is a structure that occurs when two or more
polypeptide chains are joined together by hydrogen bonds.
82
Structure of a Protein Molecule
3. Tertiary Structure• Helix structures folded with -S-S bridges to become globular
and ellipsoidal.
4. Quaternary Structure• It is formed by the combination of primary, secondary, and
tertiary formations.
83Source: McDarby M.
84Source: McDarby M.
85
General Properties of Proteins Flavors of Proteins• Pure proteins are usually sweet. Hydrolysis products are mostly
bitter.
Odor• Pure proteins are odorless.
Homogeneity• Most of the proteins are not pure but have sub-fractions.
Solubility• Soluble in water and neutral saline solutions.
• Proteins that are precipitated in an equal amount of ammonium sulfate solution are called globulin, if not it is called albumin.
• Non-soluble proteins in water and neutral salt solutions are called scleroproteins.
86
Denaturation of proteins• Denaturation is the deterioration of the natural structure of
proteins.
• In the deterioration of the natural structure, the protein molecule has to be exposed to a number of factors.
• The opening of the folds of the protein molecule, and the folding in a different way, i.e. changes in the secondary and tertiarystructures, alter the properties of the protein molecule.
• For denaturation the dissolution of peptide bonds is not necessary. In the case of deterioration of the tertiary structure, where there is a returnable denaturation, in the case of the deterioration of the secondary structure, the resulting denaturation is not reversible.
General Properties of Proteins
87
• The proteins that undergo denaturation change their
solubility, some color reactions are exacerbated, and the
biological activity of enzymes and hormones is lost.
• Treatment with acid salts, alkaline retention, dissolution
in ethanol, heat, X-rays, UV irradiation, strong agitation,
SDS (sodium dodecyl sulfate), treatment with urea salts,
freeze-thawing and high pressure are some of the reasons
for denaturation.
General Properties of Proteins
88
Normal
Protein
Denaturated
Protein
Denaturation
Renaturation
Factors: pH, Temperature, Ionic strenght, Solubility, UV rays, SDS ...
Loss of biological
activity
Recovery of
biological activity
89
Protein Structure and Denaturation - A Level Biology
90
Molecular weight• They are substances with a high molecular weight.
• Molecular weights are increased by the formation of the
quarternay structure, and by the separation of the monomers
is decreased. Therefore, the molecular weight varies
according to the conditions.
General Properties of Proteins
Protein MW (Dalton)
Insulin 12.000
Myoglobin 17.000
Hemoglobin 68.000
Albumin 69.000
Thyroglobulin 660.000
Fibrinojen 450.000
91
Molecular shape of proteins• Spherical shape to the yarn shows the changing forms.
• Most of the easy solids are spherical.
• Those in the form of yarn are insoluble proteins.
General Properties of Proteins
Shape Features
GlobularThey are easy to dissolve.
Solutions reduce viscosity.
Basil likeIt greatly increases the viscosity of the
solutions.
Fibrous Insoluble.
92
Precipitation of proteins• Proteins are precipitated by certain acids, heavy metals and
specific antibodies.
• Heavy metals; Hg, Pb, Ag, Cu, Fe, Cd, Zn.
• When the protein is given to the organism by an extrinsic
pathway, it is regarded as a foreign substance and forms
antibodies.
• Each protein is precipitated by its specific antibody, which is
formed against its own protein.
General Properties of Proteins
93
Heavy metal salts• In metal poisonings, antidote proteins are used.
Negative ions• It is used for the precipitation of blood proteins with the
purpose of analysis.
Specific antibody proteins• It is used to obtain antigen.
General Properties of Proteins
94
Hydration of proteins• They bind water. The polar groups in the peptide chain
include amino, carboxyl, hydroxyl, imino, and etc.
• Polar groups have the ability to bind with water.
Viscosity of proteins• It is directly related to the molecular shape.
• If the molecule is long, the viscosity is higher. Viscosity is
also high in large-molecule proteins.
Crystallization of proteins• Enzyme proteins such as pepsin, trypsin and urease have
been obtained in crystal form.
General Properties of Proteins
95
Classification of Proteins
Two types of classification are possible.
1.Classification according to their
Structures
2.Classification according to their
Biological Functions (Functional
Classification of Proteins)
96
Simple Proteins• Simple proteins only consist of amino acids. They are found in
the structure of polypeptide chains that only give amino acids when hydrolyzed. Simple proteins are divided into subgroups according to their different qualities; Globular and FibrillarProteins.
Conjugated Proteins (Proteids/Combined Proteins)• When it is hydrolyzed, it is proteins that give different
chemical substances together with amino acids.
Derivative Proteins• They are proteins that are formed as a result of alteration of
proteins belongs to simple or conjugated proteins.
Classification according to their Structures
97
Simple proteins are made up only of amino acids. They
are separated into two subgroups; Globular and Fibrillar
Proteins.
Globular Proteins• Proteins in which the molecule is in the form of rotational
ellipsoids of the three-dimensional shape.
• Globular proteins are divided into subgroups such as albumin,
globulins, globins, glutelines, prolamins, protamines and
histones.
Simple Proteins
98
• Albumins◦ Soluble in water and aqueous solutions.
◦ They coagulate with heat.
◦ MW<100,000.
◦ Glycine-poor proteins.
◦ Eg.: Ovalbumin, serum albumin, lactalbumin, legumelin
• Globulins◦ Not soluble in water. It dissolves in neutral saline solutions.
◦ Glycine-rich proteins.
◦ MW>100,000.
◦ Eg.: ovoglobulin, lactoglobulin, α-, β-, γ-globulins, legumin, faseolin
Simple Proteins
99
• Globin◦ They are usually found as compound, mainly in the hemoglobin
structure.
• Glutelines◦ Plant origin.
◦ Not soluble in water. Soluble in dilute acid and alkalines.
◦ They become denatured by heat.
◦ Eg.: Wheat glutenin, barley hordenin, orizenin in rice.
• Histones◦ Water soluble.
◦ It is rich in basic amino acids. It's rich in arginine. Eg.: Timothyton(gland tissue), skombron (mackerel)
Simple Proteins
100
• Prolamins◦ Plant origin.
◦ Not soluble in water. Soluble in 70-80% ethanol .
◦ They contain less Lysine and Cystine but, rich in Prolin.
◦ They are especially found in grain plants. Eg: Gliadin (wheat), zein(maize).
◦ When wheat flour dough loses its starch under running water, a very elastic material remains. This substance, which is called gluten, is a mixture of gliadin and glutenin.– Coeliac Disease (Gluten Enteropathy): Coeliac disease, also spelled celiac
disease, is a long-term autoimmune disorder primarily affecting the small intestine that occurs in people who are genetically predisposed. Coeliac disease is caused by a reaction to gluten, which are various proteins found in wheat and in other grains such as barley, and rye. Classic symptoms include gastrointestinal problems such as chronic diarrhoea, abdominal distention, malabsorption, loss of appetite, and among children failure to grow normally
Simple Proteins
101
• Protamines◦ It was obtained from fish semen.
◦ Soluble in water, dilute acids and alkalis, dilute ammonium hydroxide
solutions.
◦ It does not include tryptophan, tyrosine and sulphated amino acids.
◦ They are rich in arginine.
◦ They display strong basic characters.
◦ It is the shortest chain of proteins (MW 1000-5000).
◦ They are particularly associated with nucleic acids in tissues.
◦ Ex: Skombrin (mackerel), salmin (soma), lupine (herring).
Simple Proteins
102
Fibrillar Proteins• They are proteins in the form of three-dimensional multi-
stretched ellipsoids.
• Scleroproteins◦ It is of animal origin.
◦ They are insoluble in water, neutral salt solutions, dilute acids and
alkalis, and pure alcohol.
◦ They are resistant to enzymes such as pepsin and trypsin.
◦ Keratin (horn, hair) is not digested, collagen (connective tissue,
bone, fracture, tendo) is digested. An another example is elastin
(ligament). Keratin is very rich in sulphurous amino acids.
Simple Proteins
103
• Fibrinogen◦ It is found as dissolved protein in the blood plasma.
◦ It is the acute phase reactant involved in the coagulation of blood
(coagulation).
◦ MW is 340,000. Consists of two subunits.
◦ It has important functions in tissue repair and wound healing.
◦ During blood clotting, fibrinogen is converted to fibrin by thrombin.
◦ It is synthesized by hepatocytes in the liver.
• Myosin◦ It is found in the muscle tissue.
◦ It is involved in muscle contraction.
Simple Proteins
104
When it is hydrolyzed, it is proteins that give different chemical substances together with amino acids. It is formed by binding of polypeptide chains formed
from amino acids to the so-called prosthetic group.• Phosphoproteins
• Glycoproteins
• Proteoglycans
• Lipoproteins
• Metalloproteins
• Nucleoproteins
• Chromoproteins
Conjugated Proteins
105
• Phosphoproteins◦ Proteins that carry phosphoric acid (phosphate) as a prosthetic
group.
◦ Phosphoric acid is attached to the -OH groups of serine, threonine and
tyrosine in the protein molecule; so it is esterified.
◦ Casein in milk; vitelline, livetin and phosvitin in eggs; ihtulin in fish
eggs (haviar) are some examples.
• Glycoproteins ◦ Proteins that carry carbohydrates as a prosthetic group.
◦ They range from 1 to 80% carbohydrates.
◦ If the carbohydrate ratio is <4%, it is called glycoprotein.
Conjugated Proteins
106
◦ If the ratio is between 10-20%, it is called mucoprotein, if carbohydrate ratio is very high and protein ratio is low, it called mucoid.
◦ Some carrier proteins (seruloplazmin, transferrin) and immunoglobulins from blood plasma proteins; osseomucoprotein in bones, tendonmucoprotein in tendons, cartilago mucoprotein in cartilaginous tissue, and mucin in saliva are glycoproteins.
• Proteoglycans◦ Conjugated proteins that contain very high amount of carbohydrates
such as 80-95%.
◦ It consists of a core protein with a glycosaminoglycan (GAG) chain attached with one or more covalent bonds.– Heparin, chondroitin sulphate can be given as an example.
Conjugated Proteins
107
• Lipoproteins (Proteolipids)◦ Proteins that carry lipids such as
phospholipids, triglycerides, and
cholesterol as prosthetic groups.
◦ Easily soluble in water.
◦ Because lipids are not soluble in water,
they are bound to proteins and
transported as lipoproteins.
◦ Examples include chylomicron,
Lipovitellin, VLDL, IDL, LDL and HDL.
Conjugated Proteins
© McGraw-Hill Companies Inc.
108
Conjugated Proteins
Metalloproteins• Proteins that carry metals (Fe, Cu, Zn ...) as prostatic
groups.
• Fe carriers (ferritin, hemoglobin, cytochromes), Cu carriers (ceruloplazmin, SOD), Zn carriers (SOD), Se carriers (GPx, IDs).
Chromoproteins• They are colored proteins formed by the presence of a
metallic element in the prosthetic groups. They are formed by metal-porphyrin complex systems.
• Hemoglobin, myoglobin, cytochromes are examples.
109
• Nucleoproteins◦ Proteins that result in the binding of nucleic acids to protamines,
histones, and other simple proteins.
◦ Nucleoprotamines are the simplest nucleoproteins. The nucleic acid
and proteins are linked by arginine-phosphate linkage. They are
abundant in fish sperm.
◦ Nucleohistones which the nucleic acid and proteins are linked by
arginine-phosphate linkage are found in fish sperm and bird
erythrocytes.
◦ High nucleoproteins are found in ribosomes, covalently linked RNA-
protein, DNA-protein complex.
Conjugated Proteins
110
They are proteins that are formed as a result of alteration of proteins belongs to simple or conjugated proteins. There are two groups in this type of proteins; Primary and Secondary Derivative proteins.• Primary Derivative Proteins
◦ Peptide ligands are formed by degenerating agents without destroying them.
◦ They are also called denatured type proteins.
◦ These water-insoluble proteins are called proteans by the action of dilute acids and enzymes.
◦ Metaprotein is known to be formed by continuous effects of acids and alkalis.
◦ Boiling, agitation, UV rays and ethanol effect are called coagulation or coagulation proteins.
Derivative Proteins
111
• Secondary Derivative Proteins◦ They are formed by the action of acids or enzymes that partially
cleave peptide bonds.
◦ Protein molecules divide into smaller fragments.
◦ The big fragment is called proteose (albinoin); small pieces are called
peptones.
◦ The smaller chains are also polypeptides and peptides.
◦ These derivative proteins do not precipitate with boiling or coagulate
with heat.
Derivative Proteins
112
Catalytic Proteins
Carrier proteins (Transport proteins)
Nutrient and Storage Proteins
Contractile Proteins
Structural Proteins
Defense Proteins
Physiological Regulatory Proteins
Functional Classification of Proteins
113
Enzymes which catalyze biochemical reactions, are highly specialized proteins.
Enzymes are defined as biocatalytic substances that allow biochemical reactions to take place rapidly under normal conditions and constitute the basic character of living tissue.
Amylase, pepsin, lipase are examples of important catalytic proteins or enzymes.
Catalytic Proteins
114
Proteins that bind specific molecules or ions and transports them from one organ to another or from one side of the cell membrane to the other side.• Serum albumin, the most well known carrier protein; bilirubin,
calcium, fatty acids and many drugs are transported by binding to serum albumin.
• Hemoglobin,oxygen-carrier.• Lipoproteins, lipid-carrier.• Transferrin, iron-carrier.
The carrier proteins found in the plasma membranes and intracellular membranes of all organisms bind to glucose, amino acids and other substances; they carry them from one side of the membrane to the other side.
Transport Proteins
115
They are proteins that serve as biological reserves for
metal ions and amino acids used by the organism.• The main protein of the egg flock which is ovalbumin and the
essential protein of the milk which is casein are nutritional
proteins; amino acid stores.
• Many plant seeds also store nutrient proteins necessary for
germinating seed growth. Gluten the best-known storage
protein in wheat.
• Ferritin is iron storage protein.
Nutrient and Storage Proteins
116
They are proteins that can contract or spontaneously
move.
Myosin and actin function in the contractile system of
skeletal muscles and at the same time in many non-
muscle cells.
Tubulin is the microtubule forming protein.• The microtubules in the cells act together with the dynein
protein in the whip and eyelashes to carry the cells.
Contractile Proteins
117
The main structure of tendons and cartilage is collagen
with very high tensile strength.• Leather, almost pure collagen.
• The ligaments contain elastin, a structural protein capable of
stretching in two dimensions.
• Hair, nails and fur contain keratin.
• The main component of silk fibers and spider webs is fibroin.
The wing axes of some insects are made from the resilin.
Structural Proteins
118
Organisms are proteins that defend against invasion by
other species and protect the organism from harm.
Immunoglobulins are specialized proteins synthesized by
the lymphocytes of the vertebrates.
Immunoglobulins can recognize foreign proteins
(antigens) of another species and can precipitate or
neutralize.• Eg. Bacteria, viruses, proteins of another species.
Defense Proteins
119
• Blood clotting proteins, such as fibrinogen and thrombin, help
prevent blood loss by closing the injured site with a blood clot
when the vascular system is injured.
• Toxic plant proteins such as snake poisons, bacterial toxins and
ricin appear to have defensive functions at the same time.
• Some of the defense proteins, including fibrinogen, thrombin
and some poisons, are also enzymes.
Defense Proteins
120
They are proteins that aid in cellulite regulation or
physiological activity.
Some hormones such as insulin, growth hormone,
regulatory proteins.• Insulin is effective in regulating sugar metabolism
• The growth hormone is effective in regulating the growth
• For many hormone signals, the cellular side is often a class of
GTP-binding proteins called G-proteins.
• Some regulatory proteins surround the DNA; Regulate the
biosynthesis of enzymes and RNA molecules.
Physiological Regulatory Proteins
121
Nucleoproteins
It forms a very important group of compound proteins.
Prosthetics are proteins that are nucleic acids.
NUCLEIC ACIDS• They are hereditary-carrying genes and key features in protein
biosynthesis.
• Every particular biological event, including cell division, is of
interest to nucleic acids.
122
Nitrogenous
base Pentose Phosphate
Nucleoside
Nucleotide
(Mononucleotide)n=Nucleic acid
There are three substances in the structure of nucleic acid
Nitrogenous base + Pentose + Phosphate
+ +
123
1
5
The pentose is located in
the middle of a nucleotide
structure. 1st carbon linked to
nitrogenous base.
5th carbon linked to
phosphate.
3th carbon linked to
phosphate group of another
nucleotide.3
124
A nucleotide phosphate and pentose bond is formed by
the post-esterification of the pentose with the
phosphate of the primary alcohol (CH2OH) group on the
5th carbon atom to form a mole H2O.
Pentose is connected via its first carbon to a nitrogenous
base.
Nucleoproteins
125
The conjugation of the mononucleotides occurs via
pentose and phosphate.
The first nucleotide is generated by the esterification of
the second nucleotide phosphate with the OH group on
the third carbon of the pentose.
According to this linkage, the number n of nucleotides
continues to join and nucleic acids form.
Nucleoproteins
126
Nitrogenous bases found in a nucleotide are purine and
pyrimidine bases. • There are also rare different bases. These bases are methyl-,
dimethyl-, and N-methyl derivatives.
Purine bases are adenine and guanine.
Pyrimidine bases are cytosine, uracil and thymine. • Cytosine is found in both DNA and RNA. Uracil is found in
only RNA. Thymine is found only in DNA.
Nucleoproteins
127
128
Cells can synthesize purine and pyrimidine bases.
Nucleic acids take DNA and RNA names from the pentose
of their structure.
If there is a deoxyribose, it is called DNA
(deoxyribonucleic acid).
If there is a Ribose, it is called RNA (ribonucleic acid).
Nucleoproteins
129
130
Biologically important free nucleotides• In addition to being found in the structures of nucleic acids,
nucleotides are also found in tissues as free nucleotides, which are in close proximity to the nucleotides.
• Most of these substances have catalytic functions and work together with enzyme systems (coenzymes).
• Nitrogenous base + pentose = Nucleoside (Adenine + ribose = Adenosine)
• Adenosine + Phosphate = The nucleotide called adenosine monophosphate (AMP) is formed. Two phosphates form adenosine diphosphate (ADP), three phosphates bind adenosine triphosphate (ATP).
• In other bases, phosphate-binding nucleotides are formed.
Nucleoproteins
131
AMPADP
ATP
132
Biologically important free nucleotidesAMP (Adenosine monophosphate = Adenilic acid): Adenine - Ribose– PO4
ADP ((Adenosine diphosphate): Adenine - Ribose– PO4 – PO4
ATP (Adenosine triphosphate): Adenine - Ribose– PO4 – PO4 – PO4
NAD (Nicotinamide Adenine Dinucleotide): Adenine - Ribose– PO4 – PO4 – Ribose - Nicotinamide
NADP (Nicotinamide Adenine Dinucleotide phosphate) : Adenine – Ribose (– PO4) – PO4 – PO4 – Ribose –
Nikotinamide
FMN (Flavin mononucleotide) : Flavin – Ribitol - PO4
FAD (Flavin adenine dinucleotide) : Flavin – Ribitol - PO4 - PO4 – Ribose - Adenine
UDP-G (Uridine diphosphate-Glucose) : Uracil – Ribose - PO4 - PO4 - Glucose
Koenzim A : Adenine – Ribose (– PO4) – PO4 – PO4 – Pantothenate thiolethylamine
133
Nitrogenous
baseNucleoside Nucleotide Symbol
Adenine Adenosine Adenilic acid AMP
Guanin Guanosine Guanilic acid GMP
Cytosine Sitidin Cytidylic acid CMP
Uracil Uridin Uridylic acid UMP
Tymine Thymidine Thymidic acid TMP
134
Both DNA and RNA are common in animal tissues.
DNA is found in the nucleus and also RNAs.
The major nucleic acid fraction of the cytoplasm is RNA.
In cytoplasm, RNA is usually found in ribosomes.
Structure and Functions of Nucleic Acids
135
Building blocks; Phosphate, deoxyribose and purine and
pyrimidine bases such as Adenine (A), Guanine (G),
Cytosine (C), Timin (T).
The ratio of (A + T):(G + C) is always changed. However,
adenine and thymine or guanine and cytosine are
equally distributed.
There are three structures in the DNA molecule.• Primary structure
◦ Certain species and a certain number of nucleotides form
polynucleotide chains according to one sequence; Chain structure.
Deoxyribonucleic Acid (DNA)
136
• Secondary structure◦ It occurs when two polynucleotide chains are mutually located.
◦ These two chains are connected to each other by hydrogen bridges
between nitrogenous bases.
◦ However, this connection must be appropriate on mutual basis.
◦ It always resists adenine-thymine (A-T), guanine-cytosine (G-C).
• Tertiary structure◦ The two polynucleotides are coiled, in other words a double spiral is
formed; like twisted ladder.
◦ The same nitrogenous bases come together and are joined by two
chain H bridges.
Deoxyribonucleic Acid (DNA)
137
Molecular Structure of DNA
Primary structure
Secondary structure
Tertiary structure
138
DNA has two main functions in the organism.1. To carry genetic code.
2. Having the ability of replication.
In the cell division, genetic code are transferred
completely and unchanged to the offspring.
In order for a new DNA molecule to come into being
(DNA replication), the double helix, the tertiary
structure, has to break down and make up the
secondary structure.
Deoxyribonucleic Acid (DNA)
139
The separated DNA strands bring about a mold for the
newly formed DNA strands.
Against this pattern, a strand of DNA similar to the
structure of the peer-strand from which the strand itself
is separated may form.
Because the nitrogenous bases in the DNA strand we call
mold are only able to match their respective
nitrogenous bases.
Deoxyribonucleic Acid (DNA)
140
The strands here are called semiconservative
replicates. Semiconservative replication would
produce two copies that each contained one of the
original strands and one new strand.
In the DNA molecule, three nitrogenous bases on top of
one another encode an amino acid called codon.
Deoxyribonucleic Acid (DNA)
141
142
In order for RNAs to be formed, primary DNAs are required.
Is the RNA structure different from the DNA structure?• Instead of deoxyribose, it carries ribose.
• Uracil is found instead of thymine.
• It is not a double-helix; one strand.
There are three main types of RNA; mRNA, rRNA, tRNA
Ribonucleic Acid (RNA)
143
144
145
Transcription
DNA Transcription
146
DNAs determine the sequence of amino acids in the
structure of proteins.
All three nitrogenous bases in the polynucleotide chain
of a DNA encode an amino acid (codon).• Here, the order of the nitrogenous bases in the nucleus of the
DNA is genetic code.
The first step in protein biosynthesis is that the
genetic information in DNA is transported to
ribosomes where protein synthesis occurs. This is
done by mRNAs; Transcription.
mRNA (Messenger RNA)
147
An RNA template is formed that represents the genetic information and DNA portion necessary for protein synthesis. It passes into the cytoplasm and binds to the ribosomes.The amino acid code is valid for all forms of life,
including viruses, that have been researched up to now.The genetic code of DNA is carried by the base sequence
of RNA.The base sequence of the mRNA determines the
amino acid sequence of the protein.
mRNA (Messenger/ RNA)
148
149
The second type of RNA is found on the endoplasmic
reticulum. It is rRNA that is located in the organelle
called the ribosome. RNA forms a large part of the
ribosomes.
rRNA (Ribosomal RNA)
150
They are RNA molecules capable of
combining with specific amino acids
and transporting them to ribosomes.
There are 3 important features.• They can covalently bind a particular amino
acid.
• In their own structure, they have a
anticodon which completes the amino acid
in the mRNA code.
tRNA (Transfer RNA)
anticodon
151
152
Chromoproteins A chromoprotein is a conjugated protein that contains a
pigmented prosthetic group (or cofactor); like porphyrines. Hemoglobin and respiratory enzymes are chromoproteins
whose prosthetic group is heme. Again, the prosthetic group is riboflavin in flavoproteids,
the prosthetic group is melanin in proteins found in hair and wool. The catalase enzyme is also a chromoprotein whose
prosthetic group is heme. The chromoproteins that carry the heme structure as a
prosthetic group are called hemoproteids.• Hemoglobin, myoglobin, cytochromes and peroxidases are
hemoproteids.
153
The pyrrole ring is the first and simplest substance of porphyrins. When the side chains such as propionic acid, acetic acid or methyl, ethyl, hydroxyethyl, vinyl are added to the pyyrol ring, the structure called porphobilinogen comes to the fore. Porphobilinogen is called monopyrrol and is considered to be the precursor of porphyrins.• If the four porphobilinogen rings are connected to each other
by methine (=CH-) bridges, porphyries will form.
• Porphyrins are a group of heterocyclic macrocycle organic compounds, composed of four modified pyrrole subunits interconnected at their α carbon atoms via methine bridges.
Porphyrins
154
Pyrrole Ring Porphobilinogen (PBG)
155
If 4 acetic acid and 4 propionic
acid are attached to the
porphyrin ring, uroporphyrins
are formed.• Uroporphyrins I
• Uroporphyrins III
• Coproporphyrin I
• Coproporphyrin III
Porphyrins
Porphin Ring
156
Porphyrins
Hemoglobin• They are chromoproteins carrying HEM as a prosthetic
group.
• It is formed by four groups, each in parallel with the globin,
perpendicular to the peptide chain.
• Hemoglobin is mainly synthesized by the liver in fetus. It is
also synthesized in bone marrow in adults.
• Hemoglobin is rich in histidine, and is a good buffer.
• The most important task is to create oxyhemoglobin, which
is combined with atmospheric oxygen in the lungs to
transport oxygen to the tissues.
157
Heme Hemoglobin
158
Porphyrins• Each of the 4 groups in the hemoglobin can bind an oxygen
molecule.
• Carbaminohemoglobin is a compound of hemoglobin and carbon
dioxide, and is one of the forms in which CO2 exists in the blood.
• When combined with CO, carboxyhemoglobin is formed.
• Methemoglobin is a form of the oxygen-carrying metalloprotein
hemoglobin, in which the iron in the heme group is in the Fe3+
(ferric) state, not the Fe2+ (ferrous) of normal hemoglobin.
Methemoglobin cannot bind oxygen.
• Fe++ can be replaced with some anions. Combine with cyanide to
form cyanomethemoglobin.
• When oxyhemoglobin is treated with H2S, sulfhemoglobin forms.
159
PorphyrinsMyoglobin• Keeps the oxygen brought by
hemoglobin.
• In the structure;◦ There is a single polypeptide chain
containing 153 amino acids.
◦ Globular structure.
◦ 1 molecule of Heme as a prostatic
group.
• It is found in the muscle tissue.
160
Erythrocytes are destroyed at the end of their life for about 125 days, and as a result, the porphyrin ring is opened. It comes in an open chain containing 4 pyrrole rings, which are called bile pigments. It is assumed that all of the substances included in the group
of bile pigments are theoretically derived from a (proto) Bilin substance. In the disintegration of hemoglobin, Biliverdin results from
the breakdown of the heme moiety of hemoglobin in erythrocytes. Bilirubin is formed by the reduction of one of the methine
groups linking the porphobilinogen rings of Biliverdin to the methylene group.
Bile Pigments
161
Mesobilirubin occurs when the bilirubin vinyl groups are converted into ethyl groups. In the other two methine (=CH) groups that link the
porphobilinogen rings, mesobilirubinogen is formed by reduction to the methylene (CH2) group. In this, two side porphobilinogen rings form stercobilinogen by entering two H atoms. In clinical biochemistry, mesobilirubinogen and
stercobilinogen are called bilinogenes or urobilinogens. • Urobilinogen can be reduced to form mesobilirubinogen, and
mesobilirubinogen can be further reduced to form stercobilinogen.• Urobilin was isolated in urine and stercobilin was isolated in
stool for the first time. They are actually found in many tissues and other body fluids.
Bile Pigments
162
Bile Pigments Features• Mesobilirubinogen and stercobilirubinogen are colorless,
urobiline and stercobilin are yellow, mesobilirubin and bilirubin are orange blossom and biliverdin is bluish green color.
• The Na and K salts of biliverdin and bilirubin are dissolved in water, but salts of Ba and Ca are insoluble.
• If concentrated nitric acid and bile-colored substances are layered, green, blue, violet, red colors come into contact on the contact face. This is called the Gmelin’s test. With this test, it is possible to diagnose the jaundice.
• When the bilirubin is reacted with freshly prepared diazo reagent, azo-bilirubin in red forms. It is used to quantify bilirubin in blood.The reaction name is Van den Bergh.◦ The diazo substituent is a mixture of sulfanilic acid, HCl and sodium nitrite.
163
Bilirubin is the bile-colored substance in the plasma collection to bilirubinemi, removing the bilirubinuria urine, skin and mucosa into painting these tissues collected icterus (jaundice) is called. According to their causes icterus divided into three.1. Mechanics/retention Icterus (Post-hepatic): It is also called
obstructive jaundice and caused by an interruption to the drainage of bile containing conjugated bilirubin in the biliary system. The most common causes are gallstones in the common bile duct. Beside this, inflammation, parasites, tumors can also be reasons. both direct and indirect bilirubin levels are increased in serum. In the urine, bilirubin (+), urobilinogen is normal. Stool is colorless.
Icterus (Jaundice)
164
Icterus (Jaundice)2. Hepatocellular Icterus (Hepatic): It can be caused by acute or
chronic hepatitis, hepatotoxicity, cirrhosis, drug-induced hepatitis. Cell necrosis reduces the liver's ability to metabolize and excrete bilirubin In the serum, indirect bilirubin increased.
In the urine, urobilinogen is (+).
Stool is light color.
3. Hemolytic Jaundice (Pre-hepatic): Pre-hepaticular jaundice is caused by anything which causes an increased rate of hemolysis (breakdown of red blood cells). In the serum, indirect bilirubin increased .
In the process, urobilinogen is very high.
Stool is dark color.
165
Serum and Plasma• After the blood collected in a tube containing a suitable
anticoagulant agent that can inhibit coagulation, if to be centrifuged, it is separated into two layers; a liquid supernatant which has a yellow-pink color and a shaped elements which are cells.
• The liquid part of the blood that separates in this way is called plasma. Plasma contains 8% plasma proteins, 1% inorganic salts, and the rest contain substances such as lipids, carbohydrates and amino acids. The fibrinogen fraction of the plasma proteins that make up the 8% portion is contained in the plasma.
Major Proteins of Fluids and Tissues in Organism
166
If the fibrinogen present in the plasma passes into the
fibrin and the blood coagulates, the remaining light
yellow portion is taken as the serum..
Plasma(Water, proteins, lipids,
carbohydrates, hormones, etc.)
.)
Erythrocytes
Leukocytes and thrombocytes
Source: WikiMedia
Normal
Hematocrit
(HCT)
Anemia
(HCT )
Polycythemia
(HCT )
Major Proteins of Fluids and Tissues in Organism
167
Coagulation of blood• It occurs when the fibrinogen, a soluble protein found in
circulating blood, changes. When necessary, this fibrinogen
transforms into a fibrin by a series of reactions. This is what is
called coagulation (blood clotting/clotting).
• The conversion of fibrinogen to fibrin is provided by an enzyme
called thrombin. This enzyme is not active in the circulation.
• Many factors play a role in blood coagulation, mainly Ca.
• Coagulation of blood is not a simple event, but a complex and
controlled mechanism process; it is called Coagulation
Cascade.
Major Proteins of Fluids and Tissues in Organism
168
Thrombocytes are one of the blood cells. • When blood is taken from the circulating
blood, these platelets stick to the wall of the tube, and if it is a hemorrhage, it sticks to the edges of the wound and splits.
• This fragmentation results in the release of a substance called thromboplastin.
• Thromboplastins are found in circulating blood. Prothrombin is an inactive form of thrombin and thromboplastins convert prothrombin to thrombin. Thrombin also provides blood clotting by allowing the fibrinogen to pass into the fibrin.
Canine
Feline
Source: eClinPath
Major Proteins of Fluids and Tissues in Organism
169
Coagulation Cascade Animation
170
Plasma and serum proteins
FibrinogenIt is glycoprotein. It has ellipsoid-fibrillar structure. High
viscosity in solutions. It plays the most important role in blood
coagulation.
Serum
Albumin
It is mostly a lipoprotein structure. It's an ellipsoid shape. It is
important in preserving the osmotic pressure. It binds and
dissolves nonsoluble matters and transports them in circulating
blood.
Serum
Globulin
α-globulins: It's in glycoprotein structure. Ceruloplasmin and
prothrombin can be the examples.
β-globulins
γ-globulins: These are called antibodies or immunoglobulins.
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171
Muscle Proteins
Sarkoplasmic Proteins Myogen, Myoglobin, Myoalbumin, Globin-X
Fibrillar ProteinsMyosin, Actin (Globular actin/G-actin,
Fibrillary actin/F-actin)
Milk and Egg Proteins
Milk Proteins Casein, Lactobombin, Lactoglobulin, Immunoglobulins
Egg Proteins
Egg white: Ovalbumin, Konalbumin, Ovomucoid,
Ovoglobulins, Mucin, Avidin
Egg yolk: Vitellin, Livetin, Phosphitin (all are
phosphoprotein).
Major Proteins of Fluids and Tissues in Organism
Ası. T. 1999. Tablolarla Biyokimya, Cilt 1
Engelking LR. 2014. Textbook of Veterinary Physiological Chemistry. 3rd
edn. Academic Press.
Smith JG (2010). Organic Chemistry, 3rd Edition, McGraw-Hill.
Smith JG (2012). General, Organic, & Biological Chemistry 2nd Edition,
McGraw-Hill.
Sözbilir Bayşu N, Bayşu N. 2008. Biyokimya. Güneş Tıp Kitapevleri, Ankara
References
173
Question 1Cevap: B
Which of the following is the simplest known amino
acid?
a) Alanin
b) Glycine
c) Treonin
d) Triptofan
e) Glumatic acid
174
Question 2Cevap: C
It is called decomposition of proteins because of various
exposures.
a) Deamidation
b) Renaturation
c) Denaturation
d) Decarboxylation
e) Deamination
175
Question 3Cevap: A
Which molecule forms the first and simplest basic
substance of porphyrins?
a) Pyyrol ring
b) Porphobilinogen
c) Fibrinogen
d) Stercobilin
e) Biliverdin
Your Questions ?